pychnosz 1.1.11__cp312-cp312-win_amd64.whl

pychnosz/data/extdata/protein/Cas/Cas_aa.csv

@@ -0,0 +1,177 @@
+"protein","organism","ref","abbrv","chains","Ala","Cys","Asp","Glu","Phe","Gly","His","Ile","Lys","Leu","Met","Asn","Pro","Gln","Arg","Ser","Thr","Val","Trp","Tyr"
+"Cas6",ARCFU,O28420,Y1859,1,11,5,9,21,18,26,7,21,17,31,4,8,14,5,22,25,10,18,1,16
+"Cas11",ARCFU,O28409,Y1870,1,12,0,7,14,3,7,1,4,14,15,2,2,1,3,5,9,4,8,0,5
+"Cas7",ARCFU,O28408,O28408,1,22,3,12,31,21,25,3,14,25,17,7,13,13,4,15,21,17,39,2,15
+"Cas5",ARCFU,O28407,O28407,1,18,3,11,23,12,21,1,22,23,22,3,7,14,5,12,21,10,22,5,11
+"Cas8a1",ARCFU,O28406,Y1873,1,21,0,17,31,22,19,4,27,35,55,5,18,10,15,18,33,21,18,2,19
+"Cas3'",ARCFU,O28405,O28405,1,33,3,33,50,35,26,6,40,47,55,11,23,16,6,31,42,21,41,5,22
+"Cas3''",ARCFU,O28404,O28404,1,20,2,7,25,16,13,6,13,25,26,5,12,3,1,16,16,7,14,1,13
+"Cas2",ARCFU,O28403,CAS2A,1,5,3,7,6,5,6,1,6,5,10,1,3,2,4,9,6,2,11,0,2
+"Cas4",ARCFU,O28402,O28402,1,12,4,7,17,8,13,0,11,21,22,4,2,5,5,15,11,5,15,1,11
+"Cas1",ARCFU,O28401,CAS1A,1,30,4,20,25,9,24,5,24,28,45,7,14,7,9,30,18,4,27,2,13
+"Cas4",ARCFU,O28400,O28400,1,15,9,11,27,11,12,6,14,14,28,9,15,15,3,17,22,9,24,5,15
+"Cas6",CLOK5,A5N0X4,A5N0X4,1,6,4,12,21,12,9,3,26,24,18,6,20,6,6,10,12,15,8,1,17
+"Cas8b1",CLOK5,A5N0X3,A5N0X3,1,15,4,37,51,31,22,4,49,79,51,11,53,11,10,19,48,17,27,4,46
+"Cas7",CLOK5,A5N0X2,A5N0X2,1,17,2,23,23,17,21,2,25,36,21,5,21,8,10,6,19,20,14,2,17
+"Cas5",CLOK5,A5N0X1,A5N0X1,1,11,0,12,22,16,11,6,14,25,22,6,20,6,8,8,10,10,17,3,19
+"Cas3",CLOK5,A5N0X0,A5N0X0,1,20,8,57,79,55,27,12,89,92,69,23,86,11,17,31,61,26,39,4,54
+"Cas4",CLOK5,A5N0W9,A5N0W9,1,4,5,9,20,3,8,4,19,25,13,3,10,2,6,5,3,5,8,2,10
+"Cas1",CLOK5,A5N0W8,A5N0W8,1,11,2,16,23,21,15,10,29,36,27,8,24,10,6,17,20,9,24,2,24
+"Cas2",CLOK5,A5N0W7,A5N0W7,1,2,2,5,6,9,3,3,9,13,7,1,11,1,2,2,4,4,7,0,3
+"Cas3",HALH5,Q9KFY4,Q9KFY4,1,55,11,43,73,34,40,28,44,54,83,16,37,20,43,36,47,44,53,5,34
+"Cas5",HALH5,Q9KFY3,Q9KFY3,1,11,3,14,18,13,24,9,12,13,19,6,8,14,12,12,9,8,15,2,14
+"Cas8c",HALH5,Q9KFY2,Q9KFY2,1,48,6,45,53,24,34,14,32,51,55,9,28,23,19,39,42,32,32,12,29
+"Cas7",HALH5,Q9KFY1,Q9KFY1,1,18,1,26,16,12,18,7,18,24,17,7,13,9,8,15,29,14,22,3,6
+"Cas4",HALH5,Q9KFY0,Q9KFY0,1,7,6,8,14,5,10,5,10,20,12,8,6,8,8,10,11,4,15,0,7
+"Cas1",HALH5,Q9KFX9,Q9KFX9,1,26,2,16,24,15,22,5,11,23,44,13,18,11,15,24,16,18,21,5,14
+"Cas2",HALH5,Q9KFX8,CAS2,1,3,2,6,6,2,5,1,7,8,12,2,4,2,5,5,8,7,7,0,4
+"Cas3",GEOSL,Q74H42,Q74H42,1,93,11,74,63,32,60,22,30,39,99,15,18,55,27,78,54,45,71,16,19
+"Cas8u2",GEOSL,Q74H41,Q74H41,1,23,6,20,16,23,19,2,10,18,36,7,8,18,10,21,22,11,13,8,5
+"Cas7",GEOSL,Q74H40,Q74H40,1,42,3,26,20,13,30,6,16,23,36,3,18,19,12,23,14,17,31,2,9
+"Cas5-Cas6",GEOSL,Q74H39,Q74H39,1,59,4,33,24,15,47,18,32,18,48,12,15,39,16,45,34,17,35,14,14
+"Cas4-Cas1",GEOSL,Q74H36,CS4F1,1,48,10,27,40,22,49,14,23,11,56,16,13,35,13,59,31,29,38,6,19
+"Cas2",GEOSL,Q74H35,CAS2,1,5,2,5,5,4,4,4,11,5,9,3,4,3,4,9,4,2,8,2,2
+"Cas3'",RIPO1,B7JVN0,B7JVN0,1,44,11,31,52,33,36,13,41,41,92,14,32,23,49,45,42,32,35,10,25
+"Cas3''-Cas10d",RIPO1,B7JVM9,B7JVM9,1,70,7,53,67,38,44,17,65,58,134,13,40,39,66,46,69,50,44,21,33
+"Cas7",RIPO1,B7JVM8,B7JVM8,1,17,6,18,27,17,26,8,22,23,33,8,19,12,18,18,30,29,13,0,12
+"Cas5",RIPO1,B7JVM7,B7JVM7,1,17,4,8,9,9,15,8,16,16,28,3,19,17,17,8,18,11,9,5,21
+"Cas6",RIPO1,B7JVM6,B7JVM6,1,16,3,6,12,14,17,7,17,16,40,6,6,15,26,8,22,13,12,4,9
+"Cas4",RIPO1,B7JVM5,B7JVM5,1,9,7,9,17,5,7,10,18,13,17,5,12,5,10,15,11,7,8,3,8
+"Cas1",RIPO1,B7JVM4,B7JVM4,1,21,3,12,19,13,19,11,15,21,44,3,12,15,21,18,21,14,22,2,19
+"Cas2",RIPO1,B7JVM3,B7JVM3,1,5,2,4,5,4,5,0,6,6,14,2,6,3,5,6,5,7,5,1,6
+"Cas3",ECOLI,P38036,CAS3,1,71,17,56,51,39,52,26,43,36,100,16,41,39,54,43,59,38,56,25,26
+"Cas8e",ECOLI,Q46901,CSE1,1,37,11,18,27,25,39,14,30,25,51,9,32,29,29,25,25,25,33,8,10
+"Cas11",ECOLI,P76632,CSE2,1,15,2,10,9,5,7,3,8,5,19,6,7,6,12,19,6,7,7,5,2
+"Cas7",ECOLI,Q46899,CASC,1,42,2,25,18,13,23,8,21,21,31,14,18,8,24,17,27,14,25,5,7
+"Cas5",ECOLI,Q46898,CAS5,1,14,5,12,13,7,18,6,8,6,28,5,1,13,10,19,16,18,12,4,9
+"Cas6",ECOLI,Q46897,CAS6,1,16,4,9,8,7,13,5,13,13,23,3,7,12,14,13,10,7,15,3,4
+"Cas1",ECOLI,Q46896,CAS1,1,35,4,18,15,9,25,4,22,14,29,4,4,22,10,23,15,13,26,4,9
+"Cas2",ECOLI,P45956,CAS2,1,7,0,3,8,4,8,0,4,1,11,4,4,4,2,8,3,6,13,3,1
+"Cas1",A0A0H3B3U5,A0A0H3B3U5,NA,1,33,5,16,18,15,25,9,18,10,35,6,15,7,17,20,17,19,24,6,11
+"Cas2-Cas3",A0A0H3B287,A0A0H3B287,NA,1,90,15,71,49,34,55,44,44,53,131,20,48,48,77,79,67,55,62,27,26
+"Cas8f1",A0A0H3B0Q7,A0A0H3B0Q7,NA,1,48,4,25,32,17,21,10,18,29,51,5,21,17,33,23,31,14,24,13,12
+"Cas5f1",A0A0H3B1X5,A0A0H3B1X5,NA,1,30,7,14,18,8,24,14,15,8,40,4,12,17,12,20,18,21,17,4,13
+"Cas7f1",A0A0H3B2X2,A0A0H3B2X2,NA,1,35,2,18,19,15,22,2,16,21,30,6,18,11,21,15,24,19,24,5,11
+"Cas6f",A0A0H3B3V0,A0A0H3B3V0,NA,1,14,3,9,10,8,12,5,7,8,26,1,1,9,10,17,17,10,10,3,4
+"TnsA",UPI000637FC9D,UPI000637FC9D,NA,1,9,5,11,11,13,7,9,12,16,21,4,8,6,14,9,17,12,11,2,10
+"Cas8f3-Cas5f3",UPI00063793EA,UPI00063793EA,NA,1,49,10,35,45,28,26,23,36,41,81,9,29,29,34,40,75,29,43,13,20
+"Cas7f3",UPI000633A6D2,UPI000633A6D2,NA,1,26,8,18,28,10,24,5,15,21,34,6,16,12,11,20,22,17,21,8,21
+"Cas6f",UPI000631609A,UPI000631609A,NA,1,12,3,8,14,13,12,2,12,7,11,8,9,7,9,15,21,12,20,1,7
+"Cas1",SHEPC,A4Y6F9,A4Y6F9,1,37,5,18,18,19,19,9,14,17,35,9,13,8,24,14,10,22,16,6,12
+"Cas2-Cas3",SHEPC,A4Y6G0,A4Y6G0,1,79,13,61,60,48,41,27,61,73,98,13,58,35,49,37,65,57,63,10,30
+"Cas7f2",SHEPC,A4Y6G1,A4Y6G1,1,20,3,21,19,15,23,8,22,24,26,5,18,8,16,13,20,20,17,1,16
+"Cas5f2",SHEPC,A4Y6G2,A4Y6G2,1,16,4,17,22,17,24,0,28,32,31,10,21,9,15,11,28,19,16,3,13
+"Cas6f",SHEPC,A4Y6G3,A4Y6G3,1,11,1,13,6,11,13,6,9,16,21,4,4,7,8,9,18,6,11,2,7
+"DinG",THISK,D3SGE4,D3SGE4,1,102,4,43,54,16,61,16,23,9,100,10,14,44,34,81,50,37,43,11,14
+"Cas6",THISK,D3SGE5,D3SGE5,1,24,2,9,18,8,22,9,14,9,21,5,1,21,9,20,12,9,12,3,5
+"Cas8-like",THISK,D3SGE6,D3SGE6,1,30,5,13,19,11,22,3,5,6,27,5,4,20,14,25,6,11,14,7,5
+"Cas7",THISK,D3SGE7,D3SGE7,1,35,3,26,25,11,29,5,15,8,29,8,10,17,11,32,25,26,22,6,6
+"Cas5",THISK,D3SGE8,D3SGE8,1,20,1,11,18,4,20,2,12,4,19,8,6,14,11,22,13,11,9,9,4
+"cysH-like",RHOJR,Q0RWS5,Q0RWS5,1,21,3,20,17,7,23,17,11,5,34,3,8,19,8,26,12,20,14,8,8
+"Cas8-like",RHOJR,Q0RWS4,Q0RWS4,1,37,7,10,10,6,16,5,5,8,19,5,0,19,5,26,11,18,27,8,3
+"Cas11",RHOJR,Q0RWS3,Q0RWS3,1,14,0,6,10,0,9,2,3,3,19,1,2,9,2,17,9,13,9,6,4
+"Cas7",RHOJR,Q0RWS2,Q0RWS2,1,16,2,18,21,12,34,2,12,6,29,6,3,15,7,33,21,21,24,4,3
+"Cas5",RHOJR,Q0RWS1,Q0RWS1,1,29,5,14,13,4,23,13,6,4,28,6,0,21,3,21,12,16,10,9,4
+"Cas11",A0A3M1DV11,A0A3M1DV11,NA,1,61,10,42,35,31,32,16,32,27,78,16,23,32,28,54,47,39,52,6,14
+"Cas7",A0A3M1DW31,A0A3M1DW31,NA,1,27,3,13,28,10,28,3,21,14,38,12,10,21,18,20,18,26,21,3,9
+"Cas5",A0A3M1DYX3,A0A3M1DYX3,NA,1,25,5,19,12,13,26,6,17,10,38,3,14,29,18,27,14,20,22,7,14
+"Cas6",STAEQ,Q5HK95,Q5HK95,1,3,1,12,14,20,9,5,23,23,27,10,14,7,13,8,19,8,14,1,13
+"Cas10",STAEQ,Q5HK89,Q5HK89,1,37,8,52,55,38,39,16,61,63,79,18,57,8,26,26,66,34,22,9,43
+"Cas11",STAEQ,Q5HK90,Q5HK90,1,6,1,7,14,10,3,1,6,19,12,3,8,1,4,5,5,5,9,0,9
+"Cas7",STAEQ,Q5HK91,Q5HK91,1,9,0,13,19,11,20,5,20,16,14,4,13,4,9,12,15,13,12,0,5
+"Cas5",STAEQ,Q5HK92,Q5HK92,1,17,0,16,22,19,19,8,18,27,34,5,19,9,10,5,26,19,12,2,17
+"Cas7",STAEQ,Q5HK93,Q5HK93,1,8,2,16,20,13,22,4,25,44,26,7,28,12,18,11,22,17,20,2,23
+"csm6",STAEQ,Q5HK94,Q5HK94,1,12,4,25,44,16,12,9,41,43,46,7,37,13,9,17,23,16,23,4,21
+"Cas1",STAEQ,Q5HK87,Q5HK87,1,8,5,16,21,20,11,8,35,33,25,5,24,5,8,14,19,8,21,1,14
+"Cas2",STAEQ,Q5HK88,Q5HK88,1,2,0,5,8,4,3,0,11,11,15,2,4,4,4,6,7,4,6,0,5
+"Cas10",SYNY3,Q6ZED1,Q6ZED1,1,55,6,39,38,26,31,10,36,43,58,2,32,16,22,26,39,26,30,4,19
+"Cas7-Cas5",SYNY3,Q6ZED2,Q6ZED2,1,56,7,44,45,19,73,10,57,55,82,7,45,35,54,43,47,46,34,14,18
+"Cas11",SYNY3,Q6ZED5,Q6ZED5,1,48,6,53,50,29,66,22,44,46,61,8,43,47,39,55,46,40,42,13,37
+"Cas7-Cas7",SYNY3,Q6ZED3,Q6ZED3,1,48,5,36,24,12,47,7,37,35,62,9,26,25,23,20,26,30,29,10,11
+"Csx19",SYNY3,Q6ZED4,Q6ZED4,1,13,4,12,16,8,13,4,10,13,26,2,14,8,7,8,9,6,10,3,7
+"TPR+Caspase",A0A0B0EKL4,A0A0B0EKL4,NA,1,43,14,48,58,33,35,16,45,70,71,12,42,24,21,34,46,35,32,13,24
+"Cas7(3),Cas11",A0A0B0EGF3,A0A0B0EGF3,NA,1,62,27,120,138,76,135,39,112,160,150,17,100,76,41,110,107,86,73,28,60
+"Cas1",A0A0B0EEW2,A0A0B0EEW2,NA,1,39,8,40,47,34,67,16,52,68,84,11,31,22,23,54,54,31,48,11,28
+"Cas2",A0A0B0ELU0,A0A0B0ELU0,NA,1,2,3,7,3,5,3,0,8,13,5,2,6,1,4,7,3,6,10,0,3
+"Cas10",PSELT,A8F3D4,A8F3D4,1,25,10,37,62,37,28,16,50,61,62,5,39,25,27,33,40,23,37,15,28
+"Cas5",PSELT,A8F3D5,A8F3D5,1,7,1,11,21,14,17,2,19,27,20,2,5,9,3,5,13,9,13,0,10
+"Cas11",PSELT,A8F3D6,A8F3D6,1,4,1,10,22,9,8,1,14,18,19,2,15,5,6,15,12,9,9,5,10
+"Cas7",PSELT,A8F3D7,A8F3D7,1,22,4,12,30,13,26,4,29,31,20,4,12,15,9,11,11,9,15,2,3
+"Cas7",METTH,O26428,O26428,1,10,9,11,24,12,26,3,17,17,26,4,13,11,5,24,13,9,7,3,7
+"Cas7",METTH,O26427,O26427,1,9,1,16,20,19,25,4,14,23,26,9,12,15,4,12,14,13,10,2,13
+"Cas10",METTH,O26426,O26426,1,45,11,54,93,55,43,20,89,103,104,10,61,37,16,52,50,38,30,15,31
+"Cas7",METTH,O26425,O26425,1,19,1,16,34,13,24,2,19,20,21,2,14,13,3,19,13,16,23,4,11
+"Cas11",METTH,O26424,O26424,1,8,3,8,11,5,3,2,5,11,16,4,3,2,3,11,6,2,5,1,4
+"Cas5",METTH,O26423,O26423,1,12,1,19,19,18,25,8,25,26,19,5,15,14,5,12,20,20,16,5,16
+"Cas7",PYRFU,Q8U1S5,CMR1A,1,10,0,11,24,22,26,4,21,27,32,3,12,14,5,28,35,17,27,10,10
+"Cas10",PYRFU,Q8U1S6,CMR2,1,44,4,52,91,37,46,17,61,97,91,10,32,30,14,45,54,22,71,15,38
+"Cas5",PYRFU,Q8U1S7,CMR3,1,12,2,10,36,17,30,1,28,36,32,3,6,19,2,14,17,15,25,3,14
+"Cas7",PYRFU,Q8U1S9,CMR4,1,18,0,14,27,11,26,4,26,25,29,3,11,12,8,11,11,21,27,2,9
+"Cas11",PYRFU,Q8U1T0,CMR5,1,13,0,8,17,3,5,3,8,18,24,5,10,4,5,9,10,5,11,3,8
+"Cas6",PYRFU,Q8U1S4,CAS6,1,12,1,10,24,18,18,5,12,29,24,7,10,16,5,12,11,11,20,2,17
+"Cas7",PYRFU,Q8U1T1,CMR6,1,15,2,16,27,15,23,3,24,33,38,4,13,22,10,16,17,14,27,1,20
+"Cas9",A0AAN5PKD3,A0AAN5PKD3,NA,1,64,11,68,99,70,46,44,111,142,137,22,94,65,73,56,103,64,47,15,41
+"Cas1",A0A2U8U9X9,A0A2U8U9X9,NA,1,28,5,7,19,14,19,7,25,31,36,8,15,8,15,18,22,16,17,7,13
+"Cas2",A0A4T1YC98,A0A4T1YC98,NA,1,3,1,6,9,3,3,1,10,9,12,1,5,4,4,7,3,5,5,1,7
+"Cas4",A0A2U8U9S0,A0A2U8U9S0,NA,1,8,8,6,15,9,11,4,20,20,16,6,5,9,11,7,11,9,9,1,12
+"Cas9",STRTR,G3ECR1,CAS9,1,64,4,99,105,74,72,25,110,159,152,16,90,34,40,75,100,53,61,7,69
+"Cas1",STRTR,G3ECR2,CAS1,1,14,5,14,20,17,10,8,27,17,29,8,21,6,10,15,19,15,16,3,15
+"Cas2",STRTR,G3ECR3,CAS2,1,7,1,6,7,7,5,2,6,9,11,8,8,2,2,8,6,8,4,0,7
+"csn2",STRTR,G3ECR4,CSN2,1,4,2,16,21,11,4,1,28,14,31,4,9,4,11,6,17,10,16,0,10
+"Cas9",NEIL0,E4ZF34,E4ZF34,1,87,9,60,90,50,61,24,46,102,109,18,49,44,42,90,46,50,64,11,30
+"Cas1",NEIL0,E4ZF35,E4ZF35,1,31,2,11,19,11,14,9,19,16,48,2,16,12,22,18,11,18,11,4,10
+"Cas2",NEIL0,E4ZF36,E4ZF36,1,8,2,4,6,6,4,2,6,11,16,4,4,2,9,7,6,3,5,0,3
+"Cas9",A0A1L9GUT8,A0A1L9GUT8,NA,1,62,7,55,71,32,44,25,63,111,80,19,44,38,31,74,50,48,50,11,34
+"Cas4",A0A1L9GUY1,A0A1L9GUY1,NA,1,4,3,10,11,8,7,0,8,14,16,3,4,5,3,11,11,7,9,0,9
+"Cas2",A0A1L9GUR0,A0A1L9GUR0,NA,1,7,2,6,3,6,4,4,11,7,10,2,5,1,3,7,7,6,6,0,4
+"Cas1",A0A1L9GUR2,A0A1L9GUR2,NA,1,29,3,13,16,11,18,2,28,26,37,13,19,10,13,23,33,11,20,4,11
+"Cas12a",FRATN,A0Q7Q2,CS12A,1,63,9,99,97,87,53,19,106,173,109,13,100,28,54,35,79,51,50,8,67
+"Cas4",FRATN,A0Q7Q1,A0Q7Q1,1,7,4,14,6,6,8,5,16,21,9,4,8,3,8,4,11,8,6,0,15
+"Cas1",FRATN,A0Q7Q0,A0Q7Q0,1,12,8,17,23,28,15,4,24,34,30,7,19,6,15,16,20,12,25,3,16
+"Cas2",FRATN,A0Q7P9,A0Q7P9,1,6,0,6,6,7,2,1,7,7,9,2,6,2,2,4,6,1,9,0,7
+"Cas12e",A0A357BT59,A0A357BT59,NA,1,71,11,57,77,38,66,14,44,101,96,17,49,35,37,65,53,47,53,19,36
+"Cas4",A0A357BV01,A0A357BV01,NA,1,13,7,8,18,10,7,6,15,5,15,6,8,8,7,18,9,12,13,2,7
+"Cas1",A0A357BT84,A0A357BT84,NA,1,15,3,22,23,15,18,7,29,29,31,7,10,14,14,22,17,17,17,4,14
+"Cas2",A0A357BT86,A0A357BT86,NA,1,7,1,7,9,4,5,1,7,6,11,2,2,1,1,6,6,1,7,2,6
+"Cas12b1",ALIAG,T0D7A2,CS12B,1,88,11,69,98,45,73,29,40,70,108,21,41,44,57,111,60,35,72,25,32
+"Cas4-Cas1",A0A9E6ZHP2,A0A9E6ZHP2,NA,1,36,6,36,32,18,43,13,28,22,61,15,16,25,18,50,33,27,36,5,16
+"Cas2",ALIAG,T0C2X2,T0C2X2,1,5,2,8,3,4,5,2,6,5,10,4,1,1,8,9,5,2,11,1,5
+"Cas4-Cas1",A0A1G2YUS0,A0A1G2YUS0,NA,1,67,10,33,36,22,31,11,40,24,56,17,16,38,21,40,32,26,33,4,17
+"Cas2",A0A1G2YUR9,A0A1G2YUR9,NA,1,6,4,8,8,4,5,1,11,5,8,4,1,3,5,9,2,3,6,1,3
+"Cas12b2",A0A1G2YUT2,A0A1G2YUT2,NA,1,43,13,37,57,29,48,22,41,94,59,13,37,32,19,58,41,28,31,17,24
+"Cas12i",Ga0208225_100001036,Ga0208225_100001036,NA,1,64,14,62,74,46,53,23,63,126,98,27,72,38,39,48,78,47,60,12,49
+"Cas12h",Ga0180438_100006283,Ga0180438_100006283,NA,1,59,11,53,69,34,54,21,43,78,93,16,28,35,28,61,55,31,52,12,37
+"Cas1",UPI0007C2850C,UPI0007C2850C,NA,1,14,2,16,21,12,17,15,21,21,38,4,10,15,10,27,32,19,19,8,17
+"Cas12c",UPI0007C30103,UPI0007C30103,NA,1,91,13,65,74,59,63,33,77,86,140,17,66,51,58,67,125,58,63,13,33
+"Cas1",A0A1L9GZC2,A0A1L9GZC2,NA,1,14,3,13,21,23,25,9,24,28,29,7,9,19,11,23,28,17,16,8,20
+"Cas12d",A0A1L9GZ17,A0A1L9GZ17,NA,1,49,15,60,95,55,50,12,83,124,127,14,58,33,31,65,92,36,60,17,49
+"Cas1",A0A482D445,A0A482D445,NA,1,15,5,18,26,18,17,2,32,34,33,6,14,7,13,21,16,19,12,1,18
+"Cas2",A0A482D3L8,A0A482D3L8,NA,1,5,4,7,8,7,3,1,9,11,6,3,5,2,2,5,11,2,6,1,2
+"Cas4",A0A482D482,A0A482D482,NA,1,7,6,11,14,15,5,2,19,30,13,5,9,6,8,8,8,9,8,1,11
+"Cas12f1",A0A482D2S9,A0A482D2S9,NA,1,24,5,22,38,28,28,8,40,63,37,7,34,15,22,30,37,22,20,7,20
+"C2c10",A0A9W3JGX3,A0A9W3JGX3,NA,1,16,10,13,29,15,22,10,45,50,29,8,38,8,33,21,30,23,20,6,24
+"Cas12f",A0A482D2T6,A0A482D2T6,NA,1,17,9,24,44,27,22,7,41,90,47,7,47,11,17,34,33,14,18,3,22
+"Cas1",A0A482D3Z6,A0A482D3Z6,NA,1,11,4,17,29,18,19,2,38,34,32,5,17,8,8,17,26,13,13,1,14
+"Cas2",A0A482D4I6,A0A482D4I6,NA,1,2,4,8,7,6,4,0,18,8,6,2,6,1,3,6,6,3,3,1,4
+"Cas4",A0A482D3B0,A0A482D3B0,NA,1,9,4,7,15,7,4,1,14,28,19,7,11,9,7,11,5,9,8,0,16
+"C2c8",RIPO1,B7K606,B7K606,1,28,11,20,31,19,23,18,23,52,56,7,39,16,28,28,27,29,14,8,17
+"C2c9",A0A7D4LAR1,A0A7D4LAR1,NA,1,57,5,27,33,17,34,10,9,39,46,7,28,18,19,58,40,30,33,8,22
+"Cas1",A0A2H9L0L4,A0A2H9L0L4,NA,1,30,4,15,23,11,30,7,24,22,36,7,15,9,11,28,21,5,17,4,11
+"Cas2",A0A2H9KZH3,A0A2H9KZH3,NA,1,10,5,6,9,6,5,3,12,16,4,3,4,3,2,5,12,0,7,1,1
+"Cas4",A0A2H9KYT0,A0A2H9KYT0,NA,1,10,8,7,19,13,14,1,11,20,11,7,3,7,6,15,8,10,9,4,10
+"Cas12f3",A0A2H9KYV8,A0A2H9KYV8,NA,1,25,7,27,43,12,32,8,31,60,44,10,32,21,17,43,37,24,24,5,16
+"TnsB",RIPO1,B7JWD5,B7JWD5,1,38,4,28,58,18,30,21,54,61,50,14,41,26,46,42,43,37,31,9,26
+"TnsC",RIPO1,B7JWD6,B7JWD6,1,18,4,15,23,10,20,8,16,19,40,6,11,12,8,19,18,15,14,4,16
+"tniQ",RIPO1,B7JWD7,B7JWD7,1,7,8,1,16,7,16,5,6,13,18,6,1,10,7,11,14,3,6,4,7
+"Cas12k",RIPO1,B7JWD9,B7JWD9,1,39,9,20,30,20,20,18,49,54,77,6,45,31,73,28,43,46,16,11,25
+"Cas13a",LEPSD,P0DOC6,CS13A,1,28,7,102,145,72,37,11,176,212,116,16,148,10,24,54,60,47,49,5,70
+"Cas1",A0A510JKT1,A0A510JKT1,NA,1,14,3,20,27,13,5,8,36,26,28,6,25,6,13,12,22,4,17,2,17
+"Cas2",A0A510JQG4,A0A510JQG4,NA,1,3,0,3,12,6,4,0,9,12,10,7,2,2,7,5,8,5,4,0,6
+"Cas13d",UPI0003D9600D,UPI0003D9600D,NA,1,56,12,65,65,46,43,10,69,101,84,28,68,15,18,48,61,34,48,1,46
+"Cas1",UPI0003D863A8,UPI0003D863A8,NA,1,19,7,18,24,14,19,4,24,24,42,6,14,11,10,20,28,17,18,1,20
+"Cas2",UPI0003D92D81,UPI0003D92D81,NA,1,0,1,8,5,3,6,3,5,11,8,2,5,2,3,5,5,7,9,1,7
+"Cas13c",UPI0004817C16,UPI0004817C16,NA,1,20,7,67,119,52,28,9,121,191,116,15,95,9,25,42,63,39,42,2,59
+"Cas13b1",9BACT,E6K398,E6K398,1,52,6,61,87,70,36,28,71,118,120,30,89,41,50,66,49,52,40,14,47
+"Csx28",9BACT,E6K399,E6K399,1,13,2,4,18,8,4,3,19,18,14,5,11,1,9,10,11,8,5,1,13
+"Csx27",9FLAO,K1MDP1,K1MDP1,1,12,3,8,10,18,12,2,27,15,26,6,10,5,4,6,16,12,13,3,11
+"Cas13b2",9FLAO,K1LVU1,K1LVU1,1,57,7,70,137,67,42,20,80,175,103,13,73,32,64,52,46,45,65,9,67

pychnosz/data/extdata/protein/Cas/Cas_uniprot.csv

@@ -0,0 +1,186 @@
+Class,Subtype,Organism,"Locus tag",Accession,Legacy,Systematic,Effector,UniProt,Protein,Note
+1,I-A,"Archaeoglobus fulgidus",AF1859,,,cas6,FALSE,O28420,Y1859_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1870,,csa5,cas11,TRUE,O28409,Y1870_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1871,,,cas7,TRUE,O28408,O28408_ARCFU,"NCBI: incomplete sequence, no link out; found by interpolating UniProt accessions"
+1,I-A,"Archaeoglobus fulgidus",AF1872,,,cas5,TRUE,O28407,O28407_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1873,,,cas8a1,TRUE,O28406,Y1873_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1874,,,cas3',FALSE,O28405,O28405_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1875,,,cas3'',FALSE,O28404,O28404_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1876,,,cas2,FALSE,O28403,CAS2A_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1877,,,cas4,FALSE,O28402,O28402_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1878,,,cas1,FALSE,O28401,CAS1A_ARCFU,
+1,I-A,"Archaeoglobus fulgidus",AF1879,,csa1,cas4,FALSE,O28400,O28400_ARCFU,
+1,I-B,"Clostridium kluyveri",CKL_2758,,,cas6,FALSE,A5N0X4,A5N0X4_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2757,,csh1,cas8b1,TRUE,A5N0X3,A5N0X3_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2756,,csh2,cas7,TRUE,A5N0X2,A5N0X2_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2755,,,cas5,TRUE,A5N0X1,A5N0X1_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2754,,,cas3,FALSE,A5N0X0,A5N0X0_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2753,,,cas4,FALSE,A5N0W9,A5N0W9_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2752,,,cas1,FALSE,A5N0W8,A5N0W8_CLOK5,
+1,I-B,"Clostridium kluyveri",CKL_2751,,,cas2,FALSE,A5N0W7,A5N0W7_CLOK5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0336,,,cas3,FALSE,Q9KFY4,Q9KFY4_HALH5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0337,,,cas5,TRUE,Q9KFY3,Q9KFY3_HALH5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0338,,,cas8c,TRUE,Q9KFY2,Q9KFY2_HALH5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0339,,,cas7,TRUE,Q9KFY1,Q9KFY1_HALH5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0340,,,cas4,FALSE,Q9KFY0,Q9KFY0_HALH5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0341,,,cas1,FALSE,Q9KFX9,Q9KFX9_HALH5,
+1,I-C,"Halalkalibacterium halodurans C-125",BH0342,,,cas2,FALSE,Q9KFX8,CAS2_HALH5,
+1,I-G,"Geobacter sulfurreducens",GSU0051,,,cas3,FALSE,Q74H42,Q74H42_GEOSL,
+1,I-G,"Geobacter sulfurreducens",GSU0052,,,cas8u2,TRUE,Q74H41,Q74H41_GEOSL,
+1,I-G,"Geobacter sulfurreducens",GSU0053,,csb1,cas7,TRUE,Q74H40,Q74H40_GEOSL,
+1,I-G,"Geobacter sulfurreducens",GSU0054,,csb2,cas5-cas6,TRUE,Q74H39,Q74H39_GEOSL,
+1,I-G,"Geobacter sulfurreducens",GSU0057,,,cas4-cas1,FALSE,Q74H36,CS4F1_GEOSL,
+1,I-G,"Geobacter sulfurreducens",GSU0058,,,cas2,FALSE,Q74H35,CAS2_GEOSL,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0527,"WP_015783167, WP_012593878",,cas3',FALSE,B7JVN0,B7JVN0_RIPO1,"RefSeq and UniProt have active records for strain 8801 (not 8802)"
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0526,"WP_015783166, WP_012593877",,cas3''-cas10d,TRUE,B7JVM9,B7JVM9_RIPO1,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0525,"WP_015783165, WP_012593876",csc2,cas7,TRUE,B7JVM8,B7JVM8_RIPO1,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0524,"WP_015783164, WP_012593875",csc1,cas5,TRUE,B7JVM7,B7JVM7_RIPO1,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0523,"WP_015783163, WP_012593874",,cas6,FALSE,B7JVM6,B7JVM6_RIPO1,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0522,"WP_015783162, WP_012593873",,cas4,FALSE,B7JVM5,B7JVM5_RIPO1,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0521,"WP_015783161, WP_012593872",,cas1,FALSE,B7JVM4,B7JVM4_RIPO1,
+1,I-D,"Rippkaea orientalis (strain PCC 8801 / RF-1)",Cyan8802_0520,"WP_015783160, WP_012593871",,cas2,FALSE,B7JVM3,B7JVM3_RIPO1,
+1,I-E,"Escherichia coli K12",ygcB,,,cas3,FALSE,P38036,CAS3_ECOLI,
+1,I-E,"Escherichia coli K12","ygcL (casA)",,cse1,cas8e,TRUE,Q46901,CSE1_ECOLI,
+1,I-E,"Escherichia coli K12","ygcK (casB)",,cse2,cas11,TRUE,P76632,CSE2_ECOLI,
+1,I-E,"Escherichia coli K12","ygcJ (casC)",,,cas7,TRUE,Q46899,CASC_ECOLI,
+1,I-E,"Escherichia coli K12","ygcI (casD)",,,cas5,TRUE,Q46898,CAS5_ECOLI,
+1,I-E,"Escherichia coli K12","ygcH (casE)",,,cas6,TRUE,Q46897,CAS6_ECOLI,
+1,I-E,"Escherichia coli K12",ygbT,,,cas1,FALSE,Q46896,CAS1_ECOLI,
+1,I-E,"Escherichia coli K12",ygbF,,,cas2,FALSE,P45956,CAS2_ECOLI,
+1,I-F1,"Yersinia pseudo-tuberculosis",YPK_1644,,,cas1,FALSE,A0A0H3B3U5,A0A0H3B3U5_YERPY,
+1,I-F1,"Yersinia pseudo-tuberculosis",YPK_1645,,,cas2-cas3,FALSE,A0A0H3B287,A0A0H3B287_YERPY,
+1,I-F1,"Yersinia pseudo-tuberculosis",YPK_1646,,csy1,cas8f1,TRUE,A0A0H3B0Q7,A0A0H3B0Q7_YERPY,
+1,I-F1,"Yersinia pseudo-tuberculosis",YPK_1647,,csy2,cas5f1,TRUE,A0A0H3B1X5,A0A0H3B1X5_YERPY,
+1,I-F1,"Yersinia pseudo-tuberculosis",YPK_1648,,csy3,cas7f1,TRUE,A0A0H3B2X2,A0A0H3B2X2_YERPY,
+1,I-F1,"Yersinia pseudo-tuberculosis",YPK_1649,,csy4,cas6f,TRUE,A0A0H3B3V0,A0A0H3B3V0_YERPY,
+1,I-F3,"Vibrio crassostreae J5 20",VCR20J5_310108,CDT46946,,tnsA,FALSE,,UPI000637FC9D,"UniParc sequence"
+1,I-F3,"Vibrio crassostreae J5 20",,,,tnsB,FALSE,,,
+1,I-F3,"Vibrio crassostreae J5 20",,,,tnsC,FALSE,,,
+1,I-F3,"Vibrio crassostreae J5 20",,,,tnsD,FALSE,,,
+1,I-F3,"Vibrio crassostreae J5 20",VCR20J5_310090,CDT46719,csy2,cas8f3-cas5f3,TRUE,,UPI00063793EA,"UniParc sequence"
+1,I-F3,"Vibrio crassostreae J5 20",VCR20J5_310089,CDT46710,csy3,cas7f3,TRUE,,UPI000633A6D2,"UniParc sequence"
+1,I-F3,"Vibrio crassostreae J5 20",VCR20J5_310088,CDT46699,,cas6f,TRUE,,UPI000631609A,"UniParc sequence"
+1,I-F2,"Shewenella putrefaciens CN-32",Sputcn32_1819,,,cas1,FALSE,A4Y6F9,A4Y6F9_SHEPC,
+1,I-F2,"Shewenella putrefaciens CN-32",Sputcn32_1820,,,cas2-cas3,FALSE,A4Y6G0,A4Y6G0_SHEPC,
+1,I-F2,"Shewenella putrefaciens CN-32",Sputcn32_1821,,PBPRB1993,cas7f2,TRUE,A4Y6G1,A4Y6G1_SHEPC,
+1,I-F2,"Shewenella putrefaciens CN-32",Sputcn32_1822,,PBPRB1992,cas5f2,TRUE,A4Y6G2,A4Y6G2_SHEPC,
+1,I-F2,"Shewenella putrefaciens CN-32",Sputcn32_1823,,,cas6f,TRUE,A4Y6G3,A4Y6G3_SHEPC,
+1,IV-A,"Thioalkalivibrio sp. K90mix",TK90_2699,,csf4,dinG,FALSE,D3SGE4,D3SGE4_THISK,
+1,IV-A,"Thioalkalivibrio sp. K90mix",TK90_2700,,csf5,cas6,FALSE,D3SGE5,D3SGE5_THISK,
+1,IV-A,"Thioalkalivibrio sp. K90mix",TK90_2701,,csf1,cas8-like,TRUE,D3SGE6,D3SGE6_THISK,
+1,IV-A,"Thioalkalivibrio sp. K90mix",TK90_2702,,csf2,cas7,TRUE,D3SGE7,D3SGE7_THISK,
+1,IV-A,"Thioalkalivibrio sp. K90mix",TK90_2703,,csf3,cas5,TRUE,D3SGE8,D3SGE8_THISK,
+1,IV-B,"Rhodococcus jostii RHA1",RHA1_ro10068,,,cysH-like,FALSE,Q0RWS5,Q0RWS5_RHOJR,
+1,IV-B,"Rhodococcus jostii RHA1",RHA1_ro10069,,csf1,cas8-like,TRUE,Q0RWS4,Q0RWS4_RHOJR,
+1,IV-B,"Rhodococcus jostii RHA1",RHA1_ro10070,,,cas11,TRUE,Q0RWS3,Q0RWS3_RHOJR,
+1,IV-B,"Rhodococcus jostii RHA1",RHA1_ro10071,,csf2,cas7,TRUE,Q0RWS2,Q0RWS2_RHOJR,"Pfam: RAMP superfamily protein"
+1,IV-B,"Rhodococcus jostii RHA1",RHA1_ro10072,,csf3,cas5,TRUE,Q0RWS1,Q0RWS1_RHOJR,
+1,IV-C,"Thermoflexia bacterium",,,,LS,TRUE,,,
+1,IV-C,"Thermoflexia bacterium",D6793_05715,,,cas11,TRUE,A0A3M1DV11,A0A3M1DV11_9CHLR,
+1,IV-C,"Thermoflexia bacterium",D6793_05705,,csf2,cas7,TRUE,A0A3M1DW31,A0A3M1DW31_9CHLR,
+1,IV-C,"Thermoflexia bacterium",D6793_05700,,,cas5,TRUE,A0A3M1DYX3,A0A3M1DYX3_9CHLR,"UniProt: Type III-B CRISPR module RAMP protein Cmr6"
+1,III-A,"Staphylococcus epidermidis",SERP2455,,,cas6,FALSE,Q5HK95,Q5HK95_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2461,,,cas10,TRUE,Q5HK89,Q5HK89_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2460,,csm2,cas11,TRUE,Q5HK90,Q5HK90_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2459,,csm3,cas7,TRUE,Q5HK91,Q5HK91_STAEQ,"Pfam: RAMPs 1 hit"
+1,III-A,"Staphylococcus epidermidis",SERP2458,,csm4,cas5,TRUE,Q5HK92,Q5HK92_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2457,,csm5,cas7,TRUE,Q5HK93,Q5HK93_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2456,,,csm6,FALSE,Q5HK94,Q5HK94_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2463,,,cas1,FALSE,Q5HK87,Q5HK87_STAEQ,
+1,III-A,"Staphylococcus epidermidis",SERP2462,,,cas2,FALSE,Q5HK88,Q5HK88_STAEQ,
+1,III-D,"Synechocystis sp. 6803",sll7067,,,cas10,TRUE,Q6ZED1,Q6ZED1_SYNY3,
+1,III-D,"Synechocystis sp. 6803",sll7066,,csx10,cas7-cas5,TRUE,Q6ZED2,Q6ZED2_SYNY3,"GenBank: Regions Cas7, Cas5"
+1,III-D,"Synechocystis sp. 6803",sll7063,,csm2,cas11,TRUE,Q6ZED5,Q6ZED5_SYNY3,
+1,III-D,"Synechocystis sp. 6803",sll7065,,csm5,cas7-cas7,TRUE,Q6ZED3,Q6ZED3_SYNY3,"GenBank: Regions Cas7, Cas7"
+1,III-D,"Synechocystis sp. 6803",sll7064,,all1473,csx19,TRUE,Q6ZED4,Q6ZED4_SYNY3,
+1,III-D,"Synechocystis sp. 6803",,,csm5,cas7,TRUE,,,
+1,III-E,"Candidatus Scalindua brodae",SCABRO_02601,,,TPR+caspase,FALSE,A0A0B0EKL4,A0A0B0EKL4_9BACT,"UniProt: CHAT domain proteion"
+1,III-E,"Candidatus Scalindua brodae",SCABRO_02597,,csm3+csm2+csm5(3),"cas7(3),cas11",TRUE,A0A0B0EGF3,A0A0B0EGF3_9BACT,"Pfam: RAMPs 4 hits"
+1,III-E,"Candidatus Scalindua brodae",,,,RT,FALSE,,,
+1,III-E,"Candidatus Scalindua brodae",SCABRO_02595,,,cas1,FALSE,A0A0B0EEW2,A0A0B0EEW2_9BACT,
+1,III-E,"Candidatus Scalindua brodae",SCABRO_02593,,,cas2,FALSE,A0A0B0ELU0,A0A0B0ELU0_9BACT,
+1,III-F,"Thermotoga lettingae TMO",Tlet_0097,,,cas10,TRUE,A8F3D4,A8F3D4_PSELT,
+1,III-F,"Thermotoga lettingae TMO",Tlet_0098,,,cas5,TRUE,A8F3D5,A8F3D5_PSELT,
+1,III-F,"Thermotoga lettingae TMO",Tlet_0099,,,cas11,TRUE,A8F3D6,A8F3D6_PSELT,
+1,III-F,"Thermotoga lettingae TMO",Tlet_0100,,csm3,cas7,TRUE,A8F3D7,A8F3D7_PSELT,"Pfam: RAMPs 1 hit"
+1,III-C,"Methanothermobacter thermoautotrophicus",MTH328,,cmr1,cas7,TRUE,O26428,O26428_METTH,"Pfam: RAMPs 1 hit"
+1,III-C,"Methanothermobacter thermoautotrophicus",MTH327,,cmr6,cas7,TRUE,O26427,O26427_METTH,"Pfam: RAMPs 1 hit"
+1,III-C,"Methanothermobacter thermoautotrophicus",MTH326,,,cas10,TRUE,O26426,O26426_METTH,
+1,III-C,"Methanothermobacter thermoautotrophicus",MTH325,,cmr4,cas7,TRUE,O26425,O26425_METTH,"Pfam: RAMPs 1 hit"
+1,III-C,"Methanothermobacter thermoautotrophicus",MTH324,,cmr5,cas11,TRUE,O26424,O26424_METTH,
+1,III-C,"Methanothermobacter thermoautotrophicus",MTH323,,cmr3,cas5,TRUE,O26423,O26423_METTH,
+1,III-B,"Pyrococcus furiosus",PF1130,,cmr1,cas7,TRUE,Q8U1S5,CMR1A_PYRFU,
+1,III-B,"Pyrococcus furiosus",PF1129,,,cas10,TRUE,Q8U1S6,CMR2_PYRFU,
+1,III-B,"Pyrococcus furiosus",PF1128,,cmr3,cas5,TRUE,Q8U1S7,CMR3_PYRFU,
+1,III-B,"Pyrococcus furiosus",PF1126,,cmr4,cas7,TRUE,Q8U1S9,CMR4_PYRFU,
+1,III-B,"Pyrococcus furiosus",PF1125,,cmr5,cas11,TRUE,Q8U1T0,CMR5_PYRFU,
+1,III-B,"Pyrococcus furiosus",PF1131,,,cas6,FALSE,Q8U1S4,CAS6_PYRFU,
+1,III-B,"Pyrococcus furiosus",PF1124,,cmr6,cas7,TRUE,Q8U1T1,CMR6_PYRFU,
+2,II-B,"Legionella pneumophila str. Paris",lpp0160,,,cas9,TRUE,A0AAN5PKD3,A0AAN5PKD3_LEGPN,
+2,II-B,"Legionella pneumophila str. Paris",lpp0161,,,cas1,FALSE,A0A2U8U9X9,A0A2U8U9X9_LEGPN,
+2,II-B,"Legionella pneumophila str. Paris",lpp0162,,,cas2,FALSE,A0A4T1YC98,A0A4T1YC98_LEGPN,
+2,II-B,"Legionella pneumophila str. Paris",lpp0163,,,cas4,FALSE,A0A2U8U9S0,A0A2U8U9S0_LEGPN,
+2,II-A,"Streptococcus thermophilus",str0657,,,cas9,TRUE,G3ECR1,CAS9_STRTR,
+2,II-A,"Streptococcus thermophilus",str0658,,,cas1,FALSE,G3ECR2,CAS1_STRTR,
+2,II-A,"Streptococcus thermophilus",str0659,,,cas2,FALSE,G3ECR3,CAS2_STRTR,
+2,II-A,"Streptococcus thermophilus",str0660,,,csn2,FALSE,G3ECR4,CSN2_STRTR,
+2,II-C1,"Neisseria lactamica 020-06",NLA_17660,,,cas9,TRUE,E4ZF34,E4ZF34_NEIL0,
+2,II-C1,"Neisseria lactamica 020-06",NLA_17670,,,cas1,FALSE,E4ZF35,E4ZF35_NEIL0,
+2,II-C1,"Neisseria lactamica 020-06",NLA_17680,,,cas2,FALSE,E4ZF36,E4ZF36_NEIL0,
+2,II-C2,"Micrarchaeum acidiphilum ARMAN-1",BK997_03320,,,cas9,TRUE,A0A1L9GUT8,A0A1L9GUT8_9ARCH,
+2,II-C2,"Micrarchaeum acidiphilum ARMAN-1",BK997_03325,,,cas4,FALSE,A0A1L9GUY1,A0A1L9GUY1_9ARCH,
+2,II-C2,"Micrarchaeum acidiphilum ARMAN-1",BK997_03330,,,cas2,FALSE,A0A1L9GUR0,A0A1L9GUR0_9ARCH,
+2,II-C2,"Micrarchaeum acidiphilum ARMAN-1",BK997_03335,,,cas1,FALSE,A0A1L9GUR2,A0A1L9GUR2_9ARCH,
+2,V-A,"Francisella cf. novicida Fx1",FNFX1_1431,,cpf1,cas12a,TRUE,A0Q7Q2,CS12A_FRATN,
+2,V-A,"Francisella cf. novicida Fx1",FNFX1_1430,,,cas4,FALSE,A0Q7Q1,A0Q7Q1_FRATN,
+2,V-A,"Francisella cf. novicida Fx1",FNFX1_1429,,,cas1,FALSE,A0Q7Q0,A0Q7Q0_FRATN,
+2,V-A,"Francisella cf. novicida Fx1",FNFX1_1428,,,cas2,FALSE,A0Q7P9,A0Q7P9_FRATN,
+2,V-E,"Deltaproteobacteria bacterium",A2Z89_08250,,casX,cas12e,TRUE,A0A357BT59,A0A357BT59_UNCDE,
+2,V-E,"Deltaproteobacteria bacterium",A2Z89_08255,,,cas4,FALSE,A0A357BV01,A0A357BV01_UNCDE,
+2,V-E,"Deltaproteobacteria bacterium",A2Z89_08260,,,cas1,FALSE,A0A357BT84,A0A357BT84_UNCDE,
+2,V-E,"Deltaproteobacteria bacterium",A2Z89_08265,,,cas2,FALSE,A0A357BT86,A0A357BT86_UNCDE,
+2,V-B1,"Alicyclobacillus acidoterrestris",N007_06525,,c2c1,cas12b1,TRUE,T0D7A2,CS12B_ALIAG,
+2,V-B1,"Alicyclobacillus acidoterrestris",N007_06530,,,cas4-cas1,FALSE,A0A9E6ZHP2,A0A9E6ZHP2_ALIAG,
+2,V-B1,"Alicyclobacillus acidoterrestris",N007_06535,,,cas2,FALSE,T0C2X2,T0C2X2_ALIAG,
+2,V-B2,"Planctomycetes bacterium RBG_13_46_10",A2167_01675,,,cas4-cas1,FALSE,A0A1G2YUS0,A0A1G2YUS0_9BACT,
+2,V-B2,"Planctomycetes bacterium RBG_13_46_10",A2167_01680,,,cas2,FALSE,A0A1G2YUR9,A0A1G2YUR9_9BACT,
+2,V-B2,"Planctomycetes bacterium RBG_13_46_10",A2167_01685,,,cas12b2,TRUE,A0A1G2YUT2,A0A1G2YUT2_9BACT,
+2,V-I,"Freshwater metagenome (JGI)",Ga0208225_100001036,,,cas12i,TRUE,,Ga0208225_100001036,"Downloaded from JGI Data Portal (taxon ID: 3300020508)"
+2,V-H,"Hypersaline lake sediment metagenome (JGI )",Ga0180438_100006283,,,cas12h,TRUE,,Ga0180438_100006283,"Downloaded from JGI Data Portal (taxon ID: 3300017971)"
+2,V-C,"Oleiphilus sp.",A3715_16890,,,cas1,FALSE,,UPI0007C2850C,"UniParc sequence"
+2,V-C,"Oleiphilus sp.",A3715_16885,,c2c3,cas12c,TRUE,,UPI0007C30103,"UniParc sequence"
+2,V-D,"Bacterium CG09_39_24",BK003_02070,,,cas1,FALSE,A0A1L9GZC2,A0A1L9GZC2_UNCXX,
+2,V-D,"Bacterium CG09_39_24",BK003_02075,,casY,cas12d,TRUE,A0A1L9GZ17,A0A1L9GZ17_UNCXX,
+2,V-F1,"Uncultured archaeon",NDOCEIEL_00008,QBM01133,,cas1,FALSE,A0A482D445,A0A482D445_UNCAX,
+2,V-F1,"Uncultured archaeon",NDOCEIEL_00009,QBM01134,,cas2,FALSE,A0A482D3L8,A0A482D3L8_UNCAX,
+2,V-F1,"Uncultured archaeon",NDOCEIEL_00010,QBM01135,,cas4,FALSE,A0A482D482,A0A482D482_UNCAX,
+2,V-F1,"Uncultured archaeon",NDOCEIEL_00011,QBM01136,cas14a,cas12f1,TRUE,A0A482D2S9,A0A482D2S9_UNCAX,
+2,V-U3,"Bacillus thuringiensis HD-771",BTG_31928,,,c2c10,TRUE,A0A9W3JGX3,A0A9W3JGX3_BACTU,
+2,V-F2,"Uncultured archaeon",ICDLJNLD_00052,QBM01237,cas14b,cas12f,TRUE,A0A482D2T6,A0A482D2T6_UNCAX,
+2,V-F2,"Uncultured archaeon",ICDLJNLD_00049,QBM01234,,cas1,FALSE,A0A482D3Z6,A0A482D3Z6_UNCAX,
+2,V-F2,"Uncultured archaeon",ICDLJNLD_00050,QBM01235,,cas2,FALSE,A0A482D4I6,A0A482D4I6_UNCAX,
+2,V-F2,"Uncultured archaeon",ICDLJNLD_00051,QBM01236,,cas4,FALSE,A0A482D3B0,A0A482D3B0_UNCAX,
+2,V-U2,"Rippkaea orientalis (strain PCC 8801 / RF-1)",PCC8801_4127,ACK68059,,c2c8,TRUE,B7K606,B7K606_RIPO1,
+2,V-U4,"Rothia dentocariosa M567",HMPREF0734_01291,EFJ78236,,c2c9,TRUE,A0A7D4LAR1,A0A7D4LAR1_9MICC,
+2,V-F3,"Candidatus Micrarchaeota archaeon",COU37_03065,PIT84483,,cas1,FALSE,A0A2H9L0L4,A0A2H9L0L4_9ARCH,
+2,V-F3,"Candidatus Micrarchaeota archaeon",COU37_03060,PIT84482,,cas2,FALSE,A0A2H9KZH3,A0A2H9KZH3_9ARCH,
+2,V-F3,"Candidatus Micrarchaeota archaeon",COU37_03055,PIT84481,,cas4,FALSE,A0A2H9KYT0,A0A2H9KYT0_9ARCH,
+2,V-F3,"Candidatus Micrarchaeota archaeon",COU37_03050,PIT84480,cas14c,cas12f3,TRUE,A0A2H9KYV8,A0A2H9KYV8_9ARCH,
+2,V-U1,"Gordonia otitidis",GOOTI_RS19525,,,c2c4,TRUE,,,
+2,V-G,"Hot springs metagenome",FLYL01000025.1,,,cas12g,TRUE,,,https://www.ncbi.nlm.nih.gov/nuccore/FLYL01000025.1
+2,V-U5,"Rippkaea orientalis (strain PCC 8801 / RF-1)",PCC8801_2993,ACK66980,,tnsB,FALSE,B7JWD5,B7JWD5_RIPO1,"Transposase-like Mu"
+2,V-U5,"Rippkaea orientalis (strain PCC 8801 / RF-1)",PCC8801_2994,ACK66981,,tnsC,FALSE,B7JWD6,B7JWD6_RIPO1,
+2,V-U5,"Rippkaea orientalis (strain PCC 8801 / RF-1)",PCC8801_2995,ACK66982,,tniQ,FALSE,B7JWD7,B7JWD7_RIPO1,"Pfam: TniQ 1 hit"
+2,V-U5,"Rippkaea orientalis (strain PCC 8801 / RF-1)",PCC8801_2997,ACK66984,c2c5,cas12k,TRUE,B7JWD9,B7JWD9_RIPO1,"NCBIfam: V_Cas12k 1 hit"
+2,VI-A,"Leptotrichia shahii",B031_RS0110445,WP_018451595,c2c2,cas13a,TRUE,P0DOC6,CS13A_LEPSD,
+2,VI-A,"Leptotrichia shahii",B031_RS0110440,WP_018451594,,cas1,FALSE,A0A510JKT1,A0A510JKT1_9FUSO,
+2,VI-A,"Leptotrichia shahii",B031_RS10965,WP_018451593,,cas2,FALSE,A0A510JQG4,A0A510JQG4_9FUSO,
+2,VI-D,"Ruminococcus bicirculans",RBI_RS11595,,,WYL,FALSE,,,
+2,VI-D,"Ruminococcus bicirculans",RBI_RS12820,WP_041337480,,cas13d,TRUE,,UPI0003D9600D,"UniParc sequence"
+2,VI-D,"Ruminococcus bicirculans",RBI_RS11600,WP_041337297,,cas1,FALSE,,UPI0003D863A8,"UniParc sequence"
+2,VI-D,"Ruminococcus bicirculans",RBI_RS11605,WP_041337298,,cas2,FALSE,,UPI0003D92D81,"UniParc sequence"
+2,VI-C,"Fusobacterium perfoetens",T364_RS0105110,WP_027128616,c2c7,cas13c,TRUE,,UPI0004817C16,"UniParc sequence"
+2,VI-B1,"Segatella buccae ATCC 33574",HMPREF6485_RS00335,WP_004343973,c2c6,cas13b1,TRUE,E6K398,E6K398_9BACT,
+2,VI-B1,"Segatella buccae ATCC 33574",HMPREF6485_RS00340,WP_004343974,,csx28,FALSE,E6K399,E6K399_9BACT,
+2,VI-B2,"Bergeyella zoohelcum",HMPREF9699_02006,EKB54194,,csx27,FALSE,K1MDP1,K1MDP1_9FLAO,
+2,VI-B2,"Bergeyella zoohelcum",HMPREF9699_02005,EKB54193,c2c6,cas13b2,TRUE,K1LVU1,K1LVU1_9FLAO,

pychnosz/data/extdata/protein/Cas/download.R

@@ -0,0 +1,34 @@
+# Cas/download.R
+# Download Cas sequences from UniProt
+# 20250522
+
+dat <- read.csv("Cas_uniprot.csv")
+
+# Loop over UniProt entries
+for(UniProt in dat$UniProt) {
+  if(UniProt == "") next
+  file <- paste0(UniProt, ".fasta")
+  # Skip if already downloaded
+  if(file.exists(file.path("fasta/", file))) next
+  URL <- paste0("https://rest.uniprot.org/uniprotkb/", file)
+  cmd <- paste("wget", URL)
+  print(cmd)
+  system(cmd)
+  # Move downloaded file to fasta directory
+  file.rename(file, file.path("fasta/", file))
+}
+
+# Loop over Protein to get UniParc sequences
+for(Protein in dat$Protein) {
+  if(Protein == "") next
+  if(!grepl("^UPI", Protein)) next
+  file <- paste0(Protein, ".fasta")
+  # Skip if already downloaded
+  if(file.exists(file.path("fasta/", file))) next
+  URL <- paste0("https://rest.uniprot.org/uniparc/", file)
+  cmd <- paste("wget", URL)
+  print(cmd)
+  system(cmd)
+  # Move downloaded file to fasta directory
+  file.rename(file, file.path("fasta/", file))
+}

pychnosz/data/extdata/protein/Cas/mkaa.R

@@ -0,0 +1,34 @@
+# Cas/mkaa.R
+# Generate amino acid compositions from protein sequences
+# 20250522
+
+dat <- read.csv("Cas_uniprot.csv")
+# Use UniProt ID as the file name
+ID <- dat$UniProt
+# In case UniProt ID is missing, use alternate ID
+ID[ID == ""] <- dat$Protein[ID == ""]
+# Store ID in data frame
+dat$ID <- ID
+# Remove missing IDs
+dat <- subset(dat, ID != "")
+
+# Get amino acid composition for each protein
+aalist <- lapply(1:nrow(dat), function(iID) {
+  file <- file.path("fasta", paste0(dat$ID[iID], ".fasta"))
+  aa <- canprot::read_fasta(file)
+  # Store systematic name and ID
+  aa$protein <- dat$Systematic[iID]
+  aa$ref <- dat$ID[iID]
+  aa
+})
+
+# Convert list to data frame
+aa <- do.call(rbind, aalist)
+# Capitalize protein names
+aa$protein <- gsub("cas", "Cas", aa$protein)
+aa$protein <- gsub("csx", "Csx", aa$protein)
+aa$protein <- gsub("c2c", "C2c", aa$protein)
+aa$protein <- gsub("din", "Din", aa$protein)
+aa$protein <- gsub("tns", "Tns", aa$protein)
+# Save results
+write.csv(aa, "Cas_aa.csv", row.names = FALSE, quote = 1)

pychnosz/data/extdata/protein/POLG.csv

@@ -0,0 +1,12 @@
+protein,organism,ref,abbrv,chains,Ala,Cys,Asp,Glu,Phe,Gly,His,Ile,Lys,Leu,Met,Asn,Pro,Gln,Arg,Ser,Thr,Val,Trp,Tyr
+POLG.VP4,POL1M,UniProt,P03300,1,7,0,4,2,2,4,1,4,5,2,1,6,3,4,2,9,5,3,0,4
+POLG.VP2,POL1M,UniProt,P03300,1,21,9,10,12,8,18,5,11,5,25,8,20,18,10,13,22,24,14,8,10
+POLG.VP3,POL1M,UniProt,P03300,1,15,5,14,10,10,13,5,14,10,23,12,8,18,7,9,21,20,13,3,8
+POLG.VP1,POL1M,UniProt,P03300,1,23,2,17,11,12,17,7,12,15,20,5,14,21,9,15,24,32,26,4,16
+POLG.2A,POL1M,UniProt,P03300,1,12,6,7,9,5,16,6,8,3,8,4,8,4,7,8,8,6,10,1,13
+POLG.P2B,POL1M,UniProt,P03300,1,6,2,4,5,2,5,0,12,7,12,1,4,2,4,2,7,12,5,2,3
+POLG.P2C,POL1M,UniProt,P03300,1,22,10,15,20,14,12,8,25,23,25,13,20,15,19,19,27,15,16,4,7
+POLG.P3A,POL1M,UniProt,P03300,1,7,2,5,4,2,4,1,7,6,6,2,4,4,7,3,3,6,9,1,4
+POLG.VPg,POL1M,UniProt,P03300,1,2,0,0,0,0,2,0,1,3,1,0,2,3,1,1,0,3,2,0,1
+POLG.3C,POL1M,UniProt,P03300,1,15,3,8,9,8,18,4,13,9,11,5,9,8,7,9,9,19,13,0,5
+POLG.RNA,POL1M,UniProt,P03300,1,31,5,32,30,19,28,12,26,38,46,17,18,22,7,18,30,26,24,7,25