Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1vl2a1 | Argininosuccinate synthetase, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1ccwa_ | Glutamate mutase, small subunit | Cobalamin (vitamin B12)-binding domain | Flavodoxin-like | α/β |
Query <-- 1.669 --> IntermediateDALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
Intermediate <-- 1.559 --> HitDALI alignment (Z-score: 5.5 Raw score:439.40) d1vl2a1 1 --KEKVVLA----ysgGLDTSVILKWLCEKGFDVIAYVANvgqkddfvaikekalktgas 54 ::::::: :::::::::::::::::::::::: d1ccwa_ 1 meKKTIVLGvigsdchAVGNKILDHAFTNAGFNVVNIGVL-------------------- 40 d1vl2a1 55 kvyvedlrrefvtdyiftallgnamyegryllgtaiarplIAKRQVEIAEKEGAQYVAHG 114 :::::::::::::::::::: d1ccwa_ 41 ---------------------------------------sPQELFIKAAIETKADAILVS 61 d1vl2a1 115 ATgKGNDQVRFELTyAALNP-----NLKVISPW-----------------------KDPE 146 :: ::::::::::: ::::: :::::::: :::: d1ccwa_ 62 SL-YGQGEIDCKGL-RQKCDeagleGILLYVGGnivvgkqhwpdvekrfkdmgydrVYAP 119 d1vl2a1 147 FLakfktdlinyamekgipi 166 :: d1ccwa_ 120 GT--ppevgiadlkkdlnie 137 FAST alignment (Normalized score: 5.34 Raw score:804.70) d1vl2a1 1 --KEKVVLAYSG--------GLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALK 50 :::::: ::::::::::::::::::::: d1ccwa_ 1 MEKKTIVL----GVIGSDCHAVGNKILDHAFTNAGFNVVNI------------------- 37 d1vl2a1 51 TGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL----IAKRQVEIAEKE 106 :::::::::::: d1ccwa_ 38 --------------------------------------------GVLSPQELFIKAAIET 53 d1vl2a1 107 GAQYVAHGATGK------GNDQVRFELTYAA-LNPNLKVISPWKDPEFLAKFKTDLINYA 159 :::::::: ::::::::::::: :::::::::: d1ccwa_ 54 KADAILVS----SLYGQGEIDCKGLRQKCDEAGLEGILLYVG------------------ 91 d1vl2a1 160 MEKGIPI---------------------------------------------- 166 d1ccwa_ 92 -------GNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIADLKKDLNIE 137 TMalign alignment (TM-score: 0.36 Raw score:59.65) d1vl2a1 1 ---KEKVVLAY---SGGLDTSVILKWLCEKGFDVI-AYVANV-GQKDDFVAIKEKALKTG 52 :::::::: ::::::::::::::::::::: :::::: d1ccwa_ 1 MEKKTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQ----------------- 43 d1vl2a1 53 ASKVYVE----------------DLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIA 96 :::: :: :::::: d1ccwa_ 44 ---ELFIKAAIETKADAILVSSL----------------------------YG-QGEIDC 71 d1vl2a1 97 KRQVEIAE-KEG--AQYVAHGAT--GKGNDQV-RFELTYAALNPNLKVISPWKDPEF--- 147 :::::::: ::: ::::::::: ::::: ::::::::::: :::::::::::: d1ccwa_ 72 KGLRQKCDEAGLEGILLYVGGNIVV--GKQHWPDVEKRFKDMGY-DRVYAPGTPPEVGIA 128 d1vl2a1 148 ---------LAKFKTDLINYAMEKGIPI 166 d1ccwa_ 129 DLKKDLNIE------------------- 137 HHsearch alignment (Probability: 0.60 E-value:0.05) d1vl2a1 1 KEKVVLAYSGG----LDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGA 53 ::::::::::: ::::::::::::::::: ::::::::::::::::::::: d1ccwa_ 3 KKTIVLGVIGSDCHAVGNKILDHAFTNAGFNV----VNIGVLSPQELFIKAAIETKA 55