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 | d1e4ea1 | D-alanine:D-lactate ligase VanA, N-domain | PreATP-grasp domain | PreATP-grasp domain | 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 <-- 0.836 --> HitDALI alignment (Z-score: 3.8 Raw score:339.90) d1vl2a1 1 -KEKVVLAYS--------gGLDTSVILKWLCEKGFDVIAYVANVG-----qkddfVAIKE 46 ::::::::: :::::::::::::::::::::::::: ::::: d1e4ea1 1 nRIKVAILFGgcseehdvsVKSAIEIAANINKEKYEPLYIGITKSgvwkmcekpcAEWEN 60 d1vl2a1 47 kalktgaskvyvedlrrefvtdyiftallgnamyegryllgtaiarpliakRQVE----- 101 :::: d1e4ea1 61 ----------------------------------------------encysAVLSpdkkm 74 d1vl2a1 102 ---------iaeKEGAQYVAHGATgkGNDQ--VRFELTYAALNpnLKVISpwkdpeflak 150 :::::::::::: :::: ::::::::::: ::::: d1e4ea1 75 hgllvkknheyeINHVDVAFSALH--GKSGedGSIQGLFELSG--IPFVG---------- 120 d1vl2a1 151 fktdlinyamekgipi 166 d1e4ea1 121 ------cdiqssaicm 130 FAST alignment (Normalized score: 3.00 Raw score:441.40) d1vl2a1 1 -KEKVVLAYSG-------GLDTSVILKWLCEK-----GFDVIAYVANVGQKDDFVAIKEK 47 ::::::: ::::::::::::: ::::::::: d1e4ea1 1 NRIKVAIL---FGGCSEEHDVSVKSAIEIAA-NINKEKYEPLYIGI-------------- 42 d1vl2a1 48 ALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAE--- 104 d1e4ea1 43 ---------------------------------------------------------TKS 45 d1vl2a1 105 -----------------------------------------KEGAQYVAHGATGKGNDQ- 122 :::::::::::: d1e4ea1 46 GVWKMCEKPCAEWENENCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALH------G 99 d1vl2a1 123 -----VRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI----------- 166 ::::::::: ::::: d1e4ea1 100 KSGEDGSIQGLFEL--SGIPF----------------------------VGCDIQSSAIC 129 d1vl2a1 167 - 167 d1e4ea1 130 M 130 TMalign alignment (TM-score: 0.41 Raw score:67.91) d1vl2a1 1 -KEKVVLAYS--------GGLDTSVILKWLCEKGFDVIAYVANVGQ--KDDFVAIKEKAL 49 ::::::::: :::::::::::::::::::::::::::: : ::: :: d1e4ea1 1 NRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVW---K--MCE-KP 54 d1vl2a1 50 K------TGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQV--- 100 : ::::: ::: d1e4ea1 55 CAEWENE-----NCYSA-------------------------------------VLSPDK 72 d1vl2a1 101 ---EIA-------EKEGAQYVAHGATGKGN-DQ-VRFELTYAALNPNLKVISPWK----- 143 ::: ::::::::::::: :: :: :::::::: ::: ::::: : d1e4ea1 73 KMHGLLVKKNHEYEINHVDVAFSALH--GKSGEDGSIQGLFE-LSG-IPFVG--CDIQSS 126 d1vl2a1 144 ----DPEFLAKFKTDLINYAMEKGIPI 166 d1e4ea1 127 AICM----------------------- 130 HHsearch alignment (Probability: 0.08 E-value:0.05) d1vl2a1 1 KEKVVLAYSGG-------LDT-SVILKWLCEKGFDVIAYVANVGQ 37 ::::::::::: ::: ::::::::::::::::::::::: d1e4ea1 2 RIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSG 46