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 | d1jyka_ | CTP:phosphocholine cytidylytransferase LicC | Nucleotide-diphospho-sugar transferases | Nucleotide-diphospho-sugar transferases | 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 <-- 0.822 --> HitDALI alignment (Z-score: 3.4 Raw score:385.70) d1vl2a1 1 --KEKVVLAY---------------------sggLDTSVILKWLCEKGF-DVIAYVANvg 36 :::::::: ::::::::::::::: :::::::: d1jyka_ 1 eiRVKAIILAaglgtrlrpltentpkalvqvnqkPLIEYQIEFLKEKGInDIIIIVGY-- 58 d1vl2a1 37 qkdDFVAIkEKAL-KTGAsKVYVEDLrrefvtdyiftallgnamyegryllgtaiarpLI 95 ::::: :::: :::: ::::::: :: d1jyka_ 59 ---LKEQF-DYLKeKYGV-RLVFNDK-----------------------------yadYN 84 d1vl2a1 96 AKRQVEIAEKEG-aQYVAHGAT-------------------------------------- 116 :::::::::::: :::::::: d1jyka_ 85 NFYSLYLVKEELanSYVIDADNylfknmfrndltrstyfsvyredctnewflvygddykv 144 d1vl2a1 117 --------gkGNDQ------------------------vrfelTYAALNP---------- 134 :::: ::::::: d1jyka_ 145 qdiivdskagRILSgvsfwdaptaekivsfidkayvsgefvdlYWDNMVKdnikeldvyv 204 d1vl2a1 135 nlkvispWKDP---eflAKFKtdlinyamekgipi 166 :::: :::: d1jyka_ 205 eelegnsIYEIdsvqdyRKLE----------eilk 229 FAST alignment (Normalized score: 3.01 Raw score:587.30) d1vl2a1 1 --KEKVVLAYSGG-------------------------LDTSVILKWLCEKG-FDVIAYV 32 ::::::: :::::::::::::: ::::::: d1jyka_ 1 EIRVKAIIL----AAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIV 56 d1vl2a1 33 ANVGQK-DDFVAIKEKALKTGA--SKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTA 89 ::::::: ::::: :::::: d1jyka_ 57 ------GYLKEQFD-YLKEK--YGVRLVFN------------------------------ 77 d1vl2a1 90 I------ARPLIAKRQVEIAEKEGA---QYVAHGATGKGNDQV----------------- 123 :::::::::::: ::::::: d1jyka_ 78 -DKYADYNNFYSLYLVKEE------LANSYVIDAD--------NYLFKNMFRNDLTRSTY 122 d1vl2a1 124 ------------------------------------------------------------ 124 d1jyka_ 123 FSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSG 182 d1vl2a1 124 -----RFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI------------ 166 :::::::: d1jyka_ 183 EFVDLYWDNMVKD-----------------------------------NIKELDVYVEEL 207 d1vl2a1 167 ---------------------- 167 d1jyka_ 208 EGNSIYEIDSVQDYRKLEEILK 229 TMalign alignment (TM-score: 0.49 Raw score:81.04) d1vl2a1 1 --KEKVVLAY----------------SGG-----LDTSVILKWLCEKGF-DVIAYVANVG 36 :::::::: ::: ::::::::::::::: :::::::: d1jyka_ 1 EIRVKAIILAAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGY-- 58 d1vl2a1 37 QKDDFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIA 96 : :::::: ::::::::::::::: :: : : : d1jyka_ 59 --L-KEQFDY-LKEKYGVRLVFNDKY-AD---Y------------------------N-N 85 d1vl2a1 97 KRQVEIAEKEGA-QYVAHGAT------------------G-K--GNDQV----------- 123 :::::::::::: :::::::: : : ::::: d1jyka_ 86 FYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQ 145 d1vl2a1 124 -----------RFE---------------------------LTYAALN---P--NLKV-- 138 ::: ::::::: : :::: d1jyka_ 146 DIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVE 205 d1vl2a1 139 ISPWKDPEFLA-----------KF--KTDLINYAMEKGIPI 166 ::::::: : ::: d1jyka_ 206 ----ELEGNSIYEIDSVQDYRK-LEEILK------------ 229 HHsearch alignment (Probability: 0.00 E-value:0.83) d1vl2a1 25 G 25 : d1jyka_ 48 G 48