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: T0542_Ad2+3.pdb
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 | d1vi2a1 | Putative shikimate dehydrogenase YdiB | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.905 --> IntermediateDALI alignment (Z-score: 12.5 Raw score:953.20) query 1 dadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 ySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK----DV 157 :::::::::::::: :::::::: :::: :::: :::::: :: d1vl2a1 95 IAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpefLA 149 query 158 YK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaivaag 216 :: :::::::::: :::: d1vl2a1 150 KFkTDLINYAMEK----------GIPI--------------------------------- 166 query 217 ydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1vl2a1 167 -------------------------------------------------- 167 FAST alignment (Normalized score: 7.91 Raw score:1662.00) query 1 DADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 :::::::::::::::::::::: ::: ::::::::: d1vl2a1 1 -----------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVANV 35 query 60 KYSSDHSKGDAAELARRTG-LNFRTVSIEPMFD-AYMA---SLGLTGL-------AEENL 107 :::: ::::::::::::: ::::::::::::: :::: :::: ::::: d1vl2a1 36 -GQKD-DFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRYLLGTAI 90 query 108 QSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG---------AY 151 ::::::::::::::::: :::::::::: :::: :: d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALNPNLKVI 139 query 152 GPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 201 :: :::::::::: d1vl2a1 140 SP-----WKDPEFLAKFKTDLINYAME--------------------------------- 161 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1vl2a1 162 ------------------------------------------------------------ 162 query 262 WREGH----- 266 d1vl2a1 162 -----KGIPI 166 TMalign alignment (TM-score: 0.47 Raw score:124.53) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 YSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D--VY 158 :::::::::::::: :::::::: : :::::::: :: :::::: : :: d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEFLA 149 query 159 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 218 :::::::::::: : : ::: d1vl2a1 150 -KFKTDLINYAME-K------G-IPI---------------------------------- 166 query 219 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vl2a1 167 ------------------------------------------------ 167 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::: ::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK-GFD-VIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 83 TVSIEPMFDAYMASLGLTGLA--------EENLQSRLRGTTLMAISNQEGHIVLAPG--- 131 ::::::::::::::::::::: :::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 132 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRNRAA 173 :::::::::::::::::: ::: :::::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPNLKV-ISPWKDPEFLAKFKTDLINYAMEKGIPI 166
Intermediate <-- 0.695 --> HitDALI alignment (Z-score: 6.4 Raw score:552.90) d1vl2a1 1 -----------------KEKVVLAYSgGLDTSVILKWLCEKGF-DVIAYVANvgqkDDFV 42 ::::::::: :::::::::::::::: :::::::: :::: d1vi2a1 1 dgtghiraikesgfdikGKTMVLLGA-GGASTAIGAQGAIEGLkEIKLFNRR----DEFF 55 d1vl2a1 43 AIKEKALKTG------aSKVYVEDLrrefvtdyiftallgnamyegryllgtaiarplia 96 :::::::::: :::::::: d1vi2a1 56 DKALAFAQRVnentdcvVTVTDLAD----------------------------------q 81 d1vl2a1 97 KRQVEIAEkeGAQYVAHG--ATGK--GNDQvrFELTyAALNPN-LKVISPWK-------- 143 :::::::: :::::::: :::: :::: :::: :::::: :::::::: d1vi2a1 82 QAFAEALA--SADILTNGtkVGMKplENES--LVND-ISLLHPgLLVTECVYnphmtkll 136 d1vl2a1 144 ------------DPEFLAKFKTD-----------linyamekgipi 166 ::::::::::: d1vi2a1 137 qqaqqagcktidGYGMLLWQGAEqftlwtgkdfpleyvkqvmgfga 182 FAST alignment (Normalized score: 4.85 Raw score:843.30) d1vl2a1 1 -----------------KEKVVLAYSGGLDTSVILKWLCEKGF-DVIAYVANVGQKDDFV 42 :::::: ::::::::::::::::::: :::::: :::: ::: d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVL-LGAGGASTAIGAQGAIEGLKEIKLFN--RRDE-FFD 56 d1vl2a1 43 AIKEKALKTGA------SKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL-- 94 :::::::: ::::::: d1vi2a1 57 KALAFAQR---VNENTDCVVTVTD----------------------------------LA 79 d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATGKGNDQ-------------------------------- 122 :::::::::: :::::::: d1vi2a1 80 DQQAFAEALA--SADILTNG--------TKVGMKPLENESLVNDISLLHPGLLVTECVYN 129 d1vl2a1 123 ---VRFELTYAALNPNLKVISPWK-DPEFLAKFKTDLINYAMEKGIPI------------ 166 ::::::::: :::::: :::::::: d1vi2a1 130 PHMTKLLQQAQQ--AGCKTI----DGYGMLLWQ---------------GAEQFTLWTGKD 168 d1vl2a1 167 -------------- 167 d1vi2a1 169 FPLEYVKQVMGFGA 182 TMalign alignment (TM-score: 0.50 Raw score:83.42) d1vl2a1 1 -----------------KEKVVLAYSGGLDTSVILKWLCEKGFD-VIAYVANVGQKDDFV 42 :::::::: :::::::::::::::::: ::::: : :::::: d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVLLG-AGGASTAIGAQGAIEGLKEIKLFN-R--RDEFFD 56 d1vl2a1 43 AIKEKALKTG-----ASKVYVEDL----------------------RREFVTDYIFTALL 75 :::::::::: ::::::::: d1vi2a1 57 KALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGM-------------- 102 d1vl2a1 76 GNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGNDQVRFELTYAALNPN 135 ::::: :: ::::::: :: ::::::::: : ::::::::::::: :: d1vi2a1 103 ----------KPLEN-ES-LVNDISL-LH--PGLLVTECV-Y-NPHMTKLLQQAQQ-AG- 143 d1vl2a1 136 LKVISPWKD-PEFLAKFK-TD-------------------LINYAMEKGIPI 166 ::::::::: :::::::: : d1vi2a1 144 CKTIDGYGMLLWQGAEQFT-LWTGKDFPLEYVKQVMGFGA------------ 182 HHsearch alignment (Probability: 0.02 E-value:0.15) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTG 52 ::::::::::::::::::::: ::::: :::::::::::::::::::::: d1vi2a1 19 KTMVLLGAGGASTAIGAQGAI-EGLKE--IKLFNRRDEFFDKALAFAQRVN 66