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 | d1iowa1 | D-Ala-D-Ala ligase, N-domain | PreATP-grasp domain | PreATP-grasp domain | 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 <-- 1.442 --> HitDALI alignment (Z-score: 4.8 Raw score:336.70) d1vl2a1 1 -KEKVVLAYS--------GGLDTSVILKWLCEKGFDVIAYVANVgqkddfvaikekalkt 51 ::::::::: :::::::::::::::::::::::::: d1iowa1 1 mTDKIAVLLGgtsaerevSLNSGAAVLAGLREGGIDAYPVDPKE---------------- 44 d1vl2a1 52 gaskvyvedlrrefvtdyiftallgnamyegryllgtaiarpliakRQVEIaEKEGAQYV 111 ::::: :::::::: d1iowa1 45 ---------------------------------------------vDVTQL-KSMGFQKV 58 d1vl2a1 112 AHGATgkGNDQ--VRFELTYAALNpnLKVISpwkdpeflakfktdlinyamekgipi 166 ::::: :::: ::::::::::: ::::: d1iowa1 59 FIALH--GRGGedGTLQGMLELMG--LPYTG---------------sgvmasalsmd 96 FAST alignment (Normalized score: 5.31 Raw score:670.10) d1vl2a1 1 -KEKVVLAYSG-----------GLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKA 48 ::::::: :::::::::::::::::::::: d1iowa1 1 MTDKIAVL---LGGTSAEREVSLNSGAAVLAGLREGGIDAYPVD---------------- 41 d1vl2a1 49 LKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL----IAKRQVEIAE 104 ::::::: d1iowa1 42 ----------------------------------------------PKEVDVTQLKS--- 52 d1vl2a1 105 KEGAQYVAHGATGKGND--QVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEK 162 :::::::::: :::: :::::::::: ::::: d1iowa1 53 -MGFQKVFIAL--HGRGGEDGTLQGMLEL--MGLPY------------------------ 83 d1vl2a1 163 GIPI------------- 166 d1iowa1 84 ----TGSGVMASALSMD 96 TMalign alignment (TM-score: 0.33 Raw score:53.98) d1vl2a1 1 ---KEKVVLAYSGGLDTSVILKWLCEK-G--------FDVIAYVANVGQKDDFVAIKEKA 48 ::::::::: :::::::::::::: : ::::::: d1iowa1 1 MTDKIAVLLGGT-SAEREVSLNSGAAVLAGLREGGIDAYPVDPK---------------- 43 d1vl2a1 49 LKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGA 108 :: :::: :::::: d1iowa1 44 -------EV----------------------------------------DVTQ-LKSMGF 55 d1vl2a1 109 -QYVA-HGAT--GKGNDQVRFELTYAALNPNLKVIS----PWK-----DPEFLAKFKTDL 155 :::: :::: :::::::::: ::::::::: : d1iowa1 56 QKVFIALHGRGG----EDGTLQGMLE-LMGLPYTGSGVMA--SALSMD------------ 96 d1vl2a1 156 INYAMEKGIPI 166 d1iowa1 97 ----------- 97 HHsearch alignment (Probability: 0.02 E-value:0.14) d1vl2a1 16 VILKWLCEKGFDVIAYVAN 34 ::::::::::::::::::: d1iowa1 25 AVLAGLREGGIDAYPVDPK 43