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 | d1db3a_ | GDP-mannose 4,6-dehydratase | 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 <-- 0.743 --> HitDALI alignment (Z-score: 4.5 Raw score:485.90) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVanvgqkddfvaikekalktgASKVYVEd 60 :::::::::::::::::::::::::::::::: ::::::: d1db3a_ 1 SKVALITGVTGQDGSYLAEFLLEKGYEVHGIK------------------rpKFHLHYG- 41 d1vl2a1 61 lrrefvtdyiftallgnamyegryllgtaiARPLIAKRQVEIAEkegAQYVAHGA----- 115 :::::::::::::: :::::::: d1db3a_ 42 ----------------------------dlSDTSNLTRILREVQ---PDEVYNLGamshv 70 d1vl2a1 116 -----------tgkGNDQVRFELTYAA-LNPN-LKVISP--------------------- 141 ::::::::::::: :::: :::::: d1db3a_ 71 avsfespeytadvdAMGTLRLLEAIRFlGLEKkTRFYQAstselyglvqeipqkettpfy 130 d1vl2a1 142 ---------------------------wKDPEflaKFKT--------------------- 153 :::: :::: d1db3a_ 131 prspyavaklyaywitvnyresygmyacNGIL---FNHEsprrgetfvtrkitraiania 187 d1vl2a1 154 -------------------DLINY------------------------------------ 158 ::::: d1db3a_ 188 qglesclylgnmdslrdwgHAKDYvkmqwmmlqqeqpedfviatgvqysvrqfvemaaaq 247 d1vl2a1 159 ------------------------------------------------------------ 159 d1db3a_ 248 lgiklrfegtgveekgivvsvtghdapgvkpgdviiavdpryfrpaeetllgdptkahek 307 d1vl2a1 159 --------------------amekgipi 166 d1db3a_ 308 lgwkpeitlremvsemvandleaakkhs 335 FAST alignment (Normalized score: 3.42 Raw score:805.80) d1vl2a1 1 KEKVVLAY--SGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGA----S 54 :::::: ::::::::::::::::::::::: : d1db3a_ 1 SKVALI--TGVTGQDGSYLAEFLLEKGYEVHGI----------------------KRPKF 36 d1vl2a1 55 KVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLI------AKRQVEIAEKEGA 108 ::: ::::::::::::: d1db3a_ 37 HLH--------------------------------------YGDLSDTSNLTRILREVQP 58 d1vl2a1 109 QYVAHGATG-------------KGNDQVRFELTYAALN-------PNLKVISPWKDPEFL 148 :::::::: ::::::::::::::: ::::::: d1db3a_ 59 DEVYNLGA-MSHVAVSFESPEYTADVDAMGTLRLLEA-IRFLGLEKKTRFYQ-------- 108 d1vl2a1 149 AKFKTDLINYAMEKGIPI------------------------------------------ 166 d1db3a_ 109 ------------------ASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYR 150 d1vl2a1 167 ------------------------------------------------------------ 167 d1db3a_ 151 ESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDSLRDWGHAKD 210 d1vl2a1 167 ------------------------------------------------------------ 167 d1db3a_ 211 YVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTG 270 d1vl2a1 167 ------------------------------------------------------------ 167 d1db3a_ 271 HDAPGVKPGDVIIAVDPRYFRPAEETLLGDPTKAHEKLGWKPEITLREMVSEMVANDLEA 330 d1vl2a1 167 ----- 167 d1db3a_ 331 AKKHS 335 TMalign alignment (TM-score: 0.46 Raw score:76.29) d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVED 60 ::::::::::::::::::::::::::::::::: : ::::::::: d1db3a_ 1 SKVALITGVTGQDGSYLAEFLLEKGYEVHGIKR---------------P--KFHLHYGDL 43 d1vl2a1 61 LRR-----------------------------EFVTDYIFTALLGNAMYEGRYLLG-TAI 90 ::: ::: ::: d1db3a_ 44 SDTSNLTRILREVQPDEVYNLGAMSHVAVSFE---------------------SPEYTAD 82 d1vl2a1 91 ARPLIAKRQVEIAE-KEG--AQYVAHGATGKGN---------------------D--QVR 124 :::::::::::::: ::: ::::::::: ::: : ::: d1db3a_ 83 VDAMGTLRLLEAIRFLGLEKKTRFYQAST-SELYGLVQEIPQKETTPFYPRSPYAVAKLY 141 d1vl2a1 125 FELTYAALN---PNLKVIS----------------------------------------- 140 ::::::::: ::::::: d1db3a_ 142 AYWITVNYRESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDS 201 d1vl2a1 141 ----------P--W-------------K-------------------------------- 143 : : : d1db3a_ 202 LRDWGHAKDYVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEE 261 d1vl2a1 144 ------------------------------------------D-----PEFLAKFK-TDL 155 : :: ::::: ::: d1db3a_ 262 KGIVVSVTGHDAPGVKPGDVIIAVDPRYFRPAEETLLGDPTKAHEKLGWK-PEITLREMV 320 d1vl2a1 156 INY--AM---------EKGIPI 166 ::: : d1db3a_ 321 SEMVA-NDLEAAKKHS------ 335 HHsearch alignment (Probability: 0.20 E-value:0.01) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVAN-----VGQKDDFVAIKEKALKT 51 ::::::::::::::::::::::::::::::::: ::::::::::::::::: d1db3a_ 2 KVALITGVTGQDGSYLAEFLLEKGYEVHGIKRPKFHLHYGDLSDTSNLTRILREV 56