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 | d1id1a_ | Rck domain from putative potassium channel Kch | 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 <-- 1.328 --> HitDALI alignment (Z-score: 7.7 Raw score:545.20) d1vl2a1 1 --kEKVVLAYSgGLDTSVILKWLCEKGFDVIAYVANvgQKDDFVAIKEKALKtgaSKVYV 58 :::::::: :::::::::::::::::::::::: :::::::::::::: ::::: d1id1a_ 1 hrkDHFIVCGH-SILAINTILQLNQRGQNVTVISNL--PEDDIKQLEQRLGD--nADVIP 55 d1vl2a1 59 EdlrrefvtdyiftallgnamyegryllgtaiaRPLIaKRQVEIAEkeGAQYVAHGATgk 118 : :::: :::::::: :::::::::: d1id1a_ 56 G-------------------------------dSNDS-SVLKKAGI-dRCRAILALSD-n 81 d1vl2a1 119 GNDQVRFELTYAALNPNLKVISPW----------------KDPEflAKFK---------- 152 :::::::::::::::::::::::: :::: :::: d1id1a_ 82 DADNAFVVLSAKDMSSDVKTVLAVsdsknlnkikmvhpdiILSP--QLFGseilarvlng 139 d1vl2a1 153 tdlinyamekgipi 166 d1id1a_ 140 eeinndmlvsmlln 153 FAST alignment (Normalized score: 6.26 Raw score:997.70) d1vl2a1 1 K---EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKD-----DFVAIKEKALKTG 52 ::::: ::::::::::::::::::::::::: :::::::: d1id1a_ 1 -HRKDHFIV-CGHSILAINTILQLNQRGQNVTVIS-------NLPEDDIKQLEQR----- 46 d1vl2a1 53 A----SKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIA-----RPLIAKRQVEIA 103 :::: ::::::: d1id1a_ 47 -LGDNADVI----------------------------------PGDSNDSSVLKK----- 66 d1vl2a1 104 EKE----GAQYVAHGATG-KGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINY 158 ::::::::: ::::::::::::::::::::::: d1id1a_ 67 ---AGIDRCRAILALS--DNDADNAFVVLSAKDMSSDVKTVL------------------ 103 d1vl2a1 159 AMEKGIPI-------------------------------------------------- 166 d1id1a_ 104 --------AVSDSKNLNKIKMVHPDIILSPQLFGSEILARVLNGEEINNDMLVSMLLN 153 TMalign alignment (TM-score: 0.51 Raw score:84.07) d1vl2a1 1 --KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYV 58 ::::::::: ::::::::::::: ::::::::::: :::::::::::::: ::::: d1id1a_ 1 HRKDHFIVCGH-SILAINTILQLNQ-RGQNVTVISNL-PEDDIKQLEQRLGD---NADVI 54 d1vl2a1 59 EDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK 118 : : :::: :::::::::: :::::::::: : d1id1a_ 55 P-G-----------------------------DSND-SSVLKKAGID-RCRAILALSD-N 81 d1vl2a1 119 GNDQVRFELTYAALNPNLKVISPW----------------KDPEFLAKFK---------- 152 :::::::::::::::::::::::: :::::::::: d1id1a_ 82 DADNAFVVLSAKDMSSDVKTVLAVSDSKNLNKIKMVHPDIILSPQLFGSEILARVLNGEE 141 d1vl2a1 153 ------------TDLINYAMEKGIPI 166 d1id1a_ 142 INNDMLVSMLLN-------------- 153 HHsearch alignment (Probability: 0.03 E-value:0.17) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANV 35 ::::: :::::::::::::::::::::::::::: d1id1a_ 4 DHFIV-CGHSILAINTILQLNQRGQNVTVISNLP 36