HorA Server Transitive Detail

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


Query <-- 1.905 --> Intermediate <-- 1.461 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1lnqa1) through the intermediate protein (d1vl2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1lnqa1 Potassium channel-​related protein MthKNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.905 --> Intermediate
DALI 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 <-- 1.461 --> Hit
DALI alignment (Z-score: 7.4 Raw score:514.10) d1vl2a1 1 kEKVVLAYSgGLDTSVILKWLCekGFDVIAYVAnvgqkddFVAIKEKALKTGAsKVYVEd 60 :::::::: :::::::::::: ::::::::: ::::::::::::: ::::: d1lnqa1 1 -RHVVICGW-SESTLECLRELR--GSEVFVLAE-------DENVRKKVLRSGA-NFVHG- 47 d1vl2a1 61 lrrefvtdyiftallgnamyegryllgtaiarplIAKRQV-EIAEkeGAQYVAHGATGkG 119 :::::: :::: ::::::::::: : d1lnqa1 48 -------------------------------dptRVSDLEkANVR--GARAVIVDLES-D 73 d1vl2a1 120 NDQVRFELTYAALNPNLKVISPW----------------KDPEflAKFK----------- 152 ::::::::::::::::::::::: :::: :::: d1lnqa1 74 SETIHCILGIRKIDESVRIIAEAeryenieqlrmagadqVISP--FVISgrlmsrsiddg 131 d1vl2a1 153 ------------------------------------------------------------ 153 d1lnqa1 132 yeamfvqdvlaeestrrmvevpipegsklegvsvldadihdvtgviiigvgrgdeliidp 191 d1vl2a1 153 ----------------tdlinyamekgipi 166 d1lnqa1 192 prdysfragdiilgigkpeeierlknyisa 221 FAST alignment (Normalized score: 2.35 Raw score:450.60) d1vl2a1 1 K----------------------------------------------------------- 1 d1lnqa1 1 -RHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKAN 59 d1vl2a1 2 ----EKVVLAYSG--GLDTSVILKWLCE--KGFDVIAYVANVGQKDD-FVAIKEKALKTG 52 ::::::: ::::::::::::: ::::::::: :::::::::::: d1lnqa1 60 VRGARAVIVDL--ESDSETIHCILGIRKIDESVRIIAEA--------ERYENIEQLRMAG 109 d1vl2a1 53 ASKVYVEDLRREFVT----DYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGA 108 ::::::: :::::::::: d1lnqa1 110 ADQVISP--------FVISGRLMSRSIDD------------------------------- 130 d1vl2a1 109 QYVAHGATGKGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI-- 166 d1lnqa1 131 ----------------------------------------------------------GY 132 d1vl2a1 167 ------------------------------------------------------------ 167 d1lnqa1 133 EAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPP 192 d1vl2a1 167 ----------------------------- 167 d1lnqa1 193 RDYSFRAGDIILGIGKPEEIERLKNYISA 221 TMalign alignment (TM-score: 0.29 Raw score:48.13) d1vl2a1 1 ------------------------------------------------------------ 1 d1lnqa1 1 RHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANV 60 d1vl2a1 1 --KEKVVLAY-SGGLDTSVILKWLCEKG--FDVIAYVANVGQKDDFVAIKEKALKTGASK 55 :::::::: ::: ::::::::::::: :::::::: : : ::::::::::::: d1lnqa1 61 RGARAVIVDLESDS-ETIHCILGIRKIDESVRIIAEAE-----R-Y-ENIEQLRMAGADQ 112 d1vl2a1 56 VYVED--LRRE-----------------FVTDYIFTALLGNAMYEGRYLLGTAIARPLIA 96 ::::: :::: d1lnqa1 113 VISPFVISGRLMSRSIDDGYEAMFVQDV-------------------------------- 140 d1vl2a1 97 KRQVE-------IAEK-------------------------------------------- 105 : : d1lnqa1 141 ----LAEESTRR---MVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPR 193 d1vl2a1 106 ----------------------------EGAQYVAHGATGKGNDQVRFELTYAALNPNLK 137 d1lnqa1 194 DYSFRAGDIILGIGKPEEIERLKNYISA-------------------------------- 221 d1vl2a1 138 VISPWKDPEFLAKFKTDLINYAMEKGIPI 166 d1lnqa1 222 ----------------------------- 222 HHsearch alignment (Probability: 0.00 E-value:0.60) d1vl2a1 14 TSVILKWLCEKGFDV 28 ::::::::::::::: d1lnqa1 76 TIHCILGIRKIDESV 90