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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.613 --> Intermediate <-- 1.728 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1mo9a1) through the intermediate protein (d1ps9a3) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ps9a3 2,​4-​dienoyl-​CoA reductase,​ middle domainNucleotide-​binding domainNucleotide-​binding domainα/β
Hit d1mo9a1 NADH-​dependent 2-​ketopropyl coenzyme M oxidoreductase/​carboxylaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β

Supporting Alignments

Query <-- 1.613 --> Intermediate
DALI alignment (Z-score: 4.1 Raw score:393.70) query 1 ---------------------------------------GMENKKMNLLLfsgdydkALA 21 ::::::::::: ::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQKKNLAVVG------aGPA 54 query 22 SLIIANAAREMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreaeELPLsk 81 :::::::::::::::::::: :::: :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA---HSEI------------------------ggqFNIA-- 85 query 82 mnlgGIGKKmllemmkeekaPKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqI 141 ::::: :::::::::::::::::::: : d1ps9a3 86 --kqIPGKE--------efyETLRYYRRMIEVTGVTLKLN------------------hT 117 query 142 MDVKEYlknaLESDLQLFI----------------------------------------- 160 :::::: ::::::::: d1ps9a3 118 VTADQL----QAFDETILAsgipnralaqplidsgktvhliggcdvameldarraiaqgt 173 query 161 ------ 161 d1ps9a3 174 rlalei 179 FAST alignment (Normalized score: 3.87 Raw score:654.60) query 1 GME------------------------------------------NKKMNLLLFSGDYDK 18 :::::: d1ps9a3 1 ---INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV--------- 48 query 19 ---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLT-PREA 74 :::::::::::::::::::::: :::: d1ps9a3 49 VGAGPAGLAFAINAAARGHQVTLFD------------------------------AHSEI 78 query 75 EELPLSKMNLGGIGKKMLLEMMKEEKAP------------------KLSDLLSGARKKEV 116 :::::::::::::: d1ps9a3 79 ----------------------------GGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 query 117 KFYAXQLSVEIMGFKKEELFPE-VQIMDVKEYLKNA-LESDLQLFI-------------- 160 ::: :::::::: ::::::: d1ps9a3 111 TLK-------------------LNHTVTADQ-----LQAFDETI--LASGIPNRALAQPL 144 query 161 ----------------------------------- 161 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 TMalign alignment (TM-score: 0.44 Raw score:70.82) query 1 ---------------------------------------GMENKKMNLLLFSGDYDKALA 21 ::::::::::: :::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREA-EELPLS 80 :::::::::::::::::::: ::::: : :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA--HSEIG-------------------------GQ-FNIA- 85 query 81 KMNLGGIGKKMLLE-MMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEV 139 : :::::: :: ::::::::::::::::::::: : d1ps9a3 86 --K-QIPGKE--EFY-------ETLRYYRRMIEVTGVTLKLNH-T--------------- 117 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 :::::: :::::::::: d1ps9a3 118 ----VTADQL-QAFDETILASGIPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQG 172 query 161 ------- 161 d1ps9a3 173 TRLALEI 179 HHsearch alignment (Probability: 0.10 E-value:0.01) query 2 MENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 ::::::::::::: :::::::::::::::::::: d1ps9a3 40 AVQKKNLAVVGAG-----PAGLAFAINAAARGHQVTLF 72
Intermediate <-- 1.728 --> Hit
DALI alignment (Z-score: 11.5 Raw score:1044.00) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVGAGPAGLAFAI 60 ::::::::::::::::::: d1mo9a1 1 -kvwnarndhltinqwatrideileapdggeviynvdendpREYDAIFIGGGAAGRFGSA 59 d1ps9a3 61 NAAARGHQVTLFDAHSEIGGQ-FNIA-KQIPG---------------------------- 90 ::::::::::::::::::::: :::: ::::: d1mo9a1 60 YLRAMGGRQLIVDRWPFLGGScPHNAcVPHHLfsdcaaelmlartfsgqywfpdmtekvv 119 d1ps9a3 91 ---------keEFYETLRYYRRMIE-VTGVTLKLNHTVTAD---------qLQAFDETIL 131 :::::::::::::: ::::::::::::::: ::::::::: d1mo9a1 120 gikevvdlfraGRNGPHGIMNFQSKeQLNLEYILNCPAKVIdnhtveaagkVFKAKNLIL 179 d1ps9a3 132 ASGI----------PNRALAQPLID-----------------sGKTVHLIGGCDVAmELD 164 :::: ::::::::::: ::::::::::::: ::: d1mo9a1 180 AVGAgpgtldvpeqPRSAELAKILGldlgpkgevlvneylqtsVPNVYAVGDLIGG-PME 238 d1ps9a3 165 ARRAIAQGTRLALEI-------- 179 ::::::::::::::: d1mo9a1 239 MFKARKSGCYAARNVmgekisyt 261 FAST alignment (Normalized score: 9.57 Raw score:2068.00) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKK---------------- 44 d1mo9a1 1 --------------------------------------------KVWNARNDHLTINQWA 16 d1ps9a3 45 ---------------------------NLAVVGAGPAGLAFAINAAARGHQVTLFDAHSE 77 ::::::::::::::::::::::::::::::::: d1mo9a1 17 TRIDEILEAPDGGEVIYNVDENDPREYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPF 76 d1ps9a3 78 IGGQF--NIAKQIPG----------------------------------------KEEFY 95 ::::: ::::: ::::: d1mo9a1 77 LGGSCPHNACVP---HHLFSDCAAELMLARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRN 133 d1ps9a3 96 ETLRYYRRMI-EVTGVTLKLNHTVTAD-----------QLQAFDETILASGIPNRA---- 139 :::::::::: :::::::::::::: :::::::::::: d1mo9a1 134 GPHGIMNFQSKEQLNLEYILNCPAK--VIDNHTVEAAGKVFKAKNLILAV------GAGP 185 d1ps9a3 140 ---------LAQPLIDSG----------------------KTVHLIGGCDVAMELDARRA 168 ::::::: :::::::::: ::::::::: d1mo9a1 186 GTLDVPEQPRSAELAK--ILGLDLGPKGEVLVNEYLQTSVPNVYAVGDLI-GGPMEMFKA 242 d1ps9a3 169 IAQGTRLALEI--------- 179 :::::::::: d1mo9a1 243 RKSGCYAARN-VMGEKISYT 261 TMalign alignment (TM-score: 0.63 Raw score:113.49) d1ps9a3 1 ----------------------------------------INTCIGCNQACLDQIFVGKV 20 d1mo9a1 1 KVWNARNDHLTINQWATRIDEILEAPDGGEVIYNVDENDP-------------------- 40 d1ps9a3 21 TSCLVNPRACHETKMPILPAVQKKN-LAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIG 79 ::: :::::::::::::::::::::::::::::::::: d1mo9a1 41 ----------------------REYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLG 78 d1ps9a3 80 GQF-NI-AKQI-P--GK--------------------------------E---EF-YETL 98 ::: :: :::: : :: : : :::: d1mo9a1 79 GSCPHNACVPHHLFSDCAAELMLARTFSGQYWFPDMTEKVVGIKEVVDLFRAG-RNGPHG 137 d1ps9a3 99 RYYRRMIEVTGVTLKLNHTVTAD-----Q----LQAFDETILASGI----------PNR- 138 ::::::::::::::::::::::: : ::::::::::::: ::: d1mo9a1 138 IMNFQSKEQLNLEYILNCPAKVIDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPEQPRSA 197 d1ps9a3 139 ALAQPLID-----------------SGKTVHLIGGCDVAMELDARRAIAQGTRLALEI-- 179 :::::::: :::::::::::: ::::::::::::::::::: d1mo9a1 198 ELAKILGLDLGPKGEVLVNEYLQTS-VPNVYAVGDLIG-GPMEMFKARKSGCYAARNVMG 255 d1ps9a3 180 ------ 180 d1mo9a1 256 EKISYT 261 HHsearch alignment (Probability: 0.99 E-value:0.00) d1ps9a3 41 VQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFY----- 95 ::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1mo9a1 40 PREYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVPHHLFSDCAAEL 99 d1ps9a3 96 -----------------------ETL------------RYYRRMIEVTGVTLKLNHTVTA 120 ::: :::::::::::::::::::::: d1mo9a1 100 MLARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRNGPHGIMNFQSKEQLNLEYILNCPAKV 159 d1ps9a3 121 ---------DQLQAFDETILASGIPNRALAQPLID 146 :::::::::::::::::::::::::: d1mo9a1 160 IDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPEQP 194