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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.947 --> Intermediate <-- 1.078 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1eucb1) through the intermediate protein (d1ru8a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ru8a_ Putative N-​type ATP pyrophosphatase PF0828Adenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1eucb1 Succinyl-​CoA synthetase,​ beta-​chain,​ C-​terminal domainSuccinyl-​CoA synthetase domainsFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 0.947 --> Intermediate
DALI alignment (Z-score: 7.4 Raw score:643.70) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1ru8a_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1ru8a_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1ru8a_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1ru8a_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1ru8a_ 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALgaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1ru8a_ 1 -----------------------GLADVAVLYSGGKDSNYALYWAIKNR-fsVKFLVTMV 36 query 361 SKYS-----sDHSKGdAAELARRTGLNFRTVSIEpmfdaymaslgltglaEENLQSRLRG 415 :::: ::::: :::::::::::::::::: :::::::::: d1ru8a_ 37 SENEesymytINANL-TDLQARALGIPLVKGFTQ---------------gEKEKEVEDLK 80 query 416 TTLMAIsnqEGHIVLAPGnkselavGYSTlyGDSVG------AYGPIKDVYKTSIFRLAE 469 :::::: ::::::::: :::: ::::: :::::::::::::::::: d1ru8a_ 81 RVLSGL---KIQGIVAGA------sKYQRkrIEKVAkelgleVYTPAWGRDAKEYMRELL 131 query 470 WRN------------------------------------raaaergqtppipEASItkpd 493 ::: :::: d1ru8a_ 132 NLGfkimvvgvsaygldeswlgrildesaleelitlnekykvhvageggefeTFVL---- 187 query 494 ypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfg 553 d1ru8a_ 188 -----------------------------------dmplfkykivvdkakkvwepctssg 212 query 554 kdrrlpitnrwregh 568 d1ru8a_ 213 kliieeahleskleh 227 FAST alignment (Normalized score: 3.54 Raw score:1270.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1ru8a_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1ru8a_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1ru8a_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1ru8a_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1ru8a_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQN-----VY 355 :::::::::::::::::::::::: :: d1ru8a_ 1 -----------------------GLADVAVLYSGGKDSNYALYWAIK------NRFSVKF 31 query 356 GVSMPSKYS----SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLA---EEN 408 ::::::::: ::::::::::::::::::::::: ::: d1ru8a_ 32 LVTMVSENEESYMYTINANLTDLQARALGIPLVKGF------------------TQGEKE 73 query 409 LQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY-----GDSVG-----------A 452 :::::::::::: ::: ::::: :::: : d1ru8a_ 74 KEVEDLKRVLSG--LKI-QGIVA---------------GASKYQRKR-IEKVAKELGLEV 114 query 453 YGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP-------------------- 492 :::::::::::::::::: d1ru8a_ 115 YTPAWGRDAKEYMRELLN----------------------LGFKIMVVGVSAYGLDESWL 152 query 493 ----------DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYP 542 :::::::: d1ru8a_ 153 GRILDESALEELITLNEK------------------------------------------ 170 query 543 PGTKISAKGFGKDRRLPITNRWREGH---------------------------------- 568 d1ru8a_ 171 --------------------------YKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKV 204 query 569 ----------------------- 569 d1ru8a_ 205 WEPCTSSGKLIIEEAHLESKLEH 227 TMalign alignment (TM-score: 0.21 Raw score:120.91) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1ru8a_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1ru8a_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1ru8a_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1ru8a_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1ru8a_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 ::::::::::::::::::::::::::: ::::::::: d1ru8a_ 1 -----------------------GLADVAVLYSGGKDSNYALYWAIKNRF-SVKFLVTMV 36 query 361 SKYS-S---DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGT 416 :::: : :::::::::::::::::::::::: : : ::::::::: d1ru8a_ 37 SENEESYMYTINANLTDLQARALGIPLVKGFTQ--G-------------E-KEKEVEDLK 80 query 417 TLMAISNQEGHIVLAPGNKSELAVGYSTL-YGDSV-G------AYGPIKDVYKTSIFRLA 468 :::::: ::::::::: :: : :: :::: : ::::::::::::::::: d1ru8a_ 81 RVLSGL--KIQGIVAGA---SK--Y--QRK-RIEKVAKELGLEVYTPAWGRDAKEYMREL 130 query 469 EWRNRAAAERGQTPPIPEASITK---P-DY----------------PVLDAILELYVDRD 508 ::: : : : :::: : :: ::::: d1ru8a_ 131 LNL-G----------F-K-IMVVGVSAYGLDESWLGRILDESALEELITLN--------- 168 query 509 TGADAIVAAGYDRELV-------------------------------------------- 524 ::: :: d1ru8a_ 169 ---------EKY--KVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIE 217 query 525 ----------VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1ru8a_ 218 EAHLESKLEH-------------------------------------------- 227 HHsearch alignment (Probability: 0.87 E-value:0.00) query 324 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS---KGDAAELARRTG 380 ::::::::::::::::::::::::::::::::::::::::::::: :::::::::::: d1ru8a_ 1 GLADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYTINANLTDLQARALG 60 query 381 LNFRTVSIEPMFDAYMASL 399 ::::::::::::::::::: d1ru8a_ 61 IPLVKGFTQGEKEKEVEDL 79
Intermediate <-- 1.078 --> Hit
DALI alignment (Z-score: 3.9 Raw score:297.50) d1ru8a_ 1 ----------------glaDVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMvseneesym 44 :::::::::::::::::::::::::::::::: d1eucb1 1 epieneaakydlkyigldgNIACFVNGAGLAMATCDIIFLNGGKPANFLDL--------- 51 d1ru8a_ 45 ytinanltdlqaralgiplvkgftqgeKEKEVEDLKRVLSGL-KIQGIVAG------aSK 97 ::::::::::::::: :::::::: :: d1eucb1 52 -----------------------gggvKESQVYQAFKLLTADpKVEAILVNifggivnXA 88 d1ru8a_ 98 YQRKRIEKVAK--ELGLEVYTPAWgrdakeymrellnlgfkimvvgvsaygldeswlgri 155 ::::::::::: ::::::::::: d1eucb1 89 IIANGITKACRelELKVPLVVRLE------------------------------------ 112 d1ru8a_ 156 ldesaleelitlnekykvhvageggefetfvldmplfkykivvdkakkvwepctssgkli 215 d1eucb1 113 ------------------------------------gtnvheaqniltnsglpitsavdl 136 d1ru8a_ 216 ieeahleskleh 227 d1eucb1 137 edaakkavasvt 148 FAST alignment (Normalized score: 4.18 Raw score:765.80) d1ru8a_ 1 GL------------------ADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEES 42 ::::::::::::::::::::::::::::::::: d1eucb1 1 --EPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDL------- 51 d1ru8a_ 43 YMYTINANLTDLQARALGIPLVKGFTQGE----KEKEVEDLKRVLSGL-KIQGIVAGA-- 95 ::::::::::::::: ::::::: d1eucb1 52 -----------------------------GGGVKESQVYQAFKLLTADPKVEAILV--NI 80 d1ru8a_ 96 ------SKYQRKRIEKVAKE--LGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYGL 147 :::::::::::::: ::::::: d1eucb1 81 FGGIVNAAIIANGITKACRELELKVPLVV------------------------------- 109 d1ru8a_ 148 DESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEP 207 d1eucb1 110 ------------------------------------------------------------ 110 d1ru8a_ 208 CTSSGKLIIEEAHLESKLEH--------------------------------------- 227 d1eucb1 110 --------------------RLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT 148 TMalign alignment (TM-score: 0.28 Raw score:63.06) d1ru8a_ 1 ------------------GLADVAVLYSGGKDSNYALYWAIKNRFSVKF-LVT---MVSE 38 ::::::::::::::::::::::::::::: ::: :::: d1eucb1 1 EPIENEAAKYDLKYIGLD--GNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKES 58 d1ru8a_ 39 NEESY--MYTINANLTDLQARALGIPLVKG------------------FTQGEK-EKEVE 77 : :::: ::: ::::: d1eucb1 59 ----QVY-------------------QAFKLLTADPKVEAILVNIFGG---IVNAAIIAN 92 d1ru8a_ 78 DLKRVLS-G-LKIQGIVAGASKYQRKRIEKVAKE-LGLEVY-TPAW----------GRDA 123 ::::::: : :::::::::::::::::::::::: :::::: :::: d1eucb1 93 GITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT---- 148 d1ru8a_ 124 KEYMRELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFE 183 d1eucb1 149 ------------------------------------------------------------ 149 d1ru8a_ 184 TFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESKLEH 227 d1eucb1 149 -------------------------------------------- 149 HHsearch alignment (Probability: 0.05 E-value:0.62) d1ru8a_ 4 DVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMV 36 ::::::::::::::::::::::::::::::::: d1eucb1 20 NIACFVNGAGLAMATCDIIFLNGGKPANFLDLG 52