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 <-- 0.827 --> Intermediate <-- 1.168 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1o2da_) through the intermediate protein (d1jmva_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jmva_ Universal stress protein A,​ UspAAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1o2da_ Alcohol dehydrogenase TM0920Dehydroquinate synthase-​likeDehydroquinate synthase-​likemulti

Supporting Alignments

Query <-- 0.827 --> Intermediate
DALI alignment (Z-score: 7.9 Raw score:512.80) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVS 358 ::::::::::::::::::::::::::: :::::: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIH 37 query 359 MPS------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdayma 397 ::: :::::::::::::::: ::::::: d1jmva_ 38 VDVnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG--------- 88 query 398 slgltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVGYS------tlygdsv 450 ::::::::::::::: :::::::: :::::: d1jmva_ 89 ---------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSKLmsstrqvmntiki 131 query 451 gAYGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtg 510 :::: :::: d1jmva_ 132 dMLVV-PLRD-------------------------------------------------- 140 query 511 adaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1jmva_ 141 ---------------------------------------------------------- 141 FAST alignment (Normalized score: 3.30 Raw score:930.50) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NV 354 ::::::::::::::::::::::::: :: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKL 33 query 355 YGVSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSI 388 :::::: :::::::::::: :::: ::::: d1jmva_ 34 SIIHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG-- 86 query 389 EPMFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTL 445 :::::::::::::: :::::::: d1jmva_ 87 ------------------------SGDLGQVLSDAIEQYDVDLLVTGHH----------- 111 query 446 Y-------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP 492 :::::: d1jmva_ 112 -QDFWSKLMSSTRQVMNTIK---------------------------------------- 130 query 493 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGF 552 d1jmva_ 131 ------------------------------------------------------------ 131 query 553 GKDRRLPITNRWREGH---------- 568 d1jmva_ 131 ----------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.17 Raw score:95.23) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVS 358 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIH 37 query 359 MPSK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAY 395 :::: :: :::::::::::: ::::::::: d1jmva_ 38 VDVNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS------- 87 query 396 MASLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG-- 451 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 --------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNT 128 query 452 ----AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDR 507 ::: :: : :: d1jmva_ 129 IKIDMLV-VP-L-RD--------------------------------------------- 140 query 508 DTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREG 567 d1jmva_ 141 ------------------------------------------------------------ 141 query 568 H 568 d1jmva_ 141 - 141 HHsearch alignment (Probability: 0.04 E-value:0.35) query 19 AGNAEAILRWTRHSAEQGAHLVAF------PEMALTGYPVEDLALRSSFVEASRTALREL 72 :::::::::::::::::::::::: :::::::::::::::::::::::::::::: d1jmva_ 13 EESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDL 72 query 73 AAR 75 ::: d1jmva_ 73 AES 75
Intermediate <-- 1.168 --> Hit
DALI alignment (Z-score: 3.7 Raw score:369.20) d1jmva_ 1 --------------------------MYKHILVAVDLsEESP--ILLKKAVGIAKRHDAK 32 ::::::::::: :::: :::::::::::::::: d1o2da_ 1 vwefymptdvffgekilekrgniidlLGKRALVVTGK-SSSKknGSLDDLKKLLDETEIS 59 d1jmva_ 33 LSII-HVDVNfsdlytglidvnmssmqdristetqkalldlaesvdypiseklsgSGDLG 91 :::: ::::: ::::: d1o2da_ 60 YEIFdEVEEN--------------------------------------------pSFDNV 75 d1jmva_ 92 QVLSDAIEQYDVDLLVTGHHqdfwsklmsstrqVMNTIK------------------IDM 133 :::::::::::::::::::: :::::: ::: d1o2da_ 76 MKAVERYRNDSFDFVVGLGG----gspmdfakaVAVLLKekdlsvedlydrekvkhwLPV 131 d1jmva_ 134 LVVPLRD----------------------------------------------------- 140 ::::::: d1o2da_ 132 VEIPTTAgtgsevtpysiltdpegnkrgctlmfpvyafldprytysmsdeltlstgvdal 191 d1jmva_ 141 ------------------------------------------------------------ 141 d1o2da_ 192 shavegylsrkstppsdalaieamkiihrnlpkaiegnrearkkmfvasclagmviaqtg 251 d1jmva_ 141 ------------------------------------------------------------ 141 d1o2da_ 252 ttlahalgyplttekgikhgkatgmvlpfvmevmkeeipekvdtvnhifggsllkflkel 311 d1jmva_ 141 ----------------------------------------------- 141 d1o2da_ 312 glyekvavsseelekwvekgsrakhlkntpgtftpekirniyrealg 358 FAST alignment (Normalized score: 1.75 Raw score:392.60) d1jmva_ 1 --------------------------MYKHILVAVDL------SEESPILLKKAVGIAKR 28 :::::::::: ::::::::::::: d1o2da_ 1 VWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTG-KSSSKKNGSLDDLKKLLDE---- 55 d1jmva_ 29 HDAKLSIIHVDVNFSDL--------YTGLIDVNMSSMQDRISTETQKALLDLAESVDYPI 80 :::::::: :::: d1o2da_ 56 TEISYEIF---------DEVEENPSFDNV------------------------------- 75 d1jmva_ 81 SEKLSGSG---------------------DLGQVLSDAIEQYDV---------------- 103 :::::::::::: d1o2da_ 76 --------MKAVERYRNDSFDFVVGLGGGSPMDFAKAVAVL---LKEKDLSVEDLYDREK 124 d1jmva_ 104 ----DLLVTGHHQDFWSKLMSSTRQVMNTIKID--------------------------- 132 ::::::: d1o2da_ 125 VKHWLPVVEIP----------------------TTAGTGSEVTPYSILTDPEGNKRGCTL 162 d1jmva_ 133 ---MLVVPLRD------------------------------------------------- 140 ::::::: d1o2da_ 163 MFPVYAFLDP-RYTYSMSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAMKIIHRN 221 d1jmva_ 141 ------------------------------------------------------------ 141 d1o2da_ 222 LPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGYPLTTEKGIKHGKATGMVLPFV 281 d1jmva_ 141 ------------------------------------------------------------ 141 d1o2da_ 282 MEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTP 341 d1jmva_ 141 ----------------- 141 d1o2da_ 342 GTFTPEKIRNIYREALG 358 TMalign alignment (TM-score: 0.48 Raw score:67.20) d1jmva_ 1 ------------------------M--YKHILVAVDLSEESP-ILLKKAVGIAKRHDAKL 33 : ::::::::::::::: ::::::::::::::::: d1o2da_ 1 VWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISY 60 d1jmva_ 34 SII-HVDVNFSDLYT-GLIDVNM--------SSMQDRISTETQKALLDLAESVDYPISE- 82 ::: :::::: ::: ::::::: : d1o2da_ 61 EIFDEVEENP--SFDNVMKAVERYRNDSFDF---------------------------VV 91 d1jmva_ 83 -----KLSGSGDLGQVLSDAIE-QY-----------------DVDLLVTGHHQDFWSKLM 119 :::: ::::::: :: :::::::::: : ::: d1o2da_ 92 GLGGG-----SPMD-FAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTT-A---GTG 141 d1jmva_ 120 SSTRQVM-------------NTIK-IDMLVVP-L-RD----------------------- 140 :::::: :::: ::::::: : :: d1o2da_ 142 -SEVTPYSILTDPEGNKRGCTLMFPVYAFLDPRYTYSMSDELTLSTGVDALSHAVEGYLS 200 d1jmva_ 141 ------------------------------------------------------------ 141 d1o2da_ 201 RKSTPPSDALAIEAMKIIHRNLPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGY 260 d1jmva_ 141 ------------------------------------------------------------ 141 d1o2da_ 261 PLTTEKGIKHGKATGMVLPFVMEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVS 320 d1jmva_ 141 -------------------------------------- 141 d1o2da_ 321 SEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALG 358 HHsearch alignment (Probability: 0.04 E-value:0.11) d1jmva_ 18 LLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVD 77 :::::::::::::::::::::::: : ::::::::::::::::: d1o2da_ 16 ILEKRGNIIDLLGKRALVVTGKSS--S----------------KKNGSLDDLKKLLDETE 57 d1jmva_ 78 YPISEKLSGSGD----LGQVLSDAIEQYDVDLLVT 108 :::::::::::: ::::::::::::::::::: d1o2da_ 58 ISYEIFDEVEENPSFDNVMKAVERYRNDSFDFVVG 92