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 <-- 0.638 --> Intermediate <-- 1.086 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1rifa_) through the intermediate protein (d1tf7a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tf7a1 Circadian clock protein KaiCP-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β
Hit d1rifa_ DNA helicase UvsWP-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β

Supporting Alignments

Query <-- 0.638 --> Intermediate
DALI alignment (Z-score: 3.2 Raw score:303.50) query 1 ----------------------------------------------------sLQLRLAL 8 ::::::: d1tf7a1 1 ehqaiakmrtmiegfddishgglpigrstlvsgtsgtgktlfsiqflyngiieFDEPGVF 60 query 9 NQID------------------------------------stvgDIAGNAEAILRWTRHS 32 :::: :::::::::::::::: d1tf7a1 61 VTFEetpqdiiknarsfgwdlaklvdegklfildaspdpegqevVGGFDLSALIERINYA 120 query 33 A-EQGAHLVAFPemALTGypvedlalrssfveasrTALRELAARLAEEgfgELPVLVGYL 91 : :::::::::: :::: ::::::::::::: ::::::::: d1tf7a1 121 IqKYRARRVSID--SVTS-----vfqqydassvvrRELFRLVARLKQI---GATTVMTTE 170 query 92 drsesaqpkygqpagaprN-------aaavlhrgRVALTFAKHHLPNYgvfdefryfvpg 144 : :::::::::::::: d1tf7a1 171 ------------------RieeygpiarygveefVSDNVVILRNVLEG------------ 200 query 145 dtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlelvr 204 d1tf7a1 201 ------------------------------------------------------------ 201 query 205 kraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaaea 264 d1tf7a1 201 ------------------------------------------------------------ 201 query 265 epptgvvddglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvakng 324 d1tf7a1 201 ------------------------------------------------------------ 201 query 325 frsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtglnfr 384 d1tf7a1 201 ------------------------------------------------------------ 201 query 385 tvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgyst 444 d1tf7a1 201 ------------------------------------------------------------ 201 query 445 lygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailely 504 d1tf7a1 201 ------------------------------------------------------------ 201 query 505 vdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrw 564 d1tf7a1 201 ----------------------errrrtleilklrgtshmkgeypftitdhginifplga 238 query 565 regh 568 d1tf7a1 239 mrlt 242 FAST alignment (Normalized score: 1.90 Raw score:703.80) query 1 ----------------------------------------------------SLQLRLAL 8 :::::::: d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 query 9 NQIDST-----------------------------------------VGDIAGNAEAILR 27 : ::::::::::::: d1tf7a1 61 V-----TFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIE 115 query 28 WTRHSA-EQGAHLVAFPEMALTGYPVEDLALRSS----------FVEASRTALRELAARL 76 :::::: :::::::::: :::::::::::::::: d1tf7a1 116 RINYAIQKYRARRVSID-----------------SVTSVFQQYDASSVVRRELFRLVARL 158 query 77 AEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG---------------RVA 121 ::: :::::::::: ::: d1tf7a1 159 KQI---GATTVMTTER--------------------------IEEYGPIARYGVEEFVSD 189 query 122 LTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAG 181 :::::::: d1tf7a1 190 NVVILRNV---------------------------------------------------- 197 query 182 LLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEV 241 d1tf7a1 198 ------------------------------------------------------------ 198 query 242 VARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADR 301 d1tf7a1 198 ------------------------------------------------------------ 198 query 302 LDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 361 d1tf7a1 198 ------------------------------------------------------------ 198 query 362 KYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 421 d1tf7a1 198 ------------------------------------------------------------ 198 query 422 SNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQT 481 d1tf7a1 198 ------------------------------------------------------------ 198 query 482 PPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY 541 d1tf7a1 198 ------------------------------------------------------------ 198 query 542 PPGTKISAKGFGKDRRLPITNRWREGH--------------------------------- 568 d1tf7a1 198 ---------------------------LEGERRRRTLEILKLRGTSHMKGEYPFTITDHG 230 query 569 ------------ 569 d1tf7a1 231 INIFPLGAMRLT 242 TMalign alignment (TM-score: 0.21 Raw score:121.48) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 :: : : d1tf7a1 1 --------------EH--------------------------------Q-A--------- 4 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1tf7a1 5 ------------------------------------------------------------ 5 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1tf7a1 5 ------------------------------------------------------------ 5 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 ::::: d1tf7a1 5 ------------------------------------------IAKMR------------- 9 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 :: d1tf7a1 10 -------TM--------------------------------------------------- 11 query 301 RLDADEEVYSALVVGLRAYVAKN--------GFRSVLIGLSGG-IDSALVAAIACDALGA 351 :::::::::::: ::: : : :::::::::::::::: d1tf7a1 12 ----IEGFDDISHGGL-PIG--RSTLVSGTS-----------GTGKTLFSIQFLYNGIIE 53 query 352 -QNVYGVSMPSKYSSDHSKGDAAELAR--RTGL--NF-----RTVSIE-PMF--DAYMAS 398 ::::::::: : ::::::::::: :::: :: :::::: : d1tf7a1 54 FDEPGVFVTF---E--ETPQDIIKNARSFGWDLAKLVDEGKLFILDASP--DPE------ 100 query 399 LGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSE-L-----AV--GYSTL-YGDS 449 ::: ::::::::::::::::::::::::::::::::: : : ::::: ::: d1tf7a1 101 --GQE-VVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDA-SSVVRRELF-RLV 155 query 450 -VG----AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELY 504 :: :::::: :: ::: ::::: d1tf7a1 156 ARLKQIGATTVMT--TE--------------------------------RIE-EYGPI-- 178 query 505 VDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTK----------------IS 548 : : :: :: ::: : :::: :: d1tf7a1 179 A---------------------R--YG--VE-EFV-S-DNVVILRNVLEGERRRRTLEIL 210 query 549 AKGFGK----------------------------DRRLPITNRWREGH 568 : : :: d1tf7a1 211 K-L-RGTSHMKGEYPFTITDHGINIFPLGAMRLT-------------- 242 HHsearch alignment (Probability: 0.02 E-value:0.74) query 324 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTG--L 381 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: : d1tf7a1 26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLV 85 query 382 NFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTT 417 :::::::::::::::::::::::::::::::::::: d1tf7a1 86 DEGKLFILDASPDPEGQEVVGGFDLSALIERINYAI 121
Intermediate <-- 1.086 --> Hit
DALI alignment (Z-score: 7.7 Raw score:802.30) d1tf7a1 1 ------------------------------------------------------------ 1 d1rifa_ 1 mdikvhfhdfshvridceestfhelrdffsfeadgyrfnprfrygnwdgrirlldynrll 60 d1tf7a1 1 --------------------EHQA-IAKMrtmieGFDD---------------------- 17 :::: :::: :::: d1rifa_ 61 pfglvgqikkfcdnfgykawIDPQiNEKEelsrkDFDEwlskleiysgnkriephwyqkd 120 d1tf7a1 18 -ishgGLPIgrSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE-ETPQDIIKNAR 75 :::: ::::::::::::::::::::::::::::::::::::: ::::::::::: d1rifa_ 121 avfegLVNR--RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTtALTTQMADDFV 178 d1tf7a1 76 SFGWDLAKLV--------------DEGKLFILDAspdpegqevvggfdlSALIERiNYAI 121 :::::::::: :::::::::: :::::: :::: d1rifa_ 179 DYRLFSHAMIkkigggaskddkykNDAPVVVGTW---------------QTVVKQpKEWF 223 d1tf7a1 122 QkyRARRVSIDSVTSVfqqydassvvrreLFRLVARLKQIG---ATTVMTTERieeygpi 178 : ::::::::::::: :::::::::::: ::::::::: d1rifa_ 224 S--QFGMMMNDECHLA-------------TGKSISSIISGLnncMFKFGLSGS------- 261 d1tf7a1 179 ARYGV-eEFVSD----NVVILrnvlegerrrrtleilklrgtshmkgeypftitdhgini 233 ::::: ::::: ::::: d1rifa_ 262 LRDGKanIMQYVgmfgEIFKP--------------------------------------- 282 d1tf7a1 234 fplgamrlt 242 d1rifa_ 283 --------- 283 FAST alignment (Normalized score: 4.68 Raw score:1223.00) d1tf7a1 1 EHQAIAKMRTM------------------------------------------------- 11 d1rifa_ 1 -----------MDIKVHFHDFSHVRIDCEESTFHELRDFFSFEADGYRFNPRFRYGNWDG 49 d1tf7a1 12 ------------------------------------------------------------ 12 d1rifa_ 50 RIRLLDYNRLLPFGLVGQIKKFCDNFGYKAWIDPQINEKEELSRKDFDEWLSKLEIYSGN 109 d1tf7a1 12 ------------IEGFDDISHGGLPIG-RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPG 58 :::::: :::::::::::::::::::::::::::::::: d1rifa_ 110 KRIEPHWYQKDAVFEGLV---------NRRRILNLPTSAGRSLIQALLARYYLENYEGKI 160 d1tf7a1 59 VFVTFEE---TPQDIIKNARSFGWDLAKLV---------------------DEGKLFILD 94 ::::: ::::::::::::: :::::::: d1rifa_ 161 LIIVP--TTALTTQMADDFVDYR-------LFSHAMIKKIGGGASKDDKYKNDAPVVVG- 210 d1tf7a1 95 ASPDPEGQEVVGGFDLSALIERI----NYAIQKYRARRVSIDSVTSVFQQYDASSVVRRE 150 ::::: ::::: :::::::::::: d1rifa_ 211 ------------------TWQTVVKQPKEWFS--QFGMMMNDECHL-------------- 236 d1tf7a1 151 -LFRLVARLKQ--IGA-TTVMTTERIEEYGPIAR---------YGVEEFVS-DNVVILRN 196 :::::::::: ::: :::::: ::::::: ::::: d1rifa_ 237 ATGKSISSIISGLNNCMFKFGLS-----------GSLRDGKANIMQYVGM-FGEIFK--- 281 d1tf7a1 197 VLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT- 242 d1rifa_ 282 ----------------------------------------------P 282 TMalign alignment (TM-score: 0.50 Raw score:121.11) d1tf7a1 1 ------E----------------------------------------------------- 1 : d1rifa_ 1 MDIKVHFHDFSHVRIDCEESTFHELRDFFSFEADGYRFNPRFRYGNWDGRIRLLDYNRLL 60 d1tf7a1 2 ---------------------HQA-IAKMRT----MI--E------------------GF 15 ::: :::::: :: : :: d1rifa_ 61 PFGLVGQIKKFCDNFGYKAWIDPQINEKEELSRKDFDEWLSKLEIYSGNKRIEPHWYQKD 120 d1tf7a1 16 DDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE-ETPQDIIKNA 74 ::::::::: ::::::::::::::::::::::::::::::::::::: :::::::::: d1rifa_ 121 AVFEGLVNR---RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDF 177 d1tf7a1 75 RSFGWDLAKLV-------------D-EGKLFILDASPDPEGQEVVGGFDLSALIERINYA 120 ::::::::::: : ::::::::: : ::::::::: d1rifa_ 178 VDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTW-------------Q--TVVKQPKEW 222 d1tf7a1 121 IQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIG-A-TTVMTTERIEEYGPI 178 :: :::::::::::::: :: :::::::::: : :::::::: d1rifa_ 223 FS--QFGMMMNDECHLAT-----------GK-SISSIISGLNNCMFKFGLSGS------- 261 d1tf7a1 179 ARYGV-EEFV-S---DNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINI 233 ::::: :::: : ::::: : d1rifa_ 262 LRDGKANIMQYVGMFGEIFK-------------P-------------------------- 282 d1tf7a1 234 FPLGAMRLT 242 d1rifa_ 283 --------- 283 HHsearch alignment (Probability: 0.95 E-value:0.00) d1tf7a1 25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE-ETPQDIIKNARSFGWDLA 82 :::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: d1rifa_ 127 VNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSH 185