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 <-- 2.201 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1mt0a_) 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 d1mt0a_ Haemolysin B ATP-​binding proteinP-​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 <-- 2.201 --> Hit
DALI alignment (Z-score: 6.8 Raw score:728.70) d1tf7a1 1 ehqaiaKMRTMIEG---------fddishgGLPIGRSTLVSGTSGTGKTLFSIQFLY--- 48 :::::::: ::::::::::::::::::::::::::: d1mt0a_ 1 ------DITFRNIRfrykpdspvildninlSIKQGEVIGIVGRSGSGKSTLTKLIQRfyi 54 d1tf7a1 49 -------ngiIEFD--------ePGVFVTFeetpqdiiknarsfgwdlaklvdegklfil 93 :::: ::::::: d1mt0a_ 55 pengqvlidgHDLAladpnwlrrQVGVVLQ------------------------------ 84 d1tf7a1 94 dASPDPE----------------------------------------------gQEVVG- 106 :::::: ::::: d1mt0a_ 85 -DNVLLNrsiidnislanpgmsvekviyaaklagahdfiselregyntivgeqgAGLSGg 143 d1tf7a1 107 GFDLsALIERINYAIqkyrARRVSIDSVTSVFqqydASSVVRRELFRLvARLKQiGATTV 166 :::: :::::::::: ::::::::::::: :::::::::::: ::::: ::::: d1mt0a_ 144 QRQR-IAIARALVNN----PKILIFDEATSAL----DYESEHVIMRNM-HKICK-GRTVI 192 d1tf7a1 167 MTTErieeygpiarygVEEFVSDNVVILRNvlegerrrRTLEILKLrgtshmkgeypfti 226 :::: :::::::::::::: :::::::: d1mt0a_ 193 IIAH----------rlSTVKNADRIIVMEK--------GKIVEQGK---------hkell 225 d1tf7a1 227 tdhginifplgamrlt 242 d1mt0a_ 226 sepeslysylyqlqsd 241 FAST alignment (Normalized score: 4.79 Raw score:1157.00) d1tf7a1 1 EHQAIAKMR-TMIEGFDDISHG-------------------GLPIGRSTLVSGTSGTGKT 40 :::: ::::::::::::::::::: d1mt0a_ 1 ---------DITFR--------NIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKS 43 d1tf7a1 41 LFSIQFLYNG-----------------IIEFDE-------PGVFVTFEETPQDIIKNARS 76 :::::: :::: ::::: d1mt0a_ 44 TLTKLI----QRFYIPENGQVLIDGHDLALA--DPNWLRRQVGVV--------------- 82 d1tf7a1 77 FGWDLAKLVDEGKLFILDASPDPEGQ---------------------------------- 102 d1mt0a_ 83 --------------------------LQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLA 116 d1tf7a1 103 -----------------------EVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQ 139 :::::: :::::::::: :::::::::: d1mt0a_ 117 GAHDFISELREGYNTIVGEQGAGLSGGQR-QRIAIARALV----NNPKILIFDE------ 165 d1tf7a1 140 Q---YDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRN 196 ::::::::::::: ::::: :::::::: :::::::::::::::: d1mt0a_ 166 -ATSALDYESEHVIMRN-MHKIC-KGRTVIII----------AHRLSTVKNADRIIVM-- 210 d1tf7a1 197 VLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT-------------- 242 d1mt0a_ 211 ----------------------------------------------EKGKIVEQGKHKEL 224 d1tf7a1 243 ----------------- 243 d1mt0a_ 225 LSEPESLYSYLYQLQSD 241 TMalign alignment (TM-score: 0.39 Raw score:94.23) d1tf7a1 1 EHQAIAKMRTM-I--------------EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQ 45 ::::: : :::: ::::: :::::::::::::::::: d1mt0a_ 1 ------DITFRNIRFRYKPDSPVILDNINLS----IKQGE--VIGIVGRSGSGKSTLTKL 48 d1tf7a1 46 FLY--------NGI--IEF-DE-P--GV--FVTFEETPQDIIKNARSFGWDLAKLVDEGK 89 ::: ::: ::: :: : :: :::::: d1mt0a_ 49 IQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQ------------------------ 84 d1tf7a1 90 LFILDASPDPEGQEVVGGFDLSALIERI----------------------------NYAI 121 ::: ::::::::::::::::: d1mt0a_ 85 -----DNV---LLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTI---- 132 d1tf7a1 122 QKYRARRVSIDSVTSVF-QQ---YDASSVVRRELFRLVARLKQIGATTVMT-TERIEEYG 176 : : ::::::::::::::::::: ::::::: ::::: : d1mt0a_ 133 ----------------VG-EQGAGLSGGQRQRIAIARALVNN--PKILIFDEATSAL--D 171 d1tf7a1 177 PIARYGVEE-FV--SD----NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDH 229 : ::::::: :: :: :::::::: :::::: :: : :::::: d1mt0a_ 172 Y-ESEHVIMRNMHKICKGRTVIIIAHRL--------STVKNA-----DR-I-IVMEKG-- 213 d1tf7a1 230 GINIFPLGA---------------------MRLT 242 ::::::: d1mt0a_ 214 --KIVEQGKHKELLSEPESLYSYLYQLQSD---- 241 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF-EE---TPQDIIKNARSF 77 ::::::::::::::::::::::: ::: :::::::::::::: :: :::::::::::: d1mt0a_ 25 SIKQGEVIGIVGRSGSGKSTLTK-LIQ-RFYIPENGQVLIDGHDLALADPNWLRRQVGVV 82 d1tf7a1 78 ------------------G--WDLAKLVDEGKLFILDASPDPE----GQ-----EVVGGF 108 : ::::::::: ::::::::::: :: :::::: d1mt0a_ 83 LQDNVLLNRSIIDNISLANPGMSVEKVIYA--AKLAGAHDFISELREGYNTIVGEQGAGL 140 d1tf7a1 109 DLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMT 168 ::::::::::::::::::::::::::::::: :: :::::::::::: ::::::::: d1mt0a_ 141 SGGQRQRIAIARALVNNPKILIFDEATSALD----YE-SEHVIMRNMHKI-CKGRTVIII 194 d1tf7a1 169 TERIEEYGPIARYGVEEFVSDNVVILRN 196 :::::: :::::::::::: d1mt0a_ 195 AHRLST----------VKNADRIIVMEK 212