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 <-- 2.293 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1w0jd3) 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 d1w0jd3 Central domain of beta subunit of F1 ATP synthaseP-​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 <-- 2.293 --> Hit
DALI alignment (Z-score: 13.6 Raw score:1375.40) d1tf7a1 1 --------------------------------------------ehqAIAKMRTMIEGFD 16 ::::::::::::: d1w0jd3 1 iripvgpetlgrimnvigepidergpiktkqfaaihaeapefvemsvEQEILVTGIKVVD 60 d1tf7a1 17 DIShgGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT-FEET--PQDIIKn 73 ::: ::::::::::::::::::::::::::::::::::::::::: :::: :::::: d1w0jd3 61 LLA--PYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGvGERTreGNDLYH- 117 d1tf7a1 74 arsfgWDLA-KLVD----EGKLFILDASPDpegqEVVG-gFDLSALIERINYAIQK-yRA 126 :::: :::: :::::::::::: :::: :::::::::::::::: :: d1w0jd3 118 -----EMIEsGVINlkdaTSKVALVYGQMN---ePPGAraRVALTGLTVAEYFRDQegQD 169 d1tf7a1 127 RRVSIDSVTSVFQQYD--------------ASSVVRRELFRLVARLKQI---GATTVMTT 169 :::::::::::::::: ::::::::::::::::::: :::::::: d1w0jd3 170 VLLFIDNIFRFTQAGSevsallgripsavgYQPTLATDMGTMQERITTTkkgSITSVQAI 229 d1tf7a1 170 ERIEEygPIARY--GVEEFVSDNVVILRNVlegeRRRR-TLEI--LKLRGtshmkgeypf 224 ::::: ::::: :::::::::::::::: :::: :::: ::::: d1w0jd3 230 YVPAD--DLTDPapATTFAHLDATTVLSRA-iaeLGIYpAVDPldSTSRI---------- 276 d1tf7a1 225 titdhginifplgamrlt 242 d1w0jd3 277 ------------------ 277 FAST alignment (Normalized score: 9.58 Raw score:2476.00) d1tf7a1 1 EHQ-----------------------------------------------AIAKMRTMIE 13 :::::::::: d1w0jd3 1 ---IRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIK 57 d1tf7a1 14 GFDDISHG--GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE---TPQ 68 :::: :::::::::::::::::::::::::::::::::::::::::::: ::: d1w0jd3 58 VVDL----LAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN 113 d1tf7a1 69 DIIKNARSFGWDLAKLV--------DEGKLFILDASPDP-EGQEVV-GGFDLSALIERIN 118 :::::::: ::::::::::: ::::: ::::::::::::: d1w0jd3 114 DLYHEMIE---------SGVINLKDATSKVALVYGQ---MNEPPG-ARARVALTGLTVAE 160 d1tf7a1 119 YAIQKYRA-RRVSIDSVTSVFQQYDA------------------SSVVRRELFRLVARLK 159 :::::::: ::::::::::::: ::::::::::::::: d1w0jd3 161 YFRDQEGQDVLLFIDNIFRFTQ----AGSEVSALLGRIPSAVGYQPTLATDMGTMQERI- 215 d1tf7a1 160 Q-----IGATTVMTTERIEEYGPIAR------YGVEEFVSDNVVILRNVLEGERRRRTLE 208 :::::::::::::: ::::::::::::::: d1w0jd3 216 -TTTKKGSITSVQAIYVPAD------DLTDPAPATTFAHLDATTVLS------------- 255 d1tf7a1 209 ILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT--------------------- 242 d1w0jd3 256 ----------------------------------RAIAELGIYPAVDPLDSTSRI 276 TMalign alignment (TM-score: 0.66 Raw score:159.83) d1tf7a1 1 --------------------------------------------EHQAIAKMRTMIEGFD 16 :::::::::::::::: d1w0jd3 1 IRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVD 60 d1tf7a1 17 DISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF-EET--PQDIIKN 73 ::: :::::::::::::::::::::::::::::::::::::::::: ::: :::::: d1w0jd3 61 LLA--PYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYH- 117 d1tf7a1 74 ARSFGWDLA--KLVD----EGKLFILDASPDPEGQEVVGGFDLSALIERINYAI-QKYRA 126 ::: :::: ::::::::::::: :::::: :::::::::::::: ::::: d1w0jd3 118 ------EMIESGVINLKDATSKVALVYGQMNE-PPGARA-RVALTGLTVAEYFRDQEGQD 169 d1tf7a1 127 RRVSIDSVTSVFQQYD--------------ASSVVRRELFRLVARLK-Q--IGATTVMTT 169 :::::::::::::::: ::::::::::::::::: : ::::::::: d1w0jd3 170 VLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAI 229 d1tf7a1 170 ERIEEYGPIARY-GVEEFVSDNVVILRNVLEGERRRR-TLE--ILKLRGTSHMKGEYPFT 225 ::::: :::::: :::::::::::::::::: ::::: ::: ::::: : d1w0jd3 230 YVPAD-DLTDPAPATTFAHLDATTVLSRAIA-ELGIYPAVDPLDSTSR-I---------- 276 d1tf7a1 226 ITDHGINIFPLGAMRLT 242 d1w0jd3 277 ----------------- 277 HHsearch alignment (Probability: 0.99 E-value:0.00) d1tf7a1 5 IAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE 64 :::::::::::::::: :::::::::::::::::::::::::::::::::::::::::: d1w0jd3 49 QEILVTGIKVVDLLAP--YAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVG 106 d1tf7a1 65 ETPQDIIKNARSFGWD---LAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAI 121 :::::::::::::::: ::::::::::::::::::::::::::: ::::::::::: d1w0jd3 107 ERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVA---LTGLTVAEYFR 163 d1tf7a1 122 QK-YRARRVSIDSVTSVFQQYD--------------ASSVVRRELFRLVARLKQIG---A 163 :: ::::::::::::::::::: :::::::::::::::::::: : d1w0jd3 164 DQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSI 223 d1tf7a1 164 TTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEI 209 :::::::::::::::::::::::::::::::::::::::::::::: d1w0jd3 224 TSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDP 269