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 <-- 0.758 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1okkd2) 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 d1okkd2 GTPase domain of the signal recognition particle receptor FtsYP-​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 <-- 0.758 --> Hit
DALI alignment (Z-score: 6.5 Raw score:669.10) d1tf7a1 1 ehqaiakmrtmiegfddishGGLPIgrsTLVSgtSGTGKTLFSIQFLYNGIIEFdEPGVF 60 ::::: :::: :::::::::::::::::::: ::::: d1okkd2 1 -------------------pVEPKGrvvLVVG-vNGVGKTTTIAKLGRYYQNLG-KKVMF 39 d1tf7a1 61 VT------fEETP-QDIIknarsfgWDLAklvdegkLFILDASPdpegqevvggFDLSAL 113 :: :::: :::: :::: :::::::: :::::: d1okkd2 40 CAgdtfraaGGTQlSEWG-------KRLS-------IPVIQGPE---------gTDPAAL 76 d1tf7a1 114 IERINYAIQKYRARRVSIDSVTsvfqqydASSVVRRELFRLVARLKQIG--attvMTTER 171 :::::::::::::::::::::: :::::::::::::::::::: ::::: d1okkd2 77 AYDAVQAMKARGYDLLFVDTAG----rlhTKHNLMEELKKVKRAIAKADpeepkeVWLVL 132 d1tf7a1 172 ---IEEY-GPIAryGVEEFVSDNVVILRnvlegeRRRRtleilklrgtshmkgeypftIT 227 :::: :::: :::::::::::::: :::: :: d1okkd2 133 davTGQNgLEQA--KKFHEAVGLTGVIV-tkldgTAKG--gvlipivrtlkvpikfvgVG 187 d1tf7a1 228 DH--GINI-FPLGAM--rlt 242 :: :::: :::::: d1okkd2 188 EGpdDLQPfDPEAFVealle 207 FAST alignment (Normalized score: 5.75 Raw score:1287.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHG--GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPG 58 :::: :::::::::::::::::::::::::: ::::: d1okkd2 1 ---------------------PVEPKG-RVVLVVGVNGVGKTTTIAKLGRYYQN-LGKKV 37 d1tf7a1 59 VFVT--FEE--TPQDIIKNARSFGWDLAKLVDEG-KLFILDASPDPEGQEVVGGFD---- 109 :::: ::: ::::::: :::: :::::: d1okkd2 38 MFCAGDTFRAAGGTQLSE-------WGKR-----LSIPVIQ---------------GPEG 70 d1tf7a1 110 --LSALIERINYAIQKYRARRVSIDSVTSVFQQYDA--------SSVVRRELFRLVARLK 159 :::::::::::::::::::::: :::::::::::::::: d1okkd2 71 TDPAALAYDAVQAMKARGYDLLFV------------DTAGRLHTKHNLMEELKKVKRAIA 118 d1tf7a1 160 QIGAT------TVMTTERI-------EEYGPIAR-YGVEEFVSDN--VVILRNVLEGERR 203 : :::::: :::: :::::::: :::: d1okkd2 119 K----ADPEEPKEVWLV--LDAVTGQNGLE----QAKKFHEAV--GLTGVI--------- 157 d1tf7a1 204 RRTLEILKLRGTSHMKGEY------------------------PFTITDHGINIFPLGAM 239 :::: d1okkd2 158 -------------------VTKLDGTAKGGVLIPIVRTLKVPIKFVG------------- 185 d1tf7a1 240 RLT---------------------- 242 d1okkd2 186 ---VGEGPDDLQPFDPEAFVEALLE 207 TMalign alignment (TM-score: 0.53 Raw score:129.29) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 : : :::::::::::::: :::::::::::::::::::::::: d1okkd2 1 --------P------V-----EPKGRVVLVVGVNG-VGKTTTIAKLGRYYQNLGKKVMFC 40 d1tf7a1 61 VTF--E--ETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIER 116 ::: : ::: :::: : ::::: :::::::: : : ::: ::::: d1okkd2 41 AGDTFRAAGGT-QLSE-W------GKRLS----IPVIQGPE---G---T--DPA-ALAYD 79 d1tf7a1 117 INYAIQKYRARRVSIDSVTS-VFQQYDASSVVRRELFRLVARLKQIGATTVMTTER-IEE 174 :::::::::::::::::::: ::::::: :::::::::::::::::::::::::: ::: d1okkd2 80 AVQAMKARGYDLLFVDTAGRL-HTKHNLM-EELKKVKRAIAKADPEEPKEVWLVLDAVTG 137 d1tf7a1 175 YG--PIARYGVEEF-VSDNVVILRNV-LEGERRRRTL-E--IL---KLRGTSHMKGEYPF 224 :: ::: ::::: ::::::::::: :::::: : :: :: ::: ::: d1okkd2 138 QNGLEQA--KKFHEAVGLTGVIVTKLD----GTAKGGVLIPIVRTLKV----PIK--FVG 185 d1tf7a1 225 TITD-HGINIFPLGAM------RLT 242 :::: ::::::::::: d1okkd2 186 VGEGPDDLQPFDPEAFVEALLE--- 207 HHsearch alignment (Probability: 0.99 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEET----PQDIIKNARSFGW 79 :::::::::::::::::::::::::: :::::::::::::::: ::::::::::::: d1okkd2 4 PKGRVVLVVGVNGVGKTTTIAKLGRY-YQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSI 62 d1tf7a1 80 DLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQ 139 :::: :::::::::::::::::::::::::::::::::: d1okkd2 63 PVIQ--------------------GPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRL-- 100 d1tf7a1 140 QYDASSVVRRELFRLVARL 158 ::::::::::::::::: d1okkd2 101 --HTKHNLMEELKKVKRAI 117