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 <-- 2.260 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1w0ja3) 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 d1w0ja3 Central domain of alpha 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 <-- 2.260 --> Hit
DALI alignment (Z-score: 14.9 Raw score:1501.20) d1tf7a1 1 -------------------------------------------ehQAIA-KMRTMIEGFD 16 :::: :::::::::: d1w0ja3 1 vdvpvgeellgrvvdalgnaidgkgpigskarrrvglkapgiiprISVRePMQTGIKAVD 60 d1tf7a1 17 DIShgGLPIGRSTLVSGTSGTGKTLFSIQFLYNGiIEFD--------EPGVFVTFEE--- 65 ::: ::::::::::::::::::::::::::::: :::: :::::::::: d1w0ja3 61 SLV--PIGRGQRELIIGDRQTGKTSIAIDTIINQ-KRFNdgtdekkkLYCIYVAIGQkrs 117 d1tf7a1 66 TPQDIIKNARsfGWDLAKlvdegKLFILDASPDpegqevVGGFDLsALIERINYAIQKY- 124 :::::::::: :::::: :::::::::: :::::: ::::::::::::: d1w0ja3 118 TVAQLVKRLT--DADAMK-----YTIVVSATAS-----dAAPLQY-LAPYSGCSMGEYFr 164 d1tf7a1 125 ---RARRVSIDSVTSVFQQYD--------------ASSVVRRELFRLVARLKQ------- 160 :::::::::::::::::: :::::::::::::::::: d1w0ja3 165 dngKHALIIYDDLSKQAVAYRqmslllrrppgreaYPGDVFYLHSRLLERAAKmndafgg 224 d1tf7a1 161 iGATTVMTTERIEEygPIARY--GVEEFVSDNVVILRNVlegeRRRR-TLEI--LKLRGT 215 ::::::::::::: ::::: :::::::::::::::: :::: :::: :::::: d1w0ja3 225 gSLTALPVIETQAG--DVSAYipTNVISITDGQIFLETE-lfyKGIRpAINVglSVSRVG 281 d1tf7a1 216 Shmkgeypftitdhginifplgamrlt 242 : d1w0ja3 282 S-----------------------aaq 285 FAST alignment (Normalized score: 10.57 Raw score:2777.00) d1tf7a1 1 EHQA------------------------------------------------IAKMRTMI 12 :::::::: d1w0ja3 1 ----VDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGI 56 d1tf7a1 13 EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIE----------FDEPGVFVT 62 ::::::: ::::::::::::::::::::::::::::: ::::::::: d1w0ja3 57 KAVDSLV--PIGRGQRELIIGDRQTGKTSIAIDTIINQ---KRFNDGTDEKKKLYCIYVA 111 d1tf7a1 63 FEE---TPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVV-GGFDLSALIERIN 118 ::: ::::::::::: :::: ::::::::: :::::: ::::::::::::: d1w0ja3 112 IGQKRSTVAQLVKRLTD--ADAM-----KYTIVVSAT--ASDAAP-LQYLAPYSGCSMGE 161 d1tf7a1 119 YAIQKYRA-RRVSIDSVTSVFQQYDA------------------SSVVRRELFRLVARLK 159 :::: ::: ::::::::::::: ::::::::::::::: d1w0ja3 162 YFRD-NGKHALIIYDDLSKQAV----AYRQMSLLLRRPPGREAYPGDVFYLHSRLLERA- 215 d1tf7a1 160 QI----------GATTVMTTERIEEYGPIAR-------YGVEEFVSDNVVILRNVLEGER 202 :::::::::::: ::::::::::::::: d1w0ja3 216 --AKMNDAFGGGSLTALPVIETQA-------GDVSAYIPTNVISITDGQIFLE------- 259 d1tf7a1 203 R--------RRTLEI---LKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT------ 242 ::::: :::: d1w0ja3 260 -TELFYKGIRPAIN-VGLSVSR-----------------------------VGSAAQ 285 TMalign alignment (TM-score: 0.68 Raw score:163.97) d1tf7a1 1 --------------------------------------------EHQAIAKMRTMIEGFD 16 :::::::::::::::: d1w0ja3 1 VDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVD 60 d1tf7a1 17 DISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFD--------EPGVFVTF-EET- 66 ::: ::::::::::::::::::::::::::::: :::: :::::::: ::: d1w0ja3 61 SLV--PIGRGQRELIIGDRQTGKTSIAIDTIINQ-KRFNDGTDEKKKLYCIYVAIGQKRS 117 d1tf7a1 67 -PQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQK-- 123 :::::: :: ::: ::: :::::::::: :::: ::::: :::::::::::: d1w0ja3 118 TVAQLVK-RL---TDA-DAM--KYTIVVSATA-SDAA--PLQYL--APYSGCSMGEYFRD 165 d1tf7a1 124 Y-RARRVSIDSVTSVFQQ-Y-------------DASSVVRRELFRLVARLKQI------- 161 : :::::::::::::::: : :::::::::::::::::::: d1w0ja3 166 NGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGG 225 d1tf7a1 162 GATTVMTTERIEEYGPIARY-GVEEFVSDNVVILRNVLEGERRR-R--TLE--ILKLRGT 215 ::::::::::::: :::::: ::::::::::::::::: ::: : ::: ::::::: d1w0ja3 226 SLTALPVIETQAG-DVSAYIPTNVISITDGQIFLETEL---FYKGIRPAINVGLSVSRVG 281 d1tf7a1 216 SH--MKGEYPFTITDHGINIFPLGAMRLT 242 :: d1w0ja3 282 SAAQ------------------------- 285 HHsearch alignment (Probability: 0.99 E-value:0.00) d1tf7a1 6 AKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE-------PG 58 ::::::::::::::: :::::::::::::::::::::::::::::::::: :: d1w0ja3 50 EPMQTGIKAVDSLVP--IGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYC 107 d1tf7a1 59 VFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERIN 118 ::::::::::::::::::::::: :: ::::::::::::::::::: :::::::::: d1w0ja3 108 IYVAIGQKRSTVAQLVKRLTDAD--AM-KYTIVVSATASDAAPLQYL---APYSGCSMGE 161 d1tf7a1 119 YAIQKYRARRVSIDSVTSVFQQYDA--------------SSVVRRELFRLVARLKQ---- 160 ::::::::::::::::::::::::: ::::::::::::::::: d1w0ja3 162 YFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDA 221 d1tf7a1 161 ---IGATTVMTTERIEEYGPIAR--YGVEEFVSDNVVILRNVLEGERRRRTLEILK 211 :::::::::::: :::::: ::::::::::::::::::::::::::::::: d1w0ja3 222 FGGGSLTALPVIETQ--AGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGL 275