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 <-- 0.779 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d4tmka_) 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 d4tmka_ Thymidylate kinaseP-​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 <-- 0.779 --> Hit
DALI alignment (Z-score: 4.1 Raw score:501.30) d1tf7a1 1 ehqaiakmrtmiegfddishgglpIGRSTLVSGTSGTGKTLFSIQFLYNGIIeFDEPgvf 60 :::::::::::::::::::::::::::: :::: d4tmka_ 1 ------------------------RSKYIVIEGLEGAGKTTARNVVVETLEQ-LGIR--- 32 d1tf7a1 61 vtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvggfdlsalierinya 120 d4tmka_ 33 ------------------------------------------------------------ 33 d1tf7a1 121 iqkyraRRVSIdsVTSV-------FQQY------------------DASSVVRRELFR-L 154 ::::: :::: :::: :::::::::::: : d4tmka_ 33 ------DMVFT--REPGgtqlaekLRSLlldiksvgdevitdkaevLMFYAARVQLVEtV 84 d1tf7a1 155 VARLKQIGATTVMTTerieeygpIARY--------------------gveeFVSDNVVIL 194 ::::::::::::::: :::: ::::::::: d4tmka_ 85 IKPALANGTWVIGDR------hdLSTQayqgggrgidqhmlatlrdavlgdFRPDLTLYL 138 d1tf7a1 195 RNVLE-----------------gerrrrtleilklrgtsHMKG-----eyPFTITdHGIN 232 ::::: :::: ::::: :::: d4tmka_ 139 DVTPEvglkrarargeldrieqesfdffnrtrarylelaAQDKsihtidaTQPLE-AVMD 197 d1tf7a1 233 I---fplgamrlt 242 : d4tmka_ 198 Airttvthwvkel 210 FAST alignment (Normalized score: 3.08 Raw score:694.30) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI-GRSTLVSGTSGTGKTLFSIQFLYNGIIEFD--EP 57 :::::::::::::::::::::::::::: :: d4tmka_ 1 -------------------------RSKYIVIEGLEGAGKTTARNVVVETLEQL--GIRD 33 d1tf7a1 58 GVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDAS----------------PDPEG 101 :::: :::: d4tmka_ 34 MVFT-----------------------------------REPGGTQLAEKLRSLLLDIK- 57 d1tf7a1 102 QEV-------VGGFDLSALIERINYAIQKYRA---------RRVSID-SVTSVF-----Q 139 ::::::::::::::::::: :::::: :::::: : d4tmka_ 58 ---SVGDEVITDKAEVLMFYAARVQLVET---VIKPALANGTWVIGDRHDLSTQAYQGGG 111 d1tf7a1 140 QYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEF----VSDNVVILR 195 ::::::::::::::: ::::::::: d4tmka_ 112 RGIDQHMLATLRDAV--------------------------------LGDFRPDLTLYLD 139 d1tf7a1 196 NVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT------------- 242 d4tmka_ 140 -----------------------------------------------VTPEVGLKRARAR 152 d1tf7a1 243 ---------------------------------------------------------- 243 d4tmka_ 153 GELDRIEQESFDFFNRTRARYLELAAQDKSIHTIDATQPLEAVMDAIRTTVTHWVKEL 210 TMalign alignment (TM-score: 0.42 Raw score:101.56) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 : ::::: :::::::::::::::::::::::::::::: d4tmka_ 1 -------R----------------SKYIV-IEGLEGAGKTTARNVVVETLEQLGIRDMVF 36 d1tf7a1 61 VTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDA--SPD-PEGQ--------------E 103 :::: ::: ::: :::: : d4tmka_ 37 TREP----------------------------GGTQLAEKLRSLLLDIKSVGDEVITDKA 68 d1tf7a1 104 --VVGGFDLSALIE-RINYAIQKYRARRVSIDSV-TSVF-QQ---YDASS-VVRRELF-R 153 :::::::::::: :::::::: ::: :::::: :::: :: ::::: ::::::: : d4tmka_ 69 EVLMFYAARVQLVETVIKPALAN-GTW-VIGDRHDLSTQAYQGGGRGIDQHMLATLRDAV 126 d1tf7a1 154 LVARLKQIGATTVMTTERIEE-----------------------YGPIARYG-VEE-FVS 188 :::::: ::::::::::: ::::::: ::: ::: d4tmka_ 127 LGDFRP----DLTLYLDVTPEVGLKRARARGELDRIEQESFDFF-NRTRARYLELAAQDK 181 d1tf7a1 189 DNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINI-FP---------LGA 238 :::::::: ::: ::: ::: :: d4tmka_ 182 SIHTIDAT-------QPL----------------EAV-----MDAIRTTVTHWVKEL--- 210 d1tf7a1 239 MRLT 242 d4tmka_ 211 ---- 211 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF 63 :::::::::::::::::::::::: :::::::::::::: d4tmka_ 1 RSKYIVIEGLEGAGKTTARNVVVE-TLEQLGIRDMVFTR 38