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 <-- 1.245 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1veca_) 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 d1veca_ DEAD box RNA helicase rck/​p54P-​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 <-- 1.245 --> Hit
DALI alignment (Z-score: 5.2 Raw score:573.30) d1tf7a1 1 ehqaiakmrtmiEGFD----------------------dishgGLPIgRSTLVSGTSGtG 38 :::: :::: :::::::::: : d1veca_ 1 -------kgnefEDYClkrellmgifemgwekpspiqeesipiALSG-RDILARAKNGtG 52 d1tf7a1 39 KTLFSIQFLYNGIIEFD--ePGVFVTFE-ETPQDIIKNARsFGWD--lAKLV-------- 85 ::::::::::::::::: :::::::: ::::::::::: :::: :::: d1veca_ 53 KSGAYLIPLLERLDLKKdniQAMVIVPTrELALQVSQICI-QVSKhmgGAKVmattggtn 111 d1tf7a1 86 ---------dEGKLFILDAspdpegqevvggfdlSALIER---inYAIQkyRARRVSIDS 133 ::::::::: :::::: :::: ::::::::: d1veca_ 112 lrddimrlddTVHVVIATP---------------GRILDLikkgvAKVD--HVQMIVLDE 154 d1tf7a1 134 VTS-VFQQydassvvrrelfrlvARLKQI---GATTVMTTErieeygpiARYGVEEFVS- 188 ::: :::: :::::: ::::::::: :::::::::: d1veca_ 155 ADKlLSQD----------fvqimEDIILTlpkNRQILLYSA--------TFPLSVQKFMn 196 d1tf7a1 189 -----DNVVIlrnvlegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 ::::: d1veca_ 197 shlekPYEIN------------------------------------------------- 206 FAST alignment (Normalized score: 4.92 Raw score:1098.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------------------------------ 24 d1veca_ 1 ------------------------KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPI 36 d1tf7a1 25 --IGRSTLVSGTSGT---GKTLFSIQFLYNG-IIEFDE--PGVFVTFEE---TPQDIIKN 73 :::::::::: ::::::::::::: ::::: ::::::: :::::::: d1veca_ 37 ALSGRDILARAK---NGTGKSGAYLIPLLERLDLKKD-NIQAMVIVP--TRELALQVSQI 90 d1tf7a1 74 ARSFGWDLAKLV---------------------------DEGKLFILDASPDPEGQEVVG 106 ::: :::::::: d1veca_ 91 CIQ---------VSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIA------------- 128 d1tf7a1 107 GFDLSALIERINYAIQK------YRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQ 160 :::::::::: ::::::::::::::: :::::::::::::: d1veca_ 129 --TPGRILDLIK-----KGVAKVDHVQMIVLDEADKLL-----SQDFVQIMEDIILT--- 173 d1tf7a1 161 --IGATTVMTTERIEEYGPIA--RYGVEEF----VSDNVVILRNVLEGERRRRTLEILKL 212 ::::::::: ::::::: :::::::: d1veca_ 174 LPKNRQILLYS----------ATFPLSVQKFMNSHLEKPYEI------------------ 205 d1tf7a1 213 RGTSHMKGEYPFTITDHGINIFPLGAMRLT- 242 d1veca_ 206 ------------------------------N 206 TMalign alignment (TM-score: 0.44 Raw score:105.57) d1tf7a1 1 -------EHQAIAKMRTM-------------------IEGFDDISHGGLPIGRSTLVSGT 34 ::: :::::: :::::: ::::::: d1veca_ 1 KGNEFED--------YCLKRELLMGIFEMGWEKPSPIQEESIP-IALSGR---DILARAK 48 d1tf7a1 35 SGTGKTLFSIQFLYNGIIEFD-E-PGVFVTFE-ETPQDIIKNARSFGWD-LAKLVD---- 86 ::::::::::::::::::::: : :::::::: :::::::::::: ::: :::::: d1veca_ 49 NGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQ-VSKHMGGAKVMATT 107 d1tf7a1 87 -------------EGKLFILDASPDPEGQEVVGGFDLSALIERI-N-YAIQKYRARRVSI 131 :::::::::: :: :::::: : :::: ::::::: d1veca_ 108 GGTNLRDDIMRLDDTVHVVIATP------------GR-ILDLIKKGVAKVD--HVQMIVL 152 d1tf7a1 132 DSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEE--FV-- 187 ::::::::::: : :::::::::::::::::::::: : ::::: :: d1veca_ 153 DEADKLLSQDF----V--QIMEDIILTLPKNRQILLYSAT-------F-PLSVQKFMNSH 198 d1tf7a1 188 SD-NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 :: ::::: d1veca_ 199 LEKPYEIN------------------------------------------------ 206 HHsearch alignment (Probability: 0.95 E-value:0.00) d1tf7a1 23 LPIGRSTLVSGTSGTGKTLFS-IQFLYN-GIIEFDEPGVFVTF-EETPQDIIKNARSFGW 79 ::::::::::::::::::::: :::::: :::::::::::::: :::::::::::::::: d1veca_ 37 ALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSK 96 d1tf7a1 80 DLAKLVDE---GKLFILDASPDPEGQEVVGGFDLSALIERINY-AIQKYRARRVSIDSVT 135 :::::::: :::::::::::::::::::::::::::::::: :::::::::::::::: d1veca_ 97 HMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEAD 156 d1tf7a1 136 SVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIE 173 :::::: ::::::::::::::::::::::::::: d1veca_ 157 KLLSQD-----FVQIMEDIILTLPKNRQILLYSATFPL 189