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 <-- 1.234 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1qdea_) 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 d1qdea_ Initiation factor 4aP-​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 <-- 1.234 --> Hit
DALI alignment (Z-score: 6.0 Raw score:625.10) d1tf7a1 1 ----------------------------------ehqaiakMRTMiegfddishgGLPIg 26 :::: :::: d1qdea_ 1 iqtnydkvvykfddmeldenllrgvfgygfeepsaiqqraiMPII----------EGHD- 49 d1tf7a1 27 rsTLVSGTSGTGKTLFSIQFLYNGIIEFD--ePGVFVTFE-ETPQDIIKNARsFGWD-lA 82 ::::::::::::::::::::::::::: :::::::: ::::::::::: :::: : d1qdea_ 50 --VLAQAQSGTGKTGTFSIAALQRIDTSVkapQALMLAPTrELALQIQKVVM-ALAFhmD 106 d1tf7a1 83 KLV------dEGKLFILDAspdpegqevvggfdlSALIER---inYAIQkyRARRVSIDS 133 ::: ::::::::: :::::: :::: ::::::::: d1qdea_ 107 IKVhaciglrDAQIVVGTP---------------GRVFDNiqrrrFRTD--KIKMFILDE 149 d1tf7a1 134 VTS-VFQQydassvvrrELFRLVARLKQIG--ATTVMTTErieeygpiARYGVEEFVSD- 189 ::: :::: ::::::::::::: :::::::: ::::::::::: d1qdea_ 150 ADEmLSSG---------FKEQIYQIFTLLPptTQVVLLSA--------TMPNDVLEVTTk 192 d1tf7a1 190 -----NVVIlrnvlegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 :::: d1qdea_ 193 fmrnpVRIL------------------------------------------------- 201 FAST alignment (Normalized score: 5.38 Raw score:1186.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------------------------------ 24 d1qdea_ 1 ------------------------IQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAI 36 d1tf7a1 25 ---------IGRSTLVSGTSGTGKTLFSIQFLYNG-IIEFDE--PGVFVTFEE---TPQD 69 :::::::::::::::::::::::::: ::::: ::::::: :::: d1qdea_ 37 QQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK-APQALMLAP--TRELALQ 93 d1tf7a1 70 IIKNARS--FGWDLAKLVD----------EGKLFILDASPDPEGQEVVGGFDLSALIERI 117 ::::::: :::: ::::::: ::::: d1qdea_ 94 IQKVVMALAFHMD------IKVHACIGLRDAQIVVG-------------------TPGRV 128 d1tf7a1 118 NYAIQKY-------RARRVSIDSVTSVFQQYDASSVVRRE--LFRLVARLKQ---IGATT 165 ::::: ::::::::::::::: :::::::::: ::::: d1qdea_ 129 FDNIQ--RRRFRTDKIKMFILDEADEMLS-----------SGFKEQIYQIFTLLPPTTQV 175 d1tf7a1 166 VMTTERIEEYGPIA--RYGVEEFVS-------DNVVILRNVLEGERRRRTLEILKLRGTS 216 :::: :::::::: :::: d1qdea_ 176 VLLS----------ATMPNDVLEV-TTKFMRNPVRI------------------------ 200 d1tf7a1 217 HMKGEYPFTITDHGINIFPLGAMRLT- 242 d1qdea_ 201 --------------------------L 201 TMalign alignment (TM-score: 0.45 Raw score:107.86) d1tf7a1 1 ------------EHQAIAKMRTMIE----------------------GFDDISHGGLPIG 26 ::: ::::::::::: d1qdea_ 1 IQTNYDKVVYKF----------DDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGH-- 48 d1tf7a1 27 RSTLVSGTSGTGKTLFSIQFLYNGIIEFD--EPGVFVTFE-ETPQDIIKNARSFGWD-LA 82 :::::::::::::::::::::::::::: ::::::::: :::::::::::: ::: :: d1qdea_ 49 -DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMA-LAFHMD 106 d1tf7a1 83 KLV----D--EGKLFILDASPDPEGQEVVGGFD-LSALIERINYAIQKYRARRVSIDSVT 135 ::: : :::::: ::: : :::::::::::::::::::::::: d1qdea_ 107 IKVHACIGLRDAQIVV-GTP------------GR--VFDNIQRRRFRTDKIKMFILDEAD 151 d1tf7a1 136 SVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEE-FV--SD-NV 191 ::::::: : :::::::::::::::::::::: ::::::: :: :: :: d1qdea_ 152 EMLSSGF----K--EQIYQIFTLLPPTTQVVLLSAT-------MPNDVLEVTTKFMRNPV 198 d1tf7a1 192 VILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 ::: d1qdea_ 199 RIL------------------------------------------------ 201 HHsearch alignment (Probability: 0.94 E-value:0.00) d1tf7a1 23 LPIGRSTLVSGTSGTGKTLFS-IQFLYNG-IIEFDEPGVFVT-FEETPQDIIKNARSFGW 79 ::::::::::::::::::::: ::::::: :::::::::::: ::::::::::::::::: d1qdea_ 44 IIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAF 103 d1tf7a1 80 DLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINY-AIQKYRARRVSIDSVTSVF 138 :::::::: ::::: :::::::::::::::::: ::::::::::::::::::: d1qdea_ 104 HMDIKVHA-------CIGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML 154 d1tf7a1 139 QQYDASSVVRRELFRLVARLKQIGATTVMTTERIE 173 ::: ::::::::::::::::::::::::::: d1qdea_ 155 SSG-----FKEQIYQIFTLLPPTTQVVLLSATMPN 184