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 <-- 1.122 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d2uaga2) 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 d2uaga2 UDP-​N-​acetylmuramoyl-​L-​alanine:D-​glutamate ligase MurDMurD-​like peptide ligases,​ peptide-​binding domainMurD-​like peptide ligases,​ peptide-​binding domainα/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 <-- 1.122 --> Hit
DALI alignment (Z-score: 3.1 Raw score:363.50) d1tf7a1 1 ehqaiakmrtmiegfddishgglpigrsTLVS--------------gtsgtGKTLFSIQf 46 :::: :::::::: d2uaga2 1 -------------------------glpHRFEvvlehngvrwindskatnvGSTEAALN- 34 d1tf7a1 47 lYNGIiefdEPGVFVTF----eetpQDIIKnarsfgwdLAKLvdegKLFILDASP---dp 99 :::: :::::::: ::::: :::: ::::::::: d2uaga2 35 gLHVD----GTLHLLLGgdgksadfSPLAR-------yLNGD----NVRLYCFGRdgaql 79 d1tf7a1 100 egqevvggfdlsALIERINYAIQKYR-aRRVSIDSvTSVFQqydasSVVRRELFRLVARL 158 :::::::::::::: ::::::: ::::: :::::::::::::: d2uaga2 80 aalrpevaeqteTMEQAMRLLAPRVQpgDMVLLSPaCASLD---qfKNFEQRGNEFARLA 136 d1tf7a1 159 KQIGattvmtterieeygpiarygveefvsdnvvilrnvlegerrrrtleilklrgtshm 218 :::: d2uaga2 137 KELG-------------------------------------------------------- 140 d1tf7a1 219 kgeypftitdhginifplgamrlt 242 d2uaga2 141 ------------------------ 141 FAST alignment (Normalized score: 2.94 Raw score:541.30) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI--------------GRSTLVSGTSGTG-----KTL 41 ::::: ::: d2uaga2 1 -------------------------GLPHRFEVVLEHNGVRWIN--------DSKATNVG 27 d1tf7a1 42 FSIQFLYNGIIEF---DEPGVFVTF------EETPQDIIKNARSFGWDLAKLVDEGKLFI 92 :::::::: ::::::: :::::: :::::::::::: d2uaga2 28 STEAALNG-----LHVDGTLHLL--LGGDGKSADFSP-----------LARYLNGDNVRL 69 d1tf7a1 93 LDASPDPEGQEVVGGF-------------------DLSALIERINYAIQKYRA----RRV 129 ::: :::::::::::: ::: d2uaga2 70 YCF-------------GRDGAQLAALRPEVAEQTETMEQAMRLLAPR------VQPGDMV 110 d1tf7a1 130 SI---DSVTSVFQQYDASS---VVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGV 183 :: ::::: ::::::::::::::: d2uaga2 111 LLSPACASLD---------QFKNFEQRGNEFARLAKE----------------------- 138 d1tf7a1 184 EEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT- 242 d2uaga2 139 -----------------------------------------------------------L 139 d1tf7a1 243 - 243 d2uaga2 140 G 140 TMalign alignment (TM-score: 0.34 Raw score:83.33) d1tf7a1 1 ------EHQAIAKMRTMIEGFDDISHGGLPIG-----RSTLVSGTSGTGKTLFSIQFLYN 49 ::::: :::::::::: ::::::::: :: d2uaga2 1 GLPHRF---------------------EVVLEHNGVRWINDSKATNV-GSTEAALNG-LH 37 d1tf7a1 50 GIIEFDEPGVFVTF--E--ETPQDIIKNARSFGWDLAKLVDEGKLFILDA--SPDP---- 99 : ::::::::: : :::::::: : :: : : ::::::: :::: d2uaga2 38 V----DGTLHLLLGGDGKSADFSPLAR-Y------LN-G--D-NVRLYCFGRDGAQLAAL 82 d1tf7a1 100 --------EGQEVVGGFDLSALIERINYAIQKYR-ARRVSIDSVTSVFQQYDASSVVRRE 150 :::::::::::: : :: ::::::::::: ::::::: :::: d2uaga2 83 RPEVAEQT--------ETMEQAMRLLAP--R-VQPGDMVLLSPACA-SLDQFKN--FEQR 128 d1tf7a1 151 LFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEIL 210 :::::::::::: d2uaga2 129 GNEFARLAKELG------------------------------------------------ 140 d1tf7a1 211 KLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 d2uaga2 141 -------------------------------- 141 HHsearch alignment (Probability: 0.04 E-value:0.24) d1tf7a1 110 LSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVAR 157 ::::::::::::: ::::::::::::::::::::::::::::::::: d2uaga2 93 MEQAMRLLAPRVQ--PGDMVLLSPACASLDQFKNFEQRGNEFARLAKE 138