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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.690 --> Intermediate <-- 1.226 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1f7ua2) through the intermediate protein (d1jila_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jila_ Tyrosyl-​tRNA synthetase (TyrRS)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1f7ua2 Arginyl-​tRNA synthetase (ArgRS)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.690 --> Intermediate
DALI alignment (Z-score: 6.1 Raw score:653.80) query 1 ---dadeeVYSAL-----vvglrayvAKNGFRSVLIGLS-----ggIDSALVAAIACDAL 47 ::::: ::::::::::::: :::::::::::::: d1jila_ 1 tnvliedlKWRGLiyqqtdeqgiedlLNKEQVTLYCGADptadslhIGHLLPFLTLRRFQ 60 query 48 G-aqNVYGVSMP--SKYS----------------SDHSKGDAAELARRTG-------LNF 81 : :::::::: :::: :::::::::::::::: ::: d1jila_ 61 EhghRPIVLIGGgtGMIGdpsgkseervlqteeqVDKNIEGISKQMHNIFefgtdhgAVL 120 query 82 RTVS--IEPMfdAYMASL----------------------gltGLAEENLQSRLRGTTLM 117 :::: :::: :::::: ::::::::::::::::: d1jila_ 121 VNNRdwLGQI--SLISFLrdygkhvgvnymlgkdsiqsrlehgISYTEFTYTILQAIDFG 178 query 118 AISNQEGH-IVLAPGNkselavgystlyGDSV--------------gAYGPiKDVY---- 158 :::::::: ::::::: :::: :::: :::: d1jila_ 179 HLNRELNCkIQVGGSD---------qwgNITSgielmrrmygqtdayGLTI-PLVTksdg 228 query 159 ----------------------------------ktsifrLAEW---------------- 168 :::: d1jila_ 229 kkfgksesgavwldaektspyefyqfwinqsdedvikflkYFTFlgkeeidrleqsknea 288 query 169 --------rnRAAAerGQTPpipeasitkpdypvldailelyvdrdtgadaivaagydre 220 :::: :::: d1jila_ 289 phlreaqktlAEEV--TKFI---------------------------------------- 306 query 221 lvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jila_ 307 -----------------------------hgedalndairisqalf 323 FAST alignment (Normalized score: 2.35 Raw score:689.80) query 1 DADEEVYSA------------------LVVGLRAYVAKNGF--RSVLIGLSG-------- 32 ::::::::::: :::::: d1jila_ 1 ---------TNVLIEDLKWRGLIYQQTDEQGIEDLLNK---EQVTLYCG---ADPTADSL 45 query 33 ---GIDSALVAAIACDALGAQ-NVYGVSMPSKYS-------------------------- 62 ::::::::::::: :::::::: d1jila_ 46 HIGHLLPFLTLRRFQE-----HGHRPIVLI----GGGTGMIGDPSGKSEERVLQTEEQVD 96 query 63 --SDHSKGDAAELARRTGL-------NFRTVSIEPMFDAYMASLGLTG------------ 101 ::::::::::: ::::::::::::: d1jila_ 97 KNIEGISKQMHNI------FEFGTDHGAVLVNNRDWLGQ---------ISLISFLRDYGK 141 query 102 ---------------------LAEENLQSRLRGTTLMAISNQEGHIVLA---PGNKSELA 137 :::::::::::::::::::::::: :::: d1jila_ 142 HVGVNYMLGKDSIQSRLEHGISYTEFTYTILQAIDFGHLNRELNC----KIQVGGS---- 193 query 138 VGYSTLY-GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLD 196 :::: d1jila_ 194 -------DQWGN------------------------------------------------ 198 query 197 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRL 256 d1jila_ 199 ------------------------------------------------------------ 199 query 257 PITNRWREGH-------------------------------------------------- 266 d1jila_ 199 ----------ITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSP 248 query 267 ------------------------------------------------------------ 267 d1jila_ 249 YEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHG 308 query 267 --------------- 267 d1jila_ 309 EDALNDAIRISQALF 323 TMalign alignment (TM-score: 0.46 Raw score:121.20) query 1 ------DADEEVYSALV--VG--L--RAYVAKNGFRSVLIGLSG----G-IDSALVAAIA 43 :::::::: : : :::::::::::::::::: : :::::::::: d1jila_ 1 TNVLIE---DLKWRGLIYQ-QTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTL 56 query 44 CDALG-AQNVYGVSMPS--K------------YS----S-DHSKGDAAELARRTG----- 78 ::::: ::::::::::: : :: : ::::::::::::::: d1jila_ 57 RRFQEHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDH 116 query 79 -LNFRTVS--IEPMFDAYMASL-----------------------GLTGLAEENLQSRLR 112 ::::::: :::: ::::::: ::::::::::::: d1jila_ 117 GAVLVNNRDWLGQI-SLISFLRDYGKHVGVNYMLGKDSIQSRLEH--GISYTEFTYTILQ 173 query 113 GTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS-VG------------AYGPIKDVYK 159 :::::::::::::::::::: :: : : ::: :: ::::: ::: d1jila_ 174 AIDFGHLNRELNCKIQVGGS--DQ--W--G--NITSGIELMRRMYGQTDAYGLTI--PLV 223 query 160 TS-----IF-----------------------------R---LAEWRN------------ 170 :: :: : :::::: d1jila_ 224 TKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQ 283 query 171 -------------RAAAERGQTPP----------------IPEASITKPDYPVLDAILEL 201 ::::::::::: d1jila_ 284 SKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF-------------------- 323 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1jila_ 324 ------------------------------------------------------------ 324 query 262 WREGH 266 d1jila_ 324 ----- 324 HHsearch alignment (Probability: 0.02 E-value:0.47) query 163 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVA--AGYDRE 220 :::::::::::::::::::::::::::: ::::::::::::::::::::::: :::::: d1jila_ 203 IELMRRMYGQTDAYGLTIPLVTKSDGKK-FGKSESGAVWLDAEKTSPYEFYQFWINQSDE 261 query 221 LVVKTLRMV 229 ::::::::: d1jila_ 262 DVIKFLKYF 270
Intermediate <-- 1.226 --> Hit
DALI alignment (Z-score: 9.1 Raw score:1056.00) d1jila_ 1 TNVLiedlkwrgliyqqtdeqgiedllnKEQVTLYC-GADPTAdSLHIGHLLPFLTLRRF 59 :::: :::::::: :::::: :::::::::::::::: d1f7ua2 1 SCKL----------------------veNKKVIIEFsSPNIAK-PFHAGHLRSTIIGGFL 37 d1jila_ 60 QEHG------HRPIVLIGGgtGMIGdpsgkseeRVLQ----------------------- 90 :::: ::::::::: :::: :::: d1f7ua2 38 ANLYeklgweVIRMNYLGD--WGKQ-------fGLLAvgferygneealvkdpihhlfdv 88 d1jila_ 91 ------------------------------------------TEEQVDKNIEGISKQMHN 108 :::::::::::::::::: d1f7ua2 89 yvrinkdieeegdsipleqstngkareyfkrmedgdeealkiWKRFREFSIEKYIDTYAR 148 d1jila_ 109 -IFEFgtdhgAVLVNNRDWLgqisLISFLrDYGKH-------------vGVNY------M 148 :::: :::::::::: ::::: ::::: :::: : d1f7ua2 149 lNIKY-----DVYSGESQVS----KESML-KAIDLfkekglthedkgavLIDLtkfnkkL 198 d1jila_ 149 LGKdsiqsrlehgISYTeFTYTILQAIDFGHLNRELN--cKIQVGGSDQWGNITSGIELM 206 ::: :::: ::::::::::::::::::: :::::::::::::::::::: d1f7ua2 199 GKA------ivqkSDGT-TLYLTRDVGAAMDRYEKYHfdkMIYVIASQQDLHAAQFFEIL 251 d1jila_ 207 RRMYG--QTDAYGLTIPLVTksdgkkFGKS-ESGAVWLDaeKTSPyEFYQfwinqsdedv 263 ::::: ::::::::::::: :::: :::::::: :::: :::: d1f7ua2 252 KQMGFewAKDLQHVNFGMVQ------GMSTrKGTVVFLD--NILE-ETKE---------- 292 d1jila_ 264 ikflkyftflgkeeidrleqskneaphlreaqktlaeevtkfihgEDAL----------- 312 :::: d1f7ua2 293 -------------------------kmhevmkknenkyaqiehpeEVADlvgisavmiqd 327 d1jila_ 313 ----------ndairisqalf 323 d1f7ua2 328 mqgkrinnyefkwermlsfeg 348 FAST alignment (Normalized score: 5.63 Raw score:1888.00) d1jila_ 1 TNVLIEDLKWRGLIYQQTDEQGIEDLLN------KEQVTLY-CGADPTADSLHIGHLLPF 53 ::::::: :::::: ::::::::::: d1f7ua2 1 ----------------------------SCKLVENKKVIIEFSSPNIA-KPFHAGHLRST 31 d1jila_ 54 LTLRRFQE------HGHRPIVLIGGGTGMIGDPSGKSEERVLQ----------------- 90 :::::::: ::::::::::: d1f7ua2 32 IIGGFLANLYEKLGWEVIRMNYLGD------------------WGKQFGLLAVGFERYGN 73 d1jila_ 91 ---------------------------------------------------------TEE 93 ::: d1f7ua2 74 EEALVKDPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKR 133 d1jila_ 94 QVDKNIEGISKQMHNIFEFGTDHG-----AVLVNNRDWLGQI-----SLISFLRDYGKHV 143 ::::::::::::::: ::::::: ::::::::::: d1f7ua2 134 FREFSIEKYIDTYAR---------LNIKYDVYSGES------QVSKESMLKAIDLFKE-- 176 d1jila_ 144 GVNYMLGKDSIQSRLEHGISYTEF----------------------------------TY 169 :: d1f7ua2 177 ------------------------KGLTHEDKGAVLIDLTKFNKKLGKAIVQKSDGTTLY 212 d1jila_ 170 TILQAIDFGHLNRELNC--KIQVGGSDQWGNITSGIELMRRMYG-----QTDAYGLTIPL 222 ::::::::::::::::: :::::::::::::::::::::: ::::::::::: d1f7ua2 213 LTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQ---MGFEWAKDLQHVNFGM 269 d1jila_ 223 VTKSDGKKFGKSES--------GAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLG 274 : ::::: d1f7ua2 270 V-------------QGMSTRKGTVVFL--------------------------------- 283 d1jila_ 275 KEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF----------- 323 d1f7ua2 284 -------------------------------------------------DNILEETKEKM 294 d1jila_ 324 ------------------------------------------------------ 324 d1f7ua2 295 HEVMKKNENKYAQIEHPEEVADLVGISAVMIQDMQGKRINNYEFKWERMLSFEG 348 TMalign alignment (TM-score: 0.50 Raw score:161.61) d1jila_ 1 TN-VLIEDLKWRGLIYQQTDEQGIEDL--LNKEQVTLYCGADPTADSLHIGHLLPFLTLR 57 :: : ::::::::::::::::::::::::::::: d1f7ua2 1 SCK-----------------------LVE--NKKVIIEFSSPNIAKPFHAGHLRSTIIGG 35 d1jila_ 58 RFQEH-G---H-R-PIVLIGGGT-GMIG-------------------------------- 78 ::::: : : : ::::::::: :::: d1f7ua2 36 FLANLYEKLGWEVIRMNYLGDWGKQFGLLAVGFERYGNEEALVKDPIHHLFDVYVRINKD 95 d1jila_ 79 -DPSGKSE------------ERV--LQ-T---E------E--QVDKNIEGISKQMHN-I- 109 : : :: : : : ::::::::::::::: : d1f7ua2 96 I------EEEGDSIPLEQST--NGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYA 147 d1jila_ 110 ---FEFGTDHGAVLVNNRDWLGQISLISFLRDYGKH-VG--------VNYML--GKDSIQ 155 ::: :::::::::: :::::::::::::: :: ::::: :::::: d1f7ua2 148 RLNIKY-----DVYSGESQVS-KESMLKAIDLFKEKGLTHEDKGAVLIDLTKFNKKLGKA 201 d1jila_ 156 SRL-EHGISY-TEFTYTILQAIDFGHLNREL-N-CKIQVGGSDQWGNITSGIELMRRM-Y 210 : ::: :::::::::::::::::::: : :::::::::::::::::::::::: : d1f7ua2 202 --IV---QKSDGTTLYLTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQMGF 256 d1jila_ 211 GQ-TDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWI------------- 256 :: :::::::::::: :::::::::::: : ::::::::::: d1f7ua2 257 EWAKDLQHVNFGMVQ-----GMSTRKGTVVFL-D--NILEETKEKMHEVMKKNENKYAQI 308 d1jila_ 257 ------------NQSDEDVIKFLKYFT-----------FLGKEEIDRLEQSKNEAPHLRE 293 ::::::::: :: d1f7ua2 309 EHPEEVADLVGI------SAVMIQDMQGKRINNYEFKW--------------------ER 342 d1jila_ 294 AQKTL-AEEVTKFIHGEDALNDAIRISQALF 323 ::::: d1f7ua2 343 MLSFEG------------------------- 348 HHsearch alignment (Probability: 0.88 E-value:0.00) d1jila_ 165 TEFTYTILQAIDFGHLNRELNCK--IQVGGSDQWGNITSGIELMRRMYGQTDAYGLTIPL 222 ::::::::::::::::::::::: :::::::::::::::::::::::::::::::::: d1f7ua2 208 GTTLYLTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQMGFEWAKDLQHVN- 266 d1jila_ 223 VTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWI 256 :::::::::::::::::::::::::::::::: d1f7ua2 267 --FGMVQGMSTRKGTVVFLDNILEETKEKMHEVM 298