Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate RR42_RS00605 RR42_RS00605 glutamyl-tRNA amidotransferase
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__Cup4G11:RR42_RS00605 Length = 486 Score = 443 bits (1140), Expect = e-129 Identities = 232/484 (47%), Positives = 325/484 (67%), Gaps = 12/484 (2%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M +E VIGLE H +L T SK+FS + FGA PN+ + +DLA PGVLPV+N+ AV+ A+ Sbjct: 1 MQWEVVIGLETHTQLSTASKIFSGTSTAFGAAPNTQASPVDLALPGVLPVLNRGAVERAI 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGET-----KR 115 + +A+ IA S F RKNYFYPD PK YQISQ++ P+ + G I I+V+G+ K Sbjct: 61 QFGLAIGATIAPRSIFARKNYFYPDLPKGYQISQYELPVVQGGSISIQVEGKKGETYEKT 120 Query: 116 IGITRLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSI 173 + +TR H+EEDAGKS H+ + +DLNR GTPL+EIV+EPD+RS EA AY + L ++ Sbjct: 121 VQLTRAHLEEDAGKSLHEDFAGMTGIDLNRAGTPLLEIVTEPDMRSSAEAVAYAKALHAL 180 Query: 174 IQYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEE 233 + + G+ D M+EGS RCDAN+S+RPYG K GT+ E+KNLNSF ++++ ++YE + Q Sbjct: 181 VMWLGICDGNMQEGSFRCDANVSVRPYGSPKLGTRREIKNLNSFRFLQQAIDYEVQWQIA 240 Query: 234 ELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIP 293 E+ G EI Q T FD TG+T MR KE + DYRYFP+PD++PL ID AW ERV+ +P Sbjct: 241 EIEDGREIQQATVLFDPDTGETRAMRTKEDAHDYRYFPDPDLLPLEIDAAWIERVKSALP 300 Query: 294 ELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHG--ADVKLTSNWLMGGVNEY 351 ELP +A+ V++ GL AYDA VLT +K ++++FE+ + A+ K +NWLMG V+ Sbjct: 301 ELPVAMQARLVSQYGLSAYDASVLTASKSLANYFEAVVAEAGTANAKPAANWLMGDVSSL 360 Query: 352 LNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKK-VFPELAA--KGGNAKQIMEDNG 408 LN+ + L + P LA ++ I DGT+S+ AKK VFP + A G +A I+ G Sbjct: 361 LNREGIALEAAPVKPAQLAKLLVRIADGTVSNNTAKKDVFPAMWAGEAGADADAIIAAKG 420 Query: 409 LVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLL 468 L Q+SD L K +++ L N +SVE+++ GK KA LVGQ MKA+KG+ NP VN+LL Sbjct: 421 LKQMSDSGELEKIIDDVLAANAKSVEEFRAGKEKAFNALVGQAMKATKGKGNPAQVNELL 480 Query: 469 KQEL 472 K++L Sbjct: 481 KRKL 484 Lambda K H 0.313 0.133 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 577 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 475 Length of database: 486 Length adjustment: 34 Effective length of query: 441 Effective length of database: 452 Effective search space: 199332 Effective search space used: 199332 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 bits)
Align candidate RR42_RS00605 RR42_RS00605 (glutamyl-tRNA amidotransferase)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00133.hmm # target sequence database: /tmp/gapView.6036.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-167 541.7 0.0 7.6e-167 541.5 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS00605 RR42_RS00605 glutamyl-tRNA amido Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS00605 RR42_RS00605 glutamyl-tRNA amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 541.5 0.0 7.6e-167 7.6e-167 2 480 .. 1 484 [. 1 485 [. 0.97 Alignments for each domain: == domain 1 score: 541.5 bits; conditional E-value: 7.6e-167 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +++e+viGlE+H+ql t+sK+F+ +s+ + pNt+ +pv+l+lPG+lPvlN+ av+ A++ +la+++ lcl|FitnessBrowser__Cup4G11:RR42_RS00605 1 MQWEVVIGLETHTQLSTASKIFSGTSTAFGA-APNTQASPVDLALPGVLPVLNRGAVERAIQFGLAIGA 68 5789*************************99.9************************************ PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.....keigierlhlEeDtgksq 134 +++ s+F+RK+YfYpDlPkgyqi+q++lP++++G+++i++e+k+ k+++++r hlEeD+gks lcl|FitnessBrowser__Cup4G11:RR42_RS00605 69 T-IAPRSIFARKNYFYPDLPKGYQISQYELPVVQGGSISIQVEGKKgetyeKTVQLTRAHLEEDAGKSL 136 *.668**************************************99999999****************** PP TIGR00133 135 ykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvs 203 ++ + ++ +D+NR+g+PLlEiVt+Pd++s+ ea+a+ k l++++ +l+i dg+++eGs+R+D+Nvs lcl|FitnessBrowser__Cup4G11:RR42_RS00605 137 HED--FAGMTGIDLNRAGTPLLEIVTEPDMRSSAEAVAYAKALHALVMWLGICDGNMQEGSFRCDANVS 203 *94..4789************************************************************ PP TIGR00133 204 irlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeese 272 +r+ G+ k gtr EiKNlns++ +++ai+yE++ q++++++g+e++q+t fd + t ++R Ke+++ lcl|FitnessBrowser__Cup4G11:RR42_RS00605 204 VRPYGSPKLGTRREIKNLNSFRFLQQAIDYEVQWQIAEIEDGREIQQATVLFDPDTGETRAMRTKEDAH 272 ********************************************************************* PP TIGR00133 273 DYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkl 341 DYRYfp+Pdl p+eid ++++ v+ lpelP a+++rl+++ygls++da vl++ ++l+++fe vv lcl|FitnessBrowser__Cup4G11:RR42_RS00605 273 DYRYFPDPDLLPLEIDAAWIER-VKSALPELPVAMQARLVSQYGLSAYDASVLTASKSLANYFEAVVAE 340 *********************9.*******************************************998 PP TIGR00133 342 ikep..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksak.elleellen..k 405 ++++ k a+nW++ ++ + Ln++ i l++a +kp +la+l+ i +g++s+ +ak +++ + + lcl|FitnessBrowser__Cup4G11:RR42_RS00605 341 AGTAnaKPAANWLMGDVSSLLNREGIALEAAPVKPAQLAKLLVRIADGTVSNNTAKkDVFPAMWAGeaG 409 87665699*******************************************998862588888755669 PP TIGR00133 406 kdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevek 474 d++++i ++gl q+sd el ki+++v++ n+k+ve++++gkeka++ lvGq+mk tkg+ +p++v++ lcl|FitnessBrowser__Cup4G11:RR42_RS00605 410 ADADAIIAAKGLKQMSDSGELEKIIDDVLAANAKSVEEFRAGKEKAFNALVGQAMKATKGKGNPAQVNE 478 9******************************************************************** PP TIGR00133 475 llkell 480 llk +l lcl|FitnessBrowser__Cup4G11:RR42_RS00605 479 LLKRKL 484 ***987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (486 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.60 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory