Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013841351.1 DESRU_RS06670 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000215085.1:WP_013841351.1 Length = 479 Score = 586 bits (1510), Expect = e-172 Identities = 284/476 (59%), Positives = 370/476 (77%), Gaps = 4/476 (0%) Query: 3 FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62 +ET+IG+EVHVELKT +KIF +S T FG + NT + LG PG LPVLNK+ VE+A++A Sbjct: 4 YETIIGIEVHVELKTNTKIFCNSTTEFGGDPNTHVCPVCLGLPGTLPVLNKKVVEYAVRA 63 Query: 63 AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122 +ALNC IA +KFDRKNY+YPD K YQISQ+D PI E G+++IEV G+ KRIGITRLH Sbjct: 64 GLALNCSIANFSKFDRKNYYYPDLTKNYQISQYDLPIAEQGYLDIEVDGQEKRIGITRLH 123 Query: 123 LEEDAGKLTHTGD----GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYT 178 +EEDAGKL H G+ YSLVD+NR G PL+EIVSEPD+R+PEEA AY EKL+++IQYT Sbjct: 124 MEEDAGKLVHQGNIMTTPYSLVDYNRAGVPLIEIVSEPDMRSPEEARAYAEKLRAVIQYT 183 Query: 179 GVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLS 238 GVSDC+MEEGSLRCDANIS+RP+GQ+E GTK+E+KN+NSF +Q+ L +E +RQ VL S Sbjct: 184 GVSDCRMEEGSLRCDANISVRPVGQKELGTKSEIKNMNSFRALQRALAYEVERQIGVLES 243 Query: 239 GFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPD 298 G + QETR +DEA T+ MR KE + DYRYFP+PDLV L +D +W + ++ S+PELPD Sbjct: 244 GGQVVQETRTWDEARGITLSMRSKEQAHDYRYFPDPDLVPLVLDPQWIDFIRQSLPELPD 303 Query: 299 ERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQK 358 +RR RY++E G YDA +LTLTKEM+DFFE+T+Q+ K SNW+MGE+S LNA Sbjct: 304 QRRARYVQEFGLPVYDAGILTLTKEMSDFFEQTIQQYDNPKAVSNWMMGEMSRLLNAGGM 363 Query: 359 ELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGV 418 E+ + P LA ++KLI+KGTIS KIAK VF+E+ G D E +V+EKGLVQISDEG Sbjct: 364 EIVQCKIKPAQLASLLKLIDKGTISGKIAKTVFEEMFASGKDPEAVVQEKGLVQISDEGA 423 Query: 419 LLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474 + +V E + NP+S+EDF+ GK++AIGFLVGQ+M+A+KG+ANP +VNK+L E+++ Sbjct: 424 IAAVVDEVIAANPKSVEDFRAGKEKAIGFLVGQVMRATKGKANPELVNKLLKEKLQ 479 Lambda K H 0.314 0.134 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: 722 Number of extensions: 16 Number of successful extensions: 2 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: 476 Length of database: 479 Length adjustment: 34 Effective length of query: 442 Effective length of database: 445 Effective search space: 196690 Effective search space used: 196690 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 WP_013841351.1 DESRU_RS06670 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
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.26192.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-196 637.9 0.0 5.1e-196 637.7 0.0 1.0 1 lcl|NCBI__GCF_000215085.1:WP_013841351.1 DESRU_RS06670 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000215085.1:WP_013841351.1 DESRU_RS06670 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 637.7 0.0 5.1e-196 5.1e-196 1 480 [. 1 478 [. 1 479 [] 0.99 Alignments for each domain: == domain 1 score: 637.7 bits; conditional E-value: 5.1e-196 TIGR00133 1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 +++ye +iG+EvHv l t++K+Fc++++e+ pNt+vcpvclglPG+lPvlNk++v+ A+ +laln lcl|NCBI__GCF_000215085.1:WP_013841351.1 1 MTQYETIIGIEVHVELKTNTKIFCNSTTEFGG-DPNTHVCPVCLGLPGTLPVLNKKVVEYAVRAGLALN 68 689*****************************.9*********************************** PP TIGR00133 70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykes 138 + ++++s+FdRK+Y+YpDl k+yqi+q+dlPiae+G+l+ie++++ek+igi+rlh+EeD+gk++++++ lcl|NCBI__GCF_000215085.1:WP_013841351.1 69 CS-IANFSKFDRKNYYYPDLTKNYQISQYDLPIAEQGYLDIEVDGQEKRIGITRLHMEEDAGKLVHQGN 136 **.668*************************************************************99 PP TIGR00133 139 dk.dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirl 206 + +slvD+NR+gvPL+EiV++Pd++s++eara+ +klr++++y+++sd+ +eeGs+R+D+N+s+r+ lcl|NCBI__GCF_000215085.1:WP_013841351.1 137 IMtTPYSLVDYNRAGVPLIEIVSEPDMRSPEEARAYAEKLRAVIQYTGVSDCRMEEGSLRCDANISVRP 205 87688**************************************************************** PP TIGR00133 207 kGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275 +Gq++ gt+ EiKN+ns++++++a+ yE+eRq+ +l++g +v+qetr++de++ it+s+R+Ke+++DYR lcl|NCBI__GCF_000215085.1:WP_013841351.1 206 VGQKELGTKSEIKNMNSFRALQRALAYEVERQIGVLESGGQVVQETRTWDEARGITLSMRSKEQAHDYR 274 ********************************************************************* PP TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344 Yfp+Pdl+p+++d+++++ +++ lpelP+++r+r+++e+gl +da +l+ +e+ d fe+ + ++ lcl|NCBI__GCF_000215085.1:WP_013841351.1 275 YFPDPDLVPLVLDPQWIDF-IRQSLPELPDQRRARYVQEFGLPVYDAGILTLTKEMSDFFEQTIQQYDN 342 *****************99.************************************************* PP TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413 pk++ nW++ e+ + Ln+ +++ ++ +kp +la+l+kli++g+is+k+ak+++ee++ +kdp+++++ lcl|NCBI__GCF_000215085.1:WP_013841351.1 343 PKAVSNWMMGEMSRLLNAGGMEIVQCKIKPAQLASLLKLIDKGTISGKIAKTVFEEMFASGKDPEAVVQ 411 ********************************************************************* PP TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 ++gl+qisde ++ ++v+evi+ npk+ve++++gkeka++flvGqvm+ tkg+a+p+ v+kllke+l lcl|NCBI__GCF_000215085.1:WP_013841351.1 412 EKGLVQISDEGAIAAVVDEVIAANPKSVEDFRAGKEKAIGFLVGQVMRATKGKANPELVNKLLKEKL 478 *****************************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (479 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7.64 // [ok]
This GapMind analysis is from Apr 10 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