Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_028585866.1 G494_RS0119535 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000429965.1:WP_028585866.1 Length = 475 Score = 485 bits (1249), Expect = e-141 Identities = 251/474 (52%), Positives = 330/474 (69%), Gaps = 3/474 (0%) Query: 1 MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60 M+FE VIGLEVH ++ TKSKIF T FGA NT T + LG PG LPVLN++ VE A+ Sbjct: 1 MDFEIVIGLEVHAQMNTKSKIFCGCSTEFGAPPNTHTCPVCLGMPGSLPVLNRQVVEAAI 60 Query: 61 KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120 K A+A + I + F RKNYFYPD PK YQISQF+ PI E+G +EIEV G K IGITR Sbjct: 61 KLALATDSTINQENIFARKNYFYPDLPKGYQISQFELPIAEHGKLEIEVEGTKKTIGITR 120 Query: 121 LHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179 +H+EEDAGKL H + S VD NR GTPL+EIVSEPD+R+P EA AYL+KL +I++Y Sbjct: 121 IHMEEDAGKLVHDELEPVSHVDLNRTGTPLLEIVSEPDLRSPAEATAYLKKLHAIVRYLD 180 Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239 + D M+EGS RCDANISLRP+GQEEFG +TELKN+NSF VQ +E+E +RQ VLL G Sbjct: 181 ICDGNMQEGSFRCDANISLRPVGQEEFGIRTELKNMNSFKNVQLAMEYEVRRQRDVLLDG 240 Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299 + Q+T ++ +T MR KE + DYRYFP+PDLV + +D +W V A +PELPD Sbjct: 241 GRVIQQTLLWNPDKAQTETMRGKEEAHDYRYFPDPDLVPVVVDQDWISTVAAGLPELPDH 300 Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359 RR+R+ EELG YDA +LT ++E+AD+FE + + AK+ N++ E+ AE+ E Sbjct: 301 RRRRFCEELGLNDYDAEILTSSRELADYFELALAEYGNAKKLGNFMGTELLREYGAEEIE 360 Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419 V P LA ++K+IE TIS KIAK VF E+++KG D E IVKEKGLVQ+SDEG L Sbjct: 361 ACPV--RPSQLARLLKMIEDNTISGKIAKTVFAEMLDKGQDPEVIVKEKGLVQMSDEGEL 418 Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473 +V E + N + + F++GK + +GF VGQ+M+ +KG+ANP + NK+ +E+ Sbjct: 419 QAMVREIIAANQEQAQQFRDGKTKVMGFFVGQLMQRTKGKANPKLANKLFQQEL 472 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: 606 Number of extensions: 14 Number of successful extensions: 3 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: 475 Length adjustment: 33 Effective length of query: 443 Effective length of database: 442 Effective search space: 195806 Effective search space used: 195806 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_028585866.1 G494_RS0119535 (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.28226.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-185 603.2 0.0 1.7e-185 603.1 0.0 1.0 1 lcl|NCBI__GCF_000429965.1:WP_028585866.1 G494_RS0119535 Asp-tRNA(Asn)/Glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429965.1:WP_028585866.1 G494_RS0119535 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 ! 603.1 0.0 1.7e-185 1.7e-185 2 481 .] 1 473 [. 1 473 [. 0.98 Alignments for each domain: == domain 1 score: 603.1 bits; conditional E-value: 1.7e-185 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +++e+viGlEvH q+ntksK+Fc cs+e+ +pNt++cpvclg+PG+lPvlN+++v++A+klala++s lcl|NCBI__GCF_000429965.1:WP_028585866.1 1 MDFEIVIGLEVHAQMNTKSKIFCGCSTEFGA-PPNTHTCPVCLGMPGSLPVLNRQVVEAAIKLALATDS 68 689**************************99.************************************* PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139 i+ + +F+RK+YfYpDlPkgyqi+q++lPiae+Gkleie+e+++k+igi+r+h+EeD+gk+++ e + lcl|NCBI__GCF_000429965.1:WP_028585866.1 69 TIN-QENIFARKNYFYPDLPKGYQISQFELPIAEHGKLEIEVEGTKKTIGITRIHMEEDAGKLVHDELE 136 *76.5899*********************************************************9765 PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 s vD+NR+g+PLlEiV++Pdl+s+ ea a+lkkl++i+ryl+i dg+++eGs+R+D+N+s+r++G lcl|NCBI__GCF_000429965.1:WP_028585866.1 137 --PVSHVDLNRTGTPLLEIVSEPDLRSPAEATAYLKKLHAIVRYLDICDGNMQEGSFRCDANISLRPVG 203 ..79***************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 qe++g r E+KN+ns+k+++ a+eyE+ Rq ++l +g v q+t ++ k +t ++R Kee++DYRYf lcl|NCBI__GCF_000429965.1:WP_028585866.1 204 QEEFGIRTELKNMNSFKNVQLAMEYEVRRQRDVLLDGGRVIQQTLLWNPDKAQTETMRGKEEAHDYRYF 272 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl+p+++d++++++ v++ lpelP+++r r+ +e+gl+++da++l+s +el+d+fe + +++k lcl|NCBI__GCF_000429965.1:WP_028585866.1 273 PDPDLVPVVVDQDWIST-VAAGLPELPDHRRRRFCEELGLNDYDAEILTSSRELADYFELALAEYGNAK 340 ****************9.*************************************************** PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 + n++ +ell+e ++ +++++ ++p++la+l+k+i++++is+k+ak+++ e+l++++dp+ +++++ lcl|NCBI__GCF_000429965.1:WP_028585866.1 341 KLGNFMGTELLREYGAE--EIEACPVRPSQLARLLKMIEDNTISGKIAKTVFAEMLDKGQDPEVIVKEK 407 ************99888..7899********************************************** PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkells 481 gl+q+sde el+++v+e+i+ n+++ +++++gk k+++f+vGq m++tkg+a+pk ++kl+++ l+ lcl|NCBI__GCF_000429965.1:WP_028585866.1 408 GLVQMSDEGELQAMVREIIAANQEQAQQFRDGKTKVMGFFVGQLMQRTKGKANPKLANKLFQQELN 473 *************************************************************99885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (475 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: 00:00:00.01 # Mc/sec: 11.58 // [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