Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_018232611.1 THITHI_RS0108270 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000378965.1:WP_018232611.1 Length = 477 Score = 467 bits (1202), Expect = e-136 Identities = 233/477 (48%), Positives = 335/477 (70%), Gaps = 3/477 (0%) Query: 1 MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60 M++ETVIGLEVH +L TKSKIFS + T +GA N+Q +DLG PGVLPVLN+EAV A+ Sbjct: 1 MDWETVIGLEVHAQLATKSKIFSGASTAYGASPNSQACAVDLGLPGVLPVLNREAVRMAV 60 Query: 61 KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGIT 119 K +A+ EIA + F RKNYFYPD PK YQISQ++ P+ G +EIE+ G+TK +G+T Sbjct: 61 KFGLAIGAEIAPRSVFARKNYFYPDLPKGYQISQYELPVVGLGRLEIEMEDGETKVVGVT 120 Query: 120 RLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYT 178 R HLEEDAGK H G + +D NR GTPL+EIVSEPD+R+ +EA AYL+KL ++++Y Sbjct: 121 RAHLEEDAGKSLHEDFHGMTGIDLNRAGTPLLEIVSEPDMRSAKEAVAYLKKLHALVRYL 180 Query: 179 GVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLS 238 + D M+EGS RCDAN+S+R +G E+FGT+ E+KN+NSF FV++ + E +RQ +L Sbjct: 181 EICDGNMQEGSFRCDANVSVRRMGTEKFGTRAEIKNINSFRFVERAINFEVERQIDILEG 240 Query: 239 GFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPD 298 G + QETR +D +T MR KE ++DYRYFP+PDL+ L I E+ E V+ ++PELPD Sbjct: 241 GGAVVQETRLFDPDKGETRSMRSKEEANDYRYFPDPDLLPLEITGEFIEGVRGTLPELPD 300 Query: 299 ERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQK-GAEAKQASNWLMGEVSAYLNAEQ 357 E++ R++ G +AYDA VLT ++EM D++E V+ G AK A+NW+MGE+S LN + Sbjct: 301 EKKHRFMTHYGLSAYDAGVLTASREMGDYYEAAVKACGGHAKLAANWVMGELSGALNKDN 360 Query: 358 KELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEG 417 +E+ + ++ + L M+ IE TIS KIAK VF+ + G A++++ +KGL QI+D G Sbjct: 361 REITECPVSAQALGAMLARIEDNTISGKIAKDVFEAMWNGEGTADEVIGKKGLKQITDTG 420 Query: 418 VLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474 + ++ + + +NP +E ++ GKD+ GF VGQ+MKA+ G+ANP VN +L +++ Sbjct: 421 AIEAIIDKVMADNPGQLEQYRAGKDKLFGFFVGQVMKATGGKANPGQVNDLLKRKLQ 477 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: 617 Number of extensions: 28 Number of successful extensions: 4 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: 477 Length adjustment: 33 Effective length of query: 443 Effective length of database: 444 Effective search space: 196692 Effective search space used: 196692 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_018232611.1 THITHI_RS0108270 (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.31775.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-181 588.0 0.0 6.8e-181 587.9 0.0 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018232611.1 THITHI_RS0108270 Asp-tRNA(Asn)/G Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018232611.1 THITHI_RS0108270 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 ! 587.9 0.0 6.8e-181 6.8e-181 2 480 .. 1 476 [. 1 477 [] 0.98 Alignments for each domain: == domain 1 score: 587.9 bits; conditional E-value: 6.8e-181 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +++e viGlEvH ql tksK+F+ +s+ + +pN++ c+v+lglPG+lPvlN+eav++A+k +la+++ lcl|NCBI__GCF_000378965.1:WP_018232611.1 1 MDWETVIGLEVHAQLATKSKIFSGASTAYGA-SPNSQACAVDLGLPGVLPVLNREAVRMAVKFGLAIGA 68 57899************************99.9************************************ PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138 + +++ svF+RK+YfYpDlPkgyqi+q++lP++ G+leie+e++e k +g++r hlEeD+gks ++ lcl|NCBI__GCF_000378965.1:WP_018232611.1 69 E-IAPRSVFARKNYFYPDLPKGYQISQYELPVVGLGRLEIEMEDGEtKVVGVTRAHLEEDAGKSLHEDF 136 *.668*************************************99877999****************944 PP TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207 + ++ +D+NR+g+PLlEiV++Pd++sakea+a+lkkl++++rylei dg+++eGs+R+D+Nvs+r + lcl|NCBI__GCF_000378965.1:WP_018232611.1 137 --HGMTGIDLNRAGTPLLEIVSEPDMRSAKEAVAYLKKLHALVRYLEICDGNMQEGSFRCDANVSVRRM 203 ..5899*************************************************************** PP TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276 G+ek+gtr+EiKN+ns++ +e+ai++E+eRq+++l+ g v+qetr fd k t s+R+Kee++DYRY lcl|NCBI__GCF_000378965.1:WP_018232611.1 204 GTEKFGTRAEIKNINSFRFVERAINFEVERQIDILEGGGAVVQETRLFDPDKGETRSMRSKEEANDYRY 272 ********************************************************************* PP TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345 fp+Pdl p+ei+ e++++ v+++lpelP++k++r++++ygls++da vl++ +e+ d++e +vk+ + + lcl|NCBI__GCF_000378965.1:WP_018232611.1 273 FPDPDLLPLEITGEFIEG-VRGTLPELPDEKKHRFMTHYGLSAYDAGVLTASREMGDYYEAAVKACGGH 340 ******************.******************************************99987654 PP TIGR00133 346 .klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413 kla+nW++ el g Lnk + +++e+ +++++l ++++ i++++is+k+ak+++e + + ++ ++++i lcl|NCBI__GCF_000378965.1:WP_018232611.1 341 aKLAANWVMGELSGALNKDNREITECPVSAQALGAMLARIEDNTISGKIAKDVFEAMWNGEGTADEVIG 409 4******************************************************************** PP TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 k+gl qi+d+ ++ +i+++v+++np+++e+y++gk+k+++f+vGqvmk t g+a+p +v+ llk +l lcl|NCBI__GCF_000378965.1:WP_018232611.1 410 KKGLKQITDTGAIEAIIDKVMADNPGQLEQYRAGKDKLFGFFVGQVMKATGGKANPGQVNDLLKRKL 476 ****************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (477 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: 7.24 // [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