Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013705977.1 DESAC_RS04935 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000195295.1:WP_013705977.1 Length = 476 Score = 495 bits (1275), Expect = e-144 Identities = 250/476 (52%), Positives = 334/476 (70%), Gaps = 1/476 (0%) Query: 1 MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60 M +E VIGLEVH +L T+SKIF T FGA N+QT I LG PGVLPVLN++ VE+ + Sbjct: 1 MEYEVVIGLEVHAQLLTQSKIFCGCATTFGATPNSQTCPICLGMPGVLPVLNRKVVEYGL 60 Query: 61 KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120 K A+A +C IA+ ++F RKNYFYPD PK YQISQ++ P+ E+G ++IEV G K+IG+TR Sbjct: 61 KMALATHCLIASYSRFARKNYFYPDLPKGYQISQYELPLAEHGRVDIEVDGVKKQIGLTR 120 Query: 121 LHLEEDAGKLTHTGD-GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179 +H+EEDAGKL H S VDFNR G PL+EIVSEPD+RTP+EA AYL+ +++I+ Y Sbjct: 121 IHMEEDAGKLIHDEQLPISYVDFNRTGVPLLEIVSEPDLRTPDEAAAYLKAIRNILLYLE 180 Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239 + D MEEGSLRCDANISLRP G EFG +TELKN+NSF VQ+ LE+E +RQ +L +G Sbjct: 181 ICDGNMEEGSLRCDANISLRPQGATEFGVRTELKNMNSFRNVQRALEYEIRRQRSLLDAG 240 Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299 + QETR +D KT MR KE + DYRYFP+PDL+ L I EW + V+A++PELPD Sbjct: 241 GEVIQETRLWDANQGKTYSMRGKEEAHDYRYFPDPDLIPLVISPEWLKEVQATLPELPDA 300 Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359 +++R+I + YDA VLT K +AD+FE+ V+ + K+ SNW+M E+ L E ++ Sbjct: 301 KKERFISQYDLPEYDAGVLTQEKALADYFEDCVRDFPQPKKVSNWIMSELMRELKKEDQD 360 Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419 + + P GLA ++ L+E+ IS KIAK VF E+I G D + IVK KGL+QISD G L Sbjct: 361 IQTCPVAPTGLARLLTLVEEEVISGKIAKSVFMEMIASGNDPDAIVKAKGLIQISDTGSL 420 Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKK 475 L E L NP+ + DFK GK + +GF VG++MK +KGQANP + N++L +K+ Sbjct: 421 ETLAREILAANPKEVADFKAGKTKVMGFFVGEMMKKTKGQANPKLANQLLSRLLKE 476 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: 639 Number of extensions: 25 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: 476 Length adjustment: 33 Effective length of query: 443 Effective length of database: 443 Effective search space: 196249 Effective search space used: 196249 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_013705977.1 DESAC_RS04935 (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.9478.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-187 607.4 0.0 9.1e-187 607.2 0.0 1.0 1 lcl|NCBI__GCF_000195295.1:WP_013705977.1 DESAC_RS04935 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195295.1:WP_013705977.1 DESAC_RS04935 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 ! 607.2 0.0 9.1e-187 9.1e-187 2 480 .. 1 474 [. 1 475 [. 0.99 Alignments for each domain: == domain 1 score: 607.2 bits; conditional E-value: 9.1e-187 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +eye+viGlEvH ql t+sK+Fc c + + +pN+++cp+clg+PG+lPvlN+++v+ lk+ala+++ lcl|NCBI__GCF_000195295.1:WP_013705977.1 1 MEYEVVIGLEVHAQLLTQSKIFCGCATTFGA-TPNSQTCPICLGMPGVLPVLNRKVVEYGLKMALATHC 68 69***************************99.************************************* PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139 i +s F+RK+YfYpDlPkgyqi+q++lP+ae+G+++ie+++ +k+ig++r+h+EeD+gk+ + e+ lcl|NCBI__GCF_000195295.1:WP_013705977.1 69 LIA-SYSRFARKNYFYPDLPKGYQISQYELPLAEHGRVDIEVDGVKKQIGLTRIHMEEDAGKLIHDEQL 136 955.6************************************************************9775 PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 +s+vDfNR+gvPLlEiV++Pdl++++ea+a+lk +r+il ylei dg++eeGs+R+D+N+s+r++G lcl|NCBI__GCF_000195295.1:WP_013705977.1 137 --PISYVDFNRTGVPLLEIVSEPDLRTPDEAAAYLKAIRNILLYLEICDGNMEEGSLRCDANISLRPQG 203 ..7****************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 +++g r E+KN+ns++++++a+eyEi Rq ll g ev qetr +d ++ +t s+R Kee++DYRYf lcl|NCBI__GCF_000195295.1:WP_013705977.1 204 ATEFGVRTELKNMNSFRNVQRALEYEIRRQRSLLDAGGEVIQETRLWDANQGKTYSMRGKEEAHDYRYF 272 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl p++i++e++ke v+++lpelP+ak++r+ ++y+l e+da vl++++ l+d+fe+ v+ +pk lcl|NCBI__GCF_000195295.1:WP_013705977.1 273 PDPDLIPLVISPEWLKE-VQATLPELPDAKKERFISQYDLPEYDAGVLTQEKALADYFEDCVRDFPQPK 340 ****************9.*************************************************** PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 ++ nWi++el++eL+k++ +++ + ++p+ la+l+ l++e++is+k+ak+++ e++ ++dp+++++++ lcl|NCBI__GCF_000195295.1:WP_013705977.1 341 KVSNWIMSELMRELKKEDQDIQTCPVAPTGLARLLTLVEEEVISGKIAKSVFMEMIASGNDPDAIVKAK 409 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gliqisd+ l + +e+++ npkev ++k+gk k+++f+vG +mkktkg+a+pk +++ll ll lcl|NCBI__GCF_000195295.1:WP_013705977.1 410 GLIQISDTGSLETLAREILAANPKEVADFKAGKTKVMGFFVGEMMKKTKGQANPKLANQLLSRLL 474 ************************************************************99887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (476 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.69 // [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