Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_075388993.1 BK574_RS15990 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_002019605.1:WP_075388993.1 Length = 477 Score = 700 bits (1806), Expect = 0.0 Identities = 351/477 (73%), Positives = 401/477 (84%), Gaps = 1/477 (0%) Query: 1 MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60 M FETV+GLEVH ELKT SKIF T FGA NT T I LG+PGVLPVLNK+AVE+AM Sbjct: 1 MKFETVVGLEVHAELKTNSKIFCGCSTEFGAPPNTHTCPICLGHPGVLPVLNKQAVEYAM 60 Query: 61 KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120 +AA+ALNCEIA +TKFDRKNYFYPD+PKAYQISQFDKPIGE+G IEIEV G+ K IGITR Sbjct: 61 RAALALNCEIAEETKFDRKNYFYPDSPKAYQISQFDKPIGEHGSIEIEVNGEKKTIGITR 120 Query: 121 LHLEEDAGKLTHTGDG-YSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179 +HLEEDAGKLTH+ G YSLVDFNR GTPL+EIVSEPDIRTPEEAYAYLEKLK+I++YT Sbjct: 121 IHLEEDAGKLTHSEYGDYSLVDFNRVGTPLIEIVSEPDIRTPEEAYAYLEKLKAILEYTE 180 Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239 VSDCKMEEGSLRCDANISLRP+GQ EFGTKTELKNLNSFA VQKGL +EE RQE+ LL G Sbjct: 181 VSDCKMEEGSLRCDANISLRPVGQVEFGTKTELKNLNSFANVQKGLAYEEIRQEKELLEG 240 Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299 I QETRR+D+ K+TILMRVKEGSDDYRYFP+PDLV ++ID+EWK RV++ IPELP E Sbjct: 241 NVIHQETRRWDDGKKETILMRVKEGSDDYRYFPDPDLVSIFIDEEWKNRVRSQIPELPYE 300 Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359 R+ RYI +LG + YDA VLT +K M+DFFE+ + +AK +NWLMG+VSAYLN+ KE Sbjct: 301 RQTRYIADLGLSEYDAQVLTASKAMSDFFEQALVHDGDAKLVANWLMGDVSAYLNSNDKE 360 Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419 + DV LTPE L MI LIEKGTISSKIAK VFKE+IE GGD E IVKEKGLVQISDEG L Sbjct: 361 ITDVPLTPENLTKMIALIEKGTISSKIAKTVFKEMIENGGDPETIVKEKGLVQISDEGEL 420 Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKKR 476 +V LDNN QS++DFK GK +AIGFLVGQ+MK +KG+ANPPMVNKI++EEI KR Sbjct: 421 RNIVVAILDNNQQSVDDFKAGKQKAIGFLVGQVMKETKGKANPPMVNKIIVEEIGKR 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: 781 Number of extensions: 26 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: 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_075388993.1 BK574_RS15990 (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.4039.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-190 619.0 0.1 2.9e-190 618.8 0.1 1.0 1 lcl|NCBI__GCF_002019605.1:WP_075388993.1 BK574_RS15990 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_075388993.1 BK574_RS15990 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 ! 618.8 0.1 2.9e-190 2.9e-190 2 480 .. 1 474 [. 1 475 [. 0.98 Alignments for each domain: == domain 1 score: 618.8 bits; conditional E-value: 2.9e-190 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +++e v+GlEvH l t+sK+Fc cs+e+ +pNt++cp+clg PG+lPvlNk+av+ A+ alaln+ lcl|NCBI__GCF_002019605.1:WP_075388993.1 1 MKFETVVGLEVHAELKTNSKIFCGCSTEFGA-PPNTHTCPICLGHPGVLPVLNKQAVEYAMRAALALNC 68 689**************************99.************************************* PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139 + ++e ++FdRK+YfYpD Pk+yqi+q+d+Pi+e+G++eie+++++k+igi+r+hlEeD+gk+++ e lcl|NCBI__GCF_002019605.1:WP_075388993.1 69 E-IAEETKFDRKNYFYPDSPKAYQISQFDKPIGEHGSIEIEVNGEKKTIGITRIHLEEDAGKLTHSEYG 136 *.5679***********************************************************9775 PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 ++slvDfNR g+PL+EiV++Pd+++++ea a+l+kl++il+y+e+sd+++eeGs+R+D+N+s+r++G lcl|NCBI__GCF_002019605.1:WP_075388993.1 137 --DYSLVDFNRVGTPLIEIVSEPDIRTPEEAYAYLEKLKAILEYTEVSDCKMEEGSLRCDANISLRPVG 203 ..8****************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 q ++gt+ E+KNlns+ +++k + yE +Rq+k+l +g+ ++qetr +d+ k+ t+ +R Ke s DYRYf lcl|NCBI__GCF_002019605.1:WP_075388993.1 204 QVEFGTKTELKNLNSFANVQKGLAYEEIRQEKELLEGNVIHQETRRWDDGKKETILMRVKEGSDDYRYF 272 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl++i idee+ k++v+ ++pelP ++++r+ ++glse+da+vl++ + + d fe++ +++k lcl|NCBI__GCF_002019605.1:WP_075388993.1 273 PDPDLVSIFIDEEW-KNRVRSQIPELPYERQTRYIADLGLSEYDAQVLTASKAMSDFFEQALVHDGDAK 340 *************9.666*************************************************** PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 l++nW++ ++ ++Ln+++ +++++ l+pe+l+++i+li++g+is+k+ak++++e++en++dp+++++++ lcl|NCBI__GCF_002019605.1:WP_075388993.1 341 LVANWLMGDVSAYLNSNDKEITDVPLTPENLTKMIALIEKGTISSKIAKTVFKEMIENGGDPETIVKEK 409 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gl+qisde el +iv +++++n+++v ++k+gk+ka++flvGqvmk+tkg+a+p v+k++ e + lcl|NCBI__GCF_002019605.1:WP_075388993.1 410 GLVQISDEGELRNIVVAILDNNQQSVDDFKAGKQKAIGFLVGQVMKETKGKANPPMVNKIIVEEI 474 ************************************************************98865 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: 00:00:00.02 # Mc/sec: 7.98 // [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