Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_041277590.1 DP_RS03595 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000025945.1:WP_041277590.1 Length = 474 Score = 478 bits (1229), Expect = e-139 Identities = 245/476 (51%), Positives = 331/476 (69%), Gaps = 3/476 (0%) Query: 1 MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60 M FETVIGLE+H +LKT +KIF + T +GA N+ T I LG PGVLPVLNK+ VE+++ Sbjct: 1 MEFETVIGLEIHAQLKTNTKIFCACSTQYGAAPNSHTCPICLGMPGVLPVLNKKVVEYSI 60 Query: 61 KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120 K +A I +F RKNYFYPD PK YQ SQFD PI E G IEIEV G +K IGITR Sbjct: 61 KMGLATGSRINQWNQFARKNYFYPDLPKGYQTSQFDLPIVEGGHIEIEVDGVSKVIGITR 120 Query: 121 LHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179 +H+EEDAGKL H + S VD NR GTPL+EIVSEPD+R+P+EAYAYL+K+ +I++Y Sbjct: 121 MHMEEDAGKLVHDDVEPVSHVDLNRTGTPLLEIVSEPDMRSPQEAYAYLKKVHAILRYLD 180 Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239 + D M+EGS RCDANISLRP+GQE+ GT+TELKN+NSF VQ LE+E +RQ +LL G Sbjct: 181 ICDGNMQEGSFRCDANISLRPMGQEKLGTRTELKNMNSFKNVQAALEYEVRRQRDLLLEG 240 Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299 + Q+T +D +T MR KE + DYRYFP PDLV + I DEW E ++AS+PELP++ Sbjct: 241 EKVIQQTLLWDPDKNRTEAMRGKEDAHDYRYFPCPDLVPIEISDEWIEEIRASLPELPEQ 300 Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359 + R+I + + DA+ LT +++A FFEE V GA K+++NW+M E+ L E Sbjct: 301 CKARFIVDYALSEDDAVQLTSERDLALFFEEVVAAGAHPKKSANWIMTELLRELGGE--S 358 Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419 + D + L+ ++ ++++G IS KIAK VF E++ +G D + IVKEK L+Q+SDEG L Sbjct: 359 IVDCRVQASQLSALLLMVDQGMISGKIAKTVFAEMMAEGTDPQLIVKEKNLLQVSDEGEL 418 Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKK 475 L +V E + N Q EDF+ GK + +GF VGQ+MK +KG+ANP + N++ + + K Sbjct: 419 LAIVDEIVAANVQQAEDFRAGKTKLMGFFVGQLMKKTKGKANPGLANELFNKALNK 474 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: 595 Number of extensions: 23 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: 474 Length adjustment: 33 Effective length of query: 443 Effective length of database: 441 Effective search space: 195363 Effective search space used: 195363 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_041277590.1 DP_RS03595 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.30295.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-184 599.7 0.0 1.9e-184 599.6 0.0 1.0 1 lcl|NCBI__GCF_000025945.1:WP_041277590.1 DP_RS03595 Asp-tRNA(Asn)/Glu-tRN Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_041277590.1 DP_RS03595 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 599.6 0.0 1.9e-184 1.9e-184 2 481 .] 1 473 [. 1 473 [. 0.99 Alignments for each domain: == domain 1 score: 599.6 bits; conditional E-value: 1.9e-184 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +e+e viGlE+H ql t++K+Fc cs+++ pN+++cp+clg+PG+lPvlNk++v+ +k++la++s lcl|NCBI__GCF_000025945.1:WP_041277590.1 1 MEFETVIGLEIHAQLKTNTKIFCACSTQYGA-APNSHTCPICLGMPGVLPVLNKKVVEYSIKMGLATGS 68 689**************************99.9************************************ PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139 +i+ + +F+RK+YfYpDlPkgyq +q+dlPi+e+G++eie+++ +k igi+r+h+EeD+gk+++ lcl|NCBI__GCF_000025945.1:WP_041277590.1 69 RIN-QWNQFARKNYFYPDLPKGYQTSQFDLPIVEGGHIEIEVDGVSKVIGITRMHMEEDAGKLVHDDV- 135 *66.6**********************************************************99944. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 + s vD+NR+g+PLlEiV++Pd++s++ea a+lkk+++ilryl+i dg+++eGs+R+D+N+s+r++G lcl|NCBI__GCF_000025945.1:WP_041277590.1 136 -EPVSHVDLNRTGTPLLEIVSEPDMRSPQEAYAYLKKVHAILRYLDICDGNMQEGSFRCDANISLRPMG 203 .689***************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 qek gtr E+KN+ns+k++++a+eyE+ Rq +ll +ge+v q+t +d k++t ++R Ke+++DYRYf lcl|NCBI__GCF_000025945.1:WP_041277590.1 204 QEKLGTRTELKNMNSFKNVQAALEYEVRRQRDLLLEGEKVIQQTLLWDPDKNRTEAMRGKEDAHDYRYF 272 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p Pdl+piei++e+++e +++ lpelPe+ ++r+ +y lse+da l+s+++l+ feevv + ++pk lcl|NCBI__GCF_000025945.1:WP_041277590.1 273 PCPDLVPIEISDEWIEE-IRASLPELPEQCKARFIVDYALSEDDAVQLTSERDLALFFEEVVAAGAHPK 340 *****************.*************************************************** PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 +++nWi++ell+eL + s+ ++ +++++l +l+ ++++g is+k+ak+++ e++ +++dp+ +++++ lcl|NCBI__GCF_000025945.1:WP_041277590.1 341 KSANWIMTELLRELGGE--SIVDCRVQASQLSALLLMVDQGMISGKIAKTVFAEMMAEGTDPQLIVKEK 407 **************999..99************************************************ PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkells 481 +l q+sde el +iv+e+++ n ++ e++++gk k+++f+vGq mkktkg+a+p +++l+++ l+ lcl|NCBI__GCF_000025945.1:WP_041277590.1 408 NLLQVSDEGELLAIVDEIVAANVQQAEDFRAGKTKLMGFFVGQLMKKTKGKANPGLANELFNKALN 473 **************************************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (474 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: 00:00:00.02 # Mc/sec: 10.81 // [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