Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate Ac3H11_3339 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)
Query= metacyc::MONOMER-13956 (476 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3339 Length = 482 Score = 422 bits (1085), Expect = e-122 Identities = 220/469 (46%), Positives = 303/469 (64%), Gaps = 3/469 (0%) Query: 3 FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62 +E VIG E H +L T+SKIFS +PT FGAE NTQ +DL PG LPV+N+EAV A+K Sbjct: 9 YEVVIGFETHTQLATQSKIFSRAPTAFGAEPNTQACAVDLALPGTLPVMNREAVACAIKL 68 Query: 63 AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122 +AL IA + F RKNYFYPD PK YQISQF+ P+ + G + +G + K + + R H Sbjct: 69 GLALGSHIAEKSIFARKNYFYPDLPKGYQISQFEIPVVQGGEVSFFLGDEKKTVRLVRAH 128 Query: 123 LEEDAGKLTHTGD-GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181 LEEDAGK H G S +D NR GTPL+EIV+EPD+ + +EA AY ++L I+ + G+ Sbjct: 129 LEEDAGKSLHEDFIGQSGIDLNRAGTPLLEIVTEPDMSSSDEAVAYAKELHKIVTWIGIC 188 Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241 D M+EGS RCDAN+S+R GQ GT+ E+KNLNSF F+Q+ +++E + Q + + G Sbjct: 189 DGNMQEGSFRCDANVSVRKPGQP-LGTRREIKNLNSFKFMQQAIDYEIRWQIEQIEDGHA 247 Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301 IQQ T +D T +T MR KE + DYRYFP+PDL L+I ++W E +A + ELP Sbjct: 248 IQQATVLFDPDTGETRAMRTKEDAADYRYFPDPDLPPLHISEQWIEEQRAQMAELPRTMA 307 Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKELA 361 R++ + G YDA LT +K MA +FE + +AK ASNW+MGEVS LN + + Sbjct: 308 TRFVADYGLPEYDATTLTQSKAMAAYFEAVAKACGQAKLASNWIMGEVSRRLNMAEIGIE 367 Query: 362 DVALTPEGLAGMIKLIEKGTISSKIAKKVFKEL-IEKGGDAEKIVKEKGLVQISDEGVLL 420 ++ LA +I I GTIS+ AK+VF L +G D + +++ KGL Q++D G L Sbjct: 368 QAPVSSAQLAALIARIADGTISNNAAKQVFDALWTSEGQDVDAVIEAKGLKQMNDSGALE 427 Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469 K++ E + N ++ F+ GKD+A LVGQIMKASKG+ANP VN++L Sbjct: 428 KIIDEVIAANADNVAQFRAGKDKAFNALVGQIMKASKGKANPTQVNELL 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: 569 Number of extensions: 24 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: 482 Length adjustment: 34 Effective length of query: 442 Effective length of database: 448 Effective search space: 198016 Effective search space used: 198016 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 Ac3H11_3339 (Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7))
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.17481.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-173 561.2 0.0 9.3e-173 561.0 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 Aspartyl-tRNA(Asn) amidotransfer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamy # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 561.0 0.0 9.3e-173 9.3e-173 4 480 .. 9 480 .. 6 481 .. 0.98 Alignments for each domain: == domain 1 score: 561.0 bits; conditional E-value: 9.3e-173 TIGR00133 4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlkla 65 ye+viG+E+H+ql t+sK+F+++++ + +pNt+ c+v+l+lPG+lPv+N+eav+ A+kl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 9 YEVVIGFETHTQLATQSKIFSRAPTAFGA-EPNTQACAVDLALPGTLPVMNREAVACAIKLG 69 99*************************99.******************************** PP TIGR00133 66 lalnskivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlE 127 lal+s+ ++e+s+F+RK+YfYpDlPkgyqi+q+++P++++G+++ l +++k++++ r hlE lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 70 LALGSH-IAEKSIFARKNYFYPDLPKGYQISQFEIPVVQGGEVSFFLGDEKKTVRLVRAHLE 130 ******.668**************************************************** PP TIGR00133 128 eDtgksqykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdg 189 eD+gks ++ qs +D+NR+g+PLlEiVt+Pd++s++ea+a+ k+l++i+ +++i dg lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 131 EDAGKSLHEDFI--GQSGIDLNRAGTPLLEIVTEPDMSSSDEAVAYAKELHKIVTWIGICDG 190 ********9665..7*********************************************** PP TIGR00133 190 dleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqe 251 +++eGs+R+D+Nvs+r G + gtr EiKNlns+k +++ai+yEi q++ +++g+ ++q+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 191 NMQEGSFRCDANVSVRKPG-QPLGTRREIKNLNSFKFMQQAIDYEIRWQIEQIEDGHAIQQA 251 ****************555.5689999*********************************** PP TIGR00133 252 trafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkk 313 t fd + t ++R Ke+++DYRYfp+Pdlpp++i+e++++e ++++ elP+++ +r++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 252 TVLFDPDTGETRAMRTKEDAADYRYFPDPDLPPLHISEQWIEE-QRAQMAELPRTMATRFVA 312 *******************************************.9***************** PP TIGR00133 314 eyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpe 375 +ygl e+da +l++ + ++ +fe v+k+ +++kla nWi+ e+ ++Ln +i +++a +++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 313 DYGLPEYDATTLTQSKAMAAYFEAVAKACGQAKLASNWIMGEVSRRLNMAEIGIEQAPVSSA 374 ************************************************************** PP TIGR00133 376 elaeliklikegkisqksakelleellen.kkdpkklieklgliqisdekelvkiveevike 436 +la+li+ i +g+is+ +ak++++ l + ++d++++ie++gl q++d +l ki++evi+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 375 QLAALIARIADGTISNNAAKQVFDALWTSeGQDVDAVIEAKGLKQMNDSGALEKIIDEVIAA 436 ************************9987659******************************* PP TIGR00133 437 npkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 n+++v ++++gk+ka++ lvGq+mk +kg+a+p++v++ll+ +l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3339 437 NADNVAQFRAGKDKAFNALVGQIMKASKGKANPTQVNELLRAKL 480 ***************************************99877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (482 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: 9.96 // [ok]
This GapMind analysis is from Apr 09 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