Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_019865460.1 METMI_RS0106485 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000384075.1:WP_019865460.1 Length = 480 Score = 470 bits (1209), Expect = e-137 Identities = 236/475 (49%), Positives = 333/475 (70%), Gaps = 3/475 (0%) Query: 3 FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62 +ETVIGLE+H +L T+SKIFS + T +GAE NTQ +DLG PGVLPVLN+ AVE A+ Sbjct: 5 WETVIGLEIHTQLSTQSKIFSGASTAYGAEPNTQACAVDLGLPGVLPVLNEAAVEKAVMF 64 Query: 63 AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122 +A++ IA + F RKNYFYPD PK YQISQ D PI NG ++IEV G+TKRIGITR H Sbjct: 65 GLAIDAHIAPRSVFARKNYFYPDLPKGYQISQMDLPIVGNGHMDIEVDGETKRIGITRAH 124 Query: 123 LEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGVS 181 LEEDAGK H G S +D NR GTPL+EIVSEPD+R+ +EA AY+ KL +++Y G+ Sbjct: 125 LEEDAGKSLHESFHGMSGIDLNRAGTPLLEIVSEPDMRSAKEAVAYMRKLHELVRYLGIC 184 Query: 182 DCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGFF 241 D M+EGS RCDAN+S+RP+GQ+EFGT+ E+KN+NSF FV+K + HE +R +++ +G Sbjct: 185 DGNMQEGSFRCDANVSVRPVGQKEFGTRVEIKNINSFKFVEKAINHEVERHIELIENGGK 244 Query: 242 IQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDERR 301 I QETR YD +T MR KE ++DYRYFP+PDL+ + I +++K +VK ++PELP+ ++ Sbjct: 245 IVQETRLYDANKDETRSMRSKEEANDYRYFPDPDLLPVVITEDFKAQVKTTLPELPEAKK 304 Query: 302 KRYIEELGFAAYDAMVLTLTKEMADFFEE-TVQKGAEAKQASNWLMGEVSAYLNAEQKEL 360 +R+ ++ A +LT ++ +AD+FE V+ EAK +NW+ GE+SA LN E+ Sbjct: 305 QRFKDQYQLDNESATILTSSRPLADYFESVVVESKCEAKLCANWVTGELSAALNKADLEI 364 Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIE-KGGDAEKIVKEKGLVQISDEGVL 419 D +T LAG++ I TIS KIAK+VF+EL + A+ I++ KGL QI+D G + Sbjct: 365 TDSPVTASQLAGLLARISDDTISGKIAKQVFEELWQTPDSTADSIIEAKGLKQITDTGAI 424 Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474 ++ + + N + +E ++ G D+ GF VGQ+MKA +G+ANP VNK+L+ ++K Sbjct: 425 EAVIDQIIAANGKQVEQYRGGNDKVFGFFVGQVMKAMQGKANPAEVNKMLMAKLK 479 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: 604 Number of extensions: 11 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: 480 Length adjustment: 34 Effective length of query: 442 Effective length of database: 446 Effective search space: 197132 Effective search space used: 197132 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_019865460.1 METMI_RS0106485 (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.4075.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-184 598.7 0.0 4.1e-184 598.5 0.0 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019865460.1 METMI_RS0106485 Asp-tRNA(Asn)/Gl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019865460.1 METMI_RS0106485 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 ! 598.5 0.0 4.1e-184 4.1e-184 3 480 .. 4 478 .. 2 479 .. 0.97 Alignments for each domain: == domain 1 score: 598.5 bits; conditional E-value: 4.1e-184 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 +e viGlE+H+ql t+sK+F+ +s+ + +pNt+ c+v+lglPG+lPvlN+ av+kA++ +la++++ lcl|NCBI__GCF_000384075.1:WP_019865460.1 4 TWETVIGLEIHTQLSTQSKIFSGASTAYGA-EPNTQACAVDLGLPGVLPVLNEAAVEKAVMFGLAIDAH 71 5789************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140 +++ svF+RK+YfYpDlPkgyqi+q dlPi+ +G+++ie++++ k+igi+r hlEeD+gks +++ lcl|NCBI__GCF_000384075.1:WP_019865460.1 72 -IAPRSVFARKNYFYPDLPKGYQISQMDLPIVGNGHMDIEVDGETKRIGITRAHLEEDAGKSLHESF-- 137 .668************************************************************965.. PP TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209 + +s +D+NR+g+PLlEiV++Pd++sakea+a+++kl++++ryl+i dg+++eGs+R+D+Nvs+r++Gq lcl|NCBI__GCF_000384075.1:WP_019865460.1 138 HGMSGIDLNRAGTPLLEIVSEPDMRSAKEAVAYMRKLHELVRYLGICDGNMQEGSFRCDANVSVRPVGQ 206 579****************************************************************** PP TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278 +++gtrvEiKN+ns+k +ekai++E+eR ++l+++g +++qetr +d +k t s+R+Kee++DYRYfp lcl|NCBI__GCF_000384075.1:WP_019865460.1 207 KEFGTRVEIKNINSFKFVEKAINHEVERHIELIENGGKIVQETRLYDANKDETRSMRSKEEANDYRYFP 275 ********************************************************************* PP TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklik.epk 346 +Pdl p++i+e++ +v+++lpelPeak++r+k +y+l++e a +l+s + l+d+fe+vv +k e+k lcl|NCBI__GCF_000384075.1:WP_019865460.1 276 DPDLLPVVITEDFKA-QVKTTLPELPEAKKQRFKDQYQLDNESATILTSSRPLADYFESVVVESKcEAK 343 ************855.5******************************************876655166* PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen.kkdpkkliek 414 l +nW++ el + Lnk +++++++ +++++la l++ i++++is+k+ak+++eel ++ + ++++ie+ lcl|NCBI__GCF_000384075.1:WP_019865460.1 344 LCANWVTGELSAALNKADLEITDSPVTASQLAGLLARISDDTISGKIAKQVFEELWQTpDSTADSIIEA 412 ********************************************************99778899***** PP TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 +gl qi+d+ ++ ++++++i+ n k+ve+y+ g +k+++f+vGqvmk +g+a+p+ev+k+l +l lcl|NCBI__GCF_000384075.1:WP_019865460.1 413 KGLKQITDTGAIEAVIDQIIAANGKQVEQYRGGNDKVFGFFVGQVMKAMQGKANPAEVNKMLMAKL 478 ************************************************************998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (480 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: 10.89 // [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