Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012399480.1 BPHY_RS00275 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000020045.1:WP_012399480.1 Length = 491 Score = 447 bits (1150), Expect = e-130 Identities = 235/486 (48%), Positives = 331/486 (68%), Gaps = 15/486 (3%) Query: 3 FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62 +E VIGLE H +L T SKIFS + T FGA NTQ +DL PGVLPV+NK AVE A++ Sbjct: 5 WEVVIGLETHAQLSTVSKIFSGAATQFGAAPNTQACPVDLALPGVLPVMNKGAVERAIQF 64 Query: 63 AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-----GGKT---K 114 +A++ IA + F RKNYFYPD PK YQISQ++ P+ + G I I+V GK K Sbjct: 65 GLAIDATIAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQITIQVPANEKAGKEAYEK 124 Query: 115 RIGITRLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKS 173 I +TR HLEEDAGK H G + +D NR GTPL+EIV+EP++R+ EA AY + L Sbjct: 125 TINLTRAHLEEDAGKSLHEDFAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKALHG 184 Query: 174 IIQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQE 233 ++ + G+ D M+EGS RCDAN+S+RP+GQ+EFGT+ E+KNLNSF F+++ +++E +RQ Sbjct: 185 LVVWLGICDGNMQEGSFRCDANVSVRPVGQKEFGTRAEIKNLNSFRFLEEAIQYEVRRQI 244 Query: 234 QVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASI 293 +++ G + QETR YD ++T MR KE + DYRYFP+PDL+ L ID W ERVK + Sbjct: 245 ELIEDGGTVVQETRLYDPDKRETRSMRSKEDAHDYRYFPDPDLMPLVIDASWVERVKGEL 304 Query: 294 PELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQK--GAEAKQASNWLMGEVSA 351 PELP +KR++++ G YDA V+T K MA ++E V K A+AK A+NWLMGEVS+ Sbjct: 305 PELPAAMQKRFVDQYGLTPYDAGVVTAGKAMAAYYEAVVAKVGAAQAKVAANWLMGEVSS 364 Query: 352 YLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGD----AEKIVKE 407 LN E ++AD ++ LA +++ I GTIS+KIAK++F + E+ A++I++ Sbjct: 365 QLNREGLDIADSPVSAAQLALVLQRIADGTISNKIAKEIFLAIWEEKATDEAAADRIIEA 424 Query: 408 KGLVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNK 467 KGL QISD G L ++ E L N +S+E+F+ GK++A L+GQ MKA+KG+ANP VN+ Sbjct: 425 KGLKQISDTGALEAIIDEVLAANQKSVEEFRAGKEKAFNALIGQAMKATKGKANPQQVNE 484 Query: 468 ILLEEI 473 +L +++ Sbjct: 485 LLKKKL 490 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: 572 Number of extensions: 14 Number of successful extensions: 5 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: 491 Length adjustment: 34 Effective length of query: 442 Effective length of database: 457 Effective search space: 201994 Effective search space used: 201994 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: 52 (24.6 bits)
Align candidate WP_012399480.1 BPHY_RS00275 (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.4535.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-174 565.8 0.0 3.9e-174 565.6 0.0 1.0 1 lcl|NCBI__GCF_000020045.1:WP_012399480.1 BPHY_RS00275 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020045.1:WP_012399480.1 BPHY_RS00275 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 ! 565.6 0.0 3.9e-174 3.9e-174 2 480 .. 3 490 .. 2 491 .] 0.97 Alignments for each domain: == domain 1 score: 565.6 bits; conditional E-value: 3.9e-174 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +++e+viGlE+H ql t sK+F+ + +++ pNt+ cpv+l+lPG+lPv+Nk av+ A++ +la+++ lcl|NCBI__GCF_000020045.1:WP_012399480.1 3 TQWEVVIGLETHAQLSTVSKIFSGAATQFGA-APNTQACPVDLALPGVLPVMNKGAVERAIQFGLAIDA 70 5789*************************99.9************************************ PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke........keigierlhlEeDtg 131 +++ s+F+RK+YfYpDlPkgyqi+q+++P++++G+++i++ ++e k+i+++r hlEeD+g lcl|NCBI__GCF_000020045.1:WP_012399480.1 71 T-IAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQITIQVPANEkagkeayeKTINLTRAHLEEDAG 138 *.668************************************9998889999****************** PP TIGR00133 132 ksqykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDv 200 ks ++ + ++ +D+NR+g+PLlEiVt+P+++sa ea+a+ k l+ ++ +l+i dg+++eGs+R+D+ lcl|NCBI__GCF_000020045.1:WP_012399480.1 139 KSLHED--FAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKALHGLVVWLGICDGNMQEGSFRCDA 205 ****94..4789********************************************************* PP TIGR00133 201 NvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKe 269 Nvs+r++Gq+++gtr+EiKNlns++ +e+ai+yE+ Rq++l+++g +v+qetr +d k t s+R+Ke lcl|NCBI__GCF_000020045.1:WP_012399480.1 206 NVSVRPVGQKEFGTRAEIKNLNSFRFLEEAIQYEVRRQIELIEDGGTVVQETRLYDPDKRETRSMRSKE 274 ********************************************************************* PP TIGR00133 270 eseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeev 338 +++DYRYfp+Pdl+p++id ++v++ v+++lpelP a+++r++ +ygl +da v+++ + ++ ++e v lcl|NCBI__GCF_000020045.1:WP_012399480.1 275 DAHDYRYFPDPDLMPLVIDASWVER-VKGELPELPAAMQKRFVDQYGLTPYDAGVVTAGKAMAAYYEAV 342 ************************9.******************************************9 PP TIGR00133 339 vklikep..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen. 404 v ++ + k a+nW++ e+ ++Ln++ +++a++ +++ +la +++ i +g+is+k+ake++ + e+ lcl|NCBI__GCF_000020045.1:WP_012399480.1 343 VAKVGAAqaKVAANWLMGEVSSQLNREGLDIADSPVSAAQLALVLQRIADGTISNKIAKEIFLAIWEEk 411 988776656999**************************************************9999997 PP TIGR00133 405 ...kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpk 470 + ++++ie++gl qisd+ +l +i++ev++ n+k+ve++++gkeka++ l+Gq+mk tkg+a+p+ lcl|NCBI__GCF_000020045.1:WP_012399480.1 412 atdEAAADRIIEAKGLKQISDTGALEAIIDEVLAANQKSVEEFRAGKEKAFNALIGQAMKATKGKANPQ 480 77677899************************************************************* PP TIGR00133 471 evekllkell 480 +v++llk++l lcl|NCBI__GCF_000020045.1:WP_012399480.1 481 QVNELLKKKL 490 *******998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (491 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: 11.44 // [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