Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_090448028.1 BLS63_RS22445 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_900100495.1:WP_090448028.1 Length = 481 Score = 464 bits (1194), Expect = e-135 Identities = 229/480 (47%), Positives = 330/480 (68%), Gaps = 7/480 (1%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M +ETVIGLE+H +L T SK+FS S FGAEPN+ +++DL PGVLPV+N+ AV A+ Sbjct: 1 MQWETVIGLEIHTQLATRSKIFSASATTFGAEPNTQASLVDLGMPGVLPVLNEEAVRMAV 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119 + +A++ EI + F RKNYFYPD PK YQISQ + PI G++DI + DG KRIG+T Sbjct: 61 KFGLAIDAEIGPSNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDITLEDGTVKRIGVT 120 Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177 R H+EEDAGKS H+ + + +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y Sbjct: 121 RAHLEEDAGKSLHEDFHGMTGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYL 180 Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237 G+ D M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K + E +RQ E + Sbjct: 181 GICDGNMAEGSLRCDCNVSVRPKGQAEFGTRCEIKNVNSFRFIEKAINSEVQRQIELIED 240 Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297 GG++ Q+TR +D + +T MR KE ++DYRYFP+PD++P+ I + E R T+PELP Sbjct: 241 GGKVIQQTRLYDPNKDETRAMRSKEEANDYRYFPDPDLLPVLIGAEFLEATRATLPELPP 300 Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357 +++ ++ ++ GL AYDA VL ++E +D+FE + D KL +NW+M + LNK + Sbjct: 301 QKRERFQSQFGLSAYDASVLASSREQADYFEQVVSIAGDAKLAANWVMVELGSLLNKEGL 360 Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417 E+ ++ E L GM+ I+D T+S K+AK VF +AA G+A Q++E GL Q++D Sbjct: 361 EIEQAPVSAEQLGGMLLRIKDNTISGKLAKMVFEAMAAGEGSADQVIEARGLKQVTDSGA 420 Query: 418 LLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473 + ++E L N + VE Y+ +GK GF VGQ MKASKG+ANP VN+LLK++L+ Sbjct: 421 IESMLDEVLAANAEQVEQYRASDEAKRGKMFGFFVGQAMKASKGKANPGQVNELLKKKLE 480 Lambda K H 0.313 0.133 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: 611 Number of extensions: 20 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: 475 Length of database: 481 Length adjustment: 34 Effective length of query: 441 Effective length of database: 447 Effective search space: 197127 Effective search space used: 197127 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_090448028.1 BLS63_RS22445 (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.31126.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-172 560.6 0.0 1.5e-172 560.4 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090448028.1 BLS63_RS22445 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090448028.1 BLS63_RS22445 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 ! 560.4 0.0 1.5e-172 1.5e-172 3 480 .. 2 479 .. 1 480 [. 0.98 Alignments for each domain: == domain 1 score: 560.4 bits; conditional E-value: 1.5e-172 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 ++e viGlE+H+ql t+sK+F+ + + + +pNt+ + v+lg+PG+lPvlN+eav++A+k +la++++ lcl|NCBI__GCF_900100495.1:WP_090448028.1 2 QWETVIGLEIHTQLATRSKIFSASATTFGA-EPNTQASLVDLGMPGVLPVLNEEAVRMAVKFGLAIDAE 69 7899************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139 + + vF+RK+YfYpDlPkgyqi+q +lPi+ +G+l+i le++ k+ig++r hlEeD+gks ++ lcl|NCBI__GCF_900100495.1:WP_090448028.1 70 -IGPSNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDITLEDGTvKRIGVTRAHLEEDAGKSLHEDF- 136 .668************************************999888*******************944. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 + ++ +D+NR+g+PLlEiV++Pd++sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvs+r+kG lcl|NCBI__GCF_900100495.1:WP_090448028.1 137 -HGMTGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSVRPKG 204 .5899**************************************************************** PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 q ++gtr EiKN+ns++ iekai+ E++Rq++l+++g +v q+tr +d +k t ++R+Kee++DYRYf lcl|NCBI__GCF_900100495.1:WP_090448028.1 205 QAEFGTRCEIKNVNSFRFIEKAINSEVQRQIELIEDGGKVIQQTRLYDPNKDETRAMRSKEEANDYRYF 273 ********************************************************************* PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl p+ i e+++ ++++lpelP +kr+r+++++gls++da vl s +e +d+fe+vv+ ++++k lcl|NCBI__GCF_900100495.1:WP_090448028.1 274 PDPDLLPVLIGAEFLEA-TRATLPELPPQKRERFQSQFGLSAYDASVLASSREQADYFEQVVSIAGDAK 341 *************9999.9************************************************** PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 la+nW++ el + Lnk+ +++++a +++e+l ++ ik+++is+k ak+++e + +++++++ie++ lcl|NCBI__GCF_900100495.1:WP_090448028.1 342 LAANWVMVELGSLLNKEGLEIEQAPVSAEQLGGMLLRIKDNTISGKLAKMVFEAMAAGEGSADQVIEAR 410 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyk....sgkekalkflvGqvmkktkgradpkevekllkell 480 gl q++d ++ ++++ev++ n+++ve+y+ +++ k+++f+vGq+mk +kg+a+p +v++llk++l lcl|NCBI__GCF_900100495.1:WP_090448028.1 411 GLKQVTDSGAIESMLDEVLAANAEQVEQYRasdeAKRGKMFGFFVGQAMKASKGKANPGQVNELLKKKL 479 *****************************9887778899****************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (481 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: 10.64 // [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