Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate Pf1N1B4_1102 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 Length = 481 Score = 457 bits (1175), Expect = e-133 Identities = 227/480 (47%), Positives = 329/480 (68%), Gaps = 7/480 (1%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M +E VIGLE+H +L T SK+FS S FG+EPN+ +++DL PGVLPV+N+ AV A+ Sbjct: 1 MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119 +A++ EI + F RKNYFYPD PK YQISQ + PI G++DI + DG KR+GIT Sbjct: 61 MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIALEDGTVKRVGIT 120 Query: 120 RLHMEEDAGKSTHK--GEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177 R H+EEDAGKS H+ + +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y Sbjct: 121 RAHLEEDAGKSLHEEFNGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYL 180 Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237 G+ D M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K + E +RQ E + Sbjct: 181 GICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINTEVQRQIELIED 240 Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297 GG++ Q+TR +D + +T MR KE ++DYRYFP+PD++P+ I+D++ + VR T+PELP Sbjct: 241 GGKVIQQTRLYDPNKDETRPMRSKEEANDYRYFPDPDLLPVVIEDSFLDDVRATLPELPP 300 Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357 +++ ++ + GL YDA VL ++E +D+FE G D KL +NW+M + LNK + Sbjct: 301 QKRERFQEQFGLSVYDASVLATSREQADYFEKVASIGGDAKLAANWVMVELGSLLNKQGL 360 Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417 ++ + ++ E L GM+ I+D T+S KIAK VF +A G+A +I++ GL Q++D Sbjct: 361 DIDQSPVSAEQLGGMLLRIKDNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTGA 420 Query: 418 LLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473 + ++E L N + VE Y+ +GK GF VGQ MKASKG+ANPQ VN+LLK +L+ Sbjct: 421 ISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKLE 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: 635 Number of extensions: 17 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 Pf1N1B4_1102 (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.981585.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-174 565.7 0.0 3.9e-174 565.6 0.0 1.0 1 FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 # 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 .. 1 479 [. 1 480 [. 0.98 Alignments for each domain: == domain 1 score: 565.6 bits; conditional E-value: 3.9e-174 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 +++e+viGlE+H+ql t+sK+F+ +s+ + + +pNt+ + v+lg+PG+lPvlN+eav++A++ +la++ FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 1 MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGS-EPNTQASLVDLGMPGVLPVLNQEAVRMAVMFGLAID 67 5789***************************.************************************ PP TIGR00133 70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqyk 136 ++i + vF+RK+YfYpDlPkgyqi+q +lPi+ +G+l+i le++ k++gi+r hlEeD+gks ++ FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 68 AEIG-QHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIALEDGTvKRVGITRAHLEEDAGKSLHE 134 **55.79***********************************999888******************** PP TIGR00133 137 esdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsi 204 e + + +D+NR+g+PLlEiV++Pd++sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvsi FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 135 EFN--GATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSI 200 775..7999*********************************************************** PP TIGR00133 205 rlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeese 272 r+kGq ++gtr EiKN+ns++ iekai+ E++Rq++l+++g +v q+tr +d +k t +R+Kee++ FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 201 RPKGQVEFGTRCEIKNVNSFRFIEKAINTEVQRQIELIEDGGKVIQQTRLYDPNKDETRPMRSKEEAN 268 ******************************************************************** PP TIGR00133 273 DYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvk 340 DYRYfp+Pdl p++i+++++++ v+++lpelP +kr+r+++++gls +da vl + +e +d+fe+v++ FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 269 DYRYFPDPDLLPVVIEDSFLDD-VRATLPELPPQKRERFQEQFGLSVYDASVLATSREQADYFEKVAS 335 *******************999.********************************************* PP TIGR00133 341 likepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdp 408 +++kla+nW++ el + Lnk+ +++ ++ +++e+l ++ ik+++is+k+ak ++e + + ++++ FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 336 IGGDAKLAANWVMVELGSLLNKQGLDIDQSPVSAEQLGGMLLRIKDNTISGKIAKVVFEAMANGEGSA 403 ******************************************************************** PP TIGR00133 409 kklieklgliqisdekelvkiveevikenpkevekyk....sgkekalkflvGqvmkktkgradpkev 472 +++i+k+gl q++d+ ++ ++++e+++ n+++ve+y+ +++ k+++f+vGq+mk +kg+a+p++v FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 404 DEIIDKRGLKQVTDTGAISAVLDEMLAANAEQVEQYRaadeAKRGKMFGFFVGQAMKASKGKANPQQV 471 ************************************9888778899********************** PP TIGR00133 473 ekllkell 480 ++llk +l FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 472 NELLKSKL 479 *****988 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: 00:00:00.00 # Mc/sec: 23.25 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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