Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C; Asp/Glu-ADT subunit C; EC 6.3.5.- (uncharacterized)
to candidate BPHYT_RS01550 BPHYT_RS01550 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
Query= curated2:B4E7X5 (99 letters) >FitnessBrowser__BFirm:BPHYT_RS01550 Length = 99 Score = 166 bits (419), Expect = 8e-47 Identities = 84/99 (84%), Positives = 92/99 (92%) Query: 1 MALTLTDVKRIAHLARLEMADADAEHMLGQLNEFFGLVEQMQAVDTAGIAPLAHPIEQIQ 60 MALTLTDVKRIAHLARLE+ADADAEH L QLN+FFGLVEQMQAVDT+GIAPLAHPIEQI+ Sbjct: 1 MALTLTDVKRIAHLARLELADADAEHTLVQLNDFFGLVEQMQAVDTSGIAPLAHPIEQIE 60 Query: 61 EVAQRLRDDAVTEVVDRDDNQRPAPAVQDGLYLVPKVIE 99 +VA RLR+D VTE V+R+ QRPAPAVQDGLYLVPKVIE Sbjct: 61 DVALRLRNDVVTETVEREAFQRPAPAVQDGLYLVPKVIE 99 Lambda K H 0.319 0.135 0.371 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: 91 Number of extensions: 1 Number of successful extensions: 1 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: 99 Length of database: 99 Length adjustment: 10 Effective length of query: 89 Effective length of database: 89 Effective search space: 7921 Effective search space used: 7921 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.9 bits) S2: 39 (19.6 bits)
Align candidate BPHYT_RS01550 BPHYT_RS01550 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C)
to HMM TIGR00135 (gatC: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C 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/TIGR00135.hmm # target sequence database: /tmp/gapView.2957219.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00135 [M=93] Accession: TIGR00135 Description: gatC: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-30 89.4 0.1 8.1e-30 89.3 0.1 1.0 1 FitnessBrowser__BFirm:BPHYT_RS01550 Domain annotation for each sequence (and alignments): >> FitnessBrowser__BFirm:BPHYT_RS01550 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 89.3 0.1 8.1e-30 8.1e-30 2 93 .] 4 99 .] 3 99 .] 0.96 Alignments for each domain: == domain 1 score: 89.3 bits; conditional E-value: 8.1e-30 TIGR00135 2 skeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplels....nklReDeveeslkrke 73 + +vkr+a+Larlel ++ ae++ +L+ +++lveq+++vdt+++ p+a+p+e+ +lR+D v+e+ +r++ FitnessBrowser__BFirm:BPHYT_RS01550 4 TLTDVKRIAHLARLELADADAEHTLVQLNDFFGLVEQMQAVDTSGIAPLAHPIEQIedvaLRLRNDVVTETVEREA 79 5689**************************************************99888889************** PP TIGR00135 74 ilknapekedgfikvPkile 93 ++ ap ++dg+++vPk++e FitnessBrowser__BFirm:BPHYT_RS01550 80 FQRPAPAVQDGLYLVPKVIE 99 ******************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (93 nodes) Target sequences: 1 (99 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 4.87 // [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