Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C; Asp/Glu-ADT subunit C; EC 6.3.5.- (uncharacterized)
to candidate RR42_RS00585 RR42_RS00585 glutamyl-tRNA amidotransferase
Query= curated2:B4E7X5 (99 letters) >FitnessBrowser__Cup4G11:RR42_RS00585 Length = 99 Score = 135 bits (340), Expect = 1e-37 Identities = 68/99 (68%), Positives = 80/99 (80%) Query: 1 MALTLTDVKRIAHLARLEMADADAEHMLGQLNEFFGLVEQMQAVDTAGIAPLAHPIEQIQ 60 MAL L+DVKRIAHLAR+E+ D +A L QLN+FF LVEQMQAVDT GI PLAHP+ ++ Sbjct: 1 MALDLSDVKRIAHLARIEINDDEAGQTLVQLNQFFSLVEQMQAVDTTGIVPLAHPLSAVR 60 Query: 61 EVAQRLRDDAVTEVVDRDDNQRPAPAVQDGLYLVPKVIE 99 E++QRLRDD VTE R+D QRPAPA + GLYLVPKVIE Sbjct: 61 EMSQRLRDDVVTEPNRREDYQRPAPATEGGLYLVPKVIE 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: 74 Number of extensions: 2 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 RR42_RS00585 RR42_RS00585 (glutamyl-tRNA amidotransferase)
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.30802.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-31 93.7 0.0 3.9e-31 93.5 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS00585 RR42_RS00585 glutamyl-tRNA amido Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS00585 RR42_RS00585 glutamyl-tRNA amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 93.5 0.0 3.9e-31 3.9e-31 2 93 .] 4 99 .] 3 99 .] 0.97 Alignments for each domain: == domain 1 score: 93.5 bits; conditional E-value: 3.9e-31 TIGR00135 2 skeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplels....nklReDevees 68 + ++vkr+a+Lar+e++++ea ++ +L+++++lveq+++vdt+++ p+a+pl+++ ++lR+D v+e+ lcl|FitnessBrowser__Cup4G11:RR42_RS00585 4 DLSDVKRIAHLARIEINDDEAGQTLVQLNQFFSLVEQMQAVDTTGIVPLAHPLSAVremsQRLRDDVVTEP 74 6789*************************************************9888888*********** PP TIGR00135 69 lkrkeilknapekedgfikvPkile 93 +r++++ ap +e g+++vPk++e lcl|FitnessBrowser__Cup4G11:RR42_RS00585 75 NRREDYQRPAPATEGGLYLVPKVIE 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: 3.85 // [ok]
This GapMind analysis is from Apr 09 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