Align glutamyl-tRNAGln amidotransferase subunit C (EC 6.3.5.7) (characterized)
to candidate WP_092481822.1 BM299_RS02200 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC
Query= metacyc::MONOMER-13957 (96 letters) >NCBI__GCF_900115975.1:WP_092481822.1 Length = 93 Score = 87.0 bits (214), Expect = 4e-23 Identities = 40/92 (43%), Positives = 62/92 (67%) Query: 4 ISIEEVKHVAHLARLAITEEEAKMFTEQLDSIISFAEELNEVNTDNVEPTTHVLKMKNVM 63 +S +EV+HVA LARL +T+EE + + QL I+ +L +++T+N+ PT HVL ++NV Sbjct: 2 LSPKEVEHVALLARLKLTDEEKETYRRQLSDILDNFRKLQDLDTENIPPTAHVLPLQNVF 61 Query: 64 REDEAGKGLPVEDVMKNAPDHKDGYIRVPSIL 95 RED G + VE V+ NAP +D + +VP I+ Sbjct: 62 REDRVGGHMAVEKVLANAPQRQDNFFKVPKIV 93 Lambda K H 0.312 0.130 0.349 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: 48 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: 96 Length of database: 93 Length adjustment: 10 Effective length of query: 86 Effective length of database: 83 Effective search space: 7138 Effective search space used: 7138 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: 39 (20.5 bits) S2: 39 (19.6 bits)
Align candidate WP_092481822.1 BM299_RS02200 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC)
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.13540.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-32 97.4 0.3 2.6e-32 97.3 0.3 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092481822.1 BM299_RS02200 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092481822.1 BM299_RS02200 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 97.3 0.3 2.6e-32 2.6e-32 2 92 .. 3 93 .] 2 93 .] 0.98 Alignments for each domain: == domain 1 score: 97.3 bits; conditional E-value: 2.6e-32 TIGR00135 2 skeevkrlakLarlelseeeaekfaeeLkeilklveqlsevdtenvepmanplelsnklReDeveeslkrk 72 s +ev+++a Larl+l++ee+e++ ++L+ il+ + +l+ +dten+ p+a++l+l+n++ReD v+ + + lcl|NCBI__GCF_900115975.1:WP_092481822.1 3 SPKEVEHVALLARLKLTDEEKETYRRQLSDILDNFRKLQDLDTENIPPTAHVLPLQNVFREDRVGGHMAVE 73 5689******************************************************************* PP TIGR00135 73 eilknapekedgfikvPkil 92 ++l+nap+ +d+f+kvPki+ lcl|NCBI__GCF_900115975.1:WP_092481822.1 74 KVLANAPQRQDNFFKVPKIV 93 ******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (93 nodes) Target sequences: 1 (93 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: 3.60 // [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