Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_012465368.1 CLIM_RS02030 type 1 glutamine amidotransferase
Query= BRENDA::P20576 (201 letters) >NCBI__GCF_000020465.1:WP_012465368.1 Length = 188 Score = 241 bits (615), Expect = 6e-69 Identities = 117/190 (61%), Positives = 152/190 (80%), Gaps = 5/190 (2%) Query: 1 MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60 M+L+IDNYDSFTYNLVQY GE A +V RNDE++VE+I LAP++IV+SPGP TP++AG Sbjct: 1 MVLVIDNYDSFTYNLVQYIGESGASTEVYRNDEITVEEIIRLAPDKIVISPGPGTPDDAG 60 Query: 61 VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120 VS+ +I+ G++PLLGVCLGHQSIG A GG+VVRA+Q+MHGKTS +HH + G+F G+AN Sbjct: 61 VSVPLIKALEGRIPLLGVCLGHQSIGAALGGKVVRAQQIMHGKTSMVHHDNTGIFHGVAN 120 Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180 P TRYHSL+V+RESLP+ L V AWT+ DG+ IMG+ L + GVQFHPESI+TE Sbjct: 121 PFVATRYHSLIVERESLPDLLVVRAWTE--DGT---IMGMDCIALRLYGVQFHPESIMTE 175 Query: 181 QGHELLANFL 190 +G +++ NFL Sbjct: 176 EGKKIIGNFL 185 Lambda K H 0.319 0.137 0.403 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: 173 Number of extensions: 2 Number of successful extensions: 2 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: 201 Length of database: 188 Length adjustment: 20 Effective length of query: 181 Effective length of database: 168 Effective search space: 30408 Effective search space used: 30408 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: 41 (21.7 bits) S2: 44 (21.6 bits)
Align candidate WP_012465368.1 CLIM_RS02030 (type 1 glutamine amidotransferase)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
# 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/TIGR00566.hmm # target sequence database: /tmp/gapView.15235.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00566 [M=192] Accession: TIGR00566 Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-78 247.3 0.0 5.8e-78 247.1 0.0 1.0 1 lcl|NCBI__GCF_000020465.1:WP_012465368.1 CLIM_RS02030 type 1 glutamine am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020465.1:WP_012465368.1 CLIM_RS02030 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 247.1 0.0 5.8e-78 5.8e-78 1 191 [. 1 186 [. 1 187 [. 0.99 Alignments for each domain: == domain 1 score: 247.1 bits; conditional E-value: 5.8e-78 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 mvl+idnydsftynlvq++ e ga+ v rnd++t++ei +l+p++ ivisPGP+tPd+a++s + li+ lcl|NCBI__GCF_000020465.1:WP_012465368.1 1 MVLVIDNYDSFTYNLVQYIGESGASTEVYRNDEITVEEIIRLAPDK-IVISPGPGTPDDAGVS-VPLIK 67 79********************************************.****************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 l G++P+lGvClGhq+++ a G++vvra++++hGk+s ++h+++++f+g++nP ++atryhsl+ve lcl|NCBI__GCF_000020465.1:WP_012465368.1 68 ALEGRIPLLGVCLGHQSIGAALGGKVVRAQQIMHGKTSMVHHDNTGIFHGVANP--FVATRYHSLIVER 134 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 e+l++ll v a++e im++ +l l GvqfhPesi++e+Gk+++ nfl+ lcl|NCBI__GCF_000020465.1:WP_012465368.1 135 ESLPDLLVVRAWTEDG-TIMGMDCIALRLYGVQFHPESIMTEEGKKIIGNFLE 186 *************999.9*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (188 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.05 // [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