Align Aminodeoxychorismate/anthranilate synthase component 2; ADC synthase; ADCS; 4-amino-4-deoxychorismate synthase component 2; Aminodeoxychorismate synthase, glutamine amidotransferase component; EC 2.6.1.85; EC 4.1.3.27 (characterized)
to candidate WP_092481679.1 BM299_RS01075 aminodeoxychorismate/anthranilate synthase component II
Query= SwissProt::P28819 (194 letters) >NCBI__GCF_900115975.1:WP_092481679.1 Length = 188 Score = 238 bits (608), Expect = 4e-68 Identities = 109/182 (59%), Positives = 143/182 (78%) Query: 4 MIDNYDSFTYNLVQYLGELGEELVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAGISL 63 MIDNYDSFTYNLVQYL LGE + V+RND +T+ EI +L PD+L +SPGP +PD+AG+ L Sbjct: 1 MIDNYDSFTYNLVQYLAVLGETVAVRRNDRVTVTEIIDLRPDYLFLSPGPGTPDDAGVLL 60 Query: 64 EAIKHFAGKIPIFGVCLGHQSIAQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKNPLV 123 EA++ AG++P+FGVCLG Q+I Q +GG VVRA MHGK S + HDGK+IF GL +P Sbjct: 61 EAVQKCAGRLPVFGVCLGLQAIGQAYGGRVVRARAPMHGKISLVHHDGKSIFAGLPSPFK 120 Query: 124 ATRYHSLIVKPETLPSCFTVTAQTKEGEIMAIRHNDLPIEGVQFHPESIMTSFGKEMLRN 183 A RYHSL+V+ E+LP+C V+A T EGEIM +RH +LP+EGVQFHPES+++ G ++L N Sbjct: 121 AVRYHSLVVERESLPACLEVSAWTDEGEIMGLRHRELPVEGVQFHPESMLSEHGLDLLAN 180 Query: 184 FI 185 F+ Sbjct: 181 FL 182 Lambda K H 0.320 0.139 0.404 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: 155 Number of extensions: 3 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: 194 Length of database: 188 Length adjustment: 20 Effective length of query: 174 Effective length of database: 168 Effective search space: 29232 Effective search space used: 29232 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 (21.8 bits) S2: 44 (21.6 bits)
Align candidate WP_092481679.1 BM299_RS01075 (aminodeoxychorismate/anthranilate synthase component II)
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.835.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-79 251.2 0.0 3.6e-79 251.1 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092481679.1 BM299_RS01075 aminodeoxychorisma Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092481679.1 BM299_RS01075 aminodeoxychorismate/anthranilate synthase component II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.1 0.0 3.6e-79 3.6e-79 4 191 .. 1 183 [. 1 184 [. 0.99 Alignments for each domain: == domain 1 score: 251.1 bits; conditional E-value: 3.6e-79 TIGR00566 4 lidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehla 72 +idnydsftynlvq+l+ lg++v v+rnd +t++ei +l p+ + +sPGP+tPd+a++ le++++ a lcl|NCBI__GCF_900115975.1:WP_092481679.1 1 MIDNYDSFTYNLVQYLAVLGETVAVRRNDRVTVTEIIDLRPDY-LFLSPGPGTPDDAGVL-LEAVQKCA 67 8******************************************.***************9.******** PP TIGR00566 73 GklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetl 141 G+lP++GvClG qa++qa G+ vvra++ +hGk+s ++h+g+++fagl +P +ka ryhslvve e+l lcl|NCBI__GCF_900115975.1:WP_092481679.1 68 GRLPVFGVCLGLQAIGQAYGGRVVRARAPMHGKISLVHHDGKSIFAGLPSP--FKAVRYHSLVVERESL 134 ***************************************************..**************** PP TIGR00566 142 dtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 +++lev+a+++e eim++rhr+lp+eGvqfhPes+lse+G llanfl+ lcl|NCBI__GCF_900115975.1:WP_092481679.1 135 PACLEVSAWTDEG-EIMGLRHRELPVEGVQFHPESMLSEHGLDLLANFLR 183 ************9.**********************************96 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 5.85 // [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