Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate WP_040580301.1 A3OQ_RS0100400 aminodeoxychorismate/anthranilate synthase component II
Query= SwissProt::P00901 (198 letters) >NCBI__GCF_000385335.1:WP_040580301.1 Length = 202 Score = 196 bits (497), Expect = 3e-55 Identities = 100/197 (50%), Positives = 131/197 (66%), Gaps = 6/197 (3%) Query: 3 LMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAGV 62 +++IDNYDSF +NV +Y ELG EVKV+RND + I I L+P +V+SPGP TP +AG+ Sbjct: 5 ILVIDNYDSFVFNVARYFEELGREVKVVRNDAIDIEGIRRLDPAALVISPGPGTPQDAGI 64 Query: 63 SIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNNP 122 S+EA+ G++PILGVCLGHQ IG +G V RA++ +HG +P+ H +F GL P Sbjct: 65 SLEAVRALNGEMPILGVCLGHQCIGAMYGAPVARAKRPLHGIATPIAHNGRNLFEGLEAP 124 Query: 123 LTVTRYHSLVVKR-ETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181 L V RYHSL+V+ L L++ A E+G EIM L HK GVQFHPESILT+ Sbjct: 125 LKVGRYHSLIVEETPALKAALDIDA--VSEEG---EIMALSHKIAPTYGVQFHPESILTD 179 Query: 182 QGHELFANFLKQTGGRR 198 GH LFANFL+ R+ Sbjct: 180 HGHRLFANFLRLAEARQ 196 Lambda K H 0.320 0.138 0.411 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: 141 Number of extensions: 5 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: 198 Length of database: 202 Length adjustment: 21 Effective length of query: 177 Effective length of database: 181 Effective search space: 32037 Effective search space used: 32037 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: 45 (21.9 bits)
Align candidate WP_040580301.1 A3OQ_RS0100400 (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.1175163.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-68 215.6 0.0 3.1e-68 215.4 0.0 1.0 1 NCBI__GCF_000385335.1:WP_040580301.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000385335.1:WP_040580301.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.4 0.0 3.1e-68 3.1e-68 2 191 .. 5 190 .. 4 191 .. 0.98 Alignments for each domain: == domain 1 score: 215.4 bits; conditional E-value: 3.1e-68 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGk 74 +l+idnydsf +n+ +++eelg ev v rnd++ ++ i +l p +visPGP+tP++a+is le+++ l+G NCBI__GCF_000385335.1:WP_040580301.1 5 ILVIDNYDSFVFNVARYFEELGREVKVVRNDAIDIEGIRRLDPAA-LVISPGPGTPQDAGIS-LEAVRALNGE 75 89******************************************9.****************.********** PP TIGR00566 75 lPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvve.aetldtlle 146 +PilGvClGhq+++ Ga v ra++ hG i hng+ +f+gl P lk++ryhsl+ve + +l++ l+ NCBI__GCF_000385335.1:WP_040580301.1 76 MPILGVCLGHQCIGAMYGAPVARAKRPLHGIATPIAHNGRNLFEGLEAP--LKVGRYHSLIVEeTPALKAALD 146 *************************************************..***********72568****** PP TIGR00566 147 vtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 + a++ee eima+ h+ p GvqfhPesil+++G++l anfl+ NCBI__GCF_000385335.1:WP_040580301.1 147 IDAVSEEG-EIMALSHKIAPTYGVQFHPESILTDHGHRLFANFLR 190 *******9.**********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (202 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: 11.03 // [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