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_085637398.1 MGEO_RS11340 aminodeoxychorismate/anthranilate synthase component II
Query= SwissProt::P26922 (196 letters) >NCBI__GCF_002115805.1:WP_085637398.1 Length = 193 Score = 279 bits (714), Expect = 2e-80 Identities = 130/187 (69%), Positives = 154/187 (82%) Query: 1 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG 60 MLLLIDNYDSFTYNLVHYLGELG ++ V RND+LTV++AM L P GI+LSPGPCDPD+AG Sbjct: 1 MLLLIDNYDSFTYNLVHYLGELGTDVKVVRNDALTVQDAMGLNPSGILLSPGPCDPDQAG 60 Query: 61 ICLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLP 120 ICLPL AAA+ +PLMGVCLGHQ +GQ FGG+VVR +HGK+ M H G+GV LP Sbjct: 61 ICLPLTLAAAETGMPLMGVCLGHQTLGQAFGGSVVRHSEIVHGKMGLMHHAGKGVFAGLP 120 Query: 121 SPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHK 180 SPF ATRYHSL+V++ T+P CLEVT EDG +M LSHR+LP+HGVQFHPESI SEHGH Sbjct: 121 SPFEATRYHSLVVDKDTIPNCLEVTAWLEDGTVMGLSHRDLPMHGVQFHPESIASEHGHA 180 Query: 181 ILENFLN 187 +L+NF+N Sbjct: 181 LLKNFVN 187 Lambda K H 0.321 0.140 0.420 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: 208 Number of extensions: 12 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: 196 Length of database: 193 Length adjustment: 20 Effective length of query: 176 Effective length of database: 173 Effective search space: 30448 Effective search space used: 30448 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_085637398.1 MGEO_RS11340 (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.415699.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-75 236.7 0.0 1e-74 236.6 0.0 1.0 1 NCBI__GCF_002115805.1:WP_085637398.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085637398.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 236.6 0.0 1e-74 1e-74 1 191 [. 1 187 [. 1 188 [. 0.98 Alignments for each domain: == domain 1 score: 236.6 bits; conditional E-value: 1e-74 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaG 73 m+llidnydsftynlv++l elg++v v rnd+lt+q+ l p i++sPGPc Pd+a+i + + NCBI__GCF_002115805.1:WP_085637398.1 1 MLLLIDNYDSFTYNLVHYLGELGTDVKVVRNDALTVQDAMGLNPSG-ILLSPGPCDPDQAGICLPLTLAAAET 72 79*******************************************9.****************8777888888 PP TIGR00566 74 klPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtlle 146 +P++GvClGhq+l+qafG++vvr +++ hGk+ ++h g++vfagl +P ++atryhslvv+ +t++++le NCBI__GCF_002115805.1:WP_085637398.1 73 GMPLMGVCLGHQTLGQAFGGSVVRHSEIVHGKMGLMHHAGKGVFAGLPSP--FEATRYHSLVVDKDTIPNCLE 143 9*************************************************..********************* PP TIGR00566 147 vtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 vta+ e +m++ hrdlp++GvqfhPesi se+G++ll+nf++ NCBI__GCF_002115805.1:WP_085637398.1 144 VTAWLEDG-TVMGLSHRDLPMHGVQFHPESIASEHGHALLKNFVN 187 ****9999.9*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (193 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.43 // [ok]
This GapMind analysis is from Jul 26 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