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_011385238.1 AMB_RS14405 type 1 glutamine amidotransferase
Query= SwissProt::P26922 (196 letters) >NCBI__GCF_000009985.1:WP_011385238.1 Length = 196 Score = 281 bits (719), Expect = 5e-81 Identities = 132/190 (69%), Positives = 157/190 (82%), Gaps = 1/190 (0%) Query: 1 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG 60 M LLIDNYDSFTYNL HYLGELGAE+ V+RND++TV++ + LRP+GIV+SPGPCDPD+AG Sbjct: 1 MFLLIDNYDSFTYNLWHYLGELGAEVVVKRNDAVTVDQVLGLRPQGIVISPGPCDPDRAG 60 Query: 61 ICLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLP 120 ICL LI+ AA +PL GVCLGHQAIGQ FGG VVRAP PMHGKVD + H GV + LP Sbjct: 61 ICLELIERAA-GTIPLFGVCLGHQAIGQAFGGKVVRAPKPMHGKVDTITHDDTGVFQGLP 119 Query: 121 SPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHK 180 SPFRATRYHSL+VER + P CL V+ T DGL+M L+H+ELPI GVQFHPESIE+EHGH Sbjct: 120 SPFRATRYHSLVVERESFPDCLHVSAWTADGLVMGLAHKELPIWGVQFHPESIETEHGHA 179 Query: 181 ILENFLNTTR 190 +L NF++ T+ Sbjct: 180 MLRNFIDFTK 189 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: 197 Number of extensions: 8 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: 196 Length of database: 196 Length adjustment: 20 Effective length of query: 176 Effective length of database: 176 Effective search space: 30976 Effective search space used: 30976 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_011385238.1 AMB_RS14405 (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.2583.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-80 254.2 0.0 4.6e-80 254.0 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011385238.1 AMB_RS14405 type 1 glutamine ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385238.1 AMB_RS14405 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.0 0.0 4.6e-80 4.6e-80 1 191 [. 1 186 [. 1 187 [. 0.99 Alignments for each domain: == domain 1 score: 254.0 bits; conditional E-value: 4.6e-80 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m llidnydsftynl ++l elgaevvvkrnd++t++++ l p+ ivisPGPc Pd a+i lelie lcl|NCBI__GCF_000009985.1:WP_011385238.1 1 MFLLIDNYDSFTYNLWHYLGELGAEVVVKRNDAVTVDQVLGLRPQG-IVISPGPCDPDRAGIC-LELIE 67 679******************************************9.***************9.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 ++aG +P++GvClGhqa++qafG++vvra k +hGkv i+h++++vf+gl +P ++atryhslvve lcl|NCBI__GCF_000009985.1:WP_011385238.1 68 RAAGTIPLFGVCLGHQAIGQAFGGKVVRAPKPMHGKVDTITHDDTGVFQGLPSP--FRATRYHSLVVER 134 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 e+ +++l+v+a++ ++m++ h++lp+ GvqfhPesi +e+G+++l+nf++ lcl|NCBI__GCF_000009985.1:WP_011385238.1 135 ESFPDCLHVSAWTADG-LVMGLAHKELPIWGVQFHPESIETEHGHAMLRNFID 186 *************999.**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (196 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: 00:00:00.01 # Mc/sec: 3.39 // [ok]
This GapMind analysis is from Apr 09 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