Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate AZOBR_RS07460 AZOBR_RS07460 anthranilate synthase
Query= SwissProt::P26922 (196 letters) >FitnessBrowser__azobra:AZOBR_RS07460 Length = 196 Score = 390 bits (1003), Expect = e-114 Identities = 192/196 (97%), Positives = 193/196 (98%) Query: 1 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG 60 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG Sbjct: 1 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAG 60 Query: 61 ICLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLP 120 ICLPLIDAAAKA VPLMGVCLGHQAIGQ FGGTV+RAPVPMHGKVDRMFHQGRGVLKDLP Sbjct: 61 ICLPLIDAAAKAGVPLMGVCLGHQAIGQAFGGTVLRAPVPMHGKVDRMFHQGRGVLKDLP 120 Query: 121 SPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHK 180 SPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSH ELPIHGVQFHPESIESEHGHK Sbjct: 121 SPFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHCELPIHGVQFHPESIESEHGHK 180 Query: 181 ILENFLNTTRRLETAA 196 ILENFLNTTRRLETAA Sbjct: 181 ILENFLNTTRRLETAA 196 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: 276 Number of extensions: 6 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: 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 AZOBR_RS07460 AZOBR_RS07460 (anthranilate synthase)
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.19458.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-72 227.3 0.0 7.9e-72 227.1 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS07460 AZOBR_RS07460 anthranilate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS07460 AZOBR_RS07460 anthranilate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.1 0.0 7.9e-72 7.9e-72 1 191 [. 1 187 [. 1 188 [. 0.96 Alignments for each domain: == domain 1 score: 227.1 bits; conditional E-value: 7.9e-72 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 m+llidnydsftynlv++l elgae+ v+rndslt++e al p+ iv+sPGPc Pd+a+i l li+ lcl|FitnessBrowser__azobra:AZOBR_RS07460 1 MLLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEG-IVLSPGPCDPDKAGIC-LPLID 67 79*******************************************9.***************9.88887 PP TIGR00566 70 hla.GklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvve 137 +a +P++GvClGhqa++qafG+ v ra +hGkv + h+g++v++ l +P ++atryhsl+ve lcl|FitnessBrowser__azobra:AZOBR_RS07460 68 AAAkAGVPLMGVCLGHQAIGQAFGGTVLRAPVPMHGKVDRMFHQGRGVLKDLPSP--FRATRYHSLIVE 134 7652458************************************************..************ PP TIGR00566 138 aetldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 +tl+++levt +e +ima+ h +lp++GvqfhPesi se+G+++l+nfl+ lcl|FitnessBrowser__azobra:AZOBR_RS07460 135 RATLPACLEVTGETEDG-LIMALSHCELPIHGVQFHPESIESEHGHKILENFLN 187 ***********998888.**********************************98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.30 // [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