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_RS06415 AZOBR_RS06415 anthranilate synthase subunit I
Query= SwissProt::P26922 (196 letters) >FitnessBrowser__azobra:AZOBR_RS06415 Length = 737 Score = 136 bits (343), Expect = 8e-37 Identities = 83/195 (42%), Positives = 105/195 (53%), Gaps = 2/195 (1%) Query: 2 LLLIDNYDSFTYNLVHYLGELGAELDVRRNDSLTVEEAMALRPEGIVLSPGPCDPDKAGI 61 +LL+D+ DSF + L YL + GA + R+ A RP+ +VLSPGP P + Sbjct: 539 VLLVDHDDSFVHTLADYLRQTGASVMTLRHGHARAALAER-RPDLVVLSPGPGRPADFNV 597 Query: 62 CLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRAPVPMHGKVDRMFHQGRGVLKDLPS 121 IDAA +P+ GVCLG Q + + FGG + P P+HGK + G + LP Sbjct: 598 A-GTIDAALALGLPVFGVCLGLQGMVERFGGALDVLPEPVHGKATEVRVLGGALFAGLPE 656 Query: 122 PFRATRYHSLIVERATLPACLEVTGETEDGLIMALSHRELPIHGVQFHPESIESEHGHKI 181 R RYHSL+ R LPA L VT ET DGL+MA+ HR LP+ VQFHPESI S G Sbjct: 657 RMRVGRYHSLVARRDRLPADLTVTAETADGLVMAVEHRRLPLAAVQFHPESILSLDGGAG 716 Query: 182 LENFLNTTRRLETAA 196 L N RL A Sbjct: 717 LALLGNVMDRLAAGA 731 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: 384 Number of extensions: 19 Number of successful extensions: 3 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: 737 Length adjustment: 30 Effective length of query: 166 Effective length of database: 707 Effective search space: 117362 Effective search space used: 117362 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: 50 (23.9 bits)
Align candidate AZOBR_RS06415 AZOBR_RS06415 (anthranilate synthase subunit I)
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.4090.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-41 127.6 0.0 3.6e-41 127.1 0.0 1.2 1 lcl|FitnessBrowser__azobra:AZOBR_RS06415 AZOBR_RS06415 anthranilate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06415 AZOBR_RS06415 anthranilate synthase subunit I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 127.1 0.0 3.6e-41 3.6e-41 2 189 .. 539 723 .. 538 726 .. 0.89 Alignments for each domain: == domain 1 score: 127.1 bits; conditional E-value: 3.6e-41 TIGR00566 2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelieh 70 vll+d dsf + l ++l + ga+v+ r + + + + p+l +v+sPGP+ P++ + + lcl|FitnessBrowser__azobra:AZOBR_RS06415 539 VLLVDHDDSFVHTLADYLRQTGASVMTLR-HGHARAALAERRPDL-VVLSPGPGRPADFNVA-GTIDAA 604 9**********************998776.556667788889*99.9**********99888.667778 PP TIGR00566 71 laGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveae 139 la lP++GvClG q + fG+ + + + hGk e++ g a+fagl + ++++ryhslv + + lcl|FitnessBrowser__azobra:AZOBR_RS06415 605 LALGLPVFGVCLGLQGMVERFGGALDVLPEPVHGKATEVRVLGGALFAGLPER--MRVGRYHSLVARRD 671 8999**********************************************655..************** PP TIGR00566 140 tldtllevtaleeeeieimairhrdlpleGvqfhPesilselGk...ellanf 189 +l++ l+vta + ++ma+ hr lpl vqfhPesils G+ +ll n+ lcl|FitnessBrowser__azobra:AZOBR_RS06415 672 RLPADLTVTAETADG-LVMAVEHRRLPLAAVQFHPESILSLDGGaglALLGNV 723 *********999888.************************8776111456665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (737 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: 18.07 // [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