Align Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized, see rationale)
to candidate 209402 DVU0466 anthranilate synthase, glutamine amidotransferase component
Query= uniprot:Q72EV2_DESVH (209 letters) >MicrobesOnline__882:209402 Length = 209 Score = 433 bits (1113), Expect = e-126 Identities = 209/209 (100%), Positives = 209/209 (100%) Query: 1 MFLLIDNYDSFTFNLVQAFYGLGLAPVVVRNDDPALVACATRPDLDMVCISPGPSHPRNA 60 MFLLIDNYDSFTFNLVQAFYGLGLAPVVVRNDDPALVACATRPDLDMVCISPGPSHPRNA Sbjct: 1 MFLLIDNYDSFTFNLVQAFYGLGLAPVVVRNDDPALVACATRPDLDMVCISPGPSHPRNA 60 Query: 61 GGCLAFLDVLPRTVPVLGVCLGHQVLGLYAGATVEVGPRIMHGKTSDITHDGAGLFAGLP 120 GGCLAFLDVLPRTVPVLGVCLGHQVLGLYAGATVEVGPRIMHGKTSDITHDGAGLFAGLP Sbjct: 61 GGCLAFLDVLPRTVPVLGVCLGHQVLGLYAGATVEVGPRIMHGKTSDITHDGAGLFAGLP 120 Query: 121 QPMTVGRYHSLIVRAEEKPDLLEVTARTPEGEVMAMRYRDRPWVGVQFHPESVLTPDGVR 180 QPMTVGRYHSLIVRAEEKPDLLEVTARTPEGEVMAMRYRDRPWVGVQFHPESVLTPDGVR Sbjct: 121 QPMTVGRYHSLIVRAEEKPDLLEVTARTPEGEVMAMRYRDRPWVGVQFHPESVLTPDGVR 180 Query: 181 LLGNFPAMTGGSCPRMTPHGATVRQEVTA 209 LLGNFPAMTGGSCPRMTPHGATVRQEVTA Sbjct: 181 LLGNFPAMTGGSCPRMTPHGATVRQEVTA 209 Lambda K H 0.323 0.141 0.444 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: 349 Number of extensions: 9 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: 209 Length of database: 209 Length adjustment: 21 Effective length of query: 188 Effective length of database: 188 Effective search space: 35344 Effective search space used: 35344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 45 (21.9 bits)
Align candidate 209402 DVU0466 (anthranilate synthase, glutamine amidotransferase component)
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.10013.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-60 189.5 0.0 3e-60 189.4 0.0 1.0 1 lcl|MicrobesOnline__882:209402 DVU0466 anthranilate synthase, g Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209402 DVU0466 anthranilate synthase, glutamine amidotransferase component # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.4 0.0 3e-60 3e-60 1 189 [. 1 185 [. 1 188 [. 0.94 Alignments for each domain: == domain 1 score: 189.4 bits; conditional E-value: 3e-60 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPilG 79 m llidnydsft+nlvq + lg + vv rnd+ l + l ++isPGP++P +a+ l+ ++ l +P+lG lcl|MicrobesOnline__882:209402 1 MFLLIDNYDSFTFNLVQAFYGLGLAPVVVRNDDPALVACATRPDLDMVCISPGPSHPRNAGGC-LAFLDVLPRTVPVLG 78 679********************8888888888888777665555559*************98.9999999999***** PP TIGR00566 80 vClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeeeieim 158 vClGhq l++ Ga v +++hGk+s+i+h+ga++fagl +P ++++ryhsl+v+ae+ ++llevta + e e+m lcl|MicrobesOnline__882:209402 79 VCLGHQVLGLYAGATVEVGPRIMHGKTSDITHDGAGLFAGLPQP--MTVGRYHSLIVRAEEKPDLLEVTARTPEG-EVM 154 ********************************************..***************************99.*** PP TIGR00566 159 airhrdlpleGvqfhPesilselGkellanf 189 a+r rd p+ GvqfhPes+l+ G +ll nf lcl|MicrobesOnline__882:209402 155 AMRYRDRPWVGVQFHPESVLTPDGVRLLGNF 185 ******************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (209 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 6.06 // [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