Align 3-hydroxyanthranilate 3,4-dioxygenase; 3-hydroxyanthranilate oxygenase; 3-HAO; 3-hydroxyanthranilic acid dioxygenase; HAD; EC 1.13.11.6 (characterized)
to candidate N515DRAFT_2922 N515DRAFT_2922 3-hydroxyanthranilate 3,4-dioxygenase
Query= SwissProt::Q1LCS4 (174 letters) >FitnessBrowser__Dyella79:N515DRAFT_2922 Length = 173 Score = 171 bits (433), Expect = 6e-48 Identities = 87/167 (52%), Positives = 101/167 (60%), Gaps = 2/167 (1%) Query: 7 PFNFPRWIDEHAHLLKPPVGNRQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGNA 66 P + RWIDEH HLLKPPVGN+ + D DFIV +VGGPN RTDYH D EFFYQL G Sbjct: 6 PLDLQRWIDEHRHLLKPPVGNKCI-VDGDFIVMIVGGPNARTDYHYDEGPEFFYQLEGEM 64 Query: 67 YLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDGFEWYCD 126 L + DG ++ G +F LPP V HSPQR S LVIER+R AG DG W+C Sbjct: 65 VLKVQDDGAARDIPIRAGQMFYLPPRVPHSPQR-MPDSIGLVIERRRLAGEQDGLMWFCQ 123 Query: 127 ACGHLVHRVEVQLKSIVTDLPPLFESFYASEDKRRCPHCGQVHPGRA 173 C H ++ L SI D PP+FE FY S + R C CG VHP A Sbjct: 124 QCNHKLYEEYFTLDSIERDFPPVFERFYRSLEARTCTQCGTVHPAPA 170 Lambda K H 0.324 0.143 0.481 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: 159 Number of extensions: 6 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: 174 Length of database: 173 Length adjustment: 19 Effective length of query: 155 Effective length of database: 154 Effective search space: 23870 Effective search space used: 23870 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 44 (21.6 bits)
Align candidate N515DRAFT_2922 N515DRAFT_2922 (3-hydroxyanthranilate 3,4-dioxygenase)
to HMM TIGR03037 (nbaC: 3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6))
# 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.carbon/TIGR03037.hmm # target sequence database: /tmp/gapView.22757.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03037 [M=159] Accession: TIGR03037 Description: anthran_nbaC: 3-hydroxyanthranilate 3,4-dioxygenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-81 256.3 0.0 6.3e-81 256.1 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2922 N515DRAFT_2922 3-hydroxyanthrani Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2922 N515DRAFT_2922 3-hydroxyanthranilate 3,4-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.1 0.0 6.3e-81 6.3e-81 1 159 [] 7 164 .. 7 164 .. 0.99 Alignments for each domain: == domain 1 score: 256.1 bits; conditional E-value: 6.3e-81 TIGR03037 1 lnlkkwidehkellkppvgnkqiwqdselivtvvGGpnkrtdfhvdeseeffyqlkGemvlkvlee 66 l+l++wideh++llkppvgnk+i d ++iv++vGGpn+rtd+h+de++effyql+Gemvlkv+++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2922 7 LDLQRWIDEHRHLLKPPVGNKCI-VDGDFIVMIVGGPNARTDYHYDEGPEFFYQLEGEMVLKVQDD 71 579********************.899*************************************** PP TIGR03037 67 GkvedvpireGdifllppkvphspqraagsiglvierkrkegeldalqwfcaecgeklyraevkle 132 G ++d+pir+G++f lpp+vphspqr +siglvier+r ge+d+l+wfc++c++kly++ ++l+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2922 72 GAARDIPIRAGQMFYLPPRVPHSPQRMPDSIGLVIERRRLAGEQDGLMWFCQQCNHKLYEEYFTLD 137 ****************************************************************** PP TIGR03037 133 sivkdlppvfekfyssedartckkcGe 159 si++d+ppvfe+fy+s +artc++cG+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2922 138 SIERDFPPVFERFYRSLEARTCTQCGT 164 *************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (159 nodes) Target sequences: 1 (173 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: 7.41 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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