Align 3-hydroxyanthranilate 3,4-dioxygenase; 3-hydroxyanthranilate oxygenase; 3-HAO; 3-hydroxyanthranilic acid dioxygenase; HAD; EC 1.13.11.6 (characterized)
to candidate Echvi_1448 Echvi_1448 3-hydroxyanthranilate 3,4-dioxygenase
Query= SwissProt::Q1LCS4 (174 letters) >FitnessBrowser__Cola:Echvi_1448 Length = 170 Score = 171 bits (434), Expect = 5e-48 Identities = 81/161 (50%), Positives = 112/161 (69%), Gaps = 2/161 (1%) Query: 7 PFNFPRWIDEHAHLLKPPVGNRQVWQ-DSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGN 65 PFNF +WI+++ HLLKPPVGN+QV++ + DFIV VVGGPN R DYH + EEFFYQL G+ Sbjct: 6 PFNFKQWIEDNRHLLKPPVGNQQVYKGNDDFIVMVVGGPNSRKDYHYNEGEEFFYQLEGD 65 Query: 66 AYLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDGFEWYC 125 L + +G+ + ++KEG+IFLLPP V HSP+RP A + LV+ER R G DGF WYC Sbjct: 66 IVLKVIEEGKPKDIEIKEGEIFLLPPKVHHSPRRP-ANTVGLVMERYRKEGEKDGFIWYC 124 Query: 126 DACGHLVHRVEVQLKSIVTDLPPLFESFYASEDKRRCPHCG 166 + CG+ ++ + IV+ LPP+ E F+++ + C CG Sbjct: 125 ENCGNKLYEEYAVVTDIVSQLPPIMERFWSNPENTTCQSCG 165 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: 145 Number of extensions: 5 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: 170 Length adjustment: 18 Effective length of query: 156 Effective length of database: 152 Effective search space: 23712 Effective search space used: 23712 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 Echvi_1448 Echvi_1448 (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.14971.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-78 245.9 0.2 1e-77 245.7 0.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1448 Echvi_1448 3-hydroxyanthranilate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1448 Echvi_1448 3-hydroxyanthranilate 3,4-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 245.7 0.2 1e-77 1e-77 1 159 [] 7 166 .. 7 166 .. 0.98 Alignments for each domain: == domain 1 score: 245.7 bits; conditional E-value: 1e-77 TIGR03037 1 lnlkkwidehkellkppvgnkqiwq.dselivtvvGGpnkrtdfhvdeseeffyqlkGemvlkvleeGkvedvp 73 +n+k+wi+++++llkppvgn+q+++ ++++iv+vvGGpn r+d+h++e+eeffyql+G++vlkv+eeGk +d++ lcl|FitnessBrowser__Cola:Echvi_1448 7 FNFKQWIEDNRHLLKPPVGNQQVYKgNDDFIVMVVGGPNSRKDYHYNEGEEFFYQLEGDIVLKVIEEGKPKDIE 80 7***********************84679********************************************* PP TIGR03037 74 ireGdifllppkvphspqraagsiglvierkrkegeldalqwfcaecgeklyraevklesivkdlppvfekfys 147 i+eG+ifllppkv+hsp+r+a+++glv+er rkege+d++ w+c++cg+kly++ +++iv++lpp++e+f+s lcl|FitnessBrowser__Cola:Echvi_1448 81 IKEGEIFLLPPKVHHSPRRPANTVGLVMERYRKEGEKDGFIWYCENCGNKLYEEYAVVTDIVSQLPPIMERFWS 154 ************************************************************************** PP TIGR03037 148 sedartckkcGe 159 + ++ tc+ cG+ lcl|FitnessBrowser__Cola:Echvi_1448 155 NPENTTCQSCGT 166 **********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (159 nodes) Target sequences: 1 (170 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 4.82 // [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