Align 3-hydroxybenzoate 4-monooxygenase; 3-hydroxybenzoate 4-hydroxylase; M-hydroxybenzoate hydroxylase; EC 1.14.13.23 (characterized)
to candidate WP_234245691.1 BZY95_RS03400 FAD-dependent monooxygenase
Query= SwissProt::Q6SSJ6 (639 letters) >NCBI__GCF_002151265.1:WP_234245691.1 Length = 630 Score = 619 bits (1596), Expect = 0.0 Identities = 338/645 (52%), Positives = 422/645 (65%), Gaps = 28/645 (4%) Query: 1 MQFHLNGFRPGNPLIAPASPLAPAHTEAVPSQVDVLIVGCGPAGLTLAAQLAAFPDIRTC 60 MQ+ L+G+R G+P I P + +P +VDVLIVG GPAGL LAAQL+ FP+I T Sbjct: 2 MQYFLDGYRSGDPRIQPLAEGRSDEQGPLPEEVDVLIVGSGPAGLLLAAQLSTFPNIVTR 61 Query: 61 IVEQKEGPMELGQADGIACRTMEMFEAFEFADSILKEACWINDVTFWKPDPAQPGRIARH 120 +VE+ +GP+E+G+ADGIACRT+EMFEAF A+ + EA W+N+ FW P P RI R Sbjct: 62 VVEKSDGPLEVGRADGIACRTVEMFEAFGLAERMTSEAYWVNETHFWGPAPGDKSRITRL 121 Query: 121 GRVQDTEDGLSEFPHVILNQARVHDHYLERMRNSPSRLEPHYARRVLDVKIDHGAADYPV 180 GRV+D GLSEFPHVI+NQAR+ D LE MRNSPSRL Y L V++ D V Sbjct: 122 GRVRDVRYGLSEFPHVIVNQARLLDFLLEYMRNSPSRLRVDYRHETLKVEVPE-TPDERV 180 Query: 181 TVTLERCDAAHAGQIETVQARYVVGCDGARSNVRRAIGRQLVGDSANQAWGVMDVLAVTD 240 TV L+ + + V ARYVVGCDGA S VR +IGR G ++AWGVMDVLAVTD Sbjct: 181 TVRLKTPEGE-----KIVLARYVVGCDGAHSVVRDSIGRVPQGHGEDKAWGVMDVLAVTD 235 Query: 241 FPDVRYKVAIQS-EQGNVLIIPREGGHLVRFYVEMDKLDADERVASRNITVEQLIATAQR 299 FPD+R+K IQS E GN+L+IPREGG++VR YV+M + D +T E+++A AQ Sbjct: 236 FPDIRFKCTIQSAEAGNILLIPREGGYMVRLYVDMGNIAPDAW-----LTKEEVLAKAQA 290 Query: 300 VLHPYKLDVKNVPWWSVYEIGQRICAKYDDVADAVATPDSPLPRVFIAGDACHTHSPKAG 359 VL PY +VK W+SVY +G R+ K+DDV D +S PRVFIAGDACHTH+ KAG Sbjct: 291 VLAPYTFEVKETAWFSVYRVGHRVTDKFDDVND--NQRESRTPRVFIAGDACHTHTAKAG 348 Query: 360 QGMNFSMQDSFNLGWKLAAVLRKQCAPELLHTYSSERQVVAQQLIDFDREWAKMFSDPAK 419 QGMN SMQD+FNLGWKL +VL + LLHTY+ ER V+A+ LI+ D W++ A Sbjct: 349 QGMNVSMQDTFNLGWKLISVLEGRSPASLLHTYNDERHVIAENLIEMDTRWSR-----AI 403 Query: 420 EGGQGGVDPK-------EFQKYFEQHGRFTAGVGTHYAPSLLTGQASHQALASGFTVGMR 472 Q DP+ E Q+ F + FTAG THY P+LLTG H ALA+GF G R Sbjct: 404 GAAQDADDPEAVMKGLAEVQRQFVTNSEFTAGFATHYTPALLTGDDQHLALATGFPPGRR 463 Query: 473 FHSAPVVRVSDAKPLQLGHCGKADGRWRLYAFAGQNDLAQPESGLLALCRFLESDAASPL 532 FHSA V+R+ DAK + LGH +ADGRWRLYAFA D P S L FL SD ASP+ Sbjct: 464 FHSAEVIRLGDAKQIHLGHVHRADGRWRLYAFADMVDPRSPGSRFNRLMDFLASD-ASPI 522 Query: 533 RRFTPSGQDIDSIFDLRAIFPQAYTEVALETLPALLLPPKGQLGMIDYEKVFSPDLKNAG 592 RRFTP G D D++FD+ I Q++ EV + +L P KG LG+ DY+KV +P L Sbjct: 523 RRFTPKGADPDAVFDVHGIIQQSHLEVDWADMHDVLKPHKGPLGLQDYQKVHAPVL-GTD 581 Query: 593 QDIFELRGIDRQQGALVVVRPDQYVAQVLPLGDHAALSAYFESFM 637 +DIF+ RGIDR GALVVVRPDQYV+ VLPL AL+ +F FM Sbjct: 582 RDIFDQRGIDRGAGALVVVRPDQYVSLVLPLDGFEALTEFFSRFM 626 Lambda K H 0.321 0.137 0.419 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: 1119 Number of extensions: 39 Number of successful extensions: 8 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: 639 Length of database: 630 Length adjustment: 38 Effective length of query: 601 Effective length of database: 592 Effective search space: 355792 Effective search space used: 355792 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 (21.9 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 09 2024. 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