Align 3-hydroxybenzoate 4-monooxygenase; 3-hydroxybenzoate 4-hydroxylase; M-hydroxybenzoate hydroxylase; EC 1.14.13.23 (characterized)
to candidate WP_053936853.1 WG78_RS05840 hypothetical protein
Query= SwissProt::Q6SSJ6 (639 letters) >NCBI__GCF_001294205.1:WP_053936853.1 Length = 507 Score = 117 bits (293), Expect = 1e-30 Identities = 113/375 (30%), Positives = 155/375 (41%), Gaps = 43/375 (11%) Query: 35 VLIVGCGPAGLTLAAQLAAFPDIRTCIVEQKEGPMELGQADGIACRTMEMFEAFEFADSI 94 VLIVG GP GLTLA L + I+E+ +A + RT+EM E A Sbjct: 5 VLIVGAGPIGLTLAMALTR-QAVPVRIIEKNAVRSPYSKALIVWSRTLEMLEIEGIAQDF 63 Query: 95 LKEACWINDVTFWKPDPAQPG-RIARHGRVQDTEDGLSEFPHVILNQARVHDHYLERMRN 153 + W + R A G D G V+L Q+ + N Sbjct: 64 VAAGIPARGAAVWAEGKQRVQLRFAEAGIATDYPAG------VLLAQSETE----RLLEN 113 Query: 154 SPSRLEPHYARRVLDVKIDHGAADYPVTVTLERCDAAHAGQIETVQARYVVGCDGARSNV 213 + L H R V I H + ++ TL D G+IET QA ++ CDGA S V Sbjct: 114 HLATLGVHVEREV--ELIQHHSTPDGISATLRHAD----GRIETAQAAWLAACDGAHSTV 167 Query: 214 RRAIGR-QLVGDSANQAWGVMDVLAVTDFPDVRYKVAIQSEQGNVLIIPREGGHLVRFYV 272 R + + GD+ W + DV +D P + + + G ++ IP G RF V Sbjct: 168 RHQLDTAEFAGDTLPTHWLLADVKLASDLPRDEVSMFL-AHDGLLIAIPFGDG---RFRV 223 Query: 273 EMDKLDADERVASRNITVEQLIATAQRVLHPYK---LDVKNVPWWSVYEIGQRICAKYDD 329 D D R E +A Q +L ++ W S + I +R+ +Y Sbjct: 224 MGDIGQVD-----RASLPEPTLADIQHLLDTRSDTPAVAQDPAWISHFVINERMVREYR- 277 Query: 330 VADAVATPDSPLPRVFIAGDACHTHSPKAGQGMNFSMQDSFNLGWKLAAVLRKQCAPELL 389 RVF+ GDA H HSP GQGMN MQD+ NL WKLA LL Sbjct: 278 -----------YGRVFLLGDAAHIHSPAGGQGMNTGMQDAINLAWKLALHSHGLVGEALL 326 Query: 390 HTYSSERQVVAQQLI 404 +YSSER +A Q++ Sbjct: 327 DSYSSERSAIADQVL 341 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: 790 Number of extensions: 52 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 639 Length of database: 507 Length adjustment: 36 Effective length of query: 603 Effective length of database: 471 Effective search space: 284013 Effective search space used: 284013 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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