Align 3-hydroxybenzoate 4-monooxygenase; 3-hydroxybenzoate 4-hydroxylase; M-hydroxybenzoate hydroxylase; EC 1.14.13.23 (characterized)
to candidate Pf6N2E2_227 3-(3-hydroxy-phenyl)propionate hydroxylase (EC 1.14.13.-)
Query= SwissProt::Q6SSJ6 (639 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_227 Length = 548 Score = 117 bits (293), Expect = 1e-30 Identities = 112/373 (30%), Positives = 175/373 (46%), Gaps = 43/373 (11%) Query: 35 VLIVGCGPAGLTLAAQLAAFPDIRTCIVEQKEGPMELGQADGIACRTMEMFEAFEFADSI 94 VLI+G GP GLTLA L D+ T I+++K G + +A I ++ +A ++ Sbjct: 11 VLIIGAGPTGLTLA-NLLGQADVDTLIIDRKPGTVTEPRAVSIDDESLRTMQAIGLDAAV 69 Query: 95 LKEACWINDVTFWKPDPAQPGRIARHGRVQDTEDGLSEFPHVILNQARVHDHYLERMRNS 154 L++ V ++ +PG G+V+ T L FP + + ++ L R Sbjct: 70 LRDVVPGYGVHYF----TRPGGRC-FGKVEPTGK-LYGFPKRNAFRQPLFENTLRRGLER 123 Query: 155 PSRLEPHYARRVLDVKID-HGAADYPVTVTLERCDAAHAGQIETVQARYVVGCDGARSNV 213 + L ++ +++ D HG L R DA GQ+ V A Y+V CDG RS V Sbjct: 124 FASLTARFSHELVEFTQDPHGVC------ALVR-DAE--GQLMEVHAAYLVACDGGRSPV 174 Query: 214 RRAIGRQLVGDSANQAWGVMDVLAVTDFPDVRYKVAIQSEQGNVLIIPREGGHLVRFYVE 273 R+ +G ++VG S + W V+D D P + +V + + ++ G H R + Sbjct: 175 RKQLGIEMVGSSFSSRWLVVDT-DQDDDPFWQTRVYCDARRP---VVEVPGPHRTRRFEF 230 Query: 274 MDKLD-ADERVASRNITVEQLIATAQRVLHPYKLDVK-NVPWWSVYEIGQRICAKYDDVA 331 + K D DE+V Q +L P+K D ++ +VY R+ ++ Sbjct: 231 LLKPDETDEQVLDETCL--------QALLRPFKSDAPVSIVRKTVYTFHARVAERWQ--- 279 Query: 332 DAVATPDSPLPRVFIAGDACHTHSPKAGQGMNFSMQDSFNLGWKLAAVLRKQCAPELLHT 391 + RVF+AGDA H P AGQGMN ++D+ NLGWKL VL+ + A L + Sbjct: 280 ---------VQRVFLAGDAAHLTPPYAGQGMNSGVRDAHNLGWKLVGVLKGKMAESALLS 330 Query: 392 YSSERQVVAQQLI 404 Y SER+ A LI Sbjct: 331 YESERRDHAWALI 343 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: 796 Number of extensions: 36 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: 639 Length of database: 548 Length adjustment: 37 Effective length of query: 602 Effective length of database: 511 Effective search space: 307622 Effective search space used: 307622 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 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