Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate WP_011613086.1 TERY_RS17735 cytochrome P450
Query= metacyc::MONOMER-20332 (453 letters) >NCBI__GCF_000014265.1:WP_011613086.1 Length = 462 Score = 399 bits (1026), Expect = e-116 Identities = 204/434 (47%), Positives = 289/434 (66%), Gaps = 7/434 (1%) Query: 18 TW--ITDPVKYLETAVKDYPDLFLANIVGEGGPTVFVQHPQAVQQILTGDRQNFIASGKT 75 TW I P+ +E +Y D+F N P ++ +P+A+QQI T D F + Sbjct: 18 TWKFIFSPLSAIEERYSEYGDIFRTN-TNSLYPFIYFCNPKAIQQIFTADPDTFTSGSIN 76 Query: 76 HLLRPIIGNKSILGLDGNRHKKRRKLLLPSFHGDRIQAYGQLICDLTLQAFEQLTPNQIF 135 +L+ +G S+L DG+RHK++RKLL+P FHGDR++ YG LI ++T Q Q F Sbjct: 77 GILKYFVGLNSLLLQDGDRHKRQRKLLMPPFHGDRMRKYGDLIYNITSNVISQWKIEQPF 136 Query: 136 TGITVCKEISLQVILEAVYGLQDGDRA---LRQSVAKMADIFRSPLKTASLFFPWLQKDL 192 +EISL+VIL AV+GL ++ LR ++ + D SPL + LFF +L+KD Sbjct: 137 PIRKSTQEISLKVILAAVFGLDQEGKSYEKLRVLMSDLLDSMSSPLSSTFLFFNFLRKDW 196 Query: 193 GAWSPWGSFLRQRETIDQAIYEKIKERKANPDDSRQDILSLLISSKDEAGNSLTLLELRD 252 G WSPWG FLR+++ + + I +I+ K + R DILSLL+ ++DEAGN+++ E++D Sbjct: 197 GPWSPWGRFLRKKQELHELIIAEIQTAKKE-GNHRDDILSLLLEARDEAGNAMSDEEIKD 255 Query: 253 ELMALTFAGHETTAIAMSWALYWIHHLPEVKRKLLAEIASLGKATDPVTIAKLPYLNAVC 312 EL+ + FAGHETTA A++WALYWI +P V KL+AE+A++ +D V I KLPYL+A+C Sbjct: 256 ELLTMLFAGHETTASALAWALYWIDMIPSVGEKLMAELATIPSNSDQVAITKLPYLSAIC 315 Query: 313 QETLRIYPVGMLTLPRVVQEKTEVLGYELEPGQLVAGCIYLLHQREDVYPDAKQFKPERF 372 QETLRIYP+ M PRVVQ+ E++GY+LEPG + IYL H RED+YP+ K+FKPERF Sbjct: 316 QETLRIYPIAMNAFPRVVQKPIEIMGYQLEPGMVAIVPIYLTHHREDIYPEPKKFKPERF 375 Query: 373 LEREFSPYEFIPFGGGLRTCIGQAMAQFEVKLAIATILTNYDLELADNRPEFPKRLGARL 432 LER+FSPYE++PFGGG R CIG A A FE+KL +ATIL+ ++L+L N+ P R G + Sbjct: 376 LERQFSPYEYLPFGGGSRRCIGSAFALFEMKLVLATILSQWELKLLPNQRISPVRRGLTM 435 Query: 433 APDRGVQMVLKGKR 446 AP ++MV+K K+ Sbjct: 436 APPANMRMVVKPKK 449 Lambda K H 0.321 0.139 0.413 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: 568 Number of extensions: 25 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: 453 Length of database: 462 Length adjustment: 33 Effective length of query: 420 Effective length of database: 429 Effective search space: 180180 Effective search space used: 180180 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 (21.8 bits) S2: 51 (24.3 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