Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate WP_011610070.1 TERY_RS00790 cytochrome P450
Query= metacyc::MONOMER-20332 (453 letters) >NCBI__GCF_000014265.1:WP_011610070.1 Length = 457 Score = 410 bits (1054), Expect = e-119 Identities = 201/443 (45%), Positives = 287/443 (64%), Gaps = 5/443 (1%) Query: 5 LPKLKKHPIEQGFTWITDPVKYLETAVKDYPDLFLANIVGEGGPTVFVQHPQAVQQILTG 64 LP K + Q W P+K++E ++Y D F + P VF+ HP+A+++I Sbjct: 4 LPGPKSPALTQILQWTAKPIKFMEKCAREYGDTFEVKL---NYPIVFISHPKAIEEIFKA 60 Query: 65 DRQNFIASGKTHLLRPIIGNKSILGLDGNRHKKRRKLLLPSFHGDRIQAYGQLICDLTLQ 124 + + F L +P++G+ S+L LD H+++RKLL+P FHG R+QAYG+LIC++ + Sbjct: 61 NPKKFDCGSSNKLAQPLLGDYSLLLLDDIPHQRQRKLLMPPFHGKRMQAYGELICNVAQE 120 Query: 125 AFEQLTPNQIFTGITVCKEISLQVILEAVYGLQDGDR--ALRQSVAKMADIFRSPLKTAS 182 + Q+F+ EISL+VIL+AV+GL +G+R L + + + + SPLKT+ Sbjct: 121 VASKWEIGQVFSMREFTAEISLKVILQAVFGLYEGERYSKLEKLLGSLLESLSSPLKTSM 180 Query: 183 LFFPWLQKDLGAWSPWGSFLRQRETIDQAIYEKIKERKANPDDSRQDILSLLISSKDEAG 242 LFF +LQ DLG WSPWG+F++ RE I + + +I ER+ D R DIL++L+ ++DE G Sbjct: 181 LFFQFLQIDLGPWSPWGNFIKNREEIYELLCAEISERRQKLDPERSDILTMLLLARDEEG 240 Query: 243 NSLTLLELRDELMALTFAGHETTAIAMSWALYWIHHLPEVKRKLLAEIASLGKATDPVTI 302 ++ +ELRDELM L AGHETTA ++SWA YWIHH PE+ +KL E+ + G +P+T+ Sbjct: 241 EGMSDIELRDELMTLLIAGHETTATSLSWAFYWIHHQPEIYQKLSRELETFGDDLNPMTV 300 Query: 303 AKLPYLNAVCQETLRIYPVGMLTLPRVVQEKTEVLGYELEPGQLVAGCIYLLHQREDVYP 362 LPY+NAVC ETLRIYPV ++ PR + ++G G + CIYL H RED+YP Sbjct: 301 INLPYMNAVCSETLRIYPVVIIVSPRKTKLPITIMGQTYPAGTALTPCIYLTHHREDLYP 360 Query: 363 DAKQFKPERFLEREFSPYEFIPFGGGLRTCIGQAMAQFEVKLAIATILTNYDLELADNRP 422 + K+FKPERFLER++S YEF+PFGGG R CIG A A FE+K+ +ATIL Y L LA+ + Sbjct: 361 EPKKFKPERFLERQYSSYEFLPFGGGNRRCIGAAFAMFEMKIVLATILRRYSLALAEKQE 420 Query: 423 EFPKRLGARLAPDRGVQMVLKGK 445 P R G LAP GV+MV+ GK Sbjct: 421 VKPLRRGLTLAPAGGVKMVMTGK 443 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: 562 Number of extensions: 30 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: 457 Length adjustment: 33 Effective length of query: 420 Effective length of database: 424 Effective search space: 178080 Effective search space used: 178080 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