Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate WP_036368955.1 MVAN_RS05250 cytochrome P450
Query= metacyc::MONOMER-20332 (453 letters) >NCBI__GCF_000015305.1:WP_036368955.1 Length = 443 Score = 191 bits (485), Expect = 4e-53 Identities = 130/415 (31%), Positives = 205/415 (49%), Gaps = 26/415 (6%) Query: 43 VGEGGPTVFVQHPQAVQQILTGDRQNFIASGKTHLLRPIIGNKSILGLDGNRHKKRRKLL 102 V G V++ P ++ + GD + A +L+ ++G+ S+L +DG+ H+ RR+L+ Sbjct: 44 VASMGTLVYLTDPADIKTVFAGDPDIYHAGEANSMLKGLLGDTSVLVIDGDLHRDRRRLM 103 Query: 103 LPSFHGDRIQAYGQLICDLTLQAFEQLTPNQIFTGITVCKEISLQVILEAVYGLQDGDR- 161 L F D + A +I ++ + F EI+L+VIL V G D R Sbjct: 104 LAPFARDAVAAQAGVIAEIAADNIAGWPVGETFPVAPKMSEITLEVILRTVIGASDQARL 163 Query: 162 -ALRQSVAKMADIFRSPLKTASLFFPWLQKDLGAWSPWGSFLRQRETIDQAIYEKIKERK 220 ALR + ++ + P +T ++ +DL PW + D+ +Y +I +R+ Sbjct: 164 AALRTVMPRVLSV--GPWETLAI----ANQDLLRRRPWRAVRDAIAEADRLLYAEIADRR 217 Query: 221 ANPD-DSRQDILSLLISSKDEAGNSLTLLELRDELMALTFAGHETTAIAMSWALYWIHHL 279 A+PD D+R D L++L+ + D + ELRD+L+ L AGH+TTA A+SWAL Sbjct: 218 ADPDLDTRTDALAMLVRAGDMSDK-----ELRDQLITLLVAGHDTTATALSWAL------ 266 Query: 280 PEVKRKLLAEIASLGKATDPVTIAKLPYLNAVCQETLRIYPVGMLTLPRVVQEKTEVLGY 339 +L A L KA YL+AV +ETLR PV + + RV++ E+ GY Sbjct: 267 ----ERLTRHPAVLAKAVRAARDGDDDYLDAVAKETLRDRPV-VFDVGRVLKAPVELAGY 321 Query: 340 ELEPGQLVAGCIYLLHQREDVYPDAKQFKPERFLEREFSPYEFIPFGGGLRTCIGQAMAQ 399 L G +V + +H +YP A +F P+R L SP ++PFGGG R C+G A Sbjct: 322 RLPAGVMVIPGLVAVHADSQIYPHADRFDPDRMLGATLSPSSYLPFGGGNRRCLGATFAM 381 Query: 400 FEVKLAIATILTNYDLELADNRPEFPKRLGARLAPDRGVQMVLKGKRGALA-SPK 453 E K+ + IL +LE R E + P RG ++ ++ KR A +PK Sbjct: 382 VEFKVVLREILRRVELETTTARGEHRRLKHVIFVPHRGARIRVRAKRVVAAEAPK 436 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: 454 Number of extensions: 29 Number of successful extensions: 5 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: 443 Length adjustment: 33 Effective length of query: 420 Effective length of database: 410 Effective search space: 172200 Effective search space used: 172200 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