Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate Synpcc7942_1367 Synpcc7942_1367 cytochrome P450
Query= metacyc::MONOMER-20332 (453 letters) >FitnessBrowser__SynE:Synpcc7942_1367 Length = 455 Score = 299 bits (765), Expect = 1e-85 Identities = 159/420 (37%), Positives = 242/420 (57%), Gaps = 6/420 (1%) Query: 20 ITDPVKYLETAVKDYPDLFLANIVG-EGGPTVFVQHPQAVQQILTGDRQNFIASGKTHLL 78 IT PV +L + Y D F ++G + P VFV P+A+ I + + Sbjct: 18 ITQPVSFLLSCADRYGDWFTLRVLGPQSPPVVFVSDPEAILAIFSSLADQLELGRIADVF 77 Query: 79 RPIIGNKSILGLDGNRHKKRRKLLLPSFHGDRIQAYGQLICDLTLQAFEQLTPNQIFTGI 138 RP++GN+S++ +G+RH+++R+LL+P+ G+R+ Y + +T A Q Q Sbjct: 78 RPLVGNESLIMQNGDRHRQQRQLLMPALQGERLFDYTPAMTAITQAAIAQWPLGQPLDLR 137 Query: 139 TVCKEISLQVILEAVYGLQDGDRA--LRQSVAKMADIFRSPLKTASLFFPWLQKDLGAWS 196 +ISL VIL+ V+GL G R L Q + ++ + PL + F+P LQ+D G WS Sbjct: 138 RQMSQISLAVILQVVFGLTPGPRYRDLYQRLDQLLEAITDPLYSLQFFWPALQQDWGNWS 197 Query: 197 PWGSFLRQRETIDQAIYEKIKERKANPDDSRQDILSLLISSKDEAGNSLTLLELRDELMA 256 PWG F RQRE ID I +I+E + + RQD+L LL++++D GN L+ ELRD+LM Sbjct: 198 PWGRFCRQREAIDALITAEIQEGRQS-QQPRQDVLELLLAARDRDGNPLSDQELRDQLMT 256 Query: 257 LTFAGHETTAIAMSWALYWIHHLPEVKRKLLAEIASLGKATDPVTIAKLPYLNAVCQETL 316 L GHETTA A++WA++W+ P+ +L +E+ ++G + IAK PYL+AVC+E L Sbjct: 257 LLLLGHETTASALTWAVFWLLRHPDCLNRLQSELVAIGD--NDRAIAKAPYLDAVCREAL 314 Query: 317 RIYPVGMLTLPRVVQEKTEVLGYELEPGQLVAGCIYLLHQREDVYPDAKQFKPERFLERE 376 R+ P+ ++ PR V + GY+ G ++ C+ H+R YP+ QF+P RFLER Sbjct: 315 RLQPIALIAQPRRVASPLSLGGYDFASGTILVPCVLTAHRRAATYPNPDQFQPNRFLERR 374 Query: 377 FSPYEFIPFGGGLRTCIGQAMAQFEVKLAIATILTNYDLELADNRPEFPKRLGARLAPDR 436 FS EF+PFGGG R+CIG A++ E+K+ +AT+L + RP P R G P + Sbjct: 375 FSNGEFLPFGGGQRSCIGMALSLIEMKMVLATLLRQCQIAEVSQRPVRPARRGITFVPSQ 434 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: 515 Number of extensions: 25 Number of successful extensions: 6 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: 455 Length adjustment: 33 Effective length of query: 420 Effective length of database: 422 Effective search space: 177240 Effective search space used: 177240 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 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