Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate BPHYT_RS25265 BPHYT_RS25265 pyridoxamine 5'-phosphate oxidase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__BFirm:BPHYT_RS25265 Length = 682 Score = 132 bits (332), Expect = 3e-35 Identities = 87/245 (35%), Positives = 119/245 (48%), Gaps = 11/245 (4%) Query: 156 RIVAKTPRSALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGK 215 ++ A +A I SF EPVDG + Y+PGQ+L + + EG R Y+L+ D + Sbjct: 336 KVAAVVEETASIRSFYFEPVDGAPLPSYKPGQFLPIRVPVEGSTTPLSRTYTLSDAHDPQ 395 Query: 216 GYRIAVKREEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPML 275 YRI+VKRE G S WLH H G ++ + P G F P ISAG+G TPM+ Sbjct: 396 RYRISVKRE--GVASKWLHEHLVAGAQIEAMKPRGAFIFDEESPRPAVFISAGIGITPMM 453 Query: 276 AMLDTLAKAGHT-----AQVNWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEA 330 AML A T +V +FH A + F+ ++KEL P + H + S A Sbjct: 454 AMLRHALAASRTEGALAKRVFFFHGARSDRERPFSAQLKELAARNPALSLHLF---DSAA 510 Query: 331 DRAKGQFDSEGLMDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECF 390 D + S G + + L+ A FYLCGP FM+ + L L V E I +E F Sbjct: 511 DGVT-EGVSAGRVSIDALKRALPFDDYDFYLCGPEQFMRDLYEGLRGLNVADERIRFEAF 569 Query: 391 GPHKV 395 GP V Sbjct: 570 GPASV 574 Lambda K H 0.318 0.135 0.404 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: 609 Number of extensions: 25 Number of successful extensions: 4 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: 396 Length of database: 682 Length adjustment: 35 Effective length of query: 361 Effective length of database: 647 Effective search space: 233567 Effective search space used: 233567 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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