Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate BPHYT_RS05425 BPHYT_RS05425 oxidoreductase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__BFirm:BPHYT_RS05425 Length = 700 Score = 171 bits (433), Expect = 6e-47 Identities = 99/247 (40%), Positives = 135/247 (54%), Gaps = 4/247 (1%) Query: 153 RDFRIVAKTPRSALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKP 212 R F+++ SA I SF LEP DG + Y+ GQYL + L+P G+ IR Y+L+ Sbjct: 344 RPFKVLETIDESATIRSFILEPADGSGLVGYQAGQYLPIRLQPPGWAEPTIRTYTLSDAS 403 Query: 213 DGKGYRIAVKREEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQT 272 +G+ YRI+VKRE G S++LH+H VGD ++ +AP G F A P+ LISAGVG T Sbjct: 404 NGRTYRISVKREGKGGCSDFLHDHIVVGDTIETLAPRGAFVFDEAAGRPLALISAGVGIT 463 Query: 273 PMLAMLDT-LAKAGHT---AQVNWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPS 328 P++AML++ L G T + H+A N AFA + + G+ T H + +PS Sbjct: 464 PLIAMLNSQLVNDGRTLLHKPIYCIHSATNSKHRAFAAHLAKKGELHANLTLHVAFSRPS 523 Query: 329 EADRAKGQFDSEGLMDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYE 388 E D SEG +D + L + YLCGP GFMQ L+ LGV+ IH E Sbjct: 524 EDDVLGKTHQSEGYIDRALLRRVLPLDDYEVYLCGPPGFMQSVYDALLSLGVRDSRIHLE 583 Query: 389 CFGPHKV 395 FGP V Sbjct: 584 SFGPASV 590 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: 644 Number of extensions: 34 Number of successful extensions: 2 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: 700 Length adjustment: 35 Effective length of query: 361 Effective length of database: 665 Effective search space: 240065 Effective search space used: 240065 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