Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate PP_1163 PP_1163 Oxidoreductase, FAD-binding
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Putida:PP_1163 Length = 678 Score = 111 bits (277), Expect = 7e-29 Identities = 79/239 (33%), Positives = 112/239 (46%), Gaps = 5/239 (2%) Query: 155 FRIVAKTPRSALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDG 214 +R++ S I SF LEP G VA + PGQ+L V + +G IR YSL+ PD Sbjct: 332 WRVLRVEQESRDIRSFYLEPPAGCRVA-FAPGQHLPVQVPRDG-ESALIRTYSLSSAPDD 389 Query: 215 KGYRIAVKREEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPM 274 RI+VK + G S +LH GDV+ + P G F + P+ LI AGVG TP+ Sbjct: 390 GFLRISVKAQ--GPASRYLHERVVAGDVLNVRPPMGSFTLDQQSTRPLVLIGAGVGITPL 447 Query: 275 LAMLDTLAKAGHTAQVNWFHAAENGDVHAFADEVKELGQSL-PRFTAHTWYRQPSEADRA 333 LAML + G +++ FH A + F E+ L Q H QP + Sbjct: 448 LAMLRQQLRTGQARRIHLFHGARSLADLPFQQELAALRQQAGDLLQVHRALSQPEGHAQV 507 Query: 334 KGQFDSEGLMDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 ++ G + + +++ + FYLCGP F Q + L + V IH E FGP Sbjct: 508 GRDYEFAGRLGIEQVKATLALDDYDFYLCGPGSFTQQLYEGLRGVHVPDARIHAEAFGP 566 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: 651 Number of extensions: 33 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: 396 Length of database: 678 Length adjustment: 35 Effective length of query: 361 Effective length of database: 643 Effective search space: 232123 Effective search space used: 232123 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