Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate AZOBR_RS27900 AZOBR_RS27900 FAD-binding oxidoreductase
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__azobra:AZOBR_RS27900 Length = 690 Score = 116 bits (290), Expect = 2e-30 Identities = 85/240 (35%), Positives = 113/240 (47%), Gaps = 20/240 (8%) Query: 164 SALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKR 223 SA I SF L P DG + + GQ+L + + P G +R Y+L+ P YRI+VKR Sbjct: 345 SATIRSFHLRPNDGAGLLPHLAGQHLPIRVTPAGAEKPVVRTYTLSVAPSDGAYRISVKR 404 Query: 224 EEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAK 283 E G VS LH+H VGDV++ PAG F + P L++ GVG TP+LAML + Sbjct: 405 E--GLVSRHLHDHVRVGDVIEARGPAGGFTIDARAARPAVLLAGGVGITPLLAMLRHVVY 462 Query: 284 AGHTAQ----VNWFHAAENGDVHAFADEVKELGQS------LPRFTAHTWYRQPSEADRA 333 G Q HAA + F E+ +L + L R + P EA A Sbjct: 463 EGLRTQRIRPTILVHAARSKAERPFDREITDLVTAANGDVRLVRVLS-----DPGEA--A 515 Query: 334 KG-QFDSEGLMDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 G +D+ G +D++ L FYLCGP F Q L L + IH E FGP Sbjct: 516 PGVDYDAVGRIDMALLTRILGFNDYDFYLCGPPAFTQALYDGLRGLNIADSRIHAEAFGP 575 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: 633 Number of extensions: 30 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: 690 Length adjustment: 35 Effective length of query: 361 Effective length of database: 655 Effective search space: 236455 Effective search space used: 236455 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