Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit beta; OFOR2; EC 1.2.7.11 (characterized)
to candidate AZOBR_RS02380 AZOBR_RS02380 2-oxoglutarate synthase
Query= SwissProt::Q9YBX8 (309 letters) >FitnessBrowser__azobra:AZOBR_RS02380 Length = 276 Score = 188 bits (477), Expect = 1e-52 Identities = 94/222 (42%), Positives = 136/222 (61%), Gaps = 3/222 (1%) Query: 7 DYKTQAWVQWCPGCGDFGILNSIYRAVSELGIDPENLAVVGGIGCSGRTTYYVKGSNFHA 66 DYK+ WCPGCGD+ +L I RA++ +G++ + VV GIGCS R Y +H Sbjct: 12 DYKSDVKPIWCPGCGDYSVLAGITRAMATMGLERHDTVVVSGIGCSSRIPAYTSVYGYHT 71 Query: 67 LHGRAIPVATGVKLANPHLNVIVAGGDGDLMGIGGGHFVALGRRNLNITVLLFDNAVYGL 126 +HGR++ VA+GVKLA P LNV++ GGDGD IGG HF+ RRN+++T ++ DN VYG+ Sbjct: 72 VHGRSLAVASGVKLARPELNVLIFGGDGDGFSIGGNHFLHACRRNVDMTYIVMDNQVYGM 131 Query: 127 TKGQAAPTLPA-WVKTKALSMPNIHDNINPVLLAFAAGYTFIARGYAYHTQQLKELIKTA 185 TKGQA+PT A W ++K + I PV LA A G F+ARG++ + ++ LI Sbjct: 132 TKGQASPTTEADWCESKLTPEGPGVNPIQPVALALACGANFVARGFSNNPNEVARLIVEG 191 Query: 186 VRHRGAALVDILQPCPTYNNIMTNKWYEERIYYVDQEEGYDP 227 VRH G +++ IL PC T+ N ++ ++ +E DP Sbjct: 192 VRHPGFSVIHILSPCVTFRPEQRN--WKSTVHPYGREPTDDP 231 Lambda K H 0.322 0.140 0.441 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: 245 Number of extensions: 7 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: 309 Length of database: 276 Length adjustment: 26 Effective length of query: 283 Effective length of database: 250 Effective search space: 70750 Effective search space used: 70750 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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