Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate AZOBR_RS02380 AZOBR_RS02380 2-oxoglutarate synthase
Query= SwissProt::P72579 (305 letters) >FitnessBrowser__azobra:AZOBR_RS02380 Length = 276 Score = 181 bits (460), Expect = 1e-50 Identities = 101/269 (37%), Positives = 152/269 (56%), Gaps = 20/269 (7%) Query: 11 WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70 WCPGCG++ +L +A+ +G++ + VVVSGIGCS +IP + T + G HT+HGR++A Sbjct: 21 WCPGCGDYSVLAGITRAMATMGLERHDTVVVSGIGCSSRIPAY--TSVYGYHTVHGRSLA 78 Query: 71 FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130 A+G+KL+ P+L V++ GGDGD IG HF+ A RRNVDM I+ DN VYG+TKGQASP Sbjct: 79 VASGVKLARPELNVLIFGGDGDGFSIGGNHFLHACRRNVDMTYIVMDNQVYGMTKGQASP 138 Query: 131 TLKRG--EKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGL 188 T + E + P +N + P+ALA++ G FVARG++ + + LI ++H G Sbjct: 139 TTEADWCESKLTPEGPGVN-PIQPVALALACGANFVARGFSNNPNEVARLIVEGVRHPGF 197 Query: 189 ALIDVLQPCPTYNDINTKEWYDKRIYKLDTLPDWDPVVKKPEEVNEKIKRAIDKSLEWGD 248 ++I +L PC T+ + W ++ P DP NE ++ ++ D Sbjct: 198 SVIHILSPCVTFRP-EQRNW-KSTVHPYGREPTDDP--------NEAMRAVLE-----DD 242 Query: 249 RIPIGIFYQNELVPSYEERIKANSPAYLD 277 +GIF P E S A ++ Sbjct: 243 GFGLGIFLAGNRRPFQPESAATRSIAQIE 271 Lambda K H 0.318 0.139 0.424 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: 243 Number of extensions: 14 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: 305 Length of database: 276 Length adjustment: 26 Effective length of query: 279 Effective length of database: 250 Effective search space: 69750 Effective search space used: 69750 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: 48 (23.1 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