Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate 8499412 DvMF_0185 pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit (RefSeq)
Query= SwissProt::P72579 (305 letters) >FitnessBrowser__Miya:8499412 Length = 283 Score = 212 bits (539), Expect = 9e-60 Identities = 114/279 (40%), Positives = 165/279 (59%), Gaps = 18/279 (6%) Query: 11 WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70 WCPGCGN ++ A +QA+ L + V VSGIG + K PH+ ++G + LHGR + Sbjct: 14 WCPGCGNHDVMKAVRQALAGLDLAPNRVAHVSGIGQAAKAPHYI--DLNGFNGLHGRGLP 71 Query: 71 FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130 A IKL NP+L VI GDG G G HF+AA RRNVDM +++HDN +YGLTKGQASP Sbjct: 72 PAQAIKLCNPELTVIAQSGDGCNYGEGGNHFLAAIRRNVDMTLLVHDNQIYGLTKGQASP 131 Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190 T G+ KS P N NPIA+A++ +FVAR ++ + HL ++I+ AI+HKG AL Sbjct: 132 TTPEGQITKSQPDGVRNAPFNPIAVAVAMKCSFVARSFSGNTPHLVKMIQLAIQHKGFAL 191 Query: 191 IDVLQPCPTYNDINTKEWYDKRIYKLDTLPDWDPVVKKPEEVNEKIKRAIDKSLEWGDRI 250 +D+ PC ++N +NT WY +R +L D+DP A+ + E+G+RI Sbjct: 192 VDLFSPCVSFNKVNTFGWYKQRCQELP--EDYDPT---------DWAAAMQVAQEFGERI 240 Query: 251 PIGIFYQNELVPSYEERIKANSPAYLDYTPAKQLIEKEG 289 PIG+ Y+N+ + A+ P +Q ++++G Sbjct: 241 PIGVIYRND-----RPSLDASLPVLQKGPLGRQPVDRDG 274 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: 245 Number of extensions: 16 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: 283 Length adjustment: 26 Effective length of query: 279 Effective length of database: 257 Effective search space: 71703 Effective search space used: 71703 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