Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate 352364 BT2837 2-oxoglutarate synthase subunit korB (NCBI ptt file)
Query= SwissProt::P72579 (305 letters) >FitnessBrowser__Btheta:352364 Length = 336 Score = 185 bits (469), Expect = 1e-51 Identities = 97/212 (45%), Positives = 131/212 (61%), Gaps = 7/212 (3%) Query: 11 WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70 WCPGCG+ LN+ +A+ ELGV N+ V+SGIGCS ++P++ T G HT+HGRA A Sbjct: 18 WCPGCGDHAFLNSLHKAMAELGVAPHNIAVISGIGCSSRLPYYVNT--YGFHTIHGRAAA 75 Query: 71 FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130 ATG K++NPDL + GDGD L IG HF+ A RRN+D+ +IL +N +YGLTKGQ SP Sbjct: 76 VATGAKVANPDLTIWQISGDGDGLAIGGNHFIHAVRRNIDLNMILLNNRIYGLTKGQYSP 135 Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190 T +RG KS P + D +P LA + F AR A D E++K+A HKG ++ Sbjct: 136 TSERGFVSKSSPYGTVEDPFHPAELAFGARGRFFARCIAVDGAASVEVLKAAANHKGASV 195 Query: 191 IDVLQPCPTYND-----INTKEWYDKRIYKLD 217 ++VLQ C +ND + TKE K L+ Sbjct: 196 VEVLQNCVIFNDGTHASVATKEGRAKNAIYLE 227 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: 8 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: 305 Length of database: 336 Length adjustment: 28 Effective length of query: 277 Effective length of database: 308 Effective search space: 85316 Effective search space used: 85316 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