Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_034267069.1 AMYHA_RS01155 2-oxoacid:ferredoxin oxidoreductase subunit beta
Query= SwissProt::P72579 (305 letters) >NCBI__GCF_000504245.1:WP_034267069.1 Length = 355 Score = 185 bits (469), Expect = 2e-51 Identities = 97/225 (43%), Positives = 140/225 (62%), Gaps = 10/225 (4%) Query: 11 WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70 WCPGCG++ +LN Q + LG+ +N+V VSGIGCS + P++ T G+H++HGRA A Sbjct: 39 WCPGCGDYIVLNTMQSFLPTLGLKPENIVFVSGIGCSSRFPYYMNT--YGMHSIHGRAPA 96 Query: 71 FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130 ATG+ S PDL V V GDGD L IG H + A RRNV+ ++L +N +YGLTKGQ SP Sbjct: 97 IATGLATSRPDLSVWVITGDGDALSIGGNHLIHALRRNVNFKILLFNNRIYGLTKGQYSP 156 Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190 T + G + KS P +++ NPI+LA+ + +FV R D K L E++ +A +H+G A Sbjct: 157 TSQEGMRTKSTPMGSLDHPFNPISLALGAEASFVGRALDSDKKGLTEVLTAAAQHRGSAF 216 Query: 191 IDVLQPCPTYND-----INTKEWYDKRIYKLDTLPDWDPVVKKPE 230 +++ Q CP +ND + K+ +RI L PD +P+ PE Sbjct: 217 VEIYQNCPIFNDGAFDVLKDKDEAARRIIPL--RPD-EPITFGPE 258 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: 276 Number of extensions: 14 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: 355 Length adjustment: 28 Effective length of query: 277 Effective length of database: 327 Effective search space: 90579 Effective search space used: 90579 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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