Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; OFOR2; EC 1.2.7.11 (characterized)
to candidate WP_015947475.1 G491_RS0115625 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::Q9YBX7 (642 letters) >NCBI__GCF_000429905.1:WP_015947475.1 Length = 382 Score = 172 bits (436), Expect = 2e-47 Identities = 116/346 (33%), Positives = 176/346 (50%), Gaps = 21/346 (6%) Query: 244 GNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGYDKIAVAIVQM 303 GN+ G + G+ YPITPSS+ I +A +L +QM Sbjct: 10 GNEACMEGALYAGVQFYAGYPITPSSE------------ITEGMAMRL--PATGGKFIQM 55 Query: 304 EDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRAGPSTGM 363 EDE++SI A++GA+ G + T TSGPGFSLM E + A+ AEIP V+ MR GPSTG+ Sbjct: 56 EDEISSICAIVGASLTGHKVMTATSGPGFSLMQEGLGYAIMAEIPCVIVNVMRGGPSTGL 115 Query: 364 PTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPVIHLLDKYLA 423 PT Q D++ + + HGD + L + H + F ++AFN AE ++TPVI LLD+ + Sbjct: 116 PTHGSQGDVMQARWGVHGDHSIVALTASSHQDVFEMTVEAFNIAETYRTPVILLLDETVG 175 Query: 424 SSMVSLAREDLDPSKVP-ITRGKLLDNPPADYRRYEVVEDGISPRARLGSATMV-ITGLE 481 L E +P ++P + R + +Y Y EDG P + G +TGL Sbjct: 176 HMREKL--EIPEPGELPLVERLRTSVREGVNYHPYLPREDGRLPMSDFGDVHRYNVTGLY 233 Query: 482 HDEYGYATEDPVMREIMMFKRERKFKVIEERIPDEEKAVLHGDSEASVALVSFGSTKQPI 541 HD +G+ T DP M ++ IE R+ + + +A LVS+G + + Sbjct: 234 HDMWGFPTADPKMVHDLI---RHLIDKIENRVNVLARYKEYYLDDAERVLVSYGCSARSA 290 Query: 542 LEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQN 587 L ++ R G R +++ L+PFP +V+ +G + VI+VE N Sbjct: 291 LHVVKDRRLRGERLGLLELQTLWPFPADVVKHCCDGKKSVIVVEMN 336 Lambda K H 0.318 0.135 0.380 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: 562 Number of extensions: 31 Number of successful extensions: 4 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: 642 Length of database: 382 Length adjustment: 34 Effective length of query: 608 Effective length of database: 348 Effective search space: 211584 Effective search space used: 211584 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: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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