Align Ketoisovalerate oxidoreductase subunit VorB; VOR; 2-oxoisovalerate ferredoxin reductase subunit beta; 2-oxoisovalerate oxidoreductase beta chain; EC 1.2.7.7 (characterized)
to candidate WP_048065602.1 MA_RS16080 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000007345.1:WP_048065602.1 Length = 579 Score = 117 bits (293), Expect = 8e-31 Identities = 108/381 (28%), Positives = 170/381 (44%), Gaps = 48/381 (12%) Query: 5 MVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVY 64 ++ G A+ +GA+ +GC Y YP+TP++ IL+ + G QAE E +A+NM Sbjct: 201 LIDGVQAIGLGALMSGCKFYSAYPMTPSTGILNYLASKAEEHGLVVEQAEDEISAVNMAI 260 Query: 65 GAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQ 123 GA+ G R MT SSG G +L EG+S E P VI ++ R GP G EQAD Sbjct: 261 GASFTGVRAMTGSSGGGFALMVEGLSLAGMTETPLVIAEIQRPGPATGLPTRTEQADL-L 319 Query: 124 LVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMA------- 176 + GHG + ++ P + ++ LT AFELA+KY+ PV I +D LG Sbjct: 320 FILYAGHGEFPKVIFEPGTPKQAFYLTNRAFELAEKYQIPVFIQSDQYLGDSEWTFENFD 379 Query: 177 -EPLRFPE--------RAVEHRPDTSWAVCG------SRETMKNLVTSIFLDFDELEEFN 221 E L + + VE ++ G E K+LV + D DE +E Sbjct: 380 FEHLIYNDYRLRKKDLEGVEEYKRYKYSDTGISLLAVPGEAGKHLVVA---DSDEHDEEG 436 Query: 222 FYLQEKYAAVEENEVRYEE--------------YMVEDAEIVLVAYGISSRVAKSAVDTA 267 +++ ++ R + Y EIVLV +G + V K VD Sbjct: 437 HIIEDDETRIKMVRKRLLKKLPLIKKEIEAPLLYGDPSPEIVLVGHGSTYGVIKEVVDIL 496 Query: 268 RADGIKVGLLRPITLFPFPSERIR----ELAEGGCTFISVE-MSSGQMREDIKMASGCRD 322 D K+ ++ ++P P ER R EL E IS+E ++GQ + ++ +G Sbjct: 497 SRDR-KIAMMHFSQVYPLP-ERDRSDYIELLEKAKLTISIENNATGQFSKLVRAETGFDF 554 Query: 323 VELVNRMGGNLIELRDILRKI 343 + + G + ++ ++ Sbjct: 555 THQILKYDGRPFSIENLKEEV 575 Lambda K H 0.319 0.136 0.390 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: 429 Number of extensions: 20 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: 352 Length of database: 579 Length adjustment: 33 Effective length of query: 319 Effective length of database: 546 Effective search space: 174174 Effective search space used: 174174 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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