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 AZOBR_RS02385 AZOBR_RS02385 2-oxoglutarate synthase
Query= SwissProt::P80908 (352 letters) >FitnessBrowser__azobra:AZOBR_RS02385 Length = 555 Score = 111 bits (278), Expect = 4e-29 Identities = 97/331 (29%), Positives = 147/331 (44%), Gaps = 29/331 (8%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 + GN A +GA+ G YPITPA+EIL + G K VQAE E A+I M G Sbjct: 185 ISGNEAAGLGALKGGVKFCAAYPITPATEILEWLAPNLAKTGGKLVQAEDELASIAMCLG 244 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQL 124 A+ +G +TA++GPG+SL E I +E P VIVDV R GP G EQ+D N Sbjct: 245 ASFSGVPSITATAGPGLSLMTECIGLGVASETPVVIVDVQRGGPSTGIPTKSEQSDLNIA 304 Query: 125 VKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQ----MAEPLR 180 V G HG+ ++V+ P S+ + T A LA+ + P I+L+D +GQ + +P Sbjct: 305 VY-GLHGDAPHLVVGPTSIGDCLFTTQWAVHLAEALQTPAIVLSDQAMGQSRAIVDKPAD 363 Query: 181 FPERA-------------VEHRPDTSWAVC--------GSRETMKNLV-TSIFLDFDELE 218 P +A + DT V G T L L + Sbjct: 364 APHKANRLLATDLGGEAKYKRYADTESGVSPAAIPGMPGGEHTADGLEHAENALPSSQAS 423 Query: 219 EFNFYLQEKYAAVEENEVRYEEYMVE-DAEIVLVAYGISSRVAKSAVDTARADGIKVGLL 277 + L ++ + ++ VE + EI +V +G ++ ++ AV A G K L+ Sbjct: 424 DHQKQLDKRLRKLTSHDYGDAWADVEGEGEIAVVTWGSATGPSREAVRRLEAAGTKARLV 483 Query: 278 RPITLFPFPSERIRELAEGGCTFISVEMSSG 308 + P ++ +G + VE + G Sbjct: 484 AIRLISPVQPAKLAAALDGVSKVLVVEQTHG 514 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: 456 Number of extensions: 28 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: 555 Length adjustment: 32 Effective length of query: 320 Effective length of database: 523 Effective search space: 167360 Effective search space used: 167360 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 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