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_013259642.1 DEBA_RS14200 2-oxoglutarate ferredoxin oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000143965.1:WP_013259642.1 Length = 378 Score = 203 bits (516), Expect = 7e-57 Identities = 135/374 (36%), Positives = 201/374 (53%), Gaps = 36/374 (9%) Query: 4 QMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMV 63 ++++GN A+ GA+ AGC + GYPITPASEI R P G F+Q E E A++ Sbjct: 7 ELLQGNEAIARGALAAGCRFFAGYPITPASEISEILGRRLPARGAAFIQMEDEIASLGAC 66 Query: 64 YGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYN 122 GA+ AG + MTA+SGPG SL QE + + E P V+V+VMRAGP G P Q D Sbjct: 67 IGASLAGAKAMTATSGPGFSLMQENLGWACITETPLVLVNVMRAGPSTGMPTNPAQGDVQ 126 Query: 123 QLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFP 182 Q + G HG++ IVL P SV + +LT+ AF LA++ R PVI+LAD V+ + E + P Sbjct: 127 Q-ARWGTHGDHPAIVLCPASVAQCFELTVRAFNLAERLRTPVIVLADEVVAHLREKVSLP 185 Query: 183 E----RAVEHRPDT---SWAV------------CGSRETMKNLVTSIFLDF--------D 215 +E R + W V + + VT + D D Sbjct: 186 AEDELEIIERRKPSVPPDWYVPFKTDGGLIPHLADLGDGYRYHVTGLVHDERGFPTRRPD 245 Query: 216 ELEEFNFYLQEKYAAVEENEVRYEEYM---VEDAEIVLVAYGISSRVAKSAVDTARADGI 272 E+E F + + + N E+ + ++DAE+VL+AYG ++R A++AV ARA G+ Sbjct: 246 EVEPF---FRRLFGKIRRNFGELEQVLPMALDDAEVVLIAYGCTARAAQAAVRQARAAGM 302 Query: 273 KVGLLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDIK-MASGCRDVELVNRMGG 331 K+GLL+ + L+PFP + + G + E++ GQ+ ++K +A+G V RM G Sbjct: 303 KLGLLQIVGLWPFPRRAVEKAVLGRRAVLVPELNMGQLSREVKRVAAGRARVVHHGRMDG 362 Query: 332 NLIELRDILRKIRE 345 +I +IL +IRE Sbjct: 363 QVITPDEILNRIRE 376 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: 326 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 352 Length of database: 378 Length adjustment: 30 Effective length of query: 322 Effective length of database: 348 Effective search space: 112056 Effective search space used: 112056 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: 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