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_010876664.1 MTH_RS04890 2-oxoglutarate ferredoxin oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000008645.1:WP_010876664.1 Length = 378 Score = 195 bits (495), Expect = 2e-54 Identities = 126/367 (34%), Positives = 192/367 (52%), Gaps = 31/367 (8%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 ++GN A GA+ AGC + GYPITP++EI E + P G FVQ E E A+ V G Sbjct: 9 IQGNDACARGAIKAGCRFFAGYPITPSTEIAEEMALLLPREGGVFVQMEDEIGALGAVIG 68 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125 A +G R MTA+SGPG SL QE + + A E P VIV+V R P G P A + ++ Sbjct: 69 AVWSGVRGMTATSGPGFSLMQEHVGYAAMTETPLVIVNVQRGSPSTGQ--PTMASQSDMM 126 Query: 126 KG--GGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPE 183 + G HG+Y I L+P+SVQE D T+ AF LA++YR PV+++ D ++G M E + P+ Sbjct: 127 QARWGSHGDYEIIALSPSSVQECFDFTVRAFNLAEEYRVPVMVMGDEIVGHMREKITIPD 186 Query: 184 RAVEHR-------PDTSWAVCGSRETMKNL----------VTSI------FLDFDELEEF 220 R + P+ + + + VT + + D E Sbjct: 187 RVKIRKRRGPSVPPEEFLPFSAPEDGVPEMPAFGDGYRIPVTGLTHDEGGYPDASNPEGH 246 Query: 221 NFYLQ---EKYAAVEENEVRYEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLL 277 + ++ +K + +E + EDA I +++YG SR +AV AR DG++ G L Sbjct: 247 HRLVKRLCDKILRHRDRISDVQEELTEDAYITVISYGAPSRSVATAVKMAREDGVRAGYL 306 Query: 278 RPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDI-KMASGCRDVELVNRMGGNLIEL 336 + T +PFP +R AE + VEM+ GQM ++ ++A+G +VEL+ ++GG + Sbjct: 307 KINTPWPFPETEVRAAAERSGKLLVVEMNLGQMFYEVQRVAAGMAEVELLPKIGGEIHRP 366 Query: 337 RDILRKI 343 +IL I Sbjct: 367 EEILNMI 373 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: 340 Number of extensions: 19 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