Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit alpha; OFOR1; EC 1.2.7.11 (characterized)
to candidate WP_028313342.1 G491_RS0101620 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::Q9YA13 (639 letters) >NCBI__GCF_000429905.1:WP_028313342.1 Length = 383 Score = 165 bits (417), Expect = 4e-45 Identities = 116/352 (32%), Positives = 188/352 (53%), Gaps = 18/352 (5%) Query: 239 SGEYVVASGNDVVAMGKVVGGVRYQAYYPITPASDESVLLEEFEGLKIDGESLGSIAILQ 298 +GE+ + +G+ A G + G + YPITPA++ + E + +G I Q Sbjct: 7 TGEHYM-TGDVACAEGALAAGCLFFGGYPITPATEVA------ERMSHRLPEIGGTYI-Q 58 Query: 299 TEDEIAAVSSVIGAALTGARASTATSGPGFSLMVEALGWAGKNDVPMVITYYQRGGPSTG 358 EDEIAA++S++GA+ GA++ T+TSGPGFSLM+E LG A + P V+ QR GPSTG Sbjct: 59 MEDEIAAMASIVGASCAGAKSMTSTSGPGFSLMMENLGLAVITETPCVVVNVQRAGPSTG 118 Query: 359 LPTRGSQSDLLFSLFASHGEFPRIILSSGDHLEAFYDAIEAYNLAERFQMPVIHLLDKFL 418 LPT+G+Q D++ + + SHG++ I ++ E FY I+A+NLAE+++ PV+ + D+ + Sbjct: 119 LPTQGAQGDMMQARWGSHGDYEIIAMAPASAQEIFYQTIDAFNLAEKYRTPVLIMTDEVI 178 Query: 419 ANMVASVPFPDWKAIK-IDRGKTLFKAPTGPFKRFPR-DQPLADRPVLGSGAITWYTGDE 476 +M V PD + IK I+R K K ++ + D + G G TG Sbjct: 179 GHMSERVVIPDAREIKTIERVKA--KGRKDRYRPYAAGDLGVPPMANAGDGYKVHVTGLT 236 Query: 477 NDEYGHIDEDPVNRLVMYERRWKKMEIADREIPEDFRVKYYGDEDAEVLLVGWGSVKIPA 536 +DE G+ + M ER K++ +I R + + EDA+ ++V +G Sbjct: 237 HDEMGYPAMTVEAQAAMMERLMGKIQNNRDDI---IRYEEFMIEDADYIIVTYGVSARTG 293 Query: 537 LEAIERLREMGVNAAYLHLRMLSPLPKRRVSEVLSRFDADRVIAVEANYLGQ 588 A+E R G+ L L + P + ++ ++ S+ A ++ VE N LGQ Sbjct: 294 RAAVEEARAQGIKVGMLRLITVWPFAEEKIRDLASK--AKGMVTVEIN-LGQ 342 Lambda K H 0.320 0.138 0.400 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: 533 Number of extensions: 24 Number of successful extensions: 3 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: 639 Length of database: 383 Length adjustment: 34 Effective length of query: 605 Effective length of database: 349 Effective search space: 211145 Effective search space used: 211145 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 (21.8 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