Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; OFOR2; EC 1.2.7.11 (characterized)
to candidate 8499838 DvMF_0603 2-oxoglutarate ferredoxin oxidoreductase subunit alpha (RefSeq)
Query= SwissProt::Q9YBX7 (642 letters) >FitnessBrowser__Miya:8499838 Length = 382 Score = 191 bits (484), Expect = 7e-53 Identities = 126/394 (31%), Positives = 203/394 (51%), Gaps = 21/394 (5%) Query: 234 RRGQTMMVATGNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGY 293 +R + + A GN+ VA G ++ G YPITPS++ + + DG Sbjct: 7 KRKRRELFALGNEAVAEGALLAGCSFYAGYPITPSTEIMEVMANRLPLIEDG-------- 58 Query: 294 DKIAVAIVQMEDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTL 353 +QMEDE+AS+ A +GA+ AG +A T TSGPGF+LM E + A E P+VV Sbjct: 59 -----VFIQMEDEIASMGATIGASLAGRKAMTATSGPGFALMQEHIGYACMVEAPLVVVN 113 Query: 354 WMRAGPSTGMPTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTP 413 MR GPSTG+PT Q D+ + + HGD P IVL++ + E + AFN+AE+++TP Sbjct: 114 VMRGGPSTGLPTSPAQADVQMARWGTHGDHPIIVLSASNVQECLEMTVTAFNFAEKYRTP 173 Query: 414 VIHLLDKYLASSMVSLAREDLDPSKVPITRGKLLDNPPADYRRYEVVEDGISPRARLGSA 473 VI LLD+ A + + DP +V I PP ++ Y G+ A +GS Sbjct: 174 VILLLDEVTAHTREKITVP--DPDEVEILSRVEPTVPPEWFKPYADTARGVPAMAPIGSG 231 Query: 474 TMV-ITGLEHDEYGYATEDP-VMREIMMFKRERKFKVIEERIPDEEKAVLHGDSEASVAL 531 +TGL HD GY T+ P +++ M+ R F+ I++ D + + + +A VA+ Sbjct: 232 YRTHVTGLTHDVMGYPTQRPDEVKDAML----RLFRKIDQYYGDIQMSDEYMLDDAEVAV 287 Query: 532 VSFGSTKQPILEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQNLLGQ 591 V++GS + A+E R+ G +A ++ L+PFP VE++ V++ E N+ Sbjct: 288 VAYGSVARSAHLAVEQARERGAKAGLLTLKTLFPFPRPAVEKLTHRCHTVVVPEMNMGQM 347 Query: 592 LAMLLRAHTSIKPDSSIVKINGRPLYSFEVAGAV 625 + R + +I +++G+ + E+ A+ Sbjct: 348 SREVKRVNNGRTKVRTINRVDGQIITPSEILKAI 381 Lambda K H 0.318 0.135 0.380 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: 522 Number of extensions: 29 Number of successful extensions: 4 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: 642 Length of database: 382 Length adjustment: 34 Effective length of query: 608 Effective length of database: 348 Effective search space: 211584 Effective search space used: 211584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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