Align 2-oxoacid oxidoreductase (ferredoxin) (subunit 1/2) (EC 1.2.7.11) (characterized)
to candidate 8499839 DvMF_0604 2-oxoglutarate ferredoxin oxidoreductase subunit beta (RefSeq)
Query= BRENDA::Q4J6I8 (303 letters) >FitnessBrowser__Miya:8499839 Length = 277 Score = 165 bits (417), Expect = 1e-45 Identities = 97/267 (36%), Positives = 144/267 (53%), Gaps = 34/267 (12%) Query: 10 WCPGCGNFGILRAEEMAIQELGVDFKKVVLVSGIGCSGKMPHFVNLPVGGVHTLHGRALA 69 +C GCG+ +L + ++ LG+ VVLV+GIGCSG+M +V+ VHT HGRAL Sbjct: 22 FCAGCGHGIVLGSLIRSVHALGLPKDDVVLVAGIGCSGRMAVYVDFNT--VHTTHGRALT 79 Query: 70 FATGIKLANPSLEVIVNVGDGDGLGIGMGHFVHLGRRNIDITLIVHDNGVYGLTKGQAAP 129 FATGIK+ANP L+VI +GDGD L IG H +H RRNI +T ++ +N +YG+T GQ + Sbjct: 80 FATGIKMANPKLKVICVMGDGDALSIGGNHLIHAARRNIGVTALILNNQIYGMTGGQCSS 139 Query: 130 TLERGIKTKSLPKPNINDAVNPLAVALSAGYTFIARAYAYDVIHLKEVIKRAIKHKGSAI 189 +G + + P ++ A + + +AG +++AR ++ I L +I AI H G ++ Sbjct: 140 ATPQGDISMTTPFGSLEKAFDIADMCKAAGASYVARGTSFHAIQLDRLISSAIMHPGFSV 199 Query: 190 IDVFQPCPTY--------NDINTKEWYDKRVYKLD--KDPTWDPVVRKEEEKQSKFEKAL 239 ++VF PCPT N ++ +W K++ KDP P Sbjct: 200 VEVFSPCPTQYGRKNKFRNAVDMYKWLKSNTVKVETLKDPDQKPA--------------- 244 Query: 240 LKSMEFGEKIPIGVFYENELVPTFEER 266 +IPIGVF + E P EER Sbjct: 245 ------DGRIPIGVFRDVE-EPGLEER 264 Lambda K H 0.320 0.140 0.423 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: 211 Number of extensions: 8 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: 303 Length of database: 277 Length adjustment: 26 Effective length of query: 277 Effective length of database: 251 Effective search space: 69527 Effective search space used: 69527 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: 48 (23.1 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