Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; OFOR2; EC 1.2.7.11 (characterized)
to candidate WP_014026810.1 PYRFU_RS06240 2-oxoglutarate ferredoxin oxidoreductase subunit alpha
Query= SwissProt::Q9YBX7 (642 letters) >NCBI__GCF_000223395.1:WP_014026810.1 Length = 397 Score = 177 bits (448), Expect = 1e-48 Identities = 119/361 (32%), Positives = 187/361 (51%), Gaps = 34/361 (9%) Query: 248 VAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLG--YDKIAVAIVQMED 305 +A+G I+ G +YPI P++D +AE L + + ++Q ED Sbjct: 31 IAIGAILAGARFFAFYPIEPATD----------------IAEALVELFPRAGGVVIQTED 74 Query: 306 ELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRAGPSTGMPT 365 E++++ A +GA+ AG +A T TSGPG SLM E +S AV E PVV+ MRAGPSTG T Sbjct: 75 EISALAAAIGASWAGVKAFTATSGPGMSLMTEHISYAVMTETPVVIIDGMRAGPSTGQAT 134 Query: 366 RTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPVIHLLDKYLASS 425 + QQD++ + + HGD I + E IKAFN AE ++ P L DK Sbjct: 135 KASQQDVMQAKWGAHGDYEIIAYSPSSAQELLEYTIKAFNAAERWRVPAFILADK----- 189 Query: 426 MVSLAREDL---DPSKVPITRGKLLDNPPAD--YRRYEVVEDGISPRARLGSATMV-ITG 479 M L E++ DPS+V K PP D ++ +E ED + P R G + +TG Sbjct: 190 MTVLLMENVKVPDPSEVVRVDRKRPRVPPGDPNFKPFEPEEDLVPPMPRFGEGYGIHVTG 249 Query: 480 LEHDEYGYA-TEDPVMREIMMFKRERKFKVIEERIPDEEKAVLHGDSEASVALVSFGSTK 538 + H+E G A ++DP++ ++ + K + ++I + E + GD + +V++G Sbjct: 250 VTHNELGVAVSDDPIVHHQLVKRLCDKIRKNRDKIVEYE---VFGDENPTHVIVAYGFVA 306 Query: 539 QPILEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQNLLGQLAMLLRA 598 + A+ MLR++GV+A + L+PFPG + EK+++ E N GQ+ L+ Sbjct: 307 RAARRAVRMLREKGVKAALFRPITLWPFPGPELARFARNAEKILVAEMN-YGQVVHLVAE 365 Query: 599 H 599 H Sbjct: 366 H 366 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: 613 Number of extensions: 25 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: 397 Length adjustment: 34 Effective length of query: 608 Effective length of database: 363 Effective search space: 220704 Effective search space used: 220704 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 10 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