Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_083763501.1 AMB_RS10840 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P72578 (632 letters) >NCBI__GCF_000009985.1:WP_083763501.1 Length = 565 Score = 199 bits (507), Expect = 2e-55 Identities = 167/583 (28%), Positives = 272/583 (46%), Gaps = 75/583 (12%) Query: 9 GAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQKIDI 68 G+ G G+ TAAN+F +A A AGYY R I+GG + + + + + S DI Sbjct: 3 GSGGAGVMTAANMFLDAAAEAGYYALFGRSSGPQIRGGEAAALVRLGVEPITSVDDTFDI 62 Query: 69 LVSFDAETVFQHFYDVKDILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYETTVKG 128 +++ D + V Q F A +++ +P + + D K G + Sbjct: 63 MLAIDWQGV-QRF----------AAELPLSKNSIVICDPSAGD-VPDVYVKTGAK----- 105 Query: 129 ALEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLDVNYLIE 188 ++ ++ ++AK++ N++ + +L+G+ V L E Sbjct: 106 -----------IVHLHMKDLAKEIPGGRP----------NMIALGAVAELIGIPVGPLTE 144 Query: 189 AINSTFKQ---DLYRKMNELAVKDSYDIVESRYNLK----PSSKERRRFWLDGNTAVAIG 241 + + K+ D Y + + VK + K +K+ +R+ + GN +G Sbjct: 145 VLGKSLKKKRADAY-EASVAGVKAGAAAAATLGGAKRLAAAKAKDAKRWTVTGNYGAGLG 203 Query: 242 KIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELAAINMA 301 I GGVRF + YPITPA++ Y+ + P G V VQAEDELA+INM Sbjct: 204 AIRGGVRFCAAYPITPATEVLEYLASAL------PKVGG------VFVQAEDELASINMC 251 Query: 302 IGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTAQSDLI 361 +GA+ G + T+T+GPG SLM EGLG A +E PVV+ R GPSTG+ T+ QSDL Sbjct: 252 LGASYGGEASITSTAGPGLSLMTEGLGLAVASETPVVVVDVQRVGPSTGIATKCEQSDLN 311 Query: 362 FPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLANSYSTIPYEE 421 ++ HG+ P +V+A + W + LAE QT + + ++ L S + I + Sbjct: 312 IAVYGLHGDAPHLVVAPNSVGDCIFTTQWGVYLAESLQTACLVMSDQALGQSRAII---D 368 Query: 422 LELDKLKAERGKIVES---GDISYKRFKFTEDGISPRAFLGKATMYYTGD--EHNEEGHI 476 D + + E+ G++ +KR+ T GISP G+ YT D EH E G Sbjct: 369 APADVAFVGKRLVAEAPAEGEV-FKRYANTASGISPMPVPGQPGCQYTSDGLEHTETGTP 427 Query: 477 SEDVVNRTMMYEKRMKKLEVADKEIPEESRVKIYGDLNSRNLIITWGSPTGVLRDILEES 536 S + T+ +KR +KL D + ++ GD+ +ITWGS TG R+ + + Sbjct: 428 SSQSSDHTLQLDKRQRKLTNFDYG-NHWATIEGEGDI----AVITWGSCTGAAREAVARA 482 Query: 537 NFD---FTLLQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQ 576 D L+ +R+ SP ++ ++G KI+ VE ++ Q Sbjct: 483 KADGINAKLISLRLISPIRPQHLADALKGVSKILVVEQSHQGQ 525 Lambda K H 0.316 0.135 0.382 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: 748 Number of extensions: 32 Number of successful extensions: 7 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: 632 Length of database: 565 Length adjustment: 37 Effective length of query: 595 Effective length of database: 528 Effective search space: 314160 Effective search space used: 314160 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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