Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_099019123.1 CCS90_RS08560 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P72578 (632 letters) >NCBI__GCF_002591915.1:WP_099019123.1 Length = 609 Score = 166 bits (421), Expect = 2e-45 Identities = 168/627 (26%), Positives = 272/627 (43%), Gaps = 88/627 (14%) Query: 12 GTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQKIDILVS 71 G+G +A N+F AV G + + SNI+G ++F + I++ D +V+ Sbjct: 19 GSGSASANNLFSKAVFRLGVPVSSKNVFPSNIQGLPTWFEVRINEHGYLGRRGGYDFIVA 78 Query: 72 FDAETVFQHFYDVKD--ILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYETTVKGA 129 + +T+++ + ++ Y+ + +R+ D +Q Sbjct: 79 DNGQTMYKDYQELLPGGYFFYDSS-----------------KRLPDSFNRQ--------- 112 Query: 130 LEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLDVNYLIEA 189 +V I + EI + + + KNI+ + L +D + ++ Sbjct: 113 -------DVVPIGIPLTEICNANYTDPRQ----RQIFKNIIYVGALAYLFEMDFSVFEQS 161 Query: 190 INSTF-KQDLYRKMNELAVKDSYDIVESRYNLKPSSKERRR------FWLDGNTAVAIGK 242 I S F K+ + N A+ + E +N RR ++GN A +G Sbjct: 162 IKSLFAKKAKLIEPNIKALMLGFSYAEEHHNAVCELNIHRRDLNGEQILMEGNAAAGLGA 221 Query: 243 IYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELAAINMAI 302 ++ G +YPITP++ E + D TG K +VQAEDELAAI + I Sbjct: 222 VFAGATVAGWYPITPSTSVIEAFEKYCKAYRVDQHTGKNK---FAIVQAEDELAAIGIVI 278 Query: 303 GAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTAQSDLIF 362 GA+ G RA TATSGPG SLM E LG A +E+PV++ R GPSTG+PTRT QSDLI Sbjct: 279 GASWNGARAFTATSGPGISLMSEFLGLAYFSEIPVMLMDIQRTGPSTGMPTRTQQSDLIA 338 Query: 363 PIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLA-NSYSTIPYEE 421 +A HG+ ++L + E F + +LAE+ QTPVI + + L N + P E Sbjct: 339 AAYASHGDTKNVLLFPANPKECFDMTVKGFDLAERLQTPVILMSDLDLGMNVHQCDPIE- 397 Query: 422 LELDKLKAERGKIVESGDISYKRFKFTE------DGISPRAFLG----KATMYYTGDEHN 471 D+ +RGK++ ++ K+ DGI R G K + G H+ Sbjct: 398 -WDDQQVYDRGKVLNEKQLNELPEKWGRYLDVDGDGIPYRTIPGTHPEKGAYFTRGSSHD 456 Query: 472 EEGHISEDVVNRTMMYEKRMKKLEVADKEIPE--------ESRVKIYG--DLNSRNLIIT 521 E +ED ++ + K + A K +P + V YG D +S+ + Sbjct: 457 EYAAYTEDGEVYARGMQRLLLKWDTAKKTVPAAEISGYTCQVGVIFYGTSDYSSKEAL-- 514 Query: 522 WGSPTGVLRDILEESNFDFTLLQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQ--TSL 579 +LRD + D ++I+ F PF + V+ +E D I +E N AQ T L Sbjct: 515 -----AILRD---KQTID--SMRIKAF-PFGEE-VNTFVEKHDVIFVIEQNRDAQMKTLL 562 Query: 580 LVKMYTGKDVTNSILKWNGRPFLRDEL 606 + ++ +L +G P + L Sbjct: 563 VNELAINPQKMIEVLNIDGMPITAEYL 589 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: 860 Number of extensions: 52 Number of successful extensions: 3 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: 609 Length adjustment: 37 Effective length of query: 595 Effective length of database: 572 Effective search space: 340340 Effective search space used: 340340 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 24 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