Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_012965796.1 FERP_RS06455 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P72578 (632 letters) >NCBI__GCF_000025505.1:WP_012965796.1 Length = 528 Score = 249 bits (637), Expect = 2e-70 Identities = 199/608 (32%), Positives = 288/608 (47%), Gaps = 96/608 (15%) Query: 9 GAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQKIDI 68 GA G GI A + + GY + +EY S I+GGH+ + S++++RS+ D+ Sbjct: 10 GAAGDGIKEAGVLAAKLFSKLGYNAFVYQEYQSLIRGGHNASVVRFSERKIRSHRYYYDV 69 Query: 69 LVSFDAETVFQHFYDVKDILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYETTVKG 128 L+ + + YD R KD L KG Sbjct: 70 LICLE-----DYVYD----------------------------RHKDRL---------KG 87 Query: 129 ALEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLDVNYLIE 188 L + SK N+ V E K E + PL +N V + + + G+D E Sbjct: 88 ILIHDSKFNLDGKAVPMTEFVK----EEQKPLFF----RNAVALGVLAYVFGID----FE 135 Query: 189 AINSTFKQDLYRKMNE--LAVKDSYDIVESRYN----LKPSSKERRRFWLDGNTAVAIGK 242 + F + K ++ + ++ Y+ E + L+ +E++ GN VA+G Sbjct: 136 VLEDVFIESYGNKASDDIVLAEEGYNFAEENFERLEELEKIGEEKKVH--SGNEMVALGM 193 Query: 243 IYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELAAINMAI 302 I G+ YP+TP S ++ +DV+ P E E+AAI MAI Sbjct: 194 IKAGLERFYAYPMTPTSPILHFLVRREDVIAYQP---------------ESEIAAIMMAI 238 Query: 303 GAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTAQSDLIF 362 G+A G RAATATSG GF+LM E + AGM EVPV+I Y R PSTG+ T TAQ DL F Sbjct: 239 GSAFAGKRAATATSGGGFALMTESISLAGMAEVPVLIVYGQRSAPSTGMATYTAQEDLYF 298 Query: 363 PIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLANSYSTIPYEEL 422 + HGEFP IV + D +A+K LNLA K+QTP I L +K L SY T+ Y Sbjct: 299 ALNPAHGEFPLIVASPIDCEDAYKLGAELLNLAWKFQTPAILLSDKHLLESYETVSY--- 355 Query: 423 ELDKLKAERGKIVESGDISYKRFKFTEDGISPRAFLGKATMYYTGDEHNEEGHISEDVVN 482 K+K ER IV + +KR++ T +GISP A + A + +EH+E G ++D Sbjct: 356 --PKVKRERINIVRKSEGVFKRYEITRNGISPYA-VPPAIVKANSNEHDEYGFTTDDAEI 412 Query: 483 RTMMYEKRMKKLEVADKEIPEESRVKIYGDLNSRNLIITWGSPTGVLRDILEESNFDFTL 542 MYEKRMKK+ KEI +E R + I+TWGS G +R++ EE F + Sbjct: 413 ARKMYEKRMKKV----KEIEKEVRNSYVEEGKGSETIVTWGSNYGAVREVAEE--LGFKV 466 Query: 543 LQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQTSLLVKMYTGKDVTNSILKWNGRPFL 602 + +R P V K+ E VE NY + +++ G + IL+W+GRPF Sbjct: 467 VAVRFLKPLD---VPKIKENS---YCVECNYQGLLAGMIEKEQGIKL-RRILRWDGRPFT 519 Query: 603 RDELEEAL 610 +EL+E L Sbjct: 520 PEELKEVL 527 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: 813 Number of extensions: 40 Number of successful extensions: 7 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: 632 Length of database: 528 Length adjustment: 36 Effective length of query: 596 Effective length of database: 492 Effective search space: 293232 Effective search space used: 293232 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