Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate WP_013707104.1 DESAC_RS10780 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P72578 (632 letters) >NCBI__GCF_000195295.1:WP_013707104.1 Length = 563 Score = 276 bits (707), Expect = 1e-78 Identities = 197/611 (32%), Positives = 301/611 (49%), Gaps = 87/611 (14%) Query: 6 VIGGAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQK 65 +IGG G G+ T A I A+ +GYY+ N+ Y S I+GGH+ F++ +S + + + Q+ Sbjct: 9 LIGGEAGQGLVTIAMILTKALVRSGYYLVVNQSYQSRIRGGHNTFAIRVSTEEIIAPRQR 68 Query: 66 IDILVSFDAETVFQHFYDVKDILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYETT 125 + DFL ET Sbjct: 69 L------------------------------------------------DFLVALNQETV 80 Query: 126 VKGALEYASKNNVTLIPVNYDEIAKKVADEMKVPLS--VTERVKNIVGITISYKLLGLDV 183 E A + + L+ + + ++ +K P E+ N+ + + KLLGLD Sbjct: 81 DWHRTEIAP-DGLILLDERFADADQRC---VKAPFKQFAEEKFANVAYLAVLNKLLGLDE 136 Query: 184 NYLIEAINSTF--KQDLYRKMNELAVKDSYDIVESRYNLKPSSK-----ERRRFWLDGNT 236 + + + F K+ + N +Y+ R NL + + + L+GN Sbjct: 137 QVVFQTLEDYFGAKKPEVTEKNRQIFSAAYEWASGR-NLPETVRLAPVAPQEHLMLNGNE 195 Query: 237 AVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELA 296 A+A+G I G++F ++YP+TPA+ S+ ++A D L +VV QAEDE+A Sbjct: 196 AIALGAISAGLKFCAFYPMTPATSISLTLQAAADDL------------GLVVEQAEDEIA 243 Query: 297 AINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTA 356 AINMAIGA+ GV A ATSG GF+LMVEG+ AGM E P++I R GP+TGLPTRT Sbjct: 244 AINMAIGASYAGVPAMVATSGGGFALMVEGVSLAGMTETPILIVVAQRPGPATGLPTRTE 303 Query: 357 QSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLANSYST 416 Q DL F + AGHGEFP+ + A E F AL LAEKYQ+P+ L ++ LA+SY Sbjct: 304 QGDLEFILHAGHGEFPRAIFAPTTIEECFHLTRKALILAEKYQSPIFLLTDQFLADSYRA 363 Query: 417 I-PYEELELDKLKAERGKIVESGDISYKRFKFTEDGISPRAFLGKAT--MYYTGDEHNEE 473 + P+E LD G E + Y+R+ T+ G+SPR G++T + DEH + Sbjct: 364 VAPFEIDALDATSV--GSSPEEVSLPYQRYALTDSGVSPRLLPGQSTHLVVCDSDEHTSD 421 Query: 474 GHISEDVVNRTMMYEKRMKKLEVADKEIPEESRVKIYGDLNSRNLIITWGSPTGVLRDIL 533 GHI+ED+ R +M EKR++K E+ + + GD L +TWGS G + + Sbjct: 422 GHITEDLTVRILMVEKRLRKSAGLRAEV---TLPEYQGDNRPEVLFVTWGSSCGAVVEAA 478 Query: 534 EE----SNFDFTLLQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQTSLLVKMYTGKDV 589 E + L +++ P +S L +G D ++ VEGN AQ + ++ TG D+ Sbjct: 479 AELRLRGHRTAALCFAQVWPLIPDQFLSYL-QGADNVVMVEGNATAQFTRMICRETGLDL 537 Query: 590 TNSILKWNGRP 600 + IL+++G P Sbjct: 538 PHRILRYDGLP 548 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: 744 Number of extensions: 35 Number of successful extensions: 8 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: 563 Length adjustment: 37 Effective length of query: 595 Effective length of database: 526 Effective search space: 312970 Effective search space used: 312970 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