Align 2-oxoacid oxidoreductase (ferredoxin) (subunit 2/2) (EC 1.2.7.11) (characterized)
to candidate AZOBR_RS02385 AZOBR_RS02385 2-oxoglutarate synthase
Query= BRENDA::Q4J6I9 (621 letters) >FitnessBrowser__azobra:AZOBR_RS02385 Length = 555 Score = 197 bits (502), Expect = 8e-55 Identities = 153/568 (26%), Positives = 261/568 (45%), Gaps = 62/568 (10%) Query: 12 TSANVFSNAIARAGYYLFGNREYYSNIKGRHSYFEVVFDEKPVRSISSYTNILATFDAET 71 T+ + +A A G+Y +R I+G + V PV +I+ FD + Sbjct: 2 TAGQMLLDAAANVGWYGLMSRSTGPQIRGGEAAALVRLSPTPVHGPGDRFDIIIAFDWQ- 60 Query: 72 LFQHFTEVTDFVIYGTDYATTNIDMVKSMEPEMAEQIKQLLSENKMGYTIKDVITYLKNK 131 N++ + P + + ++++ G +V L Sbjct: 61 ---------------------NVERFAAELPLSEKSV--IITDPSQG----EVPAVLAAS 93 Query: 132 GIKVIELDYLDILKKIAAELKVQVSVVERAKNMAAVGASIGLLGLPFDILENTISSIF-- 189 G K +EL ++ +I NM +GA ++GLP ++ I Sbjct: 94 GAKQVELPIKELAGRIPGG----------RVNMVGLGAVAAIVGLPRAGIDAVIQKALGK 143 Query: 190 RNDLFVKMNVMAAKIGYNTV---NNTYHLEVINNV-KPRIQIDGNTIAAMGKIAGGLRFQ 245 + D ++ + G N L N R I GN A +G + GG++F Sbjct: 144 KGDAAIQASNAGIDAGSKEAAGWNLGLELAAPNKEGATRWNISGNEAAGLGALKGGVKFC 203 Query: 246 SYYPITPASDESVYIEANQNVDMIVEGNELRKGGVVVVQAEDELAAINMAIGAALTGART 305 + YPITPA++ ++ N L K G +VQAEDELA+I M +GA+ +G + Sbjct: 204 AAYPITPATEILEWLAPN-----------LAKTGGKLVQAEDELASIAMCLGASFSGVPS 252 Query: 306 STATSGPGFSLMAEGLSWAGMNEVPVVVTYYMRGAPSTGLPTRSGQADLKFALNAGHGEF 365 TAT+GPG SLM E + +E PVV+ RG PSTG+PT+S Q+DL A+ HG+ Sbjct: 253 ITATAGPGLSLMTECIGLGVASETPVVIVDVQRGGPSTGIPTKSEQSDLNIAVYGLHGDA 312 Query: 366 PRIVIASGDHHEIFWDSIWALNLAERYQTPVIHIIEKALANAYSLIDEDSIKGQIKIDRG 425 P +V+ + + + WA++LAE QTP I + ++A+ + +++D+ + K +R Sbjct: 313 PHLVVGPTSIGDCLFTTQWAVHLAEALQTPAIVLSDQAMGQSRAIVDKPA-DAPHKANRL 371 Query: 426 KLVKQVGD-RFNRFQPSDDGISPRVFLGQSSIFYTGD--EHNEEGHITENSLNRTKMHEK 482 G+ ++ R+ ++ G+SP G +T D EH E + + + K +K Sbjct: 372 LATDLGGEAKYKRYADTESGVSPAAIPGMPGGEHTADGLEHAENALPSSQASDHQKQLDK 431 Query: 483 RMKKLETADNEIPEELRVNVVGDADIVLITWGSPKGAILDAMSELEKDGIKTMMVQVKMF 542 R++KL + D + +V G+ +I ++TWGS G +A+ LE G K +V +++ Sbjct: 432 RLRKLTSHDY---GDAWADVEGEGEIAVVTWGSATGPSREAVRRLEAAGTKARLVAIRLI 488 Query: 543 NPYPTKLVKKLLEGKSKIVAVENNYQAQ 570 +P + L+G SK++ VE + AQ Sbjct: 489 SPVQPAKLAAALDGVSKVLVVEQTHGAQ 516 Lambda K H 0.316 0.134 0.377 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: 753 Number of extensions: 36 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 621 Length of database: 555 Length adjustment: 37 Effective length of query: 584 Effective length of database: 518 Effective search space: 302512 Effective search space used: 302512 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 Apr 09 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