Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate Ga0059261_1691 Ga0059261_1691 FAD/FMN-containing dehydrogenases
Query= BRENDA::O23240 (559 letters) >FitnessBrowser__Korea:Ga0059261_1691 Length = 484 Score = 241 bits (614), Expect = 6e-68 Identities = 149/479 (31%), Positives = 250/479 (52%), Gaps = 10/479 (2%) Query: 84 SLIQRNPLFSSLDSKDVSYFKEILGEKNVVEDKERLETANTDWMHKYKGSSKLMLLPKNT 143 S + P +S +S E LG V D++ D + ++ + P++T Sbjct: 4 SAVTTVPASASPTDPCLSALSETLGADLFVRDEDARAACLRDMTGNWPSGAQAVARPRST 63 Query: 144 QEVSQILEYCDSRRLAVVPQGGNTGLVGG-SVPV-FDEVIVNVGLMNKILSFDEVSGVLV 201 EV+++++ ++ +A+VPQGGNTGLVGG +VP ++++ + I + D + ++ Sbjct: 64 AEVARLVQAAAAQGIAIVPQGGNTGLVGGCAVPAETPALLLSTRRLRSIRAIDLHAPAVI 123 Query: 202 CEAGCILENLATFLDTKGFIMPLDLGAKGSCHIGGNVSTNAGGLRLIRYGSLHGTVLGLE 261 EAGCIL + + GF +PL LG++GS IGG VSTNAGG+R +R+G + VLGLE Sbjct: 124 AEAGCILAEVQEAVAAHGFTIPLGLGSEGSATIGGLVSTNAGGIRALRHGVMRNQVLGLE 183 Query: 262 AVTANGNVLDMLGTLRKDNTGYDLKHLFIGSEGSLGIVTKVSILTQPKLSSVNLAFIACK 321 V +G V + L TL K+N GYDLK LFIG EG+LG+VT ++ P + ++A + Sbjct: 184 VVLPDGRVWNGLRTLAKNNMGYDLKQLFIGGEGTLGVVTAAALRLVPASRQIETLWLAVE 243 Query: 322 DYLSCQKLLVEAKRNLGEILSAFEFLDNNSMDLVLNHLDGVRNPVSSSENFYILIE-TTG 380 D + LL + LG+++++FE + ++ + + G+R P S + +++L E T Sbjct: 244 DPAAALALLGALRTALGDLVTSFELIQRRGVEWGMAAVPGLRVPDSGAHGWFVLAEVATA 303 Query: 381 SDETNDREKLEAFLLKSLEKGLVSDGVIAQDINQASSFWRIREGITEALQKAGAVYKYDL 440 + R +EA L E+GL DG++A+ Q WRIRE + D+ Sbjct: 304 ATGLPLRAAVEAALADVFEQGLALDGMLAESEAQRRELWRIREAVVVGKAAGKPSISVDV 363 Query: 441 SLPVEEIYNIVNDLRGRLGDL---ANVMGYGHLGDGNLHLNI-SAAEYNDKLLGLIEPY- 495 ++P+ ++ + + L +G+GHLGDGN+H ++ A ++ G E Sbjct: 364 AVPLGQVPAFLVETEAAAAGLLPGCETLGFGHLGDGNIHFSVHRGANDTERFAGTAEAIA 423 Query: 496 --VYEWTSKHRGSISAEHGLGVMKANEIFYSKSPETVALMASIKKLLDPKGILNPYKVL 552 V + G+I AEHG+G + + + L+ ++K+ LDP +NP V+ Sbjct: 424 AKVEAIALRLGGTICAEHGVGRRMRAAVADALDAAELDLIRAVKRALDPHNRMNPGAVI 482 Lambda K H 0.317 0.136 0.390 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: 557 Number of extensions: 28 Number of successful extensions: 5 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: 559 Length of database: 484 Length adjustment: 35 Effective length of query: 524 Effective length of database: 449 Effective search space: 235276 Effective search space used: 235276 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: 52 (24.6 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