Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate BPHYT_RS13750 BPHYT_RS13750 D-2-hydroxyacid dehydrogenase
Query= BRENDA::O23240 (559 letters) >FitnessBrowser__BFirm:BPHYT_RS13750 Length = 472 Score = 303 bits (775), Expect = 1e-86 Identities = 168/461 (36%), Positives = 260/461 (56%), Gaps = 12/461 (2%) Query: 104 KEILGEKNVVEDKERLETANTDWMHKYKGSSKLMLLPKNTQEVSQILEYCDSRRLAVVPQ 163 ++ +G V+ D TDW +Y G++ +L P EV+ +++ R+A+VPQ Sbjct: 11 RDAIGAAQVLTDPHDTALYLTDWRRRYAGAACAVLCPATPDEVAALVKLAVEHRIALVPQ 70 Query: 164 GGNTGLVGGSVPVFD--EVIVNVGLMNKILSFDEVSGVLVCEAGCILENLATFLDTKGFI 221 GGNTGL GG+ P + ++++ +N++ D + + EAG IL + D G + Sbjct: 71 GGNTGLAGGATPDASGAQAVISLRRLNRVRDIDPHNNTITVEAGVILAEVQKHADEAGRL 130 Query: 222 MPLDLGAKGSCHIGGNVSTNAGGLRLIRYGSLHGTVLGLEAVTANGNVLDMLGTLRKDNT 281 PL L A+GSC IGGN++TNAGG ++RYG+ LGLE VT G + D L LRKDNT Sbjct: 131 FPLSLAAEGSCTIGGNLATNAGGTGVLRYGNARELCLGLEVVTPQGELWDGLRGLRKDNT 190 Query: 282 GYDLKHLFIGSEGSLGIVTKVSILTQPKLSSVNLAFIACKDYLSCQKLLVEAKRNLGEIL 341 GYDL+ LFIG+EG+LGI+T + P+ ++ A A + L +R G +L Sbjct: 191 GYDLRDLFIGAEGTLGIITAAVLKLHPRPAARVTALAALASPHAALDFLSLTQRVAGPLL 250 Query: 342 SAFEFLDNNSMDLVLNHLDGVRNPVSSSENFYILIETTGSD-ETNDREKLEAFLLKSLEK 400 + FE + + + LV H + +R P + +L+E + S+ E + RE E + +LE Sbjct: 251 TGFELMSDFCLRLVGRHFEQMRYPFAEPHAQVVLLELSDSESEEHARELFERLMETALES 310 Query: 401 GLVSDGVIAQDINQASSFWRIREGITEALQKAGAVYKYDLSLPVEEIYNIVNDLRGRLGD 460 GLV D V+A++++Q+ +FW +RE I A + G K+D+++P+ + + + + + Sbjct: 311 GLVQDAVVAENLSQSRAFWNLREHIPLAQAEEGLNIKHDIAVPISRVGHFIEETDAAIAQ 370 Query: 461 L---ANVMGYGHLGDGNLHLNISAAEYNDKLLGL------IEPYVYEWTSKHRGSISAEH 511 A ++ +GHLGDGNLH N+ A E D L I VY+ +HRGSISAEH Sbjct: 371 AVPGARMVTFGHLGDGNLHYNVQAPEGVDAKAFLTQYQSPINQIVYDSVHRHRGSISAEH 430 Query: 512 GLGVMKANEIFYSKSPETVALMASIKKLLDPKGILNPYKVL 552 GLG +K +E + K V LM ++K+ LDP ++NP KVL Sbjct: 431 GLGQLKIDEAMHYKQDVEVQLMRAVKRALDPLNLMNPGKVL 471 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: 592 Number of extensions: 20 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: 472 Length adjustment: 35 Effective length of query: 524 Effective length of database: 437 Effective search space: 228988 Effective search space used: 228988 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