Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate Ac3H11_2934 D-2-hydroxyglutarate dehydrogenase
Query= BRENDA::O23240 (559 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2934 Length = 474 Score = 303 bits (776), Expect = 1e-86 Identities = 176/465 (37%), Positives = 269/465 (57%), Gaps = 15/465 (3%) Query: 104 KEILGEKNVVEDKERLETANTDWMHKYKGSSKLMLLPKNTQEVSQILEYCDSRRLAVVPQ 163 + I+G +V+ + + L DW + +G + ++ P NTQEV+ +++ C + A+VPQ Sbjct: 9 RAIVGPTHVITEGD-LTAWEQDWRRRVRGKALAVVRPANTQEVAAVVKACAAVGTAIVPQ 67 Query: 164 GGNTGLVGGSVPVFD--EVIVNVGLMNKILSFDEVSGVLVCEAGCILENLATFLDTKGFI 221 GGNTGL GS P ++++++ MN + S D + + EAGCIL+NL G + Sbjct: 68 GGNTGLAVGSTPDDSGTQIVLSLTRMNAVRSVDTDNLTMTVEAGCILQNLQDVAQNAGVL 127 Query: 222 MPLDLGAKGSCHIGGNVSTNAGGLRLIRYGSLHGTVLGLEAVTANGNVLDMLGTLRKDNT 281 PL L A+GSC IGGN+ TNAGG +++RYG+ LGLE VTA G V D L LRKDNT Sbjct: 128 FPLSLAAEGSCTIGGNLGTNAGGTQVVRYGNARDLCLGLEVVTAQGEVWDGLKGLRKDNT 187 Query: 282 GYDLKHLFIGSEGSLGIVTKVSILTQPKLSSVNLAFIACKDYLSCQKLLVEAKRNLGEIL 341 GYDL+ LFIGSEG+LGI+T ++ P+ ++ A+ A LL A + LG L Sbjct: 188 GYDLRDLFIGSEGTLGIITAATMKLYPQPAANLTAWAAAPSMEHAVALLGLAHKQLGAGL 247 Query: 342 SAFEFLDNNSMDLVLNHLDGVRNPVSSSEN--FYILIETTGSD-ETNDREKLEAFLLKSL 398 + FE + ++ LV H+ +R P +N + +L+E + S+ E + R + E+ L + Sbjct: 248 TGFEVMGQFALSLVGKHMPQLRVPFLGDDNAPWCVLLENSDSESEEHARARFESLLETAF 307 Query: 399 EKGLVSDGVIAQDINQASSFWRIREGITEALQKAGAVYKYDLSLPVEEIYNIV---NDLR 455 E G V+D V+A+++ QA W IRE I A + G K+D+S+ + I V + + Sbjct: 308 EMGCVTDAVVAENLTQAHQLWHIRESIPLAQAEEGLNIKHDISIQISRIPAFVAHTDAVL 367 Query: 456 GRLGDLANVMGYGHLGDGNLHLNISAAEYNDKLLGL------IEPYVYEWTSKHRGSISA 509 R ++ +GHLGDGNLH N+ A D L + VYE ++ GS SA Sbjct: 368 QREIPGVRLVNFGHLGDGNLHYNVQAPAAGDPKAFLREQEARVNHLVYEAVAEFGGSFSA 427 Query: 510 EHGLGVMKANEIFYSKSPETVALMASIKKLLDPKGILNPYKVLPH 554 EHG+G +KA+++ +SP + +M +IK+ LDP+G++NP +VL H Sbjct: 428 EHGIGELKADKLAKYQSPVALGMMRAIKQALDPQGVMNPGRVLGH 472 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: 591 Number of extensions: 26 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: 474 Length adjustment: 35 Effective length of query: 524 Effective length of database: 439 Effective search space: 230036 Effective search space used: 230036 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