Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate RR42_RS26635 RR42_RS26635 2-hydroxyacid dehydrogenase
Query= BRENDA::O23240 (559 letters) >FitnessBrowser__Cup4G11:RR42_RS26635 Length = 466 Score = 313 bits (801), Expect = 1e-89 Identities = 175/451 (38%), Positives = 275/451 (60%), Gaps = 22/451 (4%) Query: 120 ETANTDWMHKYKGSSKLMLLPKNTQEVSQILEYCDSRRLAVVPQGGNTGLVGGSVPVFD- 178 E+ TD+ Y+G ++++++P T++VSQ++ +C + + VVPQGGNT L+GG+VP Sbjct: 18 ESYVTDYRRIYRGKAQVVVMPSTTEQVSQVMAWCHAHDVPVVPQGGNTSLMGGAVPDDSG 77 Query: 179 -EVIVNVGLMNKILSFDEVSGVLVCEAGCILENLATFLDTKGFIMPLDLGAKGSCHIGGN 237 V++++G MN++L+ D ++ + +AG L T + + + L +G++GSC IGGN Sbjct: 78 TAVLLSLGRMNRVLAVDTINDTMTVQAGVTLNAARTAAEQEQRLFALRIGSEGSCQIGGN 137 Query: 238 VSTNAGGLRLIRYGSLHGTVLGLEAVTANGNVLDMLGTLRKDNTGYDLKHLFIGSEGSLG 297 ++TNAGG ++RYG++ VLG+EAV +G + L LRKDNTGYDLK LF+GSEG+LG Sbjct: 138 LATNAGGTAVLRYGNMRDLVLGIEAVLPDGRIYSSLRGLRKDNTGYDLKQLFVGSEGTLG 197 Query: 298 IVTKVSILTQPKLSSVNLAFIACKDYLSCQKLLVEAKRNLGEILSAFEFLDNNSMDLVLN 357 I+T + P+ + +AF+A + + +LL AK++ G+ ++AFE + +++LVL Sbjct: 198 IITAAVLKLMPQPRANAVAFVAVQSPEAAVRLLGVAKQHGGQAVTAFELISAPALELVLE 257 Query: 358 HLDGVRNPVSSSENFYILIETT--GSDETNDREKLEAFLLKSLEKG----LVSDGVIAQD 411 +L V +P+ + ++ +LIE T GSDE+ L A L++ LE G LV D +A Sbjct: 258 YLGDVTSPLPARHDWMVLIELTSGGSDES-----LNATLMEILEAGLAQELVLDAAVAAS 312 Query: 412 INQASSFWRIREGITEALQKAGAVYKYDLSLPVEEIYNIVNDLRGR---LGDLANVMGYG 468 + A FWRIRE I++A + G K D+S+P+ I + D + L A ++ YG Sbjct: 313 LADAQRFWRIREEISDAQTRTGGSIKCDVSVPLSRIAAFIGDASAKVLALEPAARMVIYG 372 Query: 469 HLGDGNLHLN------ISAAEYNDKLLGLIEPYVYEWTSKHRGSISAEHGLGVMKANEIF 522 H+GDGN+H N SAA++ + I V GSISAEHG+GV K +++ Sbjct: 373 HMGDGNVHFNPLRPKDRSAADFLGQWYAPISEAVDTLAHAENGSISAEHGIGVAKRDDLK 432 Query: 523 YSKSPETVALMASIKKLLDPKGILNPYKVLP 553 KSP + LM +K+ LDPK +LNP K+LP Sbjct: 433 RYKSPVELELMWQVKRALDPKNLLNPAKMLP 463 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: 582 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: 466 Length adjustment: 34 Effective length of query: 525 Effective length of database: 432 Effective search space: 226800 Effective search space used: 226800 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