Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate RR42_RS06495 RR42_RS06495 FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__Cup4G11:RR42_RS06495 Length = 368 Score = 380 bits (975), Expect = e-110 Identities = 199/402 (49%), Positives = 270/402 (67%), Gaps = 37/402 (9%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 E+VD VVIGAGVVGLAVAR+L+++GREV+IL+A ++FGT+TS+RNSEV+HAGIYYP SL Sbjct: 2 EQVDCVVIGAGVVGLAVARQLAMQGREVIILEAENAFGTITSARNSEVIHAGIYYPAGSL 61 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 KA CVRG+ +LY YC+ + I H++ GKLIVAT +++ L+ + N V L++L Sbjct: 62 KAAMCVRGKAMLYDYCASHHIQHQRCGKLIVATTEAQVATLEAIRAKAAANGVHDLQLLS 121 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 EA +EP L+C ALLS +GI+D+H ML+L+ G+A+N Sbjct: 122 QAEAQALEPNLQCRAALLSASTGIVDSHGLMLALL------------------GDAENAG 163 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 A + + V +G V + L V S+ EA A L+ V+NSAGL A ALA+ Sbjct: 164 AMLAVQSPVASGAVMPDGIRLDVG------SQDEA-AGTTLLARTVINSAGLSAPALARS 216 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPD 377 + G+ VP +YA+GCYFTL+G PF++L+YP+PE GLGVH+T+DL G +FGP+ Sbjct: 217 IEGMPGAHVPPQYYAKGCYFTLAG--RAPFSRLIYPVPEAAGLGVHLTIDLGGQARFGPN 274 Query: 378 VEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPK 437 V WI+ + +Y V+P ++ FY E+R Y+P L DG+L+PGY+GIRPK+SGP Sbjct: 275 VRWID----------EIEYGVDPADADSFYGEVRNYWPGLADGALQPGYAGIRPKISGPG 324 Query: 438 QSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIAN 479 + ADF I G THGVPGLVNLFGIESPGLTSSLA+AEH+A+ Sbjct: 325 EPAADFRIDGPATHGVPGLVNLFGIESPGLTSSLALAEHVAS 366 Lambda K H 0.318 0.136 0.401 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: 481 Number of extensions: 18 Number of successful extensions: 4 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: 483 Length of database: 368 Length adjustment: 32 Effective length of query: 451 Effective length of database: 336 Effective search space: 151536 Effective search space used: 151536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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