Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_108358527.1 B9Z44_RS13415 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >NCBI__GCF_003063475.1:WP_108358527.1 Length = 369 Score = 342 bits (877), Expect = 1e-98 Identities = 192/404 (47%), Positives = 252/404 (62%), Gaps = 45/404 (11%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRG----REVLILDAASSFGTVTSSRNSEVVHAGIYYP 133 ++VD VVIGAGVVGLA AR L RE L+L+AA + GT TSSRNSEV+HAGIYYP Sbjct: 2 DKVDGVVIGAGVVGLATARALIQAAPETAREWLVLEAADAIGTGTSSRNSEVIHAGIYYP 61 Query: 134 PNSLKAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGL 193 SLKAK CV+GR+ LY Y +E + H++ GKLIVAT + ++P LD L+ N V+ + Sbjct: 62 QGSLKAKLCVQGRDRLYAYATERGVSHQRCGKLIVATHADQLPALDALLQKAHANGVTDV 121 Query: 194 RMLEGFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEA 253 ML +A MEP L CV AL SP +GI+D+H MLS LQG+ Sbjct: 122 VMLSAEQAQVMEPSLSCVAALHSPSTGIVDSHGLMLS------------------LQGDF 163 Query: 254 QNNHATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQA 313 +N + N+ V + + + + +AD EL+ VVN+AGL A Sbjct: 164 ENAGGIVALNSPVASAVCRDDGIVVRMADGS------------ELLAQTVVNAAGLTAPW 211 Query: 314 LAKRLHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVK 373 LAK GL + VP +++A+G YFTLSG PF+ L+YP+PE GLGVH+T+DL G K Sbjct: 212 LAKHFEGLAAQHVPQAYFAKGNYFTLSG--KSPFSHLIYPVPEAAGLGVHLTLDLGGQAK 269 Query: 374 FGPDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKL 433 FGPDV+W++ D D V+ + + FY E+RKY+P L DG+L+ GY+GIRPK+ Sbjct: 270 FGPDVQWVDRPD---------DLLVSAEHEQVFYNEVRKYWPALGDGALQAGYAGIRPKI 320 Query: 434 SGPKQSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477 SGP ++ ADF IQG HGV GLVNLFGIESPGLTS+LAI + + Sbjct: 321 SGPHEAAADFCIQGPAVHGVKGLVNLFGIESPGLTSALAIGDAV 364 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: 480 Number of extensions: 17 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: 369 Length adjustment: 32 Effective length of query: 451 Effective length of database: 337 Effective search space: 151987 Effective search space used: 151987 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 24 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