Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_011386171.1 AMB_RS19325 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >NCBI__GCF_000009985.1:WP_011386171.1 Length = 374 Score = 327 bits (839), Expect = 3e-94 Identities = 190/402 (47%), Positives = 240/402 (59%), Gaps = 43/402 (10%) Query: 76 AKERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPN 135 A ERVD VVIGAGVVGLAVAR L+ G EV+IL+A + G+ SSRNSEV+HAG+YYP Sbjct: 11 AAERVDCVVIGAGVVGLAVARSLAHAGAEVIILEAEGAIGSGISSRNSEVIHAGMYYPAG 70 Query: 136 SLKAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRM 195 SL+A+ CV G LL Y + + H GKLIVAT +E +LD ++ G N V GL Sbjct: 71 SLRARLCVEGNRLLRDYAASRGVAHAMTGKLIVATDEAEAAQLDAILAKGRANGVEGLTR 130 Query: 196 LEGFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQN 255 + A MEP L CV AL SP +GI+DTH MLSL+ GEA+ Sbjct: 131 ISAAHAREMEPDLACVAALWSPATGIIDTHGLMLSLL------------------GEAEE 172 Query: 256 NHATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALA 315 A + + V GR + M L V AE L N+V+ +AGL + L Sbjct: 173 RGAALALKSPVTGGRATDDGMLLSVGG---------AEPTTLLARNVVL-AAGLSSPRLG 222 Query: 316 KRLHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFG 375 L GL + VP +H +G YFTLSG PF +LVYP+P GLGVH T+DL G +FG Sbjct: 223 AAL-GLKN--VPPAHLCKGNYFTLSG--RTPFTRLVYPVPVAAGLGVHFTLDLGGRGRFG 277 Query: 376 PDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSG 435 PDVEW+E DY+V+P+R + FY IR+Y+PDL DG+LEP Y+GIRPK++ Sbjct: 278 PDVEWVEAE----------DYQVDPRRGDSFYAAIRRYWPDLADGALEPAYAGIRPKITA 327 Query: 436 PKQSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477 + ADF+I G GVPG+ L+GIESPGLTSSLAIA H+ Sbjct: 328 EGEPAADFLIHGPRETGVPGVAALYGIESPGLTSSLAIAGHV 369 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: 454 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: 483 Length of database: 374 Length adjustment: 32 Effective length of query: 451 Effective length of database: 342 Effective search space: 154242 Effective search space used: 154242 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: 51 (24.3 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