Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_085771178.1 B1812_RS08345 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >NCBI__GCF_002117405.1:WP_085771178.1 Length = 367 Score = 345 bits (884), Expect = 2e-99 Identities = 184/398 (46%), Positives = 246/398 (61%), Gaps = 40/398 (10%) Query: 80 VDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKA 139 VD VV+GAGV+GLAV R L+L GR V++L+ G+VTSSRNSEV+H+GIYYP SLKA Sbjct: 4 VDAVVVGAGVIGLAVVRALALTGRSVIVLETERLIGSVTSSRNSEVIHSGIYYPQGSLKA 63 Query: 140 KFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGF 199 + CV GR LY++C + + +++ GKLIVAT E P ++ L G N V L L Sbjct: 64 RLCVEGRRRLYEFCDAHGVGYQRCGKLIVATNEKERPAVEALFQKGLANGVEDLVWLSAA 123 Query: 200 EAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHAT 259 EA MEP L CV AL +P +GILD+H FML+ ++G+A+++ A Sbjct: 124 EATAMEPALHCVGALFAPSTGILDSHGFMLA------------------MRGDAEDHGAA 165 Query: 260 FSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLH 319 ++NT L+ ++E+ + + + + A ++N AGL A +A+ + Sbjct: 166 IAFNTPFLSAKIEDDGIVISAGGAEPTTLKTAA----------LINCAGLQASKVARAIV 215 Query: 320 GLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVE 379 GL+H VP + YA+G YF L+G PF +L+YP P GLGVH+T DL G V+FGPDVE Sbjct: 216 GLEHALVPETRYAKGNYFALTG--RSPFRRLIYPAPHSHGLGVHLTFDLAGQVRFGPDVE 273 Query: 380 WIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQS 439 WIE + DY V+P+R E F IR Y+P L+D +L Y+GIRPK+SGP S Sbjct: 274 WIE----------EIDYAVDPRRCEGFSEAIRSYWPGLRDDALVAAYAGIRPKISGPADS 323 Query: 440 PADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477 ADF + G E HGV GLVNLFGIESPGLTSSLAIAE + Sbjct: 324 AADFRLDGPERHGVRGLVNLFGIESPGLTSSLAIAEQV 361 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: 468 Number of extensions: 16 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: 367 Length adjustment: 32 Effective length of query: 451 Effective length of database: 335 Effective search space: 151085 Effective search space used: 151085 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 Apr 09 2024. 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