Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate 5208014 Shew_0530 FAD dependent oxidoreductase (RefSeq)
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__PV4:5208014 Length = 375 Score = 285 bits (729), Expect = 2e-81 Identities = 169/408 (41%), Positives = 227/408 (55%), Gaps = 39/408 (9%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 +++D +VIGAGVVGLAVA LS R VLI+D A + GT SSRNSEV+HAGIYYP SL Sbjct: 2 DKLDAIVIGAGVVGLAVAASLSRRFGNVLIIDRAETIGTGISSRNSEVIHAGIYYPTGSL 61 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 KA+ CV G+ LY YC + +GKLIVAT + +LD L N V L L Sbjct: 62 KAQLCVEGKRQLYAYCRRRGVAVNSLGKLIVATQVEQEAQLDALFTQARANGVDDLNPLG 121 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 + +EP L+ LLSP +GI+D+H MLSL+ ++ ++ G H Sbjct: 122 RRQLQALEPALKASAGLLSPSTGIVDSHGLMLSLLAEAEEY------------GAIFCPH 169 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 F NG F + ++ L + ++N AGL A +A R Sbjct: 170 TEFITTQADANG---------------FRVELMQQGERVSLETSFLINCAGLFATEVATR 214 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEG--GLGVHVTVDLNGLVKFG 375 + GL VP ++ +G YF G PF L+YP+PE G GLG+H T+DL G +KFG Sbjct: 215 IEGLAESLVPQLYWCKGHYFAYQG--KSPFAHLIYPVPEPGLKGLGIHATIDLGGQLKFG 272 Query: 376 PDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSG 435 PD +++ D+ DYRV ++F+ I YYP + L+ Y+GIRPKL G Sbjct: 273 PDAQYM--VPDSLE-----DYRVPEALRQRFHQAIASYYPGIAIERLQTAYAGIRPKLQG 325 Query: 436 PKQSP-ADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIANKFL 482 P + ADF+IQGE HG+PGLVNL GIESPGLT+SLAIAE ++ + + Sbjct: 326 PDDTEVADFLIQGEAQHGIPGLVNLLGIESPGLTASLAIAEQVSRQLV 373 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: 505 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 375 Length adjustment: 32 Effective length of query: 451 Effective length of database: 343 Effective search space: 154693 Effective search space used: 154693 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