Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_013403647.1 CALHY_RS08995 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >NCBI__GCF_000166355.1:WP_013403647.1 Length = 479 Score = 150 bits (379), Expect = 9e-41 Identities = 120/400 (30%), Positives = 187/400 (46%), Gaps = 52/400 (13%) Query: 81 DTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAK 140 D VIGAGVVG+++ REL+ +V L+ S NS +VHAG + KA+ Sbjct: 6 DVAVIGAGVVGMSILRELTRYRLKVCSLEKMEDVAEGASKANSGIVHAGYDPIEGTKKAR 65 Query: 141 FCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFE 200 F V G + C+E ++ +K IG L+VA EI L+ L+ G +N V GL + Sbjct: 66 FNVEGNNIFADICNELDVEYKMIGSLVVAFDDYEINVLEELLQRGKRNGVKGLEIKSQEW 125 Query: 201 AMRMEPQL-RCVK-ALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHA 258 EP L R +K AL +P SGI + + ++L E A N A Sbjct: 126 VFENEPNLSRNIKAALFAPYSGITNPYKLTVALFE------------------NAIQNGA 167 Query: 259 TFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRL 318 ++ V + ++ AD+RF +++ +++N AG+ A ++K Sbjct: 168 DVIFSFEVCKIEKDGDYFVVHSADSRFVKTK------------VLINCAGVHADEISKMA 215 Query: 319 HGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDV 378 + P RG Y+ L + P ++++ +P E G G+ VT ++G V GP+ Sbjct: 216 GARLFKIYP----RRGQYYILDKPQKMPVARVIFQVPTEKGKGILVTPTVDGNVLVGPNS 271 Query: 379 EWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQ 438 E+I+ DDT++ D + + + RK P L + +SGIR Sbjct: 272 EYIDSKDDTATTQEGLD---------EVFEKARKVLPSLSKRDVITIFSGIR-----ATP 317 Query: 439 SPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIA 478 DF+I EE V +N+ GIESPGLT+SLAI ++IA Sbjct: 318 DTHDFII--EEDEDVKNFINVAGIESPGLTASLAIGKYIA 355 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: 430 Number of extensions: 15 Number of successful extensions: 3 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: 479 Length adjustment: 34 Effective length of query: 449 Effective length of database: 445 Effective search space: 199805 Effective search space used: 199805 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 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