Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate GFF231 Psest_0232 Predicted dehydrogenase
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__psRCH2:GFF231 Length = 372 Score = 350 bits (898), Expect = e-101 Identities = 188/400 (47%), Positives = 248/400 (62%), Gaps = 40/400 (10%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 +RVD VV+GAGVVGLAVA L+L GREVL+L+A ++FGT TS+RNSEV+HAGIYYP SL Sbjct: 2 DRVDCVVVGAGVVGLAVACALALAGREVLVLEAEAAFGTATSARNSEVIHAGIYYPQGSL 61 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 K + CV GR LY +C + + +++ GKLIVAT ++I L+ L N V L+ L+ Sbjct: 62 KGRLCVAGRRQLYDFCDSHGVAYRRCGKLIVATDEAQIAALEQLQRHAQANGVDDLQRLD 121 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 G E + +EPQL V LLSP +GI+D+H+ ML+L+ G+A+ + Sbjct: 122 GHEVLALEPQLHAVAGLLSPSTGIIDSHALMLALL------------------GDAERHG 163 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 A + N V + VA + L+L+ VVN AG GA LA R Sbjct: 164 AVLALNAPVAD----------IVAASDGLRVEVGGADPLQLLARTVVNCAGHGAPVLAAR 213 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPD 377 GL P +A+G YF+LSG PF LVYP+PE GGLGVH+T+DL G +FGPD Sbjct: 214 TQGLSDAARPRQFFAKGSYFSLSG--CTPFRHLVYPLPEPGGLGVHLTLDLAGQARFGPD 271 Query: 378 VEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPK 437 V+W++ DYR+ P R+E FY IR+Y+P L D +L+P Y+GIRPK+SGP Sbjct: 272 VQWVD----------DLDYRIEPARAEGFYAAIRRYWPGLPDDALQPAYTGIRPKISGPG 321 Query: 438 QSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477 ++ ADF I G HG+ GLVNLFGIESPGLT+ LAIAEH+ Sbjct: 322 EAAADFRIDGPAQHGIAGLVNLFGIESPGLTACLAIAEHV 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: 489 Number of extensions: 23 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: 372 Length adjustment: 32 Effective length of query: 451 Effective length of database: 340 Effective search space: 153340 Effective search space used: 153340 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