Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_068168371.1 HTA01S_RS06830 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >NCBI__GCF_001592305.1:WP_068168371.1 Length = 368 Score = 340 bits (873), Expect = 4e-98 Identities = 192/405 (47%), Positives = 248/405 (61%), Gaps = 45/405 (11%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 E VD VVIGAGVVGLAVAR L+L GREV++L+ ++ GT TSSRNSEV+HAGIYYP SL Sbjct: 2 ESVDVVVIGAGVVGLAVARSLALAGREVMVLEREAAIGTGTSSRNSEVIHAGIYYPQGSL 61 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 KA+ CVRGRELLY YC+E I H++ GKL+VA +S++ L ++ N V L L Sbjct: 62 KARLCVRGRELLYAYCTERGIAHRRCGKLMVANTASQVQGLPGILARAEANGVPDLMPLT 121 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 EA +EPQL C+ AL SP +GI+D+H MLSL QG+ ++ Sbjct: 122 RAEARALEPQLECLAALHSPSTGIVDSHGLMLSL------------------QGDLEHAA 163 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 + + V + R + + + D L+ VVN+AGL A LA+ Sbjct: 164 GLVACRSGVASLRATGAGVEVLMQDGT------------ALLARGVVNAAGLHACELARN 211 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEG----GLGVHVTVDLNGLVK 373 GL+ VP + YA+G YFTLSG PF +L+YP+P+ GLGVH+T+DL G K Sbjct: 212 AQGLNPAHVPRAWYAKGSYFTLSG--RSPFGRLIYPVPDPASHLAGLGVHLTIDLGGQAK 269 Query: 374 FGPDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKL 433 FGPDV+W + DD S VNP ++ FY +R+Y+P L D +L PGY+G+RPK+ Sbjct: 270 FGPDVQWTDDPDDLS---------VNPGSADGFYAAVRQYWPGLPDAALVPGYAGMRPKI 320 Query: 434 SGPKQSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIA 478 SGP + ADF I G HGVPGLVNL GIESPGLTS LAI EH+A Sbjct: 321 SGPHEPAADFRIDGPAAHGVPGLVNLLGIESPGLTSCLAIGEHVA 365 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: 532 Number of extensions: 22 Number of successful extensions: 5 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: 368 Length adjustment: 32 Effective length of query: 451 Effective length of database: 336 Effective search space: 151536 Effective search space used: 151536 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 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