Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate Dsui_2329 Dsui_2329 putative dehydrogenase
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__PS:Dsui_2329 Length = 375 Score = 356 bits (914), Expect = e-103 Identities = 187/401 (46%), Positives = 259/401 (64%), Gaps = 35/401 (8%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 ER VVIGAGVVGLA AREL+ RG + ++++ ++FG TS+RNSEV+HAG+YYP S Sbjct: 3 ERTGAVVIGAGVVGLACARELARRGIDTVMVEKNAAFGQETSARNSEVIHAGLYYPSGSH 62 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 KA C+RGRELLY +C +++ H+ GKLIVAT +++ LD L G N V+ LR L+ Sbjct: 63 KAALCLRGRELLYAFCRTHQVAHRACGKLIVATSAAQEAGLDALQRQGEANGVTDLRRLD 122 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 +A +EP LRC ALLSP +GI+D+H FML+L+ GEA++ Sbjct: 123 AAQARVLEPALRCSAALLSPATGIVDSHGFMLALL------------------GEAESAG 164 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 A + + R + + EA LEL +++N+AGL A +A Sbjct: 165 AVLALRSPFRGARRHGGLWRISIG----------GEAPLELDTAILINAAGLHATQVAAG 214 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPD 377 + GL +P +HYA+G Y++L+G PF++LVYP+PE GGLGVH+T+DL G +FGPD Sbjct: 215 IEGLAPTAIPPAHYAKGNYYSLAG--RAPFSRLVYPLPEPGGLGVHLTLDLGGQARFGPD 272 Query: 378 VEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPK 437 VEW+ D + DYRV+P+R++ FY E+R+Y+P L D +L+P YSG+RPK+SGP Sbjct: 273 VEWLATRDPQA-----LDYRVDPRRADAFYAEVRRYWPQLADNALQPAYSGVRPKISGPG 327 Query: 438 QSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIA 478 + ADF +QG E HG+ GL+NLFGIESPGLT+SLAIAE +A Sbjct: 328 ATAADFCLQGPEQHGLAGLINLFGIESPGLTASLAIAEAVA 368 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: 499 Number of extensions: 20 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: 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