Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate AZOBR_RS33525 AZOBR_RS33525 FAD-dependent oxidoreductase
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__azobra:AZOBR_RS33525 Length = 373 Score = 366 bits (939), Expect = e-106 Identities = 196/401 (48%), Positives = 259/401 (64%), Gaps = 34/401 (8%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 ERVD VV GAGV+GLAVA L+ GREV++L+AA + GT TSSRNSEV+HAGIYYP SL Sbjct: 2 ERVDCVVAGAGVIGLAVAWRLARAGREVVVLEAADAIGTGTSSRNSEVIHAGIYYPTGSL 61 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 +A+ CV GR+ LY YC+++ + HK+IGKLIVAT +++P+L+ + N V L L Sbjct: 62 RARLCVAGRDALYAYCAQHGVEHKRIGKLIVATEEAQLPRLEAIRAQAVANGVDDLAALS 121 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 EA +EP LRCV ALLSP +GI+D+H ML+ LQG+A+ Sbjct: 122 ATEARALEPALRCVGALLSPSTGIIDSHGLMLA------------------LQGDAEAAG 163 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 A ++ + + + L V + C+ +VN+AGLGA A+ Sbjct: 164 AMLAFLSPLEHTHRRADGFELEVGGAEPTRIACDT----------LVNAAGLGAWGGARG 213 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPD 377 L G VP A+G Y+ L +A PF +LVYP+P EGGLGVH+T+DL G +FGPD Sbjct: 214 LEGFPAEHVPPRVLAKGNYYALGQGRA-PFARLVYPVPVEGGLGVHLTLDLAGQARFGPD 272 Query: 378 VEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPK 437 VEW++ D ++ DYRV+P+R++ FY E+R+Y+PDL DG+L P YSG+RPKLSGP Sbjct: 273 VEWLDPADH-----DRLDYRVDPRRADGFYGEVRRYWPDLPDGALVPAYSGVRPKLSGPG 327 Query: 438 QSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIA 478 Q ADF+IQG E HGVPGLVNLFG+ESPGLTS LAIA+ +A Sbjct: 328 QPQADFLIQGPEVHGVPGLVNLFGMESPGLTSCLAIADEVA 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: 510 Number of extensions: 19 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: 373 Length adjustment: 32 Effective length of query: 451 Effective length of database: 341 Effective search space: 153791 Effective search space used: 153791 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