Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate Pf6N2E2_261 Aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_261 Length = 369 Score = 348 bits (893), Expect = e-100 Identities = 185/400 (46%), Positives = 251/400 (62%), Gaps = 40/400 (10%) Query: 81 DTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAK 140 + VV+GAGVVGLAVARE++ G +VL+++AA + G SSRNSEV+HAGIYYP SLKA+ Sbjct: 6 ECVVVGAGVVGLAVAREMARAGHDVLLIEAAEAIGMGISSRNSEVIHAGIYYPLGSLKAQ 65 Query: 141 FCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFE 200 CV GR LY YC + + +++GKLIVAT +++ L+ L+ G +N V LR+L+ + Sbjct: 66 LCVEGRHRLYTYCESHGVATRRLGKLIVATDQAQVGGLETLLERGLKNGVDDLRLLDQEQ 125 Query: 201 AMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHATF 260 A +EP L CV AL SP +GI+D+H+ ML+ LQG+A+ A Sbjct: 126 AQALEPALACVAALYSPSTGIVDSHALMLA------------------LQGDAEAAGANI 167 Query: 261 SYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLHG 320 +++T +L R+ L + T AQ+ L L++N+AGL A ALA+R+ G Sbjct: 168 AFHTPLLGARIITGGFILELGGT----------AQMTLSCRLLINAAGLQAPALARRIEG 217 Query: 321 LDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVEW 380 L+ ++VP +G YF+L+G PF LVYP PE GLG+H+T+DL G +FGPD EW Sbjct: 218 LEMQWVPEDFLCKGNYFSLAG--RAPFRHLVYPAPEAAGLGIHMTLDLAGQARFGPDTEW 275 Query: 381 IECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQSP 440 ++C DYRV+P R+E FYP IR Y+P L D SL+P YSGIRPK+S P + Sbjct: 276 VDCE----------DYRVDPARAEAFYPAIRNYWPGLPDQSLQPAYSGIRPKISAPGEPA 325 Query: 441 ADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIANK 480 DFVI E H VPGL+NL GIESPGLTS LAIA + + Sbjct: 326 RDFVISSEAEHRVPGLINLLGIESPGLTSCLAIASRVRQR 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: 471 Number of extensions: 22 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: 369 Length adjustment: 32 Effective length of query: 451 Effective length of database: 337 Effective search space: 151987 Effective search space used: 151987 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 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