Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate Ac3H11_4104 Aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4104 Length = 365 Score = 379 bits (973), Expect = e-110 Identities = 198/401 (49%), Positives = 264/401 (65%), Gaps = 41/401 (10%) Query: 78 ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137 + VD VV+GAGVVGLAVAR L+L+GREV++L+AA + GT SSRNSEV+HAG+YYP S+ Sbjct: 3 DAVDCVVVGAGVVGLAVARALALQGREVMVLEAADAIGTGISSRNSEVIHAGLYYPTGSI 62 Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197 KA+ CVRG+ELLY YC+E +PH++ GKL+VAT ++++ ++ + N V L+ L Sbjct: 63 KAQLCVRGKELLYAYCAERGVPHRRCGKLLVATSAAQLASVESIQARAQANGVLDLQWLS 122 Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257 EA+ +EP L CV AL SP +GI+D+H+ ML+ LQG+ +N Sbjct: 123 RDEALALEPALECVGALYSPSTGIVDSHALMLA------------------LQGDLENAG 164 Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317 + N+ + + E ++L +D ++R VVN+AGL A ALA R Sbjct: 165 GLVAVNSPLARAHIAEGAINLEASDGTRLQAR------------TVVNAAGLYAPALAAR 212 Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPD 377 GLD VP++H+A+G YFTL+G PF+ L+YP+PE GLGVH+T+DL G KFGPD Sbjct: 213 FVGLDPAHVPTAHFAKGSYFTLTG--KAPFSHLIYPVPEAAGLGVHLTLDLGGQAKFGPD 270 Query: 378 VEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPK 437 V+W+ D D V+P R + FY E+RKY+P L+DG+L PGY+GIRPK+ G Sbjct: 271 VQWVTSAD---------DLLVDPARGDAFYAEVRKYWPGLRDGALAPGYAGIRPKIHGAS 321 Query: 438 QSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIA 478 Q ADFVIQG HGVPGLVNLFGIESPGLTSSLAIAEH+A Sbjct: 322 QPAADFVIQGPAVHGVPGLVNLFGIESPGLTSSLAIAEHVA 362 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: 481 Number of extensions: 16 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: 365 Length adjustment: 32 Effective length of query: 451 Effective length of database: 333 Effective search space: 150183 Effective search space used: 150183 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