Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate CCNA_03278 CCNA_03278 aminobutyraldehyde dehydrogenase
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__Caulo:CCNA_03278 Length = 372 Score = 288 bits (737), Expect = 2e-82 Identities = 167/400 (41%), Positives = 224/400 (56%), Gaps = 39/400 (9%) Query: 81 DTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAK 140 D VV+GAG VGLA LS RG V +L+ G SSRNSEV+H G+YYP SLKAK Sbjct: 7 DVVVVGAGAVGLACGYALSRRGLVVAVLEEQGRIGEGVSSRNSEVIHGGLYYPTGSLKAK 66 Query: 141 FCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFE 200 CV+GR LY +C +++P+KK GKL+VAT EI +LD + N V G+ L G + Sbjct: 67 LCVQGRRALYAFCDAHKVPYKKCGKLVVATSEDEIARLDTIWEQALANDVEGMERLTGAQ 126 Query: 201 AMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHATF 260 A +EP L ALLSPESG+ +H +ML+L QGE + Sbjct: 127 ARALEPGLNAHAALLSPESGVFASHDYMLAL------------------QGEIEA----- 163 Query: 261 SYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLHG 320 + VVL+ E + +A F AE +L L+V + GL +QA+A R+ G Sbjct: 164 AGGAVVLSTPFEGAEP---LAGGGFRVRAGGAEPT-DLTCRLLVTAPGLSSQAVAGRIEG 219 Query: 321 LDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVEW 380 +P +H+ +G YF LSG PF +L+YP P G LG H D+ G FGPD+E+ Sbjct: 220 YPAEQIPKAHFGKGIYFRLSG--KAPFQRLIYPPPIHGALGTHYRNDMGGQAVFGPDLEY 277 Query: 381 IECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQSP 440 + D Y V+P +++ F IRK++PDL L P Y+G+RPKL GP + Sbjct: 278 VAAPD----------YSVDPAKADAFAAYIRKFWPDLPADRLVPDYAGVRPKLHGPGEPQ 327 Query: 441 ADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIANK 480 DF ++G E HG+ GL+ LFGIESPGLTSSLAI E +A + Sbjct: 328 PDFQLRGVEDHGLAGLMALFGIESPGLTSSLAIGETVAER 367 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: 503 Number of extensions: 17 Number of successful extensions: 4 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: 372 Length adjustment: 32 Effective length of query: 451 Effective length of database: 340 Effective search space: 153340 Effective search space used: 153340 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