Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate HSERO_RS20665 HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >FitnessBrowser__HerbieS:HSERO_RS20665 Length = 262 Score = 201 bits (510), Expect = 2e-56 Identities = 115/246 (46%), Positives = 152/246 (61%) Query: 12 ERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGADIKEMA 71 E V +TLNRP NAL Q + E+ AL + E D + +V++G+ KAFAAGAD+ EM Sbjct: 17 EHVLHLTLNRPALRNALRNQSLREIVAALARAEEDDSVRVVVISGNEKAFAAGADLNEMI 76 Query: 72 ELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNARFGQPE 131 LD IA KP++AAV GYALG GCEL + D+ AA A+ GQPE Sbjct: 77 HKDAIATQLDVRAQYWRAIARFPKPILAAVNGYALGAGCELLMHADIAIAARGAKIGQPE 136 Query: 132 VNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAESLLEETLK 191 +N+G LPG GGTQRL R VGK AM M L+G + A +A +AGLVA V ++ LE TL Sbjct: 137 INVGTLPGAGGTQRLIRTVGKPLAMKMVLSGEFISADQALQAGLVAEVVDDDATLERTLA 196 Query: 192 AARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMAAFSEKRK 251 A IA+KS A + KE++ ++FE L G+ FER+ F + A+AD++EG+AAF EKR Sbjct: 197 LAHSIAQKSPLAVRLAKEAMLQSFELGLEAGLLFERKSFSLMAASADRQEGIAAFQEKRA 256 Query: 252 PEFTNR 257 F+ R Sbjct: 257 AVFSGR 262 Lambda K H 0.321 0.135 0.375 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: 145 Number of extensions: 4 Number of successful extensions: 2 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: 257 Length of database: 262 Length adjustment: 24 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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 (21.9 bits) S2: 47 (22.7 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