Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate NP_349233.1 CA_C2626 3-ketoacyl-ACP reductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000008765.1:NP_349233.1 Length = 248 Score = 100 bits (250), Expect = 2e-26 Identities = 77/263 (29%), Positives = 120/263 (45%), Gaps = 37/263 (14%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAV-------------LLDLPNSGGEAQAKKLGN 56 G VA+ITG + G+G + AE + G V L + NSGG A+ K Sbjct: 7 GKVALITGSSRGIGKSIAEEMAKMGIEVVINYRNDEKGALDTLKSIKNSGGIAEVYK--- 63 Query: 57 NCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQR 116 D+TS +V+ KFG++D+ VN AGI+ ++K+ D+ Sbjct: 64 ------CDITSYSEVKNMFEFIISKFGKIDLLVNNAGISKIGLFIDMKEN------DYNE 111 Query: 117 VLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIV 176 ++D + G FN L M + + G IIN +S+ G + YSA+KG + Sbjct: 112 IMDNDFRGVFNCTSLAVKYMLERKS------GSIINISSIWGNVGASCEVLYSAAKGAVN 165 Query: 177 GMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHL 236 T + ++LAP GIRV I+PG+ T + S N L +++P R G +E A + Sbjct: 166 SFTKALGKELAPSGIRVNAISPGVIDTEMNGSFSNDEKNDLENEIPM-CRFGKTSEIAKI 224 Query: 237 V--QAIIENPFLNGEVIRLDGAI 257 A E ++ +VI DG + Sbjct: 225 AIFLASEEASYITAQVITADGGM 247 Lambda K H 0.318 0.135 0.385 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: 144 Number of extensions: 7 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: 261 Length of database: 248 Length adjustment: 24 Effective length of query: 237 Effective length of database: 224 Effective search space: 53088 Effective search space used: 53088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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