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 SMa0335 SMa0335 3-ketoacyl-ACP reductase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Smeli:SMa0335 Length = 258 Score = 108 bits (271), Expect = 9e-29 Identities = 86/259 (33%), Positives = 126/259 (48%), Gaps = 24/259 (9%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLL----DLPNSGGEAQA---KKLGNNCVFAP 62 G V ++TG +SG+G A A R GA AV++ + P GGE A +KLG VF Sbjct: 9 GKVVIVTGASSGIGRAIAIRAAEHGAKAVIVSDVVEAPREGGEPTASEIRKLGAESVFVK 68 Query: 63 ADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNL 122 ADV+ + D AL A +FG VDV V AGI + + + + +D++R++ VNL Sbjct: 69 ADVSRKVD-NDALVAAAEEFGGVDVMVANAGITLKTDGAEVPE------DDYRRLMSVNL 121 Query: 123 MGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPI 182 G L + + ++G I+ AS+ G AYS SKGG+V M + Sbjct: 122 DGP-----LFGAQAAARQMKALNKQGSIVLMASMGGISGAGITVAYSTSKGGVVLMAKSL 176 Query: 183 ARDLAPIGIRVMTIAPGLFGTPLLTSLP--EKVCNFLASQVPFPSRLGDPAEYAHLVQAI 240 A L P GIRV +APG T LL + P + + P RLG PAE V + Sbjct: 177 ADALGPDGIRVNAVAPGTIDTELLRTSPGIAQASEGFRQRTPL-RRLGKPAEVGDAVAFL 235 Query: 241 IE--NPFLNGEVIRLDGAI 257 + +++G + +DG + Sbjct: 236 GSDLSSYVSGTALLVDGGL 254 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: 160 Number of extensions: 11 Number of successful extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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 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