Align 3-keto-5-aminohexanoate cleavage enzyme; EC 2.3.1.247 (characterized)
to candidate SM_b20275 SM_b20275 hypothetical protein
Query= SwissProt::B0VHH0 (276 letters) >FitnessBrowser__Smeli:SM_b20275 Length = 286 Score = 115 bits (288), Expect = 1e-30 Identities = 79/277 (28%), Positives = 141/277 (50%), Gaps = 11/277 (3%) Query: 1 MEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRL 60 ++ + + A G T+AD P +P+TPEE A A+ C +AGA +IH+H+R+ DG Sbjct: 7 LQGISIAVAPNGGRRTKADHPAIPLTPEELALTARDCLDAGAAMIHVHVRKGDGSHLLDA 66 Query: 61 DRFQEAISAIREVVPE-IIIQISTGGAVGESFDKRLAPL-ALKPEMATLNAGTLNFGDDI 118 D ++ A +AIR V + ++IQI++ S +++A + A++PE +L L + Sbjct: 67 DAYRAATAAIRAAVGDRMVIQITSEALGIYSPGEQIAVVKAVRPEAVSLALRELVPDE-- 124 Query: 119 FINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLG-VPG 177 H A L + V P++ +Y+ + + ++G+++++ + + +VLG Sbjct: 125 --THEAAFADLLSWAAREKVTPQIILYDPEEAVRLDGMRRRGLLSRDDIPVLYVLGRYTP 182 Query: 178 GMSGKPKNLMYMMEHLKEEIPTAT-WAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYH 236 G P++L + L ++P T W+V GR +A + GGH+R GFE+N++ Sbjct: 183 GQRSLPRDL---LPFLAPDMPAFTHWSVCAFGRHEAACVTVAALLGGHVRVGFENNLWLP 239 Query: 237 KGVIAESNAQLVARLARIAKEIGRPLATPEQAREILA 273 +G A SNA LV + + PL E+ A Sbjct: 240 EGTAAGSNADLVRTVTAALLPLSVPLLQGPALAEMFA 276 Lambda K H 0.320 0.137 0.396 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: 240 Number of extensions: 6 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: 276 Length of database: 286 Length adjustment: 26 Effective length of query: 250 Effective length of database: 260 Effective search space: 65000 Effective search space used: 65000 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 (21.8 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