Align 3-keto-5-aminohexanoate cleavage enzyme; EC 2.3.1.247 (characterized)
to candidate AZOBR_RS23055 AZOBR_RS23055 hypothetical protein
Query= SwissProt::B0VHH0 (276 letters) >FitnessBrowser__azobra:AZOBR_RS23055 Length = 314 Score = 154 bits (389), Expect = 2e-42 Identities = 95/298 (31%), Positives = 162/298 (54%), Gaps = 29/298 (9%) Query: 4 LILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDD-GRPSQRLDR 62 +I+T A+TG+ T + P+LP+TP++ A EA A EAGA ++HLH R+ + GRP+Q D Sbjct: 11 VIITCAVTGSIHTPSMSPHLPVTPDQIAAEAIAAVEAGAAIVHLHARDPETGRPTQDPDL 70 Query: 63 FQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLA-LKPEMATLNAGTLNFG------ 115 FQ + I++ + ++ I+TGG+ + + RL P A +PE+A+LN G++NFG Sbjct: 71 FQRFLPRIKQAT-KAVVNITTGGSAAMTVEDRLRPAAQFQPEVASLNMGSMNFGLFPMLN 129 Query: 116 ------------------DDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLI 157 D +F N DI + + E E Y+ + +A + Sbjct: 130 RFSAFQHDWERTYLENSRDLVFKNTFKDIEHILKTCSGNGTRFEFECYDISHLYTLAHFL 189 Query: 158 KKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTA-TWAVAGIGRWHIPTSL 216 + ++T PL +Q V G+ GG+ P+++M+M W+V G GR +P + Sbjct: 190 DRKLVTP-PLFVQSVFGILGGIGPHPEDVMHMKRTADRLFGDQYVWSVLGAGRNQMPIAT 248 Query: 217 IAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILAL 274 ++ GG++R G EDN++ G +A SNA+ VA + ++ + + +ATP++AR +L+L Sbjct: 249 QSLALGGNVRVGLEDNLWAGPGRLATSNAEQVAMVRKLIEGLALEVATPDEARAMLSL 306 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: 243 Number of extensions: 14 Number of successful extensions: 4 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: 314 Length adjustment: 26 Effective length of query: 250 Effective length of database: 288 Effective search space: 72000 Effective search space used: 72000 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: 48 (23.1 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