Align 3-keto-5-aminohexanoate cleavage enzyme; EC 2.3.1.247 (uncharacterized)
to candidate Pf1N1B4_5996 Transposase
Query= curated2:E3PRK0 (273 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5996 Length = 350 Score = 116 bits (291), Expect = 6e-31 Identities = 91/309 (29%), Positives = 147/309 (47%), Gaps = 40/309 (12%) Query: 1 MEKLIITAAICGAEVTKEHNP-NVPYTVEEIVREAKSAYDAGASVIHLHVREDDGTPTQS 59 MEK++IT A G E E P ++P T++E V++A Y+AGA+V+HLHVRE DG ++ Sbjct: 13 MEKVVITVAPYGPEWMPEDFPEDIPLTMDEQVQKAVECYEAGATVLHLHVRELDGKGSKR 72 Query: 60 KERFKMCVDAIKEACPDAIIQ--------PSTGG--AVGMTDEER--LQPVFLKPEMASL 107 +F + ++EA PD IIQ P + G A ++D+ R L + KP+ ++ Sbjct: 73 LSKFNELIAGVREAVPDMIIQVGGSISFAPESDGEAAKWLSDDTRHMLAELTPKPDQVTV 132 Query: 108 DCGTCNFGGDEIF-------VNTEN-----------------MIINFSKYMIKNGVKPEC 143 T E+ + N + K ++ NG++P Sbjct: 133 AINTTQMNIMELLYPEYLEGTSLANPAYQAAYSEMTVPAGPAWVAEHLKRLMDNGIQPHF 192 Query: 144 EVFDKSMIDMAIRLAKKGHIQTPMHFNFVMGVNGGISA-TPRDLVFLIGSIPSESSFTVS 202 ++ ++ RL +KG + P++ ++ G+ GG P + I P + T Sbjct: 193 QLTGMHAMETLERLVRKGVYKGPLNLTWI-GIGGGFDGPNPFNFFNFIHRAPDGCTLTSE 251 Query: 203 AMGRNQFPMAAMAIITGGHVRVGFEDNVYIEKGVPAKSNGELVEKVVRLAKEFGRPVATP 262 ++ +N P MA+ G H RVG ED + KG S + +++ VR+A E GR +AT Sbjct: 252 SLLKNVMPFNTMAMAMGMHPRVGNEDTIIDHKGDRFGSVAQ-IKQTVRIAHELGREIATG 310 Query: 263 SEAREILGI 271 EAREI I Sbjct: 311 KEAREIYRI 319 Lambda K H 0.318 0.135 0.390 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: 248 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 273 Length of database: 350 Length adjustment: 27 Effective length of query: 246 Effective length of database: 323 Effective search space: 79458 Effective search space used: 79458 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: 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