Align crotonase (EC 4.2.1.150) (characterized)
to candidate 6939547 Sama_3635 naphthoate synthase (RefSeq)
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__SB2B:6939547 Length = 300 Score = 97.4 bits (241), Expect = 3e-25 Identities = 79/270 (29%), Positives = 131/270 (48%), Gaps = 26/270 (9%) Query: 10 KDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKA------FVA 63 KD I NRP LNA T+ E+ A++ + +V V++TG+G + F + Sbjct: 31 KDQGTVRIAFNRPDCLNAFRPKTVDELYTALDHARQWSDVGCVLLTGNGPSAKGQYSFSS 90 Query: 64 GADIA-EMKDLTAVEGRK-----FSVLGN----KIFRKLENLEKPVIAAINGFALGGGCE 113 G D KD EG + + +G ++ R + + K VIA + G+A+GGG Sbjct: 91 GGDQRIRGKDGYKYEGEEAGKADVARMGRLHILEVQRLIRFMPKVVIAVVPGWAVGGGHS 150 Query: 114 LSLSCDIRIASSK-AKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEA 172 L + CD+ +AS + A F Q + + G+ LA+ +G A+E+ + G +A+EA Sbjct: 151 LHVVCDLTLASKEHAVFKQTDPDVASFDSGYGSAYLAKMVGQKRAREIFFLGFNYSADEA 210 Query: 173 LRIGLVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVF 232 + +G+VN+ + +L EA I +P A+RM K N D G+ + Sbjct: 211 VAMGMVNRSIPHAELETEALRWAKEINSKSPTAMRMLKYGFNLP-----DDGLVGQQLFA 265 Query: 233 GE----CFATEDRVEGMTAFVEKRDKAFKN 258 GE + T++ EG AF+EKRD+ + + Sbjct: 266 GEATRLAYGTDEAREGRDAFLEKRDQDYSH 295 Lambda K H 0.318 0.136 0.376 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: 168 Number of extensions: 11 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: 259 Length of database: 300 Length adjustment: 26 Effective length of query: 233 Effective length of database: 274 Effective search space: 63842 Effective search space used: 63842 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