Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate 3609504 Dshi_2888 putative esterase/lipase/thioesterase (RefSeq)
Query= BRENDA::M0RC77 (306 letters) >FitnessBrowser__Dino:3609504 Length = 257 Score = 105 bits (262), Expect = 1e-27 Identities = 77/250 (30%), Positives = 120/250 (48%), Gaps = 18/250 (7%) Query: 50 QATQKARATRRNQLDVSYGDGVGEKMDIYFPDEDSKAFPLFMFLHGGYWQSGSKDDSAFM 109 +A R R ++ +++G EK+D++ P+ L +F+HGGYW+ + D + + Sbjct: 25 RAAAAFREGARGEIGIAHGAHPREKLDLFLPEGTPAG--LVVFVHGGYWRRFDRTDWSHL 82 Query: 110 VNPLTAQGIVVAVVAYDIAPKGTLDQMVDQVSRSVVFLQRRYPSNEGIYLCGHSAGAHLA 169 A+G VA+ Y + P+ T+ ++ V R + L R+ + I L GHSAG HL Sbjct: 83 AAGPLARGWAVAMPGYPLCPEVTIPEITASV-RGAIALAARHVAGP-IRLTGHSAGGHLV 140 Query: 170 AMMLLASWTKHGVTPNIQGLLLVSGIYDLEPLVFTSQNDLLHMTLEDAERNSPQRLLEVA 229 A M A V + ++ +S + DLEPL+ T + L +T E A SP A Sbjct: 141 ARMPAAGLAPE-VLSRVARIVPISPVSDLEPLLRTEMAETLRLTPEIAAAESPLH----A 195 Query: 230 PARPVVPAYPVLVFVAQHDSPEFHRQSKEFCETLRLAGWKASFQELCGVDHFDIIENLTR 289 PA P PV V+V + P F Q++ E W A + G HFD+I++L Sbjct: 196 PA----PDCPVTVWVGAEERPVFLDQARWLAE-----AWGAQHRIAAGRHHFDVIDDLAE 246 Query: 290 EDYALTQIIL 299 D LT +L Sbjct: 247 PDGPLTSALL 256 Lambda K H 0.320 0.135 0.405 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: 167 Number of extensions: 8 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: 306 Length of database: 257 Length adjustment: 26 Effective length of query: 280 Effective length of database: 231 Effective search space: 64680 Effective search space used: 64680 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