Align arylesterase (EC 3.1.1.2); 1,4-lactonase (EC 3.1.1.25); aryldialkylphosphatase (EC 3.1.8.1) (characterized)
to candidate 17442 b3379 predicted hydrolase (NCBI)
Query= BRENDA::Q4J6Z8 (315 letters) >FitnessBrowser__Keio:17442 Length = 292 Score = 148 bits (373), Expect = 2e-40 Identities = 98/301 (32%), Positives = 159/301 (52%), Gaps = 20/301 (6%) Query: 18 GFTLIHEHLRVFSEPVRYQWPHLYNEDEELKNAV---NEVKTIMSYGVKTIVDPTVMGLG 74 G+TL HEHL + + N D L E+ +M+ GV+ +++ T +G Sbjct: 7 GYTLAHEHLHIDLSGFKN------NVDCRLDQYAFICQEMNDLMTRGVRNVIEMTNRYMG 60 Query: 75 RDIRFSEKVVKETGINVIAATGLYTYTDLPFFFNGRSLEEIAELLIHDIKKGIQGTNNRA 134 R+ +F V++ETGINV+A TG Y P RS++E+A+ ++ +I++GI GT +A Sbjct: 61 RNAQFMLDVMRETGINVVACTGYYQDAFFPEHVATRSVQELAQEMVDEIEQGIDGTELKA 120 Query: 135 GFI-KVAADEPGITRDVERAIRAAAIAQKETNVPIITHSNAHNGTGLEQQRILMEEGVDP 193 G I ++ E IT E+ AAA+A +T PI TH+ + + GLEQ +L GVD Sbjct: 121 GIIAEIGTSEGKITPLEEKVFIAAALAHNQTGRPISTHT-SFSTMGLEQLALLQAHGVDL 179 Query: 194 GRVLIGHLGDTDNVDYIKKIADKGSFVGLDRYGLDLFLPIDKRNEVLLKLIKDGYLDRIM 253 RV +GH DN+D I K+ D G++V D G + + P +KR +L L G L+R+M Sbjct: 180 SRVTVGHCDLKDNLDNILKMIDLGAYVQFDTIGKNSYYPDEKRIAMLHALRDRGLLNRVM 239 Query: 254 VSQDYCCTIDWGIAKPEYKPKLAPKWSMSLIFTDVIPSIKRAGVTDEQLHVIFVKNPARL 313 +S D I + + K + + T IP ++++G + + V+ +NP++ Sbjct: 240 LSMD--------ITRRSHL-KANGGYGYDYLLTTFIPQLRQSGFSQADVDVMLRENPSQF 290 Query: 314 F 314 F Sbjct: 291 F 291 Lambda K H 0.320 0.140 0.412 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: 229 Number of extensions: 10 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: 315 Length of database: 292 Length adjustment: 27 Effective length of query: 288 Effective length of database: 265 Effective search space: 76320 Effective search space used: 76320 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