GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Escherichia coli BW25113

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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