GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Escherichia coli BW25113

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 16203 b2096 tagatose-bisphosphate aldolase 1 (VIMSS)

Query= BRENDA::Q5HE75
         (286 letters)



>FitnessBrowser__Keio:16203
          Length = 284

 Score =  221 bits (564), Expect = 1e-62
 Identities = 121/287 (42%), Positives = 176/287 (61%), Gaps = 5/287 (1%)

Query: 1   MPLVSMKEMLIDAKENGYAVGQYNINNLEFTQAILEASQEENAPVILGVSEGAARYMSGF 60
           M +VS K+ML +A+  GYAV  +NI+NLE  Q ++E +   +APVI+  + G   + +G 
Sbjct: 1   MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTH-AGT 59

Query: 61  YTIVKMVEGLMHDLNITIPVAIHLDHGSSFEKCKEAIDAGFTSVMIDASHSPFEENVATT 120
             ++ +V  +    +   P+AIHLDH + F+   + + +G  SVMIDASH PF +N++  
Sbjct: 60  ENLLALVSAMAKQYHH--PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLPFAQNISRV 117

Query: 121 KKVVEYAHEKGVSVEAELGTVGGQEDDVVAD--GIIYADPKECQELVEKTGIDALAPALG 178
           K+VV++ H   VSVEAELG +GGQEDDV  +    +Y +P + +E  E TGID+LA A+G
Sbjct: 118 KEVVDFCHRFDVSVEAELGQLGGQEDDVQVNEADALYTNPAQAREFAEATGIDSLAVAIG 177

Query: 179 SVHGPYKGEPKLGFKEMEEIGLSTGLPLVLHGGTGIPTKDIQKAIPFGTAKINVNTENQI 238
           + HG Y   P L F  +E I     LPLVLHG +G+ TKDIQ+ I  G  KINV TE + 
Sbjct: 178 TAHGMYASAPALDFSRLENIRQWVNLPLVLHGASGLSTKDIQQTIKLGICKINVATELKN 237

Query: 239 ASAKAVRDVLNNDKEVYDPRKYLGPAREAIKETVKGKIKEFGTSNRA 285
           A ++A+++ L    E  DPR YL  A+ A+++ V   I + G   RA
Sbjct: 238 AFSQALKNYLTEHPEATDPRDYLQSAKSAMRDVVSKVIADCGCEGRA 284


Lambda     K      H
   0.312    0.133    0.370 

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: 234
Number of extensions: 9
Number of successful extensions: 3
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: 286
Length of database: 284
Length adjustment: 26
Effective length of query: 260
Effective length of database: 258
Effective search space:    67080
Effective search space used:    67080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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.

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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