GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-B in Pseudomonas fluorescens FW300-N1B4

Align PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; EC 2.7.1.202 (characterized)
to candidate Pf1N1B4_1144 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= SwissProt::D4GYE1
         (158 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1144
          Length = 579

 Score = 97.4 bits (241), Expect = 3e-25
 Identities = 53/121 (43%), Positives = 80/121 (66%), Gaps = 3/121 (2%)

Query: 2   KLVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVII 61
           +LVAVT+CPTG+AH+ MAAE L QA +RLG+D+ VE QG++G ++ L+++AIA+AD V++
Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAEAIADADVVLL 180

Query: 62  TSDTSVSRDRFDGKLVLKGTVKDGVNNAEAVVQKAVELAEAGKTGSVTFGSGDDGEDADV 121
            +D  V+ +RF GK + +      +  AEA + KA  LAE GK  S + G+    +    
Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLNKA--LAE-GKQESASTGAKGPAKQEKT 237

Query: 122 G 122
           G
Sbjct: 238 G 238



 Score = 62.4 bits (150), Expect = 1e-14
 Identities = 36/101 (35%), Positives = 54/101 (53%)

Query: 1   MKLVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVI 60
           MKL  VT+CP G+  S + A  L  A +R G    VEV  A   + +L++  I  A+ V+
Sbjct: 1   MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVL 60

Query: 61  ITSDTSVSRDRFDGKLVLKGTVKDGVNNAEAVVQKAVELAE 101
           + +   V   RF GK V + T    + + EAV+++ VE AE
Sbjct: 61  LVTSAPVDMSRFVGKRVFQSTPAQALQDVEAVLRRGVEEAE 101


Lambda     K      H
   0.309    0.128    0.345 

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: 152
Number of extensions: 4
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 158
Length of database: 579
Length adjustment: 26
Effective length of query: 132
Effective length of database: 553
Effective search space:    72996
Effective search space used:    72996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 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