GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-B in Pseudomonas putida KT2440

Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate PP_0795 PP_0795 fructose PTS permease - IIBC component

Query= TCDB::D2RXA4
         (150 letters)



>lcl|FitnessBrowser__Putida:PP_0795 PP_0795 fructose PTS permease -
           IIBC component
          Length = 580

 Score = 90.5 bits (223), Expect = 4e-23
 Identities = 49/109 (44%), Positives = 69/109 (63%), Gaps = 1/109 (0%)

Query: 2   KFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVII 61
           + VAVT+CPTG+AH+ MAAE L+Q A   G+++ VE QG++G  N LS++AIA AD V++
Sbjct: 119 RIVAVTACPTGVAHTFMAAEALQQAAQQLGYQLTVETQGSVGARNPLSAEAIAAADVVLL 178

Query: 62  AADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSA 110
           AAD  V   RF GK +       A+      L++A+A A  E   AD+A
Sbjct: 179 AADIEVPTARFAGKRIYRCGTGIALKQARATLDKALAQATVENG-ADAA 226



 Score = 62.0 bits (149), Expect = 1e-14
 Identities = 42/118 (35%), Positives = 57/118 (48%), Gaps = 3/118 (2%)

Query: 1   MKFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVI 60
           M    VT+CP G   S ++A  L   A  RG    VEVQ     E +LS+  IAEAD V+
Sbjct: 1   MNIAIVTACPNGQVSSVLSARLLSAAAQRRGWSTSVEVQNTEHPERQLSAAQIAEADWVL 60

Query: 61  IAADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAAD---GETSTADSAQSEGA 115
           + +   V+  RF GK +  +    A+ D E  L+ A A A+     T    +A S GA
Sbjct: 61  VVSTGPVDLARFVGKRLYQSTPSQALADREGFLDEAAANAELLAAVTGAPAAASSAGA 118


Lambda     K      H
   0.307    0.122    0.323 

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: 130
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: 150
Length of database: 580
Length adjustment: 26
Effective length of query: 124
Effective length of database: 554
Effective search space:    68696
Effective search space used:    68696
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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