GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglB in Pseudomonas fluorescens FW300-N1B4

Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf1N1B4_4386 Inositol transport system sugar-binding protein

Query= TCDB::P0AEE5
         (332 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4386 Inositol transport
           system sugar-binding protein
          Length = 308

 Score =  120 bits (302), Expect = 3e-32
 Identities = 93/312 (29%), Positives = 145/312 (46%), Gaps = 29/312 (9%)

Query: 23  AADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKG 82
           AA  RIGV+I + DDNFM+ VR  +E DA    +VQ+   D+Q D  +Q +Q+   L + 
Sbjct: 20  AASYRIGVSIARVDDNFMTYVRSGLE-DAARKENVQIQFEDAQGDVVRQLNQVQGFLGQK 78

Query: 83  VKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQ 142
           V A+ +  VD AA   +   A    +P+V+ N+ P  + L        V ++  E+G +Q
Sbjct: 79  VDAVIVLPVDTAATANMTRAAVEAKIPLVYVNRHPDERVLPK--GVVTVASNDVEAGQLQ 136

Query: 143 GDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELND-KGIKTEQLQL 201
              +A+  A          G+    ++KG+      + RT  V + L D  GIK  + Q 
Sbjct: 137 MRYLAEKMA----------GKGNIAIIKGDLAQNSTQDRTEGVNQVLKDYPGIKIVEQQ- 185

Query: 202 DTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKS--SIPVFGVD 259
            +A W   +  D    WL        + ++ANND MA+GA  AL+   K+   I + G+D
Sbjct: 186 -SAEWQRNKGMDLTSNWLLA--GADFDAIVANNDEMAIGAAMALQQAGKAKGEIAIVGID 242

Query: 260 ALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYV 319
            LP+ LA +K G L  +V  D   QA +    A  +  G+              V VP+ 
Sbjct: 243 GLPDGLAAIKRGMLVASVFQDPKAQATSALQAAIKMIKGEPVETD---------VWVPFQ 293

Query: 320 GVDKDNLAEFSK 331
            +  D +A F +
Sbjct: 294 LITPDQVAVFEQ 305


Lambda     K      H
   0.313    0.129    0.363 

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: 245
Number of extensions: 12
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: 332
Length of database: 308
Length adjustment: 28
Effective length of query: 304
Effective length of database: 280
Effective search space:    85120
Effective search space used:    85120
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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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