GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate Pf6N2E2_2891 Glucose ABC transport system, inner membrane component 1

Query= reanno::WCS417:GFF4323
         (302 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2891
          Length = 297

 Score =  583 bits (1503), Expect = e-171
 Identities = 286/297 (96%), Positives = 292/297 (98%)

Query: 6   VFSKASPFDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQY 65
           VFSKASPFDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFT STFLP YKWAGLAQY
Sbjct: 1   VFSKASPFDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFLPNYKWAGLAQY 60

Query: 66  ARLFDNDRWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSM 125
           ARL DNDRWWVASKNLA+FGG+FIGITLVIGV LA+FLDQ+IRREGFIRTIYLYPMALSM
Sbjct: 61  ARLMDNDRWWVASKNLALFGGLFIGITLVIGVLLAVFLDQRIRREGFIRTIYLYPMALSM 120

Query: 126 IVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMF 185
           IVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMF
Sbjct: 121 IVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMF 180

Query: 186 LAGLRGVDQSIVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMT 245
           LAGLRGVDQSI+RAAQIDGASMPRIYW VVLPSLRPVFFSAVMILAHIAIKSFDLVAAMT
Sbjct: 181 LAGLRGVDQSIIRAAQIDGASMPRIYWKVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMT 240

Query: 246 AGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKRND 302
           AGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKR+D
Sbjct: 241 AGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKRHD 297


Lambda     K      H
   0.330    0.141    0.455 

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: 505
Number of extensions: 5
Number of successful extensions: 1
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: 302
Length of database: 297
Length adjustment: 27
Effective length of query: 275
Effective length of database: 270
Effective search space:    74250
Effective search space used:    74250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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