GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate AO353_03390 AO353_03390 sugar ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895
         (302 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03390
          Length = 302

 Score =  593 bits (1529), Expect = e-174
 Identities = 292/302 (96%), Positives = 300/302 (99%)

Query: 1   MSSVAVFSKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWV 60
           MSSVAVFSKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTF+LSFTNSSFMPSYKWV
Sbjct: 1   MSSVAVFSKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFVLSFTNSSFMPSYKWV 60

Query: 61  GLQQYMRLMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYP 120
           GLQQY+RLM+NDRWWVASKNLA+FGGMFI ISLVLGVFLAVLLDQRIRKEGFIRT+YLYP
Sbjct: 61  GLQQYVRLMENDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRTIYLYP 120

Query: 121 MALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGF 180
           MALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGF
Sbjct: 121 MALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGF 180

Query: 181 VMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDL 240
           VMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDL
Sbjct: 181 VMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDL 240

Query: 241 VAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKR 300
           VAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAM+MLGA+L ILVPYLYSELRGKR
Sbjct: 241 VAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMMMLGAILAILVPYLYSELRGKR 300

Query: 301 HD 302
           H+
Sbjct: 301 HE 302


Lambda     K      H
   0.329    0.141    0.448 

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: 539
Number of extensions: 9
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: 302
Length adjustment: 27
Effective length of query: 275
Effective length of database: 275
Effective search space:    75625
Effective search space used:    75625
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.

Links

Downloads

Related tools

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