GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_21725 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate AO353_21725 AO353_21725 ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21725 AO353_21725
           ATP-binding protein
          Length = 265

 Score =  519 bits (1337), Expect = e-152
 Identities = 265/265 (100%), Positives = 265/265 (100%)

Query: 1   MTQAQVSTQNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC 60
           MTQAQVSTQNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC
Sbjct: 1   MTQAQVSTQNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRC 60

Query: 61  VNMLEEFQGGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQ 120
           VNMLEEFQGGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQ
Sbjct: 61  VNMLEEFQGGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQ 120

Query: 121 NVTLGLLKVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS 180
           NVTLGLLKVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS
Sbjct: 121 NVTLGLLKVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPS 180

Query: 181 LMLFDEVTSALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE 240
           LMLFDEVTSALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE
Sbjct: 181 LMLFDEVTSALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE 240

Query: 241 QGPPKELFERPQSPRLAEFLKNTRF 265
           QGPPKELFERPQSPRLAEFLKNTRF
Sbjct: 241 QGPPKELFERPQSPRLAEFLKNTRF 265


Lambda     K      H
   0.319    0.135    0.379 

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: 353
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: 265
Length of database: 265
Length adjustment: 25
Effective length of query: 240
Effective length of database: 240
Effective search space:    57600
Effective search space used:    57600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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