GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02871 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized)
to candidate AO353_25125 AO353_25125 sugar ABC transporter permease

Query= reanno::Smeli:SMc02871
         (279 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25125
          Length = 280

 Score =  140 bits (354), Expect = 2e-38
 Identities = 90/264 (34%), Positives = 139/264 (52%), Gaps = 15/264 (5%)

Query: 23  LIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYETVLKQGDFIGYFQNSIIVTV 82
           L A+FP +  IV S K  +A+F     + +P+ FS   Y  VL Q  F+    NS++V +
Sbjct: 24  LYAVFPFYYAIVTSLKPSSALFEVSYWIDSPD-FS--NYAAVLHQSSFLRAIGNSLVVAL 80

Query: 83  VSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGI-MIPIRLGTVAILQGMV----ATG 137
             + L L     AA+AL   +FRG   + L + LG+ M P     VA+L G+     A G
Sbjct: 81  CVVTLALFLSLTAAYALGRVKFRGRGTV-LMMVLGVSMFP----QVAVLSGLFEVIRALG 135

Query: 138 LVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLSEYAIFLRLVLPLIRP 197
           L NT  ALIL YT   LP  V++L+ FM  +  +L+ A  +DG S +    R++LPL+ P
Sbjct: 136 LYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWP 195

Query: 198 AMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLGSQIFIG--QFVTNWNAVLSALSLAI 255
           A+ T  +   I  WN+  F L     +  +TV +   +  G       W  +++A  L  
Sbjct: 196 ALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVLVT 255

Query: 256 FPVLVLYVIFSRQLIRGITAGAVK 279
            P+++L +IF R+++ G+TAGA+K
Sbjct: 256 VPLVILVLIFQRRIVSGLTAGALK 279


Lambda     K      H
   0.330    0.142    0.409 

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: 264
Number of extensions: 13
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 279
Length of database: 280
Length adjustment: 26
Effective length of query: 253
Effective length of database: 254
Effective search space:    64262
Effective search space used:    64262
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: 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:

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