GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate AO353_25125 AO353_25125 sugar ABC transporter permease

Query= reanno::Dino:3607127
         (272 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25125
          Length = 280

 Score =  178 bits (451), Expect = 1e-49
 Identities = 91/263 (34%), Positives = 149/263 (56%), Gaps = 4/263 (1%)

Query: 13  LLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSL 72
           L+ +++   VFPFY+ + TSLK      E    WI  P  SNY   L +   LR + NSL
Sbjct: 18  LIGILLLYAVFPFYYAIVTSLKPSSALFEVS-YWIDSPDFSNYAAVLHQSSFLRAIGNSL 76

Query: 73  IIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGL 132
           ++A+    LAL L + AA+AL R +FRG+  +    +   M   + +    F + R LGL
Sbjct: 77  VVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRALGL 136

Query: 133 LDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPG 192
            +    LIL Y  F LP  +W++T     +P++L+EAA ++GAS +  + ++ LPL  P 
Sbjct: 137 YNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWPA 196

Query: 193 VAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEG---YNLPYGKIMATSTLIVI 249
           +  + + +FI +WNE +F L  T ++ +    +A++ + G   + LP+G +MA S L+ +
Sbjct: 197 LVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVLVTV 256

Query: 250 PVLIFALIASKQLVRGLTMGAVK 272
           P++I  LI  +++V GLT GA+K
Sbjct: 257 PLVILVLIFQRRIVSGLTAGALK 279


Lambda     K      H
   0.331    0.143    0.431 

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: 243
Number of extensions: 14
Number of successful extensions: 3
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: 272
Length of database: 280
Length adjustment: 25
Effective length of query: 247
Effective length of database: 255
Effective search space:    62985
Effective search space used:    62985
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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