GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Escherichia coli BW25113

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate 15246 b1124 spermidine/putrescine ABC transporter membrane protein (NCBI)

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



>FitnessBrowser__Keio:15246
          Length = 264

 Score = 97.1 bits (240), Expect = 4e-25
 Identities = 67/215 (31%), Positives = 110/215 (51%), Gaps = 3/215 (1%)

Query: 55  YREALFEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMI 114
           Y   +  D +L+   +SL +A+ +   A ++G   A AL R+ FRGK  +        M 
Sbjct: 47  YSLLMNNDSLLQAAQHSLTMAVFSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMS 106

Query: 115 SPIVLALPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEG 174
             IV+A+   ++   LG+     +L+  ++TF LP V+  V  + +G    + EAA+  G
Sbjct: 107 PDIVMAISLLVLFMLLGIQLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLG 166

Query: 175 ASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYN 234
           AS+FTI+RKI LPLAMP VA   + SF  S ++++    +T    +  P    S ++   
Sbjct: 167 ASEFTILRKIILPLAMPAVAAGWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGV 226

Query: 235 LPYGKIMATSTLIVIPVLIFALIASKQLVRGLTMG 269
            P    +AT  L++  V++   IAS+ + R  T G
Sbjct: 227 SPEVNALATILLVLSLVMV---IASQLIARDKTKG 258


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: 196
Number of extensions: 11
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: 272
Length of database: 264
Length adjustment: 25
Effective length of query: 247
Effective length of database: 239
Effective search space:    59033
Effective search space used:    59033
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