GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Escherichia coli BW25113

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 16238 b2130 predicted transporter subunit: membrane component of ABC superfamily (NCBI)

Query= TCDB::Q9KKE2
         (285 letters)



>FitnessBrowser__Keio:16238
          Length = 385

 Score =  102 bits (255), Expect = 1e-26
 Identities = 65/197 (32%), Positives = 104/197 (52%), Gaps = 16/197 (8%)

Query: 90  DLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPS---FVYLIPA 146
           D   Q L L+  A + ++VIGVP+GI    S   +     +L+V+QT+PS   F  LI  
Sbjct: 175 DALAQHLTLLFGAVLPALVIGVPLGIWCYFSTARQGAIFSLLNVIQTVPSVALFGLLIAP 234

Query: 147 LM-------------LFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGG 193
           L              + G G  PA++A ++YA+ PL+R   +G+ Q+  +V+E+A A G 
Sbjct: 235 LAALVTAFPWLGTLGIAGTGMTPALIALVLYALLPLVRGVVVGLNQIPRDVLESARAMGM 294

Query: 194 SPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKG 253
           S  Q    V+LPLA P  +  L   ++  + M V+A++IGA G G  V  G+ +  +   
Sbjct: 295 SGAQRFLHVQLPLALPVFLRSLRVVMVQTVGMAVIAALIGAGGFGALVFQGLLSSAIDLV 354

Query: 254 LEAGIGIVILAVVLDRI 270
           L   I +++LAV+ D +
Sbjct: 355 LLGVIPVIVLAVLTDAL 371


Lambda     K      H
   0.327    0.142    0.422 

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: 332
Number of extensions: 19
Number of successful extensions: 2
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: 285
Length of database: 385
Length adjustment: 28
Effective length of query: 257
Effective length of database: 357
Effective search space:    91749
Effective search space used:    91749
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 (21.7 bits)
S2: 49 (23.5 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