GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Klebsiella michiganensis M5al

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate BWI76_RS14600 BWI76_RS14600 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__Koxy:BWI76_RS14600
          Length = 260

 Score =  190 bits (482), Expect = 3e-53
 Identities = 96/237 (40%), Positives = 157/237 (66%), Gaps = 4/237 (1%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           +E+ ++ K++G++++L GV++E+  GEV+ L+GDNGAGKSTL K++SG   P  G +  +
Sbjct: 11  VEMINITKTYGSIRSLRGVNLELAPGEVLGLVGDNGAGKSTLTKVLSGAVIPSGGTIRID 70

Query: 65  GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI----FLNKKKMMEE 120
           G++  F +P D+R   IE +YQDL+L   + +  N+F+ RE    +    FL++ KM  +
Sbjct: 71  GEQQQFANPADSRRCHIEMVYQDLSLCDTVDVAGNLFMGREPMKSVLGIPFLDEAKMHAD 130

Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180
           ++++L  L I IPD  + V NLSGGQRQA+A+ARA  F  K+++MDEPTAAL+V E   V
Sbjct: 131 AREMLKGLGISIPDTRLLVRNLSGGQRQAIAIARAAAFDPKVLIMDEPTAALAVAEVEAV 190

Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237
           LEL R +  +G+ V++ITH +   + V DRI V+  G  +  ++  +T++ +I  ++
Sbjct: 191 LELIRRVSARGVSVILITHRLQDLFLVCDRIMVMYEGTNVADRRVADTSLSDIVNLI 247


Lambda     K      H
   0.318    0.137    0.371 

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: 134
Number of extensions: 4
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: 251
Length of database: 260
Length adjustment: 24
Effective length of query: 227
Effective length of database: 236
Effective search space:    53572
Effective search space used:    53572
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 (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