GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Dethiosulfovibrio salsuginis USBA 82

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085543671.1 B9Y55_RS01935 sugar ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_900177735.1:WP_085543671.1
          Length = 252

 Score =  183 bits (464), Expect = 3e-51
 Identities = 98/239 (41%), Positives = 157/239 (65%), Gaps = 6/239 (2%)

Query: 1   MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60
           M  ++E++ + KSFG+V+AL  V   +N GEVVALLGDNGAGKSTLIKI+SG+H  DRG 
Sbjct: 1   MEAMVEMKGIGKSFGSVEALRQVDFRLNPGEVVALLGDNGAGKSTLIKILSGFHSADRGS 60

Query: 61  LVFEGKKVIFNS--PNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK--IFLNKKK 116
           ++ +G+++ F +     ARSLG+ET+YQ+ +L    P++ N+F+ R   N+  +   K++
Sbjct: 61  MMVKGREIDFKAYDVTVARSLGVETVYQERSLGERQPLWRNVFIGRHRLNRWGLIDVKRE 120

Query: 117 MMEESKKLLDSLQIRIPDI--NMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSV 174
            ME  + L   L +R   +  +  VE LSGG+RQ +A+ RA++F A +I++DEPT AL++
Sbjct: 121 KMETMELLSSVLGLRGAGLSPDASVETLSGGERQGLAIGRAMHFGADIIVLDEPTTALAL 180

Query: 175 VEARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233
            E  KVL    ++++ G   ++I+H++   Y+VADR  ++DRG  +   +K +   EE+
Sbjct: 181 SEVGKVLSFIGSIREDGRSCIVISHDLGHVYKVADRFVLMDRGSTVGDYRKGDITPEEL 239


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: 176
Number of extensions: 7
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: 251
Length of database: 252
Length adjustment: 24
Effective length of query: 227
Effective length of database: 228
Effective search space:    51756
Effective search space used:    51756
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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