GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Dethiosulfovibrio salsuginis USBA 82

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085543660.1 B9Y55_RS01865 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_900177735.1:WP_085543660.1
          Length = 358

 Score =  233 bits (595), Expect = 5e-66
 Identities = 137/333 (41%), Positives = 195/333 (58%), Gaps = 11/333 (3%)

Query: 23  AVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRDI 82
           AV+E+ LD+  GE +  +GPSGCGK+TTLRM+AG ET T G + ++ + +  V    R I
Sbjct: 23  AVKELDLDVKGGELVTFLGPSGCGKTTTLRMVAGFETPTSGRILIDGQDVTDVMVNKRHI 82

Query: 83  AMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLSG 142
             VFQ+YAL+PH +V  N+++GL        D I+ +V +  +M+G+S +  R P QLSG
Sbjct: 83  GFVFQNYALFPHMTVGDNVAYGLRMRNESAKD-IKTKVVQGLEMVGLSQVEKRYPNQLSG 141

Query: 143 GQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQTE 202
           G+QQRVAL R +V  P+V LMDEPLSNLDAKLR  MRTE++R+Q +L +T +YVTHDQ E
Sbjct: 142 GEQQRVALARVLVMRPKVLLMDEPLSNLDAKLRIHMRTEIRRIQKQLDITCLYVTHDQKE 201

Query: 203 AMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGS---LSGDTFRG 259
           A+TM DR+ V++ G+++Q+GTP   Y  P + FVA FIG+   N+ +G+   L G T R 
Sbjct: 202 ALTMADRIMVMNKGQVEQIGTPFQIYTAPESTFVADFIGQ--ANILEGTLDDLDGLTSRI 259

Query: 260 DGFDYPLSGATRDQLGGASG--LTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNENAV 317
                 LS    +      G  ++L +RPE +++ +   G       V  V   G+    
Sbjct: 260 STGGSNLSARLLEGKSYRKGEKVSLVLRPETLSLSQ---GGGLLGGTVTQVVFSGDRMEY 316

Query: 318 HLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSF 350
            LR  DG           G    + GD   +SF
Sbjct: 317 TLRLGDGQSLLAMENFYPGIKVWQEGDSVDLSF 349


Lambda     K      H
   0.316    0.136    0.384 

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: 407
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: 383
Length of database: 358
Length adjustment: 30
Effective length of query: 353
Effective length of database: 328
Effective search space:   115784
Effective search space used:   115784
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: 42 (22.0 bits)
S2: 49 (23.5 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