GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Pseudomonas litoralis 2SM5

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  214 bits (544), Expect = 4e-60
 Identities = 109/236 (46%), Positives = 161/236 (68%), Gaps = 3/236 (1%)

Query: 20  DIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQD 79
           D +AV++++L I+ GE   L+G SG GKST LR++AG ET +EG + L+ + +  +    
Sbjct: 32  DALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLDGQNITALPPHK 91

Query: 80  RDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQ 139
           R I M+FQSYAL+PH +V  N++FGL++   L + EI +RV E   ++ ++    RKP Q
Sbjct: 92  RPINMMFQSYALFPHMTVEQNIAFGLKQDK-LSNTEISERVAEMLKLVHMAKYAKRKPHQ 150

Query: 140 LSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHD 199
           LSGGQ+QRVAL R++ + P++ L+DEP+  LD KLR++M+ EL  +   +GVT + VTHD
Sbjct: 151 LSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERVGVTCIMVTHD 210

Query: 200 QTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255
           Q EAMTM  R+A++D G + QVGTP+D Y  P N  VA F+G  S+N+F+G +  D
Sbjct: 211 QEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVG--SVNIFEGEIVAD 264


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: 396
Number of extensions: 14
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: 378
Length adjustment: 30
Effective length of query: 353
Effective length of database: 348
Effective search space:   122844
Effective search space used:   122844
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: 50 (23.9 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