GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Pseudomonas simiae WCS417

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__WCS417:GFF5028
          Length = 370

 Score =  229 bits (583), Expect = 1e-64
 Identities = 134/296 (45%), Positives = 178/296 (60%), Gaps = 16/296 (5%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78
           G+ + V++++L+I  GEFL L+GPSG GK+T+L M+AG ET T GE++L  R +N V   
Sbjct: 22  GENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLAGRSINNVPPH 81

Query: 79  DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138
            RDI MVFQ+YAL+PH +V  N++F L     L   +I +RV+    M+ +     R P 
Sbjct: 82  KRDIGMVFQNYALFPHMTVAENLAFPLSVRA-LSKTDISERVKRVLSMVQLDAFAQRYPA 140

Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198
           QLSGGQQQRVAL RA+V +P++ LMDEPL  LD +LR  M+ E++ L   LGVT VYVTH
Sbjct: 141 QLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVTVVYVTH 200

Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSG---- 254
           DQ EA+TM DRVAV   GE+QQ+  P   Y  P N FVA FIGE   N  +G L      
Sbjct: 201 DQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFIGE--NNRLNGRLHSHSGE 258

Query: 255 ----DTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTV-GERRSGQRTFDAEV 305
               +  RG+  +         Q+GG   +TL +RPE V++ G   S    F   V
Sbjct: 259 RCVVELARGEKVE--ALAVNVGQVGGP--VTLSVRPERVSLNGSSESCVNRFSGRV 310


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: 392
Number of extensions: 15
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: 370
Length adjustment: 30
Effective length of query: 353
Effective length of database: 340
Effective search space:   120020
Effective search space used:   120020
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 17 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