GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Shewanella loihica PV-4

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  219 bits (558), Expect = 1e-61
 Identities = 115/252 (45%), Positives = 170/252 (67%), Gaps = 8/252 (3%)

Query: 4   LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63
           L ++ V+K++ D     + AV+++SL+I+ GE   L+G SG GKST LRM+AG E  TEG
Sbjct: 21  LKIERVSKLFDD-----VRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEG 75

Query: 64  ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123
            + L+ + +  +   +R I M+FQSYAL+PH +V  N++FGL++   +P  EI QRV+E 
Sbjct: 76  RIYLDGQDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDK-MPKAEIEQRVKEM 134

Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183
             ++ +     RKP QLSGGQ+QRVAL R++ + P++ L+DEP+  LD KLR +M+ E+ 
Sbjct: 135 LKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVV 194

Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243
            +   +GVT V VTHDQ EAMTM +R+A+++DG + Q G+P+D Y  P N  VA FIG  
Sbjct: 195 DILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIG-- 252

Query: 244 SMNLFDGSLSGD 255
           S+NLF+G +  D
Sbjct: 253 SVNLFEGDIVED 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: 385
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: 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 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