GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Phaeacidiphilus oryzae TH49

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  176 bits (445), Expect = 1e-48
 Identities = 106/295 (35%), Positives = 160/295 (54%), Gaps = 6/295 (2%)

Query: 21  DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQ 80
           DL +  G   VL+GP+  GK++ +R++AGL+    G+I     DVT +P + R++AMV+Q
Sbjct: 25  DLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPKDRDIAMVFQ 84

Query: 81  QFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRT 140
            +  YP +TV +N+   ++I+G + A I  +V +AA++L LT +LDR P  LSGGQ+QR 
Sbjct: 85  NYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKALSGGQRQRV 144

Query: 141 ALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLGG 200
           A+ RA+V+   + LMDEPL+NLD KLR   R ++  +  + G   VY T +  EA+ +G 
Sbjct: 145 AMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHDQVEAMTMGD 204

Query: 201 NTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDV-TKSGNVFTRPSGVTI-- 257
             A L  G + Q      +Y RP NL  AG    P +N ++V    G V    S V +  
Sbjct: 205 RVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVKFGESVVQVSR 264

Query: 258 PVPSHLAVVPDGPVTIAFHPHHLGLAPQT---GDAARLQARTLVSEITGSESFVH 309
                 A   D  VT+   P HL +   T   G+   L     V E  G++ +V+
Sbjct: 265 DAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEELGADGYVY 319


Lambda     K      H
   0.319    0.136    0.392 

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: 338
Number of extensions: 15
Number of successful extensions: 1
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: 358
Length of database: 369
Length adjustment: 29
Effective length of query: 329
Effective length of database: 340
Effective search space:   111860
Effective search space used:   111860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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