GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pedobacter sp. GW460-11-11-14-LB5

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate CA265_RS25055 CA265_RS25055 6-phosphogluconolactonase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__Pedo557:CA265_RS25055
          Length = 369

 Score =  237 bits (604), Expect = 5e-67
 Identities = 138/387 (35%), Positives = 220/387 (56%), Gaps = 22/387 (5%)

Query: 1   MRRLPTLCLLALAPLTGVAPQAQAASLYNLLVGTYTE-GSSEGIQVYRFDGADGSVKGPL 59
           M+++ +L LL++      A +A     YNL+VGTYT  G SEGI  Y F+ +  +     
Sbjct: 1   MKKISSLFLLSILSTLTFAQKAN----YNLIVGTYTAPGKSEGIYTYNFNASTAATTIKS 56

Query: 60  RVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLA 119
              +T+NPSYL  +PDQ+ ++VVNE G           ++++++  SG L  +++V +  
Sbjct: 57  ITKNTANPSYLAVSPDQKFVYVVNETG------ATSTVSAFKYNAASGALTFLNKVDSHG 110

Query: 120 DHPTYSSLSHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVHP--RQV 177
             P + ++  D + + VANYS    GS+A+   +ADG+L   +Q   H    + P  RQ 
Sbjct: 111 ADPCFITV--DAKNVIVANYS---GGSLAIFSRKADGALTEALQTIEHTGKSIDPKGRQE 165

Query: 178 SGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLI 237
           S HVH V  +PD ++L   DLG D++++Y Y P   E  L     + + T  G+GPRH+ 
Sbjct: 166 SAHVHMVKFTPDYKHLIVNDLGEDRIYIYNYKPAAKENILTVK--SVIKTNAGTGPRHIT 223

Query: 238 FSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFL 297
           FS +G+FAYL  E +G +  FA+  NG L ++Q        F GKV A  +H+SADG+FL
Sbjct: 224 FSPNGKFAYLAHEFNGSITAFAYS-NGSLTKIQEIGTTSKDFTGKVDAADIHVSADGKFL 282

Query: 298 GVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRV 357
              NRGD N +  F+V P +G+L+F+E  S  G  PR F   P G+F+L+ +Q ++ + +
Sbjct: 283 YETNRGDANSISAFSVLP-TGKLKFIETVSTLGKGPRNFTIDPTGKFLLIGHQYTNNIVI 341

Query: 358 FARDPQSGQVGKTLQSVEVGSPSDLRF 384
           F R+  +G++  + + ++VG+P  L F
Sbjct: 342 FKRNKTTGKLSDSGKRIDVGAPVCLVF 368


Lambda     K      H
   0.318    0.135    0.395 

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: 444
Number of extensions: 33
Number of successful extensions: 10
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: 388
Length of database: 369
Length adjustment: 30
Effective length of query: 358
Effective length of database: 339
Effective search space:   121362
Effective search space used:   121362
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: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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