GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Bacteroides thetaiotaomicron VPI-5482

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate 350650 BT1122 conserved hypothetical protein (NCBI ptt file)

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__Btheta:350650
          Length = 384

 Score =  163 bits (413), Expect = 7e-45
 Identities = 110/363 (30%), Positives = 188/363 (51%), Gaps = 22/363 (6%)

Query: 30  LLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGG 89
           LLVG Y +   EG+++YRFDG    V  P  +   SNP++LT       ++ + ++   G
Sbjct: 37  LLVGCYMKPDEEGVRMYRFDGQTADVDYPCGLRGISNPAFLTSDSTGNRIYAIGDDE--G 94

Query: 90  KGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAV 149
           K  T   A +  FD  SG L  ++   T  + P Y +LS    ++  ANY     GS+ V
Sbjct: 95  KSST---ANALLFDKESGLLSLLNSQSTDGELPIYITLSPKEYFVLTANYK---GGSITV 148

Query: 150 LPVRADGSL---APVVQVESHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVY 206
                 G L     +++   +  +K   RQ   H+H V  +PDG++L A DLG D ++++
Sbjct: 149 FSQDKKGKLQRDTKIIRFAGNGPNK--KRQEQSHLHCVTFTPDGKFLLATDLGTDCIYLF 206

Query: 207 RYA--PE--QAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEG 262
                PE  +A   L  +    +    GSGPRH+ F  +GRFAYL  ELSG++ VF++  
Sbjct: 207 PIGKRPEAGKAHSLLDESRVVRIQMDSGSGPRHICFHPNGRFAYLISELSGKITVFSY-N 265

Query: 263 NGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRF 322
            G+L +LQT    P   +G      +H+S+DG+FL       ++ ++ +++D   G L  
Sbjct: 266 EGKLERLQTIVCDPFVAEGNAD---IHVSSDGKFLYASKHLKEDGIIVYSIDSQKGTLVQ 322

Query: 323 VERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDL 382
           +  +   G  PR FA SP G ++ V  ++++ +++F R+  +G +  T +++ +  P+ +
Sbjct: 323 IGFQPT-GLYPRSFAISPDGCYLAVVCRDANCIQIFERNRNTGLLKNTGKNIRLERPAFV 381

Query: 383 RFV 385
           +F+
Sbjct: 382 KFL 384


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: 488
Number of extensions: 36
Number of successful extensions: 9
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: 384
Length adjustment: 30
Effective length of query: 358
Effective length of database: 354
Effective search space:   126732
Effective search space used:   126732
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.

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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