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 353925 BT4399 conserved hypothetical protein (NCBI ptt file)

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__Btheta:353925
          Length = 383

 Score =  191 bits (485), Expect = 3e-53
 Identities = 125/397 (31%), Positives = 210/397 (52%), Gaps = 28/397 (7%)

Query: 1   MRRLPTLCLLALAPLTGVAPQA-------QAASLYNLLVGTYTEGSSEGIQVYRFDGADG 53
           ++   T+C++ +   +  + +A       +A     ++VGTYT G S+G+  +RF+  +G
Sbjct: 2   LKTFATICIIGMFTSSCTSKKASRTEGSHEAEQDLTMIVGTYTSGDSKGLYSFRFNEENG 61

Query: 54  SVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQIS 113
           +    L  A   NPSYL  + D + ++ V+E       +    A ++ F+   G  + ++
Sbjct: 62  TATA-LSEAEVENPSYLVPSADGKFIYAVSEFS-----NEQAAANAFAFNKEEGTFRLLN 115

Query: 114 QVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVH 173
             +T  + P Y  +  +G  +  ANYS    GS++V P+  DGSL P  +V   + S   
Sbjct: 116 TQKTGGEDPCY--IITNGSNVVTANYS---GGSISVFPIDKDGSLLPASEVVKFKGSGAD 170

Query: 174 P-RQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAP----EQAERPLQAADPAFVPTP 228
             RQ   H+H V  +PDG+YLFA DLG D++  +   P    +  +  L+   PA     
Sbjct: 171 KERQEKPHLHCVRITPDGKYLFADDLGTDQIHKFIVNPNAKADNEDVFLKEGSPASYKVE 230

Query: 229 PGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGAL 288
            GSGPRHL F+ +G +AYL  ELSG V+ F +  +G L+++QT     A   G  G+G +
Sbjct: 231 AGSGPRHLTFAPNGSYAYLINELSGTVIAFEY-NDGELKEIQT---IAADTVGAKGSGDI 286

Query: 289 HLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVA 348
           H+S DG+FL   NR   + L  F++ P +G L  V  + + G  PR F  +P G+++LVA
Sbjct: 287 HISPDGKFLYASNRLKADGLAIFSIHPENGMLTKVGYQ-LTGIHPRNFIITPNGKYLLVA 345

Query: 349 NQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFV 385
            ++S+ ++V+ RD  +G +    + ++V  P  ++FV
Sbjct: 346 CRDSNVIQVYERDTDTGLLTDIRKDIKVDKPVCIKFV 382


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: 526
Number of extensions: 48
Number of successful extensions: 11
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: 383
Length adjustment: 30
Effective length of query: 358
Effective length of database: 353
Effective search space:   126374
Effective search space used:   126374
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