GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Tatumella morbirosei LMG 23360

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_052752433.1 HA49_RS04380 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_000757425.2:WP_052752433.1
          Length = 405

 Score =  204 bits (520), Expect = 3e-57
 Identities = 133/400 (33%), Positives = 214/400 (53%), Gaps = 31/400 (7%)

Query: 4   LPTLCLLALAPLTGVAPQAQAAS---LYNLLVGTYT-EGSSEGIQ--------VYRFD-G 50
           +P L    ++     +P AQ A        LVG++T + + E +Q        +YR    
Sbjct: 18  IPLLLSTGISYAENSSPLAQPAHHLPTQTFLVGSWTGQATGEMVQKAIYPSQGIYRVRLN 77

Query: 51  ADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQ 110
           +DGS+  PL +   ++PS++ F+ + +  +  NEN  G         T+ R     G+L 
Sbjct: 78  SDGSLL-PLDMLKLASPSWIVFSHNNKFAYTTNENDAGS-------VTALRVGK-QGKLS 128

Query: 111 QISQVQTLADHPTYSSLSHDGRYLFVANYSVQP-EGSVAVLPVRADGSLAPVVQ----VE 165
            I+Q  +L   PT+++++ D +YL  ANYSV P    + + P+R DG++   VQ    ++
Sbjct: 129 TINQADSLGSQPTHATITLDDKYLIAANYSVAPGHAGITLFPLRTDGAIEDAVQHIPFID 188

Query: 166 SHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFV 225
                K   RQ  GH HSV  +PDG+ LF  DLGAD V  + Y  E+++ PL       +
Sbjct: 189 GSHVVK--DRQDGGHAHSVNMTPDGKMLFVADLGADTVHAFSYHGEKSQ-PLTPEPDFDL 245

Query: 226 PTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGA 285
              PG GPRH+ FS+DG+FAY++ E+S +V V+  E + +L ++Q  DL  +      G 
Sbjct: 246 HFKPGEGPRHMTFSSDGKFAYISTEMSAKVHVYRIE-HDKLSEIQVADLTESKNPDDKGG 304

Query: 286 GALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFV 345
             +  S D +FL V NR   NQ+V F  DP +G+L    R S  G EPR FAF   G+++
Sbjct: 305 AGILFSPDHKFLYVGNRRKVNQIVVFKADPVTGKLTLTRRFSSGGIEPRAFAFDKTGQYM 364

Query: 346 LVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFV 385
           +VAN  S+ +    R+ ++G +  T  ++++G+P+D++FV
Sbjct: 365 IVANVFSNNVVELRRNTENGDLTPTAVTLQIGTPTDIKFV 404


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: 495
Number of extensions: 48
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: 405
Length adjustment: 31
Effective length of query: 357
Effective length of database: 374
Effective search space:   133518
Effective search space used:   133518
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 24 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