GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Bacteroides clarus YIT 12056

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_009122468.1 BUB52_RS02845 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_900129655.1:WP_009122468.1
          Length = 372

 Score =  194 bits (492), Expect = 4e-54
 Identities = 128/384 (33%), Positives = 212/384 (55%), Gaps = 28/384 (7%)

Query: 8   CLLALAPLTGVAPQAQAAS---LYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHT 64
           C+L L+ +    PQ    S     ++L+GTYT+G+S+GI  +RF+   G+   PL     
Sbjct: 6   CMLGLS-MAACTPQKTVNSGEDELSMLIGTYTDGTSKGIYSFRFNQKTGTAT-PLGSVEL 63

Query: 65  SNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTY 124
           SNPSYLT + D + ++ V+E       D+     +  FD  +G L+ ++  +T    P Y
Sbjct: 64  SNPSYLTPSEDGKFIYAVSE-----MNDSTAAVNALAFDKQTGNLRLLNSERTPGAAPCY 118

Query: 125 SSLSHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHS 183
             +S +G+ +  ANYS    G+++V  +R DG+L+P   +    A+     RQ+  H+H 
Sbjct: 119 --VSTNGKEVLTANYS---GGNMSVFRLRKDGTLSPAEALFKGTANGPDTIRQIVPHIHC 173

Query: 184 VVSSPDGQYLFAPDLGADKVFVYRYAPEQ--AERPLQAADPAFVPTPPGSGPRHLIFSAD 241
            + SPDG+Y+FA D  AD++  +  + E   +  P +A D       P SGPRHL FS +
Sbjct: 174 ALFSPDGKYIFATDFSADRILRFTLSSEGNISRLPGEATD-----ITPDSGPRHLTFSPN 228

Query: 242 GRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLN 301
           G+FAYL  ELSG+V+ F +  +G+L Q+Q+  +A    Q + G+  +HLS DG+FL   N
Sbjct: 229 GKFAYLINELSGKVIAFGYT-DGKLEQIQS--IAADSLQAR-GSADIHLSPDGKFLYASN 284

Query: 302 RGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARD 361
           R + + +  F VD  +G L     +   G  PR F  +P G+++L A ++S+ ++V+ RD
Sbjct: 285 RLEGDGIAIFTVDTVNGTLTRAGYQPT-GIHPRHFNITPNGKYLLAACRDSNVIQVYERD 343

Query: 362 PQSGQVGKTLQSVEVGSPSDLRFV 385
            ++G +  T Q + +  P  ++F+
Sbjct: 344 TENGLLKDTQQDILIDKPVCVQFI 367


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: 519
Number of extensions: 52
Number of successful extensions: 14
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 388
Length of database: 372
Length adjustment: 30
Effective length of query: 358
Effective length of database: 342
Effective search space:   122436
Effective search space used:   122436
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