GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gnl in Pseudomonas simiae WCS417

Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate GFF2903 PS417_14855 gluconolactonase

Query= metacyc::MONOMER-13276
         (356 letters)



>lcl|FitnessBrowser__WCS417:GFF2903 PS417_14855 gluconolactonase
          Length = 365

 Score =  129 bits (324), Expect = 1e-34
 Identities = 102/319 (31%), Positives = 155/319 (48%), Gaps = 51/319 (15%)

Query: 65  IEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDA-GVSIFLKPSGHAEPIPAGQ 123
           +E +A+ ++W+EGPVW+ +G +LL SD P N + +W      +S++ + +          
Sbjct: 70  VERLATGLRWAEGPVWIGDGRYLLVSDIPNNRIVRWDEVTDSLSVYRENANF-------- 121

Query: 124 FREPGSNGMKVGPDGKIWVADSGT-----RAIMKVDPVTRQRSVVVDNYKGKRFNSPNDL 178
                SNGM     G++ V +  T     R I + +      +V+ D++ GK FNSPND+
Sbjct: 122 -----SNGMCRDRQGRLLVCEGSTTTREGRRITRTEH-NGSLTVLADSFDGKPFNSPNDI 175

Query: 179 FFSKSGAVYFTDPPYGLTNLDES-DIKEMNYNGVFRLSPD-GRLDLIEAGLSRPNGLALS 236
              + G+V+FTDPP+  +N  E   I     +GV+R+  + G +  +   L+ PNGL  S
Sbjct: 176 VCKRDGSVWFTDPPFQTSNNYEGHKIAPTQPHGVYRIDGESGTVTRVIDDLNGPNGLCFS 235

Query: 237 PDETKLYVSNSDRASPN--IWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNIDK 294
           PDE  LYV    RA PN  IW   +  +G   +R      RK       A L DG+  D+
Sbjct: 236 PDEKVLYVVEG-RAKPNRLIWAIDVKDDGTLGAR------RKHIEGFDYAAL-DGIKCDE 287

Query: 295 QGNLFASAPG------------GIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQTLFI 341
            GNL+    G            G+ +F P G+ +G IS     P  N CF G +G  LF+
Sbjct: 288 SGNLWCGWGGNGDPKADLEKLDGVRVFNPQGKAIGHISLPERCP--NLCFGGREGNRLFM 345

Query: 342 SASHNV----VRVRTKTFG 356
           + SH++    V  R   FG
Sbjct: 346 AGSHSIYSLFVNTRDAGFG 364


Lambda     K      H
   0.317    0.135    0.409 

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: 437
Number of extensions: 28
Number of successful extensions: 4
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: 356
Length of database: 365
Length adjustment: 29
Effective length of query: 327
Effective length of database: 336
Effective search space:   109872
Effective search space used:   109872
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 (21.6 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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