GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2903
          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:

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