GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas putida KT2440

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate PP_3180 PP_3180 Smp-30/Cgr1 family protein

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__Putida:PP_3180
          Length = 346

 Score =  131 bits (330), Expect = 2e-35
 Identities = 82/269 (30%), Positives = 132/269 (49%), Gaps = 7/269 (2%)

Query: 16  IGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGGYVLAMGN 75
           +GES VW+E+ G L FVDI+G ++    P  +        A IG++AL   G  +     
Sbjct: 71  LGESLVWDERSGVLYFVDISGGRINGLTPDGEVDCLYESAARIGALALTDRGNLIFTEDA 130

Query: 76  TFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPAVVERNQGSLF 135
           + +  +   + V+  +     +   RFNDG  DP+GRF+ G M + +       N G+LF
Sbjct: 131 SVAIFDVPTRKVSQHSASVHPRSTYRFNDGACDPQGRFVTGLMDEALSD-----NTGALF 185

Query: 136 TLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTGKSSNRRTLYK 195
                 S     D + +  GL WS D  T+Y++DS +  +   +Y ++ G+        +
Sbjct: 186 RFDWQLSDQVIHDDMGLPTGLAWSHDGHTVYFVDSAARAIYRAEYLIE-GRLGAVTLFAE 244

Query: 196 LQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKTTSCCFGGPDY 255
              + G PDG+ +D EG LWV  Y+G  ++R D   G     V +P+   TSCCFGGP  
Sbjct: 245 TPAELGRPDGLALDREGGLWVCQYHGSCLLRYDRH-GYLTDQVLMPVPCPTSCCFGGPGM 303

Query: 256 SEMYVTSACDGMDEDWKKRQPQSGGIYKI 284
           + +Y+++A   M  +     P +G +Y I
Sbjct: 304 NTLYISTARYDMTPEDLHHYPDAGDLYAI 332


Lambda     K      H
   0.316    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: 305
Number of extensions: 20
Number of successful extensions: 5
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: 299
Length of database: 346
Length adjustment: 28
Effective length of query: 271
Effective length of database: 318
Effective search space:    86178
Effective search space used:    86178
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: 48 (23.1 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