GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas fluorescens FW300-N2C3

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate AO356_23060 AO356_23060 gluconolactonase

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23060
          Length = 301

 Score =  147 bits (371), Expect = 3e-40
 Identities = 95/301 (31%), Positives = 151/301 (50%), Gaps = 11/301 (3%)

Query: 4   IKIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVAL 63
           ++ E +V     +GESPVW  +E  L +V+I    + RW+ S+ K+Q       +  +A 
Sbjct: 1   MQAELIVDARNAVGESPVWVPEENALYWVNIPSGGLQRWNASSGKIQGWEAPEMLACIAR 60

Query: 64  RKSGGYVLAMGNTFSALNWEDQ---SVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQ 120
            + GG+V  M + F  L+  D           V+  + + R NDG+ D +GRF AG+M  
Sbjct: 61  HQDGGWVAGMESGFFRLHPHDDGSLDSELCGSVEHSRVDMRLNDGRCDRQGRFWAGSMVL 120

Query: 121 EIRPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDS--LSFKVDAL 178
            +  A V+  +   +       V        + NGL +S D +T+Y  DS  LS ++ A 
Sbjct: 121 NM-AANVDEGRMYRYEAGQRSPVEAQLSGFIVPNGLGFSPDGRTMYLSDSHPLSQQIWAF 179

Query: 179 DYDMKTGKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTV 238
           DYD+ +G  SNRR    +    G PDG  +DA+G  W+   + G + R  P+ G+  +++
Sbjct: 180 DYDIDSGTPSNRRLFVDMLPLAGRPDGAAVDADGCYWICANDAGLIHRFTPD-GRLDRSL 238

Query: 239 KLPIDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFA 298
           ++P+ K T C FGG     ++VTS   G D D    Q  +GG++ +   GVKG+A   F 
Sbjct: 239 EVPVKKPTMCAFGGSRLDTLFVTSIRPGDDND---PQSLAGGVFALKP-GVKGLAEPVFG 294

Query: 299 G 299
           G
Sbjct: 295 G 295


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: 343
Number of extensions: 26
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: 301
Length adjustment: 27
Effective length of query: 272
Effective length of database: 274
Effective search space:    74528
Effective search space used:    74528
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