GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Caulobacter crescentus NA1000

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate CCNA_01882 CCNA_01882 SMP-30/gluconolaconase/LRE-like protein

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__Caulo:CCNA_01882
          Length = 293

 Score =  153 bits (387), Expect = 4e-42
 Identities = 95/294 (32%), Positives = 144/294 (48%), Gaps = 13/294 (4%)

Query: 6   IECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRK 65
           +E +  E  ++GESP+W+   G L +VD     + R+DP T + +S+    PIGSV L +
Sbjct: 5   VEIIGKERCRLGESPLWDADAGVLYWVDSMAPAIWRYDPFTSEQRSIPAPKPIGSVVLGR 64

Query: 66  SGGYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPA 125
            G  +  + +    +  +  + T +A  D   P  RFNDGK D +GRF+ GTM+      
Sbjct: 65  PGELIAGLADGVYRVQLDTGAFTPIALPDTLAPIERFNDGKADRQGRFVTGTMAMHNETG 124

Query: 126 VVER----NQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYD 181
            + +    + G  + + P        + ++I+N   +S    TLY+ DSL   V A  YD
Sbjct: 125 RIGKLYRFSAGGAWEVLPT-------EPIEIANSTCFSPSGDTLYFADSLRHMVWAFSYD 177

Query: 182 MKTGKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLP 241
            KTG    +R  +        PDG  +DAEG +W+A     ++IRI P+ G+  + V+ P
Sbjct: 178 PKTGAVGEKRDFFDTTGFNSAPDGATVDAEGHIWLALVQAQKLIRISPD-GRLDRVVESP 236

Query: 242 IDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPT 295
               +   FGG D   +YVTS  D      K     SG +    GLGV+GIA T
Sbjct: 237 APFCSCPAFGGEDLDILYVTSISDSGGR-LKTDVDASGRLMAFHGLGVRGIAET 289


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: 312
Number of extensions: 18
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: 293
Length adjustment: 26
Effective length of query: 273
Effective length of database: 267
Effective search space:    72891
Effective search space used:    72891
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