GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Sphingomonas koreensis DSMZ 15582

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate Ga0059261_1893 Ga0059261_1893 Gluconolactonase

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__Korea:Ga0059261_1893
          Length = 295

 Score =  146 bits (368), Expect = 6e-40
 Identities = 86/265 (32%), Positives = 128/265 (48%), Gaps = 7/265 (2%)

Query: 18  ESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGGYVLAMGNTF 77
           E PVW +++  L FVDI   ++ R+DP++ + +S    A +G      +G +V  +    
Sbjct: 20  EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79

Query: 78  SALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPAVVERNQGSLFTL 137
           +  +  D+S T L   +   P NR NDG VDP GR   GTM      A      G ++ L
Sbjct: 80  AIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEAT-----GRIYRL 134

Query: 138 YPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTGKSSNRRTLYKLQ 197
             D   V     V ISNG   S D +TLY++D+L   + +       G   + R    + 
Sbjct: 135 GGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG-DDGILGDSRVFATIP 193

Query: 198 QDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKTTSCCFGGPDYSE 257
             EG PDG  +DAEG +W+  YNG  V R  P  G+ +  V  P+   T   FGGPD   
Sbjct: 194 NSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSP-AGELLDVVAFPVGAITKVAFGGPDLRT 252

Query: 258 MYVTSACDGMDEDWKKRQPQSGGIY 282
           +Y T+A   +D D +  +P +G ++
Sbjct: 253 VYATTASKHLDADGRAEEPHAGDLF 277


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: 282
Number of extensions: 17
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: 295
Length adjustment: 26
Effective length of query: 273
Effective length of database: 269
Effective search space:    73437
Effective search space used:    73437
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