GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas simiae WCS417

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate GFF1427 PS417_07255 calcium-binding protein

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__WCS417:GFF1427
          Length = 292

 Score =  168 bits (425), Expect = 2e-46
 Identities = 101/297 (34%), Positives = 161/297 (54%), Gaps = 8/297 (2%)

Query: 4   IKIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVAL 63
           ++IE +V     +GE PVW+ ++  L ++D    ++ R     +++++  V   IGS+AL
Sbjct: 1   MRIEVLVDVKTTLGEGPVWDVEQQRLYWIDSADGRILRCTDDGRELRAWEVGQKIGSMAL 60

Query: 64  RKSG-GYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEI 122
           R+ G   ++A+ N    L+ +   +  +A  +   P+NR NDGKVD +GRF+ G+M  + 
Sbjct: 61  RQDGESAIVALQNGVHTLDLKSGELNLIADPEPHLPDNRLNDGKVDRQGRFIFGSMDTQ- 119

Query: 123 RPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDM 182
                +     L+ L  D S+    + + +SNG  WS    T Y+ D+ S ++ A DYD+
Sbjct: 120 ----EDNASAKLYRLDADLSLHTLDEGIIVSNGPCWSPSGDTFYFCDTWSGEIWAYDYDL 175

Query: 183 KTGKSSNRRTLYKLQ-QDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLP 241
            TG  SNRRT  K+  +  G  DG  +DAEG LW A    G+++R  PE G   + +++P
Sbjct: 176 ATGNVSNRRTFAKVDTRGGGAADGCTVDAEGCLWQALVYAGKLVRYTPE-GVVDRIIQMP 234

Query: 242 IDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFA 298
           + K TS  FGGP+   ++VTS        +     Q G ++ ITGLGV+GIA   FA
Sbjct: 235 VKKVTSLTFGGPNLDTLFVTSMAKPPLPRFPADGQQRGALFAITGLGVQGIAERRFA 291


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: 310
Number of extensions: 27
Number of successful extensions: 7
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: 292
Length adjustment: 26
Effective length of query: 273
Effective length of database: 266
Effective search space:    72618
Effective search space used:    72618
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.

Links

Downloads

Related tools

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