GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas fluorescens FW300-N1B4

Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate Pf1N1B4_413 L-arabinolactonase (EC 3.1.1.15)

Query= SwissProt::Q9I922
         (299 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_413
          Length = 314

 Score =  113 bits (283), Expect = 5e-30
 Identities = 88/300 (29%), Positives = 138/300 (46%), Gaps = 23/300 (7%)

Query: 9   VVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGG 68
           V     ++GE P W+     L +VDI G++  R   +  ++  +     + +    +SG 
Sbjct: 29  VTGHRAQLGEGPFWDAPTQALYWVDIAGKQALRLIGANVEIWQMPEH--VSAFIPCESGD 86

Query: 69  YVLAMGNTFSALNWEDQSVT---TLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEI--- 122
            ++ + +    L+     +    TL  V + +P NR N+ + D +GR   GTM   I   
Sbjct: 87  ALVTLSSGVYRLDLASPGLEPRLTLFCVADPQPGNRPNEARCDAQGRLWLGTMQNNIGEQ 146

Query: 123 -RPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYD 181
                V R  G LF +  D  V      + I N L WS D  TLY+ DSL    D+  Y 
Sbjct: 147 GEDLPVVRRSGGLFRIDRDARVTPLLRGLGIPNTLLWSDDGTTLYFADSL----DSTLYR 202

Query: 182 MKTGKSSNRRTLYKL--QQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVK 239
                  N  T Y      + G PDG  +DAEG +W A ++G  ++R++P+ G   + ++
Sbjct: 203 HFIHTDGNLDTAYVWFGPHERGGPDGSAMDAEGYVWNARWDGSCLLRLNPD-GYVDRVIE 261

Query: 240 LPIDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299
           LP+ + TSC FGG D+  +Y+TSA   ++       P  G +  I  + V G A   FAG
Sbjct: 262 LPVSRPTSCVFGGEDFKTLYITSAASPLN------HPLDGALLSIR-VDVPGKACQRFAG 314


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: 331
Number of extensions: 23
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: 314
Length adjustment: 27
Effective length of query: 272
Effective length of database: 287
Effective search space:    78064
Effective search space used:    78064
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