GapMind for catabolism of small carbon sources

 

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

Align LacI family transcriptional regulator (characterized, see rationale)
to candidate Pf1N1B4_6035 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)

Query= uniprot:A0A161ZH48
         (318 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6035
          Length = 318

 Score =  603 bits (1556), Expect = e-177
 Identities = 318/318 (100%), Positives = 318/318 (100%)

Query: 1   MKLPFAGRLLAVAMLAAASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQ 60
           MKLPFAGRLLAVAMLAAASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQ
Sbjct: 1   MKLPFAGRLLAVAMLAAASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQ 60

Query: 61  KDHSGDFELISNGIKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGI 120
           KDHSGDFELISNGIKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGI
Sbjct: 61  KDHSGDFELISNGIKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGI 120

Query: 121 TVINIDNQLDPAVVKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTN 180
           TVINIDNQLDPAVVKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTN
Sbjct: 121 TVINIDNQLDPAVVKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTN 180

Query: 181 AQQRTAGFKDAMEAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGA 240
           AQQRTAGFKDAMEAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGA
Sbjct: 181 AQQRTAGFKDAMEAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGA 240

Query: 241 VSAVRAAGKAGKVQVVGYDNINAIKPMLKDGRVLATADQFAARQAVFGIETALKIIKGET 300
           VSAVRAAGKAGKVQVVGYDNINAIKPMLKDGRVLATADQFAARQAVFGIETALKIIKGET
Sbjct: 241 VSAVRAAGKAGKVQVVGYDNINAIKPMLKDGRVLATADQFAARQAVFGIETALKIIKGET 300

Query: 301 VDSGANGVIETPVELVTK 318
           VDSGANGVIETPVELVTK
Sbjct: 301 VDSGANGVIETPVELVTK 318


Lambda     K      H
   0.314    0.130    0.348 

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: 428
Number of extensions: 8
Number of successful extensions: 1
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: 318
Length of database: 318
Length adjustment: 27
Effective length of query: 291
Effective length of database: 291
Effective search space:    84681
Effective search space used:    84681
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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