GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6035 Ribose ABC transport
           system, periplasmic ribose-binding protein RbsB (TC
           3.A.1.2.1)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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