GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate Pf1N1B4_4792 Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)

Query= reanno::BFirm:BPHYT_RS07675
         (229 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4792
          Length = 371

 Score =  276 bits (706), Expect = 4e-79
 Identities = 144/223 (64%), Positives = 181/223 (81%)

Query: 3   LYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPD 62
           L G+GP+LL GT  T++LS LSL  ++ LGL GAAAKLS  + L   AT YTTLIR VPD
Sbjct: 15  LQGYGPLLLHGTWVTLKLSALSLLVSMALGLLGAAAKLSPLKLLNLPATFYTTLIRGVPD 74

Query: 63  LVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPR 122
           LVLMLL+FYS+Q  +++LT+A++ P  +IDPFVAGV+TLGFIYGAYFTETFRGA L+VPR
Sbjct: 75  LVLMLLIFYSLQGWLSSLTEAMDWPYMEIDPFVAGVVTLGFIYGAYFTETFRGAILSVPR 134

Query: 123 GQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQ 182
           GQ EA +++G++  + F  ++FPQMMRFALP +GNNW VL+KATALVSIIGL+D+VK AQ
Sbjct: 135 GQQEAAASFGLNRWQRFRFVVFPQMMRFALPSLGNNWLVLLKATALVSIIGLSDLVKVAQ 194

Query: 183 DAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGVR 225
           +AGKSTFNM  F+L+A  +YL IT+ASN VL  LE+RY+ GVR
Sbjct: 195 EAGKSTFNMLDFLLLAGALYLLITSASNYVLRVLERRYNQGVR 237


Lambda     K      H
   0.329    0.142    0.411 

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: 249
Number of extensions: 9
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: 229
Length of database: 371
Length adjustment: 26
Effective length of query: 203
Effective length of database: 345
Effective search space:    70035
Effective search space used:    70035
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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