GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4792 Histidine ABC
           transporter, permease protein HisQ (TC 3.A.1.3.1)
          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 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