GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate AO353_01535 AO353_01535 amino acid ABC transporter permease

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



>FitnessBrowser__pseudo3_N2E3:AO353_01535
          Length = 242

 Score =  296 bits (757), Expect = 3e-85
 Identities = 150/225 (66%), Positives = 185/225 (82%)

Query: 3   LYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPD 62
           L GFGP+LL G+  T++LS+LSL  +VLLGL GA+AKLS  + LR  A  YTTLIR VPD
Sbjct: 16  LKGFGPLLLEGSWMTVKLSILSLLLSVLLGLIGASAKLSSVKLLRIPAQLYTTLIRGVPD 75

Query: 63  LVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPR 122
           LVLMLL+FYS+Q  + + T+AL     +I+PF AG++TLGFIYGAYFTETFRGA LAVPR
Sbjct: 76  LVLMLLIFYSLQTWLTSFTEALGWEYIEINPFAAGIITLGFIYGAYFTETFRGAILAVPR 135

Query: 123 GQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQ 182
           GQ+EA +AYG+S A+ F  ++FPQMMRFALPGIGNNW V++KATALVSIIGLAD+VKAAQ
Sbjct: 136 GQMEAATAYGLSRAQRFRFVVFPQMMRFALPGIGNNWMVILKATALVSIIGLADLVKAAQ 195

Query: 183 DAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGVRHA 227
           DAGKS++ +FFF+++AALIYL IT+ASN VL WLE+ Y+ G R A
Sbjct: 196 DAGKSSYQLFFFLVLAALIYLVITSASNYVLRWLERHYAAGSREA 240


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: 202
Number of extensions: 3
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: 242
Length adjustment: 23
Effective length of query: 206
Effective length of database: 219
Effective search space:    45114
Effective search space used:    45114
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: 46 (22.3 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