GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisM in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate Pf1N1B4_3433 Arginine/ornithine ABC transporter, permease protein AotM

Query= reanno::pseudo5_N2C3_1:AO356_09910
         (229 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3433 Arginine/ornithine
           ABC transporter, permease protein AotM
          Length = 232

 Score =  218 bits (555), Expect = 8e-62
 Identities = 112/221 (50%), Positives = 158/221 (71%), Gaps = 1/221 (0%)

Query: 2   NWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFR 61
           +++VI + LP    G   TL+L+A+++  GLL A+PLG+ R S+   V    + + +  R
Sbjct: 4   DYNVIWEALPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIR 63

Query: 62  GTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAI 121
           GTP+LVQLFL+YYGLAQF+AVR S LWP+L    +CA +   ++T+AY AEI+ G+++A 
Sbjct: 64  GTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRAT 123

Query: 122 PKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGM 181
           P GEIEAA+A+GMSR K    I+LP A R  LP YSNEVI+ML+ ++LAS VTL+++TG 
Sbjct: 124 PNGEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGA 183

Query: 182 ARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLE-RWL 221
           ART+ A+ YLP E +  AG+FYL ++F+LV+ FK  E RWL
Sbjct: 184 ARTVNAQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHRWL 224


Lambda     K      H
   0.331    0.141    0.434 

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: 175
Number of extensions: 4
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: 232
Length adjustment: 23
Effective length of query: 206
Effective length of database: 209
Effective search space:    43054
Effective search space used:    43054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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