GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fru2-IIC in Pseudomonas fluorescens GW456-L13

Align PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized)
to candidate PfGW456L13_5073 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::Q3JZE4
         (367 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5073
          Length = 579

 Score =  213 bits (543), Expect = 8e-60
 Identities = 121/345 (35%), Positives = 192/345 (55%), Gaps = 20/345 (5%)

Query: 6   KKANFKGHLLTAISYLIPIVCGAGFLVAIGMAMGGRAQDALVIGNFSFWDTMATM----- 60
           +K     HLLT +S+++P+V   G ++A+    G        I  F    T+A       
Sbjct: 235 EKTGVYKHLLTGVSFMLPMVVAGGLMIALSFVFG--------ITAFKEEGTLAAALMQIG 286

Query: 61  GGKALGLLPVIIATGIAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGI 120
           G  A  L+  ++A  IA+SIA +PG+APG + GL+A+ + AGFIGGI+ G++AG+ A  I
Sbjct: 287 GDSAFKLMVPLLAGYIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFLAGYAARAI 346

Query: 121 LKNVKVPNWAKGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLV 180
            +  ++P   + L P LI+P  A+L + L+MIY++G P++     LT+FL S+G T+ ++
Sbjct: 347 NRYARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTNFLDSMGTTNAIL 406

Query: 181 MGAVIGVLSGVDLGGPLNKTVYAFVLTLQAEGVKEPLTALQLVNTATPVGFGLAYFIAKL 240
           +G ++G +  VDLGGP+NK  YAF + L A     P+ A        P+G G+A FIA  
Sbjct: 407 LGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIA-- 464

Query: 241 FKKNIYTNDEIETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTMGA 300
             +  +   E E  K+A+ +G+  I EG IP    + +  I A   GGA+ GA+SM  G 
Sbjct: 465 --RRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGC 522

Query: 301 DSAVPFGG--ILMIP-TMTRPIAGICGLLSNILVTGLVYSLAKKP 342
               P GG  +L IP  +   +  +  +++  L+T + Y+L K+P
Sbjct: 523 KLMAPHGGLFVLAIPNAINHALLYLLAIVAGSLLTAVAYALVKRP 567


Lambda     K      H
   0.323    0.143    0.415 

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: 615
Number of extensions: 41
Number of successful extensions: 6
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: 367
Length of database: 579
Length adjustment: 33
Effective length of query: 334
Effective length of database: 546
Effective search space:   182364
Effective search space used:   182364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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