GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fru2-IIC in Pseudomonas stutzeri RCH2

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 GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component

Query= TCDB::Q3JZE4
         (367 letters)



>lcl|FitnessBrowser__psRCH2:GFF3289 Psest_3353 PTS system,
           fructose-specific, IIB component/PTS system, fructose
           subfamily, IIC component
          Length = 579

 Score =  213 bits (541), Expect = 1e-59
 Identities = 121/344 (35%), Positives = 196/344 (56%), Gaps = 20/344 (5%)

Query: 6   KKANFKGHLLTAISYLIPIVCGAGFLVAIGMAMGGRAQDALVIGNFSFWDTMAT----MG 61
           +K     H+LT +SY++P+V   G L+A+    G  A        F    T+A     +G
Sbjct: 236 EKTGVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEA--------FKEEGTLAAALMKIG 287

Query: 62  GK-ALGLLPVIIATGIAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGI 120
           G+ A  L+  ++A  IA+SIA +PG+APG + GL+A  + AGFIGGI+ G++AG+ A  +
Sbjct: 288 GETAFQLMVPLLAGYIAYSIADRPGLAPGMIGGLLAGTLGAGFIGGIIAGFVAGYAAKAV 347

Query: 121 LKNVKVPNWAKGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLV 180
            + + +P   + L P LI+P  A+L++ L+MIY++G P++     LT+FL ++G ++ ++
Sbjct: 348 SRWIPLPASIESLKPILIIPLLASLVTGLVMIYIVGTPVAKLLAGLTEFLDTMGTSNAIL 407

Query: 181 MGAVIGVLSGVDLGGPLNKTVYAFVLTLQAEGVKEPLTALQLVNTATPVGFGLAYFIAKL 240
           +G ++G +  VDLGGP+NK  YAF + L A     P+ A        P+G G+A  IA  
Sbjct: 408 LGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGMGIATLIA-- 465

Query: 241 FKKNIYTNDEIETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTMGA 300
             +  +   E E  K+A+ +G   I EG IP    + +  I A   GGA+ GA+SM  GA
Sbjct: 466 --RRKFAQTEREAGKAALVLGCCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMAFGA 523

Query: 301 DSAVPFGG--ILMIP-TMTRPIAGICGLLSNILVTGLVYSLAKK 341
               P GG  +L+IP  +   +  +  +L+  LVTG++Y++ K+
Sbjct: 524 KLLAPHGGLFVLLIPNAINHALLYLVAILAGSLVTGVIYAVIKQ 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: 657
Number of extensions: 43
Number of successful extensions: 10
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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