GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Pseudomonas fluorescens FW300-N2C3

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate AO356_28385 AO356_28385 ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28385
          Length = 293

 Score =  125 bits (314), Expect = 1e-33
 Identities = 91/309 (29%), Positives = 160/309 (51%), Gaps = 24/309 (7%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60
           ME+F + LI GL  G +Y L+AIG+ ++Y   G+ NFA G + +  A    +TF+++   
Sbjct: 1   MEFFFEVLIGGLLAGVMYALVAIGFVLIYKASGVFNFAQGAMVLFSA----LTFVSLLER 56

Query: 61  GIT-WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119
           G+  W  LA ++ L A +L        VER+  RPL +   +   ++ +G+S  ++ + Q
Sbjct: 57  GVPFW--LAFVISLAAMVLIAV----AVERVVLRPLVNRSPITLFMATLGLSYVIEGFAQ 110

Query: 120 ILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179
            L GA+   L+ +   +  L  G + +S   +   V    L+   + L  +T LG + RA
Sbjct: 111 ALWGAQVHGLE-LGISDEPLELGGMLLSQFDIFAAVTAAFLVLLLSWLFNKTRLGLSLRA 169

Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGV---IDFYIGFLAGVKAF 236
              D   A  +G+ + RV    +V+  A+A   G++  L++G    + F +  L  +KA 
Sbjct: 170 VADDPLAALAVGIRLQRV----WVVVWAVAGFVGLVAGLLWGARLGVQFSLS-LVVLKAL 224

Query: 237 TAAVLGGIGSLPGAMLGGVVIG----LIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292
              ++GG  S+ GA++GG++IG    L E +   ++GS  ++   + + +L L+ RP GL
Sbjct: 225 PVLIIGGFTSISGAIVGGLIIGASEKLAEVYLGPFIGSGIENWFPYVLALLFLLVRPAGL 284

Query: 293 LGRPEIEKV 301
            G   IE+V
Sbjct: 285 FGERAIERV 293


Lambda     K      H
   0.329    0.144    0.425 

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: 289
Number of extensions: 22
Number of successful extensions: 4
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: 301
Length of database: 293
Length adjustment: 26
Effective length of query: 275
Effective length of database: 267
Effective search space:    73425
Effective search space used:    73425
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 (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