GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08235 in Pseudomonas fluorescens FW300-N2E2

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Pf6N2E2_1432 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

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



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1432 High-affinity
           branched-chain amino acid transport system permease
           protein LivH (TC 3.A.1.4.1)
          Length = 293

 Score =  126 bits (317), Expect = 5e-34
 Identities = 94/309 (30%), Positives = 163/309 (52%), 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----LTFVSLVER 56

Query: 61  GIT-WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119
           G+  W  LA L+ L A+ML  AV    VER+  RPL +   +   ++ +G+S  ++ + Q
Sbjct: 57  GVPFW--LAFLISL-AAMLLIAV---AVERVVLRPLINRSPITLFMATLGLSYVIEGFAQ 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+ RP GL
Sbjct: 225 PVLIIGGFTSISGAIVGGLIIGASEKLAEVYLGPFIGSGIENWFPYVLALVFLLVRPAGL 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: 291
Number of extensions: 23
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 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