GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate Pf1N1B4_5114 Maltose/maltodextrin ABC transporter, permease protein MalG

Query= reanno::Smeli:SM_b20327
         (276 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5114 Maltose/maltodextrin
           ABC transporter, permease protein MalG
          Length = 280

 Score =  380 bits (976), Expect = e-110
 Identities = 184/269 (68%), Positives = 227/269 (84%)

Query: 8   RTAFYALVAVIILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSHGTFVRN 67
           R  F+ L+ V++L AVFPFYYAI+TSLK  +ALF + YW  +   +NYA + +  +F+R 
Sbjct: 12  RLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPDFSNYAAVLNQASFLRA 71

Query: 68  LGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELI 127
           +GNSL+VA  VV ++L L++TAAYAL RV+FRGRG +L+ +L VSMFPQ+AVL+GLFE+I
Sbjct: 72  IGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVI 131

Query: 128 RFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMP 187
           R +G++NT  ALI SY IFTLPFTVWVLTTFM  LP E+EEAAI+DGASPWV +TRV +P
Sbjct: 132 RALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLP 191

Query: 188 LMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAAS 247
           L+WPALVTTGLLAFIAAWNEFLFALTFT ++TQRTVPVAIAL+SGGS  E+PWG +MAAS
Sbjct: 192 LLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAAS 251

Query: 248 VIVTVPLVVLVLIFQRRIISGLTAGGVKG 276
           V+VTVPLV+LVLIFQRRI+SGLTAG +KG
Sbjct: 252 VVVTVPLVILVLIFQRRIVSGLTAGALKG 280


Lambda     K      H
   0.332    0.143    0.426 

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: 274
Number of extensions: 10
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: 276
Length of database: 280
Length adjustment: 25
Effective length of query: 251
Effective length of database: 255
Effective search space:    64005
Effective search space used:    64005
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: 47 (22.7 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