GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Pseudomonas fluorescens FW300-N2E3

Align MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate AO353_25125 AO353_25125 sugar ABC transporter permease

Query= TCDB::Q8DT26
         (278 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25125
          Length = 280

 Score =  127 bits (318), Expect = 4e-34
 Identities = 89/279 (31%), Positives = 147/279 (52%), Gaps = 9/279 (3%)

Query: 3   RKKQLQIGSIYALLILLSFIWLFPIIWVILTSFRGEGTAY-VPYIIPKTWTLDNYIKLFT 61
           +K  L++G  + L+ +L    +FP  + I+TS +     + V Y I       NY  +  
Sbjct: 7   KKALLRLG-FWCLIGILLLYAVFPFYYAIVTSLKPSSALFEVSYWIDSP-DFSNYAAVLH 64

Query: 62  NSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFM 121
            SSF   R   N+L+V+     L+  +++  AY+L R+KF+ R   L + L ++MFP   
Sbjct: 65  QSSFL--RAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVA 122

Query: 122 SMIAVYYILKALNLTQTLTSLVLVYSSGAA-LTFYIAKGFFDTIPYSLDESAMIDGATRK 180
            +  ++ +++AL L  T  +L+L Y+      T ++   F   +P+ L+E+A++DGA+  
Sbjct: 123 VLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPW 182

Query: 181 DIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVI-LGDATSKYTVAIGLFSMLQADTI 239
               ++ LPL  P +V T LLAFIA W +F+FA    L D      VAI L S      +
Sbjct: 183 VTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHEL 242

Query: 240 NNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278
             W +  AA SVL+ +P+ IL +  Q+  V G+T G++K
Sbjct: 243 -PWGLLMAA-SVLVTVPLVILVLIFQRRIVSGLTAGALK 279


Lambda     K      H
   0.330    0.142    0.428 

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: 236
Number of extensions: 19
Number of successful extensions: 3
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: 278
Length of database: 280
Length adjustment: 26
Effective length of query: 252
Effective length of database: 254
Effective search space:    64008
Effective search space used:    64008
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: 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 (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