GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Bb in Pseudomonas fluorescens FW300-N1B4

Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate Pf1N1B4_5114 Maltose/maltodextrin ABC transporter, permease protein MalG

Query= uniprot:Q6MNM1
         (272 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5114
          Length = 280

 Score =  174 bits (442), Expect = 1e-48
 Identities = 91/267 (34%), Positives = 150/267 (56%), Gaps = 4/267 (1%)

Query: 8   WISILLFSLFSIYPILYVLSVSLRPDNAFQTQSLEIIGPNASFKNFVDLFATTDFLIWMR 67
           W  I +  L++++P  Y +  SL+P +A    S  I  P+  F N+  +     FL  + 
Sbjct: 16  WCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPD--FSNYAAVLNQASFLRAIG 73

Query: 68  NSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYIILSK 127
           NSLVV+     L + L+ T+AYAL R +FRGR  +L  +L   MFP   ++   + ++  
Sbjct: 74  NSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRA 133

Query: 128 LRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIILPVS 187
           L L ++ W L L Y+   LPF +W +  +   +P ELEEAA++DG S W+   +++LP+ 
Sbjct: 134 LGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLL 193

Query: 188 SPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQASLATQ--WGLYAAGALI 245
            PALV T L +F+++W+E++ A          T+P+ +         +  WGL  A +++
Sbjct: 194 WPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVV 253

Query: 246 VSVPVLILFISISRYLVSGLTMGSVKG 272
           V+VP++IL +   R +VSGLT G++KG
Sbjct: 254 VTVPLVILVLIFQRRIVSGLTAGALKG 280


Lambda     K      H
   0.329    0.139    0.421 

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: 250
Number of extensions: 15
Number of successful extensions: 2
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: 272
Length of database: 280
Length adjustment: 25
Effective length of query: 247
Effective length of database: 255
Effective search space:    62985
Effective search space used:    62985
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