GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Pseudomonas fluorescens FW300-N2E2

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate Pf6N2E2_1648 Maltose/maltodextrin ABC transporter, permease protein MalG

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1648
          Length = 280

 Score =  143 bits (361), Expect = 4e-39
 Identities = 87/268 (32%), Positives = 144/268 (53%), Gaps = 10/268 (3%)

Query: 6   LYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAW--EAFRPKF 63
           L G LLL A F   P Y  ++T+LK  +   L  V  W   P + ++       +F    
Sbjct: 18  LIGILLLYAVF---PFYYAIVTSLKPSS--ALFQVSYWIDNPDFSNYAAVLGQASFLRAI 72

Query: 64  QNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMK 123
            NS+V+A+    L+ L+     Y L +  FRG G++  ++L     P  ++L  LF+ ++
Sbjct: 73  GNSLVVALCVVALALLLSLTAAYALGRVKFRGRGVVLMMVLGVSMFPQVAVLSGLFEVIR 132

Query: 124 SIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPL 183
           ++GLY + + L+L + I+ +P    +   +  ++P EL EAA +DGA  +     V+LPL
Sbjct: 133 ALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPL 192

Query: 184 SVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQ-PITVALAQLAGG--EAVKWNLPMAGAI 240
             PA V   +  F   WNEFLFA+T T  +SQ  + VA+A ++GG    + W L MA ++
Sbjct: 193 LWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHELPWGLLMAASV 252

Query: 241 LAALPTLLVYILLGRYFLRGLLAGSVKG 268
           L  +P +++ ++  R  + GL AG++KG
Sbjct: 253 LVTVPLVILVLIFQRRIVSGLTAGALKG 280


Lambda     K      H
   0.330    0.146    0.461 

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: 11
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: 268
Length of database: 280
Length adjustment: 25
Effective length of query: 243
Effective length of database: 255
Effective search space:    61965
Effective search space used:    61965
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