GapMind for catabolism of small carbon sources

 

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

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 AO353_25125 AO353_25125 sugar ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25125
          Length = 280

 Score =  141 bits (355), Expect = 2e-38
 Identities = 86/273 (31%), Positives = 144/273 (52%), Gaps = 10/273 (3%)

Query: 1   MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWE--A 58
           +G   L G LLL A F   P Y  ++T+LK  +   L  V  W   P + ++       +
Sbjct: 13  LGFWCLIGILLLYAVF---PFYYAIVTSLKPSS--ALFEVSYWIDSPDFSNYAAVLHQSS 67

Query: 59  FRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPL 118
           F     NS+V+A+    L+  +     Y L +  FRG G +  ++L     P  ++L  L
Sbjct: 68  FLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGL 127

Query: 119 FQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRH 178
           F+ ++++GLY + + L+L + I+ +P    +   +  ++P EL EAA +DGA  +     
Sbjct: 128 FEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTR 187

Query: 179 VILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQ-PITVALAQLAGG--EAVKWNLP 235
           V+LPL  PA V   +  F   WNEFLFA+T T  ++Q  + VA+A ++GG    + W L 
Sbjct: 188 VLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLL 247

Query: 236 MAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           MA ++L  +P +++ ++  R  + GL AG++KG
Sbjct: 248 MAASVLVTVPLVILVLIFQRRIVSGLTAGALKG 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: 234
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