GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0326 in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1896 Glucose ABC transport system, inner membrane component 2

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1896
          Length = 281

 Score =  263 bits (673), Expect = 2e-75
 Identities = 132/268 (49%), Positives = 177/268 (66%), Gaps = 2/268 (0%)

Query: 3   RALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRPK 62
           R  +Y  LLL A  +L+P+ +++LT+ K P  I    +  WP       +  AW+     
Sbjct: 14  RIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDVVGGY 73

Query: 63  FQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122
           F NSV + V A L+S  +G++NGYVL+ W FRGS L F L+LFG F+P+Q++L+P    +
Sbjct: 74  FWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133

Query: 123 KSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILP 182
              GL  +  GLVLVHV+YG+   TL FRNYY  IPD LV+AAR+DGAGFF IF  ++LP
Sbjct: 134 GKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKILLP 193

Query: 183 LSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAGGE--AVKWNLPMAGAI 240
           +S+P  +V  IWQFTQIWN+FLF V     ++QPITVAL  L      A ++N+ MA A+
Sbjct: 194 MSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAKEYNVDMAAAM 253

Query: 241 LAALPTLLVYILLGRYFLRGLLAGSVKG 268
           +A LPTLLVYI  G+YFLRGL +G+VKG
Sbjct: 254 IAGLPTLLVYIFAGKYFLRGLTSGAVKG 281


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: 303
Number of extensions: 10
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: 268
Length of database: 281
Length adjustment: 25
Effective length of query: 243
Effective length of database: 256
Effective search space:    62208
Effective search space used:    62208
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