GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TT_C0326 in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_594 Glucose ABC transport system, inner membrane component 2

Query= TCDB::Q72KX4
         (268 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_594 Glucose ABC transport
           system, inner membrane component 2
          Length = 281

 Score =  261 bits (668), Expect = 9e-75
 Identities = 132/268 (49%), Positives = 178/268 (66%), Gaps = 2/268 (0%)

Query: 3   RALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRPK 62
           R  +Y  LLL A  +L+P+ +++LT+ K P  I    +   P       +  AW++    
Sbjct: 14  RIAIYATLLLAAAIYLIPLVVMLLTSFKSPEDIRTGNLLSLPQVIDGIGWIKAWDSVGSY 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
             IGL  +  GLVLVHV+YG+   TL FRNYY  IPD LV+AAR+DGAGFF IF  ++LP
Sbjct: 134 GKIGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFWKILLP 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: 297
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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