GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Pseudomonas putida KT2440

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__Putida:PP_2456
          Length = 331

 Score =  147 bits (371), Expect = 4e-40
 Identities = 93/303 (30%), Positives = 163/303 (53%), Gaps = 13/303 (4%)

Query: 27  ALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLSV 86
           ALL ++++ S ++ HFW         +G+   + N+   + +LA+GMT V+  GGIDLSV
Sbjct: 32  ALLAMIVLFSFLSSHFWS--------YGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSV 83

Query: 87  GAVMAIAGATTAAMTVAGFSLPIVLLSALGTGI--LAGLWNGILVAILKIQPFVATLILM 144
           G+V+A+A A+T ++ + G+   ++  + LG  +  LAG   G +    +I  F+ +L ++
Sbjct: 84  GSVLALA-ASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVL 142

Query: 145 VAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMF 204
              RG+A   T  +   +     +WF +     +    IIA+L ++L  L+  +T  G +
Sbjct: 143 EMARGLAYQFTDSR-TAYIGDAYAWFSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRY 201

Query: 205 IEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDA 264
           +  +G N  A + AG++ R   +L + L GL A +A +   + +  AD N AG  LEL  
Sbjct: 202 LIGIGTNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPN-AGSGLELQV 260

Query: 265 ILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQ 324
           I AVVIGG SLMGGR +++ +  G LII  +  G+   G      +++   V++  +++ 
Sbjct: 261 IAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLD 320

Query: 325 SQR 327
           + R
Sbjct: 321 TYR 323


Lambda     K      H
   0.327    0.142    0.416 

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: 269
Number of extensions: 17
Number of successful extensions: 4
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: 341
Length of database: 331
Length adjustment: 28
Effective length of query: 313
Effective length of database: 303
Effective search space:    94839
Effective search space used:    94839
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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