GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Burkholderia phytofirmans PsJN

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__BFirm:BPHYT_RS16055
          Length = 335

 Score =  184 bits (467), Expect = 3e-51
 Identities = 113/338 (33%), Positives = 181/338 (53%), Gaps = 23/338 (6%)

Query: 3   PQSLPDTTTPKR-------RFRWP-----TGMPQLVALLLVLLVDSLVAPHFWQVVLQDG 50
           P S P T+T          RF W      T     + LL+V +V          V   D 
Sbjct: 6   PSSSPKTSTVNSDTPGAPVRFTWAALKRSTLFYPFIGLLVVCIV---------MVFASDS 56

Query: 51  RLFGSPID-ILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPI 109
            L G+ I+ +L + +  A++A+GMT VI TGGIDLSVG+VMA+AG   A + VAG +   
Sbjct: 57  FLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALAGTLAAGLMVAGMNAVA 116

Query: 110 VLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSW 169
            L   +  G+  G  NG  VA   + P + TL  M   RG+A + T G  +      +S+
Sbjct: 117 ALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALIYTGGYPIDGLPDWVSF 176

Query: 170 FGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLT 229
           FGSG +L +  PV+I  +  ++ W+L  +   G ++ A+G N +A + +GV    + ++ 
Sbjct: 177 FGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIV 236

Query: 230 YVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGA 289
           Y ++GL +A A I++ A +      NAG+  ELDAI AVV+GG S+ GGR +++ +++GA
Sbjct: 237 YTIAGLTSAFAAIVLTARLMSGQP-NAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGA 295

Query: 290 LIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQR 327
           L++  +N G+ + G  P +  V+K  ++L  + +   R
Sbjct: 296 LLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDR 333


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: 316
Number of extensions: 16
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: 341
Length of database: 335
Length adjustment: 28
Effective length of query: 313
Effective length of database: 307
Effective search space:    96091
Effective search space used:    96091
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