GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate BPHYT_RS22780 BPHYT_RS22780 sugar ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__BFirm:BPHYT_RS22780
          Length = 283

 Score =  142 bits (357), Expect = 1e-38
 Identities = 86/235 (36%), Positives = 131/235 (55%), Gaps = 7/235 (2%)

Query: 146 PPRFTL-DNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLL 204
           P  F + DNY E L+ + +   F NS+ + VP+ V  I +AA A +ALA   F G + L 
Sbjct: 55  PKHFAMFDNYREALTTSPMLHYFWNSVLITVPAVVGSIALAAMAGFALAIYRFRGNSTLF 114

Query: 205 AVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMA 264
           A  V    VP+Q+ +IP+  L   +G F  VSA     + L H  F        LRN++ 
Sbjct: 115 ATFVAGNFVPVQVLMIPVRDLSLQLGLFNTVSA-----LILFHVSFQTGFCALFLRNFIK 169

Query: 265 GLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDD 324
            LP E++E+AR++GA+++ +F KI+LPL  PALA+ AI  F + WND   A+  L  GDD
Sbjct: 170 QLPFELVEAARIEGANEWTVFFKIVLPLIRPALAALAILVFTFVWNDYFWALC-LTQGDD 228

Query: 325 KLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
              +T  +  L G     W +++A + +  +  + +FFA+Q++ V GL  G+ KG
Sbjct: 229 AAPITVGVAALKGQWTTAWNLVSAGSILAALPSVAMFFAMQKHFVAGLTFGATKG 283


Lambda     K      H
   0.324    0.139    0.418 

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: 274
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 380
Length of database: 283
Length adjustment: 28
Effective length of query: 352
Effective length of database: 255
Effective search space:    89760
Effective search space used:    89760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 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