GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21219 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21219
         (281 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28580
          Length = 280

 Score =  144 bits (364), Expect = 2e-39
 Identities = 90/268 (33%), Positives = 146/268 (54%), Gaps = 12/268 (4%)

Query: 18  LLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASL 77
           +L V  + P  + ++ S+ P++ L    +++W    D S Y  +L+       A+F+ ++
Sbjct: 21  ILLVYAVFPFYYAIVTSLKPSSALFQ--VSYWIDQPDFSNYAAVLNQ------ASFLRAI 72

Query: 78  LNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYMLPPVALAVPLYMGLA 135
            NS+ VA      A+ +++ AA+A+ R         L  V+   M P VA+   L+  + 
Sbjct: 73  GNSLVVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGVSMFPQVAVLSGLFEVIR 132

Query: 136 YFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILTLPL 195
             GL N+ + L L Y     PFT W+L +    +P E+E AA++DGA     L  + LPL
Sbjct: 133 ALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPL 192

Query: 196 AAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSD--YGLIATAGV 253
             P + T+ L AF+ AW+EF +AL FT     +T+ VAIA ++GG   +  +GL+  A V
Sbjct: 193 LWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHELPWGLLMAASV 252

Query: 254 LAALPPVLIGLIMQRALISGLTSGGVKG 281
           L  +P V++ LI QR ++SGLT+G +KG
Sbjct: 253 LVTVPLVILVLIFQRRIVSGLTAGALKG 280


Lambda     K      H
   0.325    0.136    0.402 

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: 212
Number of extensions: 17
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: 281
Length of database: 280
Length adjustment: 26
Effective length of query: 255
Effective length of database: 254
Effective search space:    64770
Effective search space used:    64770
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 (21.7 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