GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21104 in Pantoea rwandensis LMG 26275

Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_084934373.1 HA51_RS09975 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21104
         (298 letters)



>NCBI__GCF_002095475.1:WP_084934373.1
          Length = 290

 Score =  125 bits (313), Expect = 1e-33
 Identities = 88/282 (31%), Positives = 139/282 (49%), Gaps = 16/282 (5%)

Query: 11  LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLW-VFIGFRNYVNVLTNAEFWVAF 69
           L LLPA +V AVF++LPL+ SL  SFT +  T     W +F G  NY+ +  +  FWVA 
Sbjct: 11  LYLLPAVLVYAVFLLLPLLASLGISFTEWDGTS----WPIFTGVSNYLRMFQDPVFWVAL 66

Query: 70  GRTVLLLTVALNAEMFLGLGLALLVNKATYGQR------ALRTAMMFPMMFSPVLVGFQF 123
           G   LL+         L +G+ LL+    Y  R       LR     P +    ++G  +
Sbjct: 67  GNNALLMLFYT----LLPIGVGLLLCSFLYDTRNNKERSVLRILFFLPYIMPMAVLGVVW 122

Query: 124 KFLFNDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLA 183
           ++L+N   G ++  L+++GL   A+ WL D   AL ++     W       +L +AGL  
Sbjct: 123 RWLYNPAFGPIDQFLRAIGLPQLALSWLGDFTWALPAVGFVATWYFFGFCLVLFMAGLQR 182

Query: 184 MPKDPVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAK 243
           M    +EAA +DG +  Q F  +T P L P   IA+ +  +   +A+D+V +MT GGP  
Sbjct: 183 MDPSLLEAADLDGSSRRQKFMRITLPSLRPELRIALLLTVIASLKAFDLVYVMTQGGPGT 242

Query: 244 RTELLWTLIGRTAYGDARMGMANAMAYVAILLSIFF-TVYFF 284
            T +    + +  +     G A+A+A  ++L+ +   TV  F
Sbjct: 243 STMVTNIFMYKQGFDLHYFGYASAVAVFSMLIVLMINTVIHF 284


Lambda     K      H
   0.331    0.142    0.441 

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: 264
Number of extensions: 21
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: 298
Length of database: 290
Length adjustment: 26
Effective length of query: 272
Effective length of database: 264
Effective search space:    71808
Effective search space used:    71808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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