GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21104 in Halopiger salifodinae KCY07-B2

Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_049989937.1 LT39_RS07855 sugar ABC transporter permease

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



>NCBI__GCF_000784335.1:WP_049989937.1
          Length = 308

 Score =  140 bits (352), Expect = 5e-38
 Identities = 85/279 (30%), Positives = 147/279 (52%), Gaps = 9/279 (3%)

Query: 11  LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFG 70
           L ++P  +++ VFI+ P+  ++YSSF    L  PD    F+G  NY  + TN +      
Sbjct: 26  LPIVPVMVLVGVFILYPIAQAIYSSFFDKSLLSPDEA-EFVGLANYQEIWTNPDLHQVLW 84

Query: 71  RTVLLLTVALNAEMFLGLGLA-LLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFND 129
            T + ++V   A +  G  L  LL  K  Y   A    ++ P +   V+    ++F+F  
Sbjct: 85  NTFVWVSVGSIAAIVFGFVLGWLLYEKFPYTSVA-SAIVLIPWVLPRVVGASIWQFMFGG 143

Query: 130 NIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPV 189
           + G +N  L  LG+ D  +  L  G+L+L+  I+  +W    +FA+L L  L  + +   
Sbjct: 144 DQGIINELLVQLGVIDEYMVMLGSGDLSLWPPIIGMIWRLAPLFALLTLTSLQGIDEHLY 203

Query: 190 EAAHVDGCTPWQTFRYVTWP---YLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTE 246
           EAA +DG TPW+ FRY+T P   Y +   F+ M I ++   R + +V +MT+GGP   + 
Sbjct: 204 EAARMDGATPWERFRYITLPMMRYNLAIGFLLMLIYNI---RNFSMVWVMTEGGPGVSSS 260

Query: 247 LLWTLIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFR 285
            L  +I RTA+ D  +G+A+A++ +  ++ + F+ Y+ +
Sbjct: 261 TLPVMIYRTAFVDFNVGLASALSVLLFVVLLVFSYYYIK 299


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: 286
Number of extensions: 11
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: 308
Length adjustment: 27
Effective length of query: 271
Effective length of database: 281
Effective search space:    76151
Effective search space used:    76151
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