GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21104 in Phaeobacter inhibens BS107

Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease

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



>FitnessBrowser__Phaeo:GFF726
          Length = 315

 Score =  129 bits (324), Expect = 9e-35
 Identities = 90/279 (32%), Positives = 137/279 (49%), Gaps = 10/279 (3%)

Query: 8   APTLLLLPAFIVLAVFIVLPLIFSLYSSFTPFR-LTKPDSLWVFIGFRNYVNVLTNAEFW 66
           AP L L P  I    +++ P++ S   SF  +  L  P     FIG  NY  ++ +  F 
Sbjct: 32  APWLFLAPGVIFFLFYVIFPILQSFNLSFYRWDGLGDPQ----FIGMENYRELMDDRAFE 87

Query: 67  VAFGRTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFL 126
           V+    +  L + L A +  GL +AL +N+   G R  ++   FP + S V+VG  F + 
Sbjct: 88  VSLWNNLKWLLLYLLA-IPAGLFIALFLNQTVTGIRLYKSLFFFPFVISQVVVGLVFSWF 146

Query: 127 FNDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPK 186
           ++   G +N  L  +GL    I  L D  L  + II+A +W  TA   IL L GL A+  
Sbjct: 147 YDPTFGLLNQVLAWVGLGP--INVLGDPTLVTYGIIIAGLWPQTAYCMILYLTGLNAVDP 204

Query: 187 DPVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTE 246
           + VEAA +DG    +   YV  P L P  F+A  +  +   R++D++ IMT+GGP   + 
Sbjct: 205 EQVEAARLDGAKGAKMLWYVIIPQLRPATFVAFVVTIIGALRSFDLISIMTNGGPFGSSR 264

Query: 247 LLWTLIGRTAYGD--ARMGMANAMAYVAILLSIFFTVYF 283
           +L   +   A  +   RMG   A+A V  L+ + F  YF
Sbjct: 265 VLSFYMFEKALSEYGFRMGYGAAIAVVLFLIMLCFIAYF 303


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: 277
Number of extensions: 10
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: 315
Length adjustment: 27
Effective length of query: 271
Effective length of database: 288
Effective search space:    78048
Effective search space used:    78048
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 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