GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treU in Phaeobacter inhibens BS107

Align TreU, component of Trehalose porter (characterized)
to candidate GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component

Query= TCDB::Q97ZC1
         (267 letters)



>FitnessBrowser__Phaeo:GFF1646
          Length = 283

 Score =  124 bits (311), Expect = 2e-33
 Identities = 81/257 (31%), Positives = 129/257 (50%), Gaps = 5/257 (1%)

Query: 15  YFLFPLYILVLLAFNSPKYTVLAKFPSLLPVSLTLNNLLTALQGTAFIDPFIKSLETATL 74
           + LFPLY L+ +A  +P   + ++   +LP ++T  N  T L  T F+  F  SL  +  
Sbjct: 28  FALFPLYWLMKIAI-TPDALIFSEGTRMLPSAVTFENFATVLFETEFLAYFRNSLTVSLG 86

Query: 75  VGIITIALAIPAGYGLSRLPRAIAYSIIILLLVTNMMPAIVIGIPIAVDFLKLHLFESVV 134
               T  +A  AGY  SR   A    II ++L+T M P ++I  PI      L L  S+ 
Sbjct: 87  TAFFTTLIAAGAGYAFSRFVFAGKRIIIAVMLITQMFPLLMIIAPIYKIVADLGLLNSLT 146

Query: 135 GLALAQTLITLPLATFILQGTFSSIPIDLEHQARVDGANLFNRLFSVLLPLAAPGIAAAF 194
            L +  T   +P ATF++Q  F  IP DLE  A +DG + F  L +V+ PL  PG+ A  
Sbjct: 147 SLIVVYTAFNIPFATFLMQSFFDGIPKDLEEAAMMDGCSRFQALRTVVFPLTLPGLGATL 206

Query: 195 LISWMFSWDEFTYAILLIPYHS--TLPVTIYQDVTRGNLLAG--IAFSLIFTLPVIILTF 250
              +  +W E  +A++LI  +   T PV +   V++ ++  G  +A  ++  +P  +   
Sbjct: 207 GFVFTAAWSELLFALMLISKNDAMTFPVGLLTFVSKFSVDWGQMMAAGVLALVPSCLFFI 266

Query: 251 ALQKYLRGEYLAGGIKG 267
            +Q+YL     +G +KG
Sbjct: 267 FIQRYLVQGLTSGAVKG 283


Lambda     K      H
   0.330    0.146    0.431 

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: 176
Number of extensions: 7
Number of successful extensions: 1
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: 267
Length of database: 283
Length adjustment: 25
Effective length of query: 242
Effective length of database: 258
Effective search space:    62436
Effective search space used:    62436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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