GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Dinoroseobacter shibae DFL-12

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__Dino:3609043
          Length = 327

 Score =  133 bits (334), Expect = 7e-36
 Identities = 101/285 (35%), Positives = 146/285 (51%), Gaps = 17/285 (5%)

Query: 25  LVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDL 84
           L+A +L+LL  +L+A  F   +            + N  +P+ LLAIG  +VI T  IDL
Sbjct: 13  LIAAILLLL--ALIASRFPAFIAPSNLAH-----VFNDTSPLILLAIGQMIVILTRCIDL 65

Query: 85  SVGAVMAIAGATTAAMTVAGFSLPIV--LLSALGTGILAGLWNGILVAILKIQPFVATLI 142
           SV A +A+ G   + + VA   LPIV  L  A+G G L G++NG+LV  L+I P V TL 
Sbjct: 66  SVAANLALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLG 125

Query: 143 LMVAGRGVAQLITAGQIVTFN--SPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTA 200
            M   RG+  LI+ G+ V  +  SP    F    LL LP    IA+L +ILF ++  +T 
Sbjct: 126 TMTIFRGIIFLISDGKWVNSHEMSPAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTT 185

Query: 201 LGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWL 260
           LG    A G N  AA  AG++        + +SG  A + G +  +    +  + AG   
Sbjct: 186 LGRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAG-GF 244

Query: 261 ELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFP 305
           ELD + A VIGG S+MGG     +  VG  ++  +  GI+ +  P
Sbjct: 245 ELDVVAACVIGGVSIMGG-----VGTVGGALLGALFLGIIKNALP 284


Lambda     K      H
   0.327    0.142    0.416 

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: 319
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 341
Length of database: 327
Length adjustment: 28
Effective length of query: 313
Effective length of database: 299
Effective search space:    93587
Effective search space used:    93587
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 (21.7 bits)
S2: 49 (23.5 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