GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3609043 Dshi_2432
           Monosaccharide-transporting ATPase (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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