GapMind for catabolism of small carbon sources

 

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

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate 3607096 Dshi_0518 Monosaccharide-transporting ATPase (RefSeq)

Query= TCDB::B8H230
         (332 letters)



>FitnessBrowser__Dino:3607096
          Length = 336

 Score =  164 bits (415), Expect = 3e-45
 Identities = 106/332 (31%), Positives = 172/332 (51%), Gaps = 22/332 (6%)

Query: 19  LLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGI 78
           LL  A ++  ++ L  L+  F  A   FL   +A  +L  V+I GI+A+G+T  +++GG 
Sbjct: 5   LLDIAIRYGFLMLLFGLIVYFSLAAPGFLGPLSAAFVLQSVAITGILALGVTCTLVVGGF 64

Query: 79  DVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAF 138
           D+++G++   A + +AY  + V+ + PA  ++A+L+   +G   G++ G  +    VP  
Sbjct: 65  DLSIGAVATSALMLSAY--SMVILEHPA--IVAVLLCLAMGALVGFINGLLIVKFRVPDL 120

Query: 139 IVTLGGMTVWRGAT------------LLLNDGGPISG-FNDAYRWWGSGEI-----LFLP 180
           + TLG M +  G              + L+DG    G F+ A+ W G           LP
Sbjct: 121 LATLGMMFLLIGLQRIPTQGNSIATGMTLSDGTVAEGTFSAAFLWLGRHRFDVVIERLLP 180

Query: 181 VPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGL 240
           +PVVIF  +A    + L +TR+GR +YA+G N  AA L G  V+    + Y I G  A +
Sbjct: 181 MPVVIFVGIAVLIWLFLGFTRHGRLMYAIGSNERAAGLVGTPVNRYKIAAYMISGVTASI 240

Query: 241 SGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLV 300
            G LL+ARLG  +  +G    L  +A+ +IG A L        GT +GAL +G+L  G+ 
Sbjct: 241 GGILLAARLGRGDIASGNNLLLDSVAAALIGFAVLGAARPNAFGTAMGALFVGILLQGMT 300

Query: 301 MLHVTSYVQQVVIGLIIVAAVAFDHYARTHKA 332
           M++   Y Q  V G ++VAA+ F  Y  + ++
Sbjct: 301 MMNAPYYTQDFVKGAVLVAALVFTFYLSSRRS 332


Lambda     K      H
   0.325    0.140    0.413 

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: 264
Number of extensions: 18
Number of successful extensions: 4
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: 332
Length of database: 336
Length adjustment: 28
Effective length of query: 304
Effective length of database: 308
Effective search space:    93632
Effective search space used:    93632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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