GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01112 in Dinoroseobacter shibae DFL-12

Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)

Query= reanno::Burk376:H281DRAFT_01112
         (364 letters)



>lcl|FitnessBrowser__Dino:3609042 Dshi_2431
           Monosaccharide-transporting ATPase (RefSeq)
          Length = 328

 Score =  137 bits (344), Expect = 5e-37
 Identities = 91/307 (29%), Positives = 154/307 (50%), Gaps = 14/307 (4%)

Query: 48  RNPEWFTVALIVVTCLIVGA--INPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGID 105
           R   W T+ L+V   + V     +P F     L D   + T  ++ A    +++ SG ID
Sbjct: 19  RLKSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEID 78

Query: 106 VSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVT 165
           +S  +I AL    +  AV       P  +++  G   G++ G  NG+LV R+  PS++VT
Sbjct: 79  LSVASIIALASTAMGAAV-QMGVGTPGLVLIGLGV--GLLCGAFNGVLVTRMGLPSIVVT 135

Query: 166 IGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAV 225
           IGT  L+RG+    +G   F   P S   FG+  +++         V+   ++     AV
Sbjct: 136 IGTMSLFRGISYIVLGDQAFRGYPESFSWFGQGYVWW---------VISFELVLFAIIAV 186

Query: 226 VTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRL 285
           +   LL++T  GRAVYA+G +   A   G  ++ +   +F  TG+++G+A I   +    
Sbjct: 187 IYAMLLHKTNFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGS 246

Query: 286 ANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKV 345
             P   +G EL+V+  V+LGG  I GG+GT++G ++   ++ L+   L L+ VP     +
Sbjct: 247 TRPSIAMGWELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSI 306

Query: 346 IIGAFIL 352
           +IGA ++
Sbjct: 307 VIGALLI 313


Lambda     K      H
   0.328    0.141    0.426 

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: 306
Number of extensions: 18
Number of successful extensions: 4
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: 364
Length of database: 328
Length adjustment: 29
Effective length of query: 335
Effective length of database: 299
Effective search space:   100165
Effective search space used:   100165
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.

Links

Downloads

Related tools

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, 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