GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05255 in Dinoroseobacter shibae DFL-12

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)

Query= uniprot:D8J112
         (347 letters)



>lcl|FitnessBrowser__Dino:3606962 Dshi_0389
           Monosaccharide-transporting ATPase (RefSeq)
          Length = 357

 Score =  186 bits (473), Expect = 6e-52
 Identities = 111/303 (36%), Positives = 167/303 (55%), Gaps = 10/303 (3%)

Query: 38  LAFASLLLMILFFS-FASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTM 96
           +A   LLL   FFS FA         L  ILQ   + G++A A + VI+T+GIDLSVG +
Sbjct: 56  IAVFGLLLGSKFFSPFA---------LTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAI 106

Query: 97  MTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLK 156
           M   +V+ G     +G+P+ + +A  +  G L G+I+G ++AK+K+PPFI TLGM  ++ 
Sbjct: 107 MVMSSVVMGQFTFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQIVL 166

Query: 157 GLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTV 216
             + + S    I   D    + + Q       I    +   V+ + L+ I  +  L  T 
Sbjct: 167 AANFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARLTYGVIFMVLLVIVLAYALRHTA 226

Query: 217 FGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYE 276
           +GR+ +A+G + EA  LSGV+V    ++VY  SG IC  AG  +  R+ S  P  GQ   
Sbjct: 227 WGRHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIGSVSPTSGQLAN 286

Query: 277 LDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAV 336
           +++I AVVIGG SL GG G+ILG   GA I+ V   GLR++    +W  ++ G++II AV
Sbjct: 287 IESITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTFLLIGLLIIAAV 346

Query: 337 YLD 339
            +D
Sbjct: 347 AVD 349


Lambda     K      H
   0.326    0.139    0.398 

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: 273
Number of extensions: 16
Number of successful extensions: 3
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: 347
Length of database: 357
Length adjustment: 29
Effective length of query: 318
Effective length of database: 328
Effective search space:   104304
Effective search space used:   104304
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