GapMind for catabolism of small carbon sources

 

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

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)

Query= TCDB::P23200
         (336 letters)



>FitnessBrowser__Dino:3606962
          Length = 357

 Score =  155 bits (391), Expect = 2e-42
 Identities = 106/335 (31%), Positives = 170/335 (50%), Gaps = 32/335 (9%)

Query: 7   KSFLTYLKEGGIYVVLLVLLAII----IFQDPTFLSLLNLSNILTQSSVRIIIALGVAGL 62
           + F   L +    V L+VL+A I    +     F S   L+ IL Q  +  I+A   + +
Sbjct: 34  RKFQHALHQTPALVPLIVLVAAIAVFGLLLGSKFFSPFALTLILQQVQIVGIVAAAQSLV 93

Query: 63  IVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLI 122
           I+T G DLS G  + +++VV              F     +P+ + +      G ++G I
Sbjct: 94  ILTAGIDLSVGAIMVMSSVVMGQ-----------FTFRYGLPVEVAVACGLLCGTLLGFI 142

Query: 123 NGLIIAYLNVTPFITTLGTMIIVYGINSLY--------YDFVGASPISGFDSGFSTFAQG 174
           NG ++A + + PFI TLG   IV   N LY         D    +P+  F   F T  + 
Sbjct: 143 NGWLVAKVKLPPFIVTLGMWQIVLAANFLYSRNETIRSQDIRDQAPLLQF---FGTTLE- 198

Query: 175 FVALGSFRLSY-ITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLM 233
              +G  RL+Y + F  L+ +   + L   T +G++++A+G +PEAA++SGV V   L+ 
Sbjct: 199 ---IGGARLTYGVIFMVLLVIVLAYAL-RHTAWGRHVYAVGDDPEAAELSGVQVSRTLIS 254

Query: 234 IYALSGVFYAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGV 293
           +Y LSG+  AF G    GRIGS +   G +  +++I A V+GG+S  GG G+++G   G 
Sbjct: 255 VYMLSGLICAFAGWALIGRIGSVSPTSGQLANIESITAVVIGGISLFGGRGSILGAFFGA 314

Query: 294 IIFTVINYGLTYIGVNPYWQYIIKGAIIIFAVALD 328
           +I  V   GL  +G +  W +++ G +II AVA+D
Sbjct: 315 LIVGVFTLGLRLLGADAQWTFLLIGLLIIAAVAVD 349


Lambda     K      H
   0.327    0.143    0.415 

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: 289
Number of extensions: 18
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: 336
Length of database: 357
Length adjustment: 29
Effective length of query: 307
Effective length of database: 328
Effective search space:   100696
Effective search space used:   100696
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