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 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)

Query= TCDB::P23200
         (336 letters)



>FitnessBrowser__Dino:3609043
          Length = 327

 Score =  168 bits (426), Expect = 2e-46
 Identities = 105/324 (32%), Positives = 173/324 (53%), Gaps = 19/324 (5%)

Query: 14  KEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAG 73
           +E  +   +L+LLA+I  + P F++  NL+++   +S  I++A+G   +I+T+  DLS  
Sbjct: 9   RETLLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVA 68

Query: 74  RQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVT 133
             + L  +V + +       N   P +   PI +++ I   +G ++G+ NGL++  L + 
Sbjct: 69  ANLALTGMVVSMV-------NVAAPGL---PIVVILAIAIGLGTLLGMFNGLLVWKLQIP 118

Query: 134 PFITTLGTMIIVYGINSLYYD--FVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYAL 191
           P + TLGTM I  GI  L  D  +V +  +S     F  F +  + LG   LS+I   A+
Sbjct: 119 PIVVTLGTMTIFRGIIFLISDGKWVNSHEMS---PAFKAFPRAEL-LGLPVLSWI---AI 171

Query: 192 IAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAG 251
           +AV    ++  +T  G+  +A GGNP AA  +G++VG      + +SG      G L   
Sbjct: 172 LAVILFTIVMTRTTLGRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVS 231

Query: 252 RIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPY 311
           R   +  ++   +ELD +AACV+GGVS  GGVGTV G + G +   +I   L  + ++P+
Sbjct: 232 RFAVSYVDIAGGFELDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPF 291

Query: 312 WQYIIKGAIIIFAVALDSLKYARK 335
           WQ  I G  II AVAL++    +K
Sbjct: 292 WQLAISGGAIIIAVALNAQANRKK 315


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: 265
Number of extensions: 15
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: 327
Length adjustment: 28
Effective length of query: 308
Effective length of database: 299
Effective search space:    92092
Effective search space used:    92092
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