GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluP in Sphingomonas koreensis DSMZ 15582

Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate Ga0059261_2650 Ga0059261_2650 glucose/galactose transporter

Query= reanno::SB2B:6936374
         (413 letters)



>FitnessBrowser__Korea:Ga0059261_2650
          Length = 425

 Score =  315 bits (808), Expect = 1e-90
 Identities = 177/410 (43%), Positives = 252/410 (61%), Gaps = 24/410 (5%)

Query: 14  AAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFL 73
           AAPA    +     + SLFF+WGFIT +N+ L+PHL+ +FDL YT+  L++  +F AYF+
Sbjct: 12  AAPAPESYRRALALLASLFFMWGFITVINNTLLPHLRSVFDLDYTRTTLIESVWFIAYFV 71

Query: 74  VSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQV 133
            S  +  LI RIGY R ++ GL  MA G      A+S+  Y + L  LFV+ASGIT+LQV
Sbjct: 72  ASIPSARLIERIGYQRSLVAGLLVMAAGSAGMMLAASIPSYGVTLAMLFVIASGITLLQV 131

Query: 134 SANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFG-AAAGTHEA-------- 184
           +ANP+VA +G   TA+SRLNL QA+NS G  L P FG+ LI G +  GT EA        
Sbjct: 132 AANPYVAVVGRPETASSRLNLVQAMNSAGTMLAPAFGAWLILGRSKGGTSEAGTVLTQAE 191

Query: 185 -------VQLPYLLLAAVIGIIAVGFI-----FLGGKVKHADMGVDHRHKGSLLSHKRLL 232
                  V LPY L+A  + ++A+         +G   +   +  + R   SL  H+ L+
Sbjct: 192 RFADAQSVILPYGLVAVALVMLALVIACFPLPAMGAATRR--LAKEERRNHSLWKHRNLV 249

Query: 233 LGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTR 292
            G  AIF+Y+ AE+ + +  VN+ ++P I  L  + A   +++ WGG M GRFAG+AL +
Sbjct: 250 FGVPAIFIYLIAEIGVANLFVNFVSQPDIANLTHEQAGHYLTFLWGGMMAGRFAGSALMQ 309

Query: 293 RFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELT 352
           RF+ A VLA  A+ A  ++++   ++G  A+ A++ VGFF+SIMFPTIFTL I GLG LT
Sbjct: 310 RFDAAHVLAVFAIGAFAVMLVATFATGPTAMWALILVGFFHSIMFPTIFTLGIRGLGPLT 369

Query: 353 SRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWYAFF 402
             GSGLL  AI GGAL+ ++QG +AD  G+QLSF++   C  Y+ +YA +
Sbjct: 370 EEGSGLLIMAIAGGALV-IVQGWLADQWGLQLSFLLTAACEVYVLFYALW 418


Lambda     K      H
   0.329    0.142    0.425 

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: 443
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: 413
Length of database: 425
Length adjustment: 32
Effective length of query: 381
Effective length of database: 393
Effective search space:   149733
Effective search space used:   149733
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 (21.8 bits)
S2: 50 (23.9 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