GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Sphingomonas koreensis DSMZ 15582

Align Glucose/galactose porter (characterized)
to candidate Ga0059261_0767 Ga0059261_0767 glucose/galactose transporter

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__Korea:Ga0059261_0767
          Length = 434

 Score =  376 bits (965), Expect = e-109
 Identities = 202/389 (51%), Positives = 258/389 (66%), Gaps = 13/389 (3%)

Query: 31  LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90
           LFF++G IT LND++IP LK +F LNYTQ+ML+QFCFF AY ++ +P  +LVK++ Y RG
Sbjct: 33  LFFIFGGITSLNDVIIPKLKELFTLNYTQAMLVQFCFFTAYLVIGIPGAKLVKKLGYMRG 92

Query: 91  IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150
            V GL+   +GC LFIPA+ Y  Y +FL ALFVLASGV I+QV ANP +++LGKPETA S
Sbjct: 93  AVAGLLTMMVGCLLFIPASQYATYGVFLFALFVLASGVVIVQVVANPLISLLGKPETAHS 152

Query: 151 RLTLTQAFNSLGTTVAPVFGAVLILSAATDATVN------------AEADAVRFPYLLLA 198
           RLT  QAFNSLGTTV P+ G++LIL +    T +            AE+ A+   YL +A
Sbjct: 153 RLTFAQAFNSLGTTVFPIVGSILILGSLATVTADQLSGPALEAYRVAESKAIMHGYLGIA 212

Query: 199 LAFTVLAIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFL 258
            A  V+A +  + +     E   A +               GA+ IF+YVGAEVS+GS +
Sbjct: 213 AALAVVAGVVWLFRNRLKGERHQASAGLAGLDLLGRPRFGFGALCIFLYVGAEVSIGSLI 272

Query: 259 VNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILLF 318
           VN+L  P V GL E  A   + ++WGGAMVGRFIGS  MR I  GK LAF A  A+ L+ 
Sbjct: 273 VNYLMQPGVMGLQEQAAGKLIGFYWGGAMVGRFIGSGLMRVISPGKLLAFVAVGAVALIL 332

Query: 319 ITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLI 378
           I+  TTGH+A +S+LAIGL NSIMFPTIFSLA   LG   + GSGI+ +AI GGA+VPL 
Sbjct: 333 ISTNTTGHVAGYSLLAIGLMNSIMFPTIFSLASEKLGGRAADGSGIINIAIFGGAVVPLA 392

Query: 379 QGALADAIG-IHLAFLMPIICYAYIAFYG 406
            GALADA G + LA ++P ICYA IA +G
Sbjct: 393 TGALADATGSLGLALILPAICYAIIAGFG 421


Lambda     K      H
   0.328    0.141    0.420 

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: 600
Number of extensions: 36
Number of successful extensions: 4
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: 412
Length of database: 434
Length adjustment: 32
Effective length of query: 380
Effective length of database: 402
Effective search space:   152760
Effective search space used:   152760
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: 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