GapMind for catabolism of small carbon sources

 

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

Align The glucose uptake porter, GluP (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= TCDB::Q0SE66
         (483 letters)



>FitnessBrowser__Korea:Ga0059261_1777
          Length = 458

 Score =  279 bits (713), Expect = 2e-79
 Identities = 171/472 (36%), Positives = 258/472 (54%), Gaps = 25/472 (5%)

Query: 10  AESPGDTAEGTSVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASA 69
           A +P + A  T   +  A  AALGGLLFG+D+AVI+GA  A++ +F +  A+LGF +ASA
Sbjct: 9   AGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASA 68

Query: 70  LLGAAAGAMLAGRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGL 129
           L+G   G+++AG  ADR+GR   M   A+ +++S++GTG A ++   + FR +GG+ +G 
Sbjct: 69  LIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGA 128

Query: 130 ASVIAPAYIAEISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEA 189
           ASV+ P YIAE+SPAR RGRL ++ QL IV GI ++ L +Y    IAG  Q ++     A
Sbjct: 129 ASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNY---IIAGLVQYDV-----A 180

Query: 190 WRWMFLAMCVPALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRS 249
           WRWMF  + VP+  + L++L +PESPR+L   G+   AR ++  L      D + E  R 
Sbjct: 181 WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRL---GFADPRAELARI 237

Query: 250 TLARETQPSIRDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSS 309
            LA   + +    +         V   I +++F Q  GIN + YY+  +++  G    S+
Sbjct: 238 ELAEAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSA 297

Query: 310 LQITVITSVVNIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGV 369
           L  ++     N+  T+ A+  IDR GRRPLL +GS   A TL  + +   +A     DG 
Sbjct: 298 LLQSIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKP---DG- 353

Query: 370 TTPQLTGLQGPIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAAN 429
            T  L GL G         F+ AF MS G V+WV + E FP+ +R    +L +   W   
Sbjct: 354 -TLILFGLLG---------FIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMA 403

Query: 430 WLITVTFPSMKDFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAMHSDS 481
             IT  FP       G  + F+    +L L++  +++ ET G+ LE M+  S
Sbjct: 404 AAITWAFPVFAASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGS 455


Lambda     K      H
   0.324    0.138    0.405 

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: 598
Number of extensions: 29
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: 483
Length of database: 458
Length adjustment: 33
Effective length of query: 450
Effective length of database: 425
Effective search space:   191250
Effective search space used:   191250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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