GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP in Sphingomonas koreensis DSMZ 15582

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= SwissProt::P96710
         (464 letters)



>FitnessBrowser__Korea:Ga0059261_1777
          Length = 458

 Score =  278 bits (712), Expect = 2e-79
 Identities = 154/436 (35%), Positives = 250/436 (57%), Gaps = 6/436 (1%)

Query: 23  VILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISGF 82
           +IL +  A LGGLL+G+DTAVISGA   L+  + L+  M G  ++S +IG V+G  I+G 
Sbjct: 22  IILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGA 81

Query: 83  LSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAA 142
            +DRFGR+ +++T A+ + +S++ + L+ D++  ++ R +GGL IG  S ++  YI E +
Sbjct: 82  PADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVS 141

Query: 143 PPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPSVIFFL 202
           P   RG L ++ QL  +LGI   +  N  +  +G  ++ V   WRWM     VPS IF L
Sbjct: 142 PARFRGRLVAMNQLNIVLGILIAFLSNYII--AGLVQYDV--AWRWMFGIVAVPSTIFLL 197

Query: 203 VLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLSQLFKPG 262
           V L++PESPRWLA  G+ + A  ++ R+ G    + EL  IE +   E+     +LF+  
Sbjct: 198 VTLLLPESPRWLAIHGQADRARDVMQRL-GFADPRAELARIELAEAREEAAGKPRLFQRS 256

Query: 263 LRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVIFTVIAV 322
               +   I +A+FNQ+ G+NA+ YY P IF++ G G ++  + +  VG   ++FTV A+
Sbjct: 257 HFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAAL 316

Query: 323 LLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVSVGPITW 382
            LID+ GR+ L+ +GS   A  ++L+G         G +++  +LGF+AAF +S G + W
Sbjct: 317 FLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIW 376

Query: 383 IMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVINILCFLF 442
           + ISE+FP+ +R +   + +   W    AI    P+   S G  + F  F  + +L  L+
Sbjct: 377 VFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLW 435

Query: 443 VVTICPETKNKSLEEI 458
                PET   +LE++
Sbjct: 436 TWKFMPETNGIALEDM 451


Lambda     K      H
   0.327    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: 516
Number of extensions: 28
Number of successful extensions: 5
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: 464
Length of database: 458
Length adjustment: 33
Effective length of query: 431
Effective length of database: 425
Effective search space:   183175
Effective search space used:   183175
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: 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