GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP in Echinicola vietnamensis KMM 6221, DSM 17526

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family

Query= SwissProt::P96710
         (464 letters)



>FitnessBrowser__Cola:Echvi_2810
          Length = 450

 Score =  246 bits (628), Expect = 1e-69
 Identities = 153/429 (35%), Positives = 225/429 (52%), Gaps = 12/429 (2%)

Query: 32  LGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGG-VVGVGISGFLSDRFGRR 90
           L G L+G+DTAVISGA   LK L+  S +  G  I S+ + G V+G  + G      GR+
Sbjct: 14  LTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHLGRK 73

Query: 91  KILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAAPPAIRGSL 150
             L    ++F +SA+ +AL+ D       R +GG+ IG  S  + TY++E +    RG  
Sbjct: 74  NTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQRGRR 133

Query: 151 SSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPSVIFFLVLLVVPES 210
             LYQ+  + GI   Y  N  +Q  G      H  WRWMLA  ++P++I+   +L +PES
Sbjct: 134 VGLYQINIVSGILVAYVSNYLLQGVGD-----HNDWRWMLAAEIIPAIIYLAFILDIPES 188

Query: 211 PRWLAKAGKTNEAL-KILTRINGETVAKEELKNIENSLKIEQMGSLSQLFKPGLRKALVI 269
           PRWL    K   A  K+L +I    + +  L    +SL+ ++M    +LF    R  L +
Sbjct: 189 PRWLILKQKDESAAQKVLKKITTGKIDQLLLSIKHDSLRSKKM----KLFSAKNRLPLFL 244

Query: 270 GILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVIFTVIAVLLIDKVG 329
             ++A+FNQ+ G+N I YY PEI +  GF      +    +G   +IFT+I + LIDK G
Sbjct: 245 AGIIAIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLIGMSLIDKTG 304

Query: 330 RKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVSVGPITWIMISEIF 389
           RK+LM IGS    I + L+   FY + +S + ++  IL F+AA  +  G + W+ ISEIF
Sbjct: 305 RKQLMLIGSMGYIISLGLVSYGFY-DSSSPLFILTSILIFIAAHGIGQGAVIWVFISEIF 363

Query: 390 PNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVINILCFLFVVTICPE 449
           PN +RA          WG    I  F  ++ID+      F +F  + IL F+FV    PE
Sbjct: 364 PNKVRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIFMVFMALMILQFVFVWRYMPE 423

Query: 450 TKNKSLEEI 458
           TK   LE +
Sbjct: 424 TKGLELENL 432


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: 562
Number of extensions: 30
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: 450
Length adjustment: 33
Effective length of query: 431
Effective length of database: 417
Effective search space:   179727
Effective search space used:   179727
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