GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family

Query= SwissProt::A0A0H2VG78
         (446 letters)



>FitnessBrowser__Cola:Echvi_2805
          Length = 448

 Score =  271 bits (692), Expect = 4e-77
 Identities = 158/451 (35%), Positives = 265/451 (58%), Gaps = 13/451 (2%)

Query: 1   MKANKYLIF--ILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVG 58
           M + KY+IF  I+ ALGG L+G+D  VISGA  FI +   L+  T G+ V+  L G ++G
Sbjct: 1   MNSKKYVIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSDWTHGMAVAIALYGTVIG 60

Query: 59  AGSSGPLADKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPV 118
           A   G  ADK GR+  ++ I +++ I AL  A + ++   +  R I GL VG S    P+
Sbjct: 61  ALFGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPM 120

Query: 119 YLSEMAPTEYRGSLGSLNQLMITIGILAAYLVNY--AFADI-EGWRWMLGLAVVPSVILL 175
           Y+SE+AP + RG L +L Q  I  GIL AY  NY    AD+ E WRWM+G+  +P++I  
Sbjct: 121 YISEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNESWRWMMGMEAIPALIYT 180

Query: 176 VGIYFMPESPRWLLENRNE-EAARQVMKITYDDSEIDKELK---EMKEINAISESTWTVI 231
           +    +P+SPRWL+ + N+ E A Q+++ T D   +D+ +    E +    I      + 
Sbjct: 181 LLSIRVPKSPRWLIAHHNKVEEATQILRKT-DPEGVDEAIHLAIEERNREKIKVGFAVLF 239

Query: 232 KSPWLGRILIVGCIFAIFQQFIGINAVIFYSSSIFAKAGLGEAASILGSVGIGTINVLVT 291
           K   L +  ++  + A+F Q  GINA+I+++  +F  AG+ + +++L ++GIG +N++ T
Sbjct: 240 KHSHL-KTTLLAIMIALFNQLSGINAIIYFAPRVFEMAGIDQKSALLSTIGIGVVNMIAT 298

Query: 292 IVAIFVVDKIDRKKLLVGGNIGMIASLLIMAILIWTIGIASSAWIIIVCLSLFIVFFGIS 351
           ++ ++++D+I RKKL+V G+IG I SLL+MA   ++ G+ +S ++ +  + +FI    + 
Sbjct: 299 MIGLYLIDRIGRKKLMVIGSIGYIISLLLMA-YSFSGGVINSGYLPLF-VFVFIASHAVG 356

Query: 352 WGPVLWVMLPELFPMRARGAATGISALVLNIGTLIVSLFFPILSDALSTEWVFLIFAFIG 411
            G V+WV + E+FP   R     I      I   +++  FP  +++     +F  FA + 
Sbjct: 357 QGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPASIFGFFAVMM 416

Query: 412 VLAMIFVIKFLPETRGRSLEEIEYELRERTG 442
            L +++V+  +PET+GRSLEEI+ +L+ + G
Sbjct: 417 GLQLLWVLTKMPETKGRSLEEIQQDLKIKQG 447


Lambda     K      H
   0.327    0.144    0.422 

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: 560
Number of extensions: 33
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: 446
Length of database: 448
Length adjustment: 33
Effective length of query: 413
Effective length of database: 415
Effective search space:   171395
Effective search space used:   171395
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