GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Methanobacterium lacus AL-21

Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate WP_013644894.1 METBO_RS06515 sugar porter family MFS transporter

Query= SwissProt::A0A0H2VG78
         (446 letters)



>NCBI__GCF_000191585.1:WP_013644894.1
          Length = 453

 Score =  367 bits (941), Expect = e-106
 Identities = 187/431 (43%), Positives = 289/431 (67%), Gaps = 3/431 (0%)

Query: 7   LIFILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVGAGSSGPLA 66
           L+  + ++GGLL+GYD GVISGA+LFI +D  L++T + + VS++LIGA++GA  SG LA
Sbjct: 16  LVAAITSIGGLLFGYDTGVISGAILFIREDFLLSTTAQEVTVSAVLIGAVIGASISGILA 75

Query: 67  DKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPVYLSEMAPT 126
           D+ GR+ +++L +I+F IGA+  + S N+  LII R+++G+A+G +   VP+Y++E+AP 
Sbjct: 76  DRYGRKIMIVLASIIFGIGAIFSSVSPNVNALIISRVVVGIAIGMASFIVPLYIAEVAPI 135

Query: 127 EYRGSLGSLNQLMITIGILAAYLVNYAFADIEGWRWMLGLAVVPSVILLVGIYFMPESPR 186
             RG+L SLNQL IT+GI+ +Y+V+  FA    WRWMLGLAV+PS+IL +G++FMP SPR
Sbjct: 136 NIRGALVSLNQLAITLGIVISYMVDLYFAPNGSWRWMLGLAVIPSLILALGMFFMPPSPR 195

Query: 187 WLLENRNEEAARQVMKITYDDSEIDKELKEMKEINAI-SESTWTVIKSPWLGRILIVGCI 245
           WL+    E  A  V+K       +DKE+ E+++   + +E  W+ +  P +   LI+G  
Sbjct: 196 WLISKGFESKAVAVLKKIRGIDNVDKEVNEIEQTLLLENEGKWSDLLEPKIRSALIIGIG 255

Query: 246 FAIFQQFIGINAVIFYSSSIFAKAGLGEA-ASILGSVGIGTINVLVTIVAIFVVDKIDRK 304
            A FQQ  GIN VI+Y+ +I   AGL  A  +I  +VGIG +NVL+T+V+I ++D++ R+
Sbjct: 256 LAAFQQLTGINTVIYYAPTILEFAGLQTATVTIFATVGIGVVNVLLTVVSILLIDRLGRR 315

Query: 305 KLLVGGNIGMIASLLIMAILIWTIGIASS-AWIIIVCLSLFIVFFGISWGPVLWVMLPEL 363
            LL+ G  GMI SL IM +     G+ SS  W+ ++CL L++  F IS GP+ W+M+ E+
Sbjct: 316 PLLLAGITGMIVSLGIMGLAFIIPGLTSSLGWLAVICLMLYVGSFAISLGPIFWLMIAEI 375

Query: 364 FPMRARGAATGISALVLNIGTLIVSLFFPILSDALSTEWVFLIFAFIGVLAMIFVIKFLP 423
           +P+R RG A  I  ++     L+V++ F  + + L     F ++  I VL+++FV   +P
Sbjct: 376 YPLRIRGRAMSIVTMINWATNLVVAITFLTIIELLGASGTFWLYGVIAVLSLLFVYYRVP 435

Query: 424 ETRGRSLEEIE 434
           ET+G+SLEEIE
Sbjct: 436 ETKGKSLEEIE 446


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: 632
Number of extensions: 36
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: 453
Length adjustment: 33
Effective length of query: 413
Effective length of database: 420
Effective search space:   173460
Effective search space used:   173460
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 Apr 09 2024. 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