GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Sphingobium czechense LL01

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_066601288.1 V473_RS05365 sugar porter family MFS transporter

Query= TCDB::P15729
         (468 letters)



>NCBI__GCF_001046645.1:WP_066601288.1
          Length = 470

 Score =  426 bits (1095), Expect = e-124
 Identities = 229/465 (49%), Positives = 313/465 (67%), Gaps = 5/465 (1%)

Query: 8   SQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGS 67
           S    N+ FV  I  VA +GGF+FG+D+ VING    L+  F    L  G++V   L+GS
Sbjct: 5   SAEKVNMAFVAAIVAVATIGGFMFGYDSGVINGTQKGLEAAFDLGKLGIGVNVGAILVGS 64

Query: 68  ALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVI 127
           ++GAFGAG +AD  GR   M+L+A+LF  S++ +G   +   FIF R++GG+GVGAASVI
Sbjct: 65  SIGAFGAGRMADIIGRRGVMMLSAILFLGSALLAGAAGSSAIFIFARIIGGLGVGAASVI 124

Query: 128 APAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRW 187
           +P YI+EV+PA++RGRL S+QQ+ I+SG+  A ++N+ +A  AGGS    WL    AWRW
Sbjct: 125 SPVYISEVTPANVRGRLSSVQQVMIISGLTGAFIANFVLARYAGGSTAPLWL-DYPAWRW 183

Query: 188 MFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGG-DVPSRIEEIQATVS 246
           MFW + IPA +Y +    IPESPRYLVA+G+   A A+L ++ G  +   ++ EI+A++S
Sbjct: 184 MFWLQAIPAAIYFLALLAIPESPRYLVARGRDADALAVLTRLFGSLEAARKVGEIRASLS 243

Query: 247 LD-HKPRFSDLLSR-RGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSL 304
            D H+P+ SDL+S+  G + PIVW G+GL+  QQ VGINV+FYY + LW +VGF+E+ +L
Sbjct: 244 ADHHRPKLSDLISKTTGKIRPIVWTGIGLAVFQQLVGINVVFYYGATLWEAVGFSEDNAL 303

Query: 305 LITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGA-TVVNGQPT 363
            I +++G ++I   L  I  VDK GRKPLLL+GS GM +TL I++  F  A T  +G  +
Sbjct: 304 QINILSGVLSIGACLGTIMLVDKIGRKPLLLVGSAGMAVTLAIVAYAFSTAVTGADGAVS 363

Query: 364 LTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIIS 423
           L G  G++AL+ ANLYV  F  SWGPI+WVLLGEMF N+IR + L+VA   QWIAN  IS
Sbjct: 364 LPGHNGLMALIAANLYVVFFNLSWGPIMWVLLGEMFPNQIRGSGLAVAGFAQWIANAAIS 423

Query: 424 TTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
            +FP L  + GL   Y  YA  AAIS FF+   V ETKG+ LE M
Sbjct: 424 VSFPALAVSPGLVMTYTGYALFAAISFFFVRKMVHETKGRELEDM 468


Lambda     K      H
   0.325    0.140    0.430 

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: 602
Number of extensions: 32
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: 468
Length of database: 470
Length adjustment: 33
Effective length of query: 435
Effective length of database: 437
Effective search space:   190095
Effective search space used:   190095
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 24 2021. The underlying query database was built on Sep 17 2021.

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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