GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Flavobacterium glycines Gm-149

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_066323743.1 BLR17_RS10195 sugar porter family MFS transporter

Query= TCDB::P15729
         (468 letters)



>NCBI__GCF_900100165.1:WP_066323743.1
          Length = 465

 Score =  298 bits (762), Expect = 3e-85
 Identities = 177/466 (37%), Positives = 280/466 (60%), Gaps = 25/466 (5%)

Query: 13  NVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQ--TDSLLTGLSVSLALLGSALG 70
           N  ++L IS V+ALGG LFG+D  VI GA    ++ F   T + L   ++S AL+G  LG
Sbjct: 9   NNNYLLAISMVSALGGLLFGYDWVVIGGAKPFYERFFDITTSANLQAWAMSSALIGCILG 68

Query: 71  AFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPA 130
           A  +G I+D+ GR   ++L+A LFT++S+G+GL    W F+ +R++GG+G+G AS ++P 
Sbjct: 69  AVVSGVISDKFGRKWPLLLSAFLFTVASLGTGLASAYWIFVVFRIVGGVGIGLASALSPM 128

Query: 131 YIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIA--LMAGGS---AQNPWLFGAAAW 185
           YIAEV+P+HLRGR  +L Q+ +V GI  A + N  IA  + AG S    ++ W  G   W
Sbjct: 129 YIAEVAPSHLRGRFVALNQMTLVVGILAAQIVNLLIADKVPAGVSDAFIRSSW-NGQMGW 187

Query: 186 RWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRIEEIQATV 245
           RWMF+   +P++++ +  F +PESPR+L+  G+ +KA   L K+ GG+V +  E      
Sbjct: 188 RWMFFACAVPSVVFFLLVFTLPESPRWLMKAGKADKAFPTLQKI-GGEVYAHEEMANIKA 246

Query: 246 SLD---HKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEK 302
           +LD    K  F  L + +     ++ IG+ ++  QQ+ GIN +F Y+  ++ + G+    
Sbjct: 247 TLDDVTEKIDFKALFNPK--FKDVLVIGIVIAVFQQWCGINTVFNYAEEIFTAAGYGVSD 304

Query: 303 SLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQP 362
           +L   VITG +N++ TLVA+  VDK+GRK L++ G++G+TIT  +L   F          
Sbjct: 305 TLFNIVITGTVNLIFTLVAMFTVDKWGRKKLMVFGALGLTITYLLLGSAF--------YF 356

Query: 363 TLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFII 422
            L G A +++LV   + V++   S  PI WV+L E+F N++R AA+++A    W+A FI+
Sbjct: 357 DLKGVA-VLSLVVIAIAVYA--MSLAPITWVILSEIFPNRVRGAAMALATFALWVACFIL 413

Query: 423 STTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
           + TFP L  T+G    + +YA    +   F+   + ETKGKTLE++
Sbjct: 414 TYTFPLLNKTLGAAGTFWVYAGICVLGFLFVLIRLPETKGKTLEEI 459


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: 551
Number of extensions: 31
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: 465
Length adjustment: 33
Effective length of query: 435
Effective length of database: 432
Effective search space:   187920
Effective search space used:   187920
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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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