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_066326767.1 BLR17_RS06040 sugar porter family MFS transporter

Query= TCDB::P15729
         (468 letters)



>NCBI__GCF_900100165.1:WP_066326767.1
          Length = 439

 Score =  265 bits (678), Expect = 2e-75
 Identities = 155/456 (33%), Positives = 255/456 (55%), Gaps = 28/456 (6%)

Query: 15  KFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSV-SLALLGSALGAFG 73
           K ++  S VA+  GFLFGFDT VI+GA  ALQ  + +     G  V ++AL G+ +GA  
Sbjct: 3   KKIMSWSIVASFAGFLFGFDTVVISGADKALQILWDSSDFFHGSVVMAMALWGTVIGAIF 62

Query: 74  AGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIA 133
            G   ++ GR  T+++  +LF++S++GS L    W F F+R +GG+G+GA+++ APAYI+
Sbjct: 63  GGIPTNKIGRKSTLLIIGILFSISALGSSLANGPWIFAFFRFIGGLGIGASTIAAPAYIS 122

Query: 134 EVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTEL 193
           E++PA  RGRL  L Q  IV GI  A LSN+ ++ +           G  AWRWM   ++
Sbjct: 123 EIAPAKDRGRLVGLYQFNIVFGILTAFLSNYLLSDI-----------GENAWRWMLGIQV 171

Query: 194 IPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGDVPSRIEEIQATVSLDHKPRF 253
            P+++Y V AF IPESPR+L+ Q Q ++A  IL K+   +    ++ I   +S D+K   
Sbjct: 172 FPSVVYTVLAFYIPESPRWLLTQSQIDEARVILNKINSKE---DVQSIIDNISEDNKNTS 228

Query: 254 SD-LLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGF 312
           SD  +  +    P++ + + ++A  Q  GIN   YY+  ++   G   + +LL ++  GF
Sbjct: 229 SDENIFMKKYSFPLILVFL-IAAFNQLSGINAFLYYAPRIFEEAGLGAKTALLSSIGIGF 287

Query: 313 INILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIA 372
           +N++ TL+ +  +D+ GR+ L++ GS+G   +L ++++ F          + TG A  I 
Sbjct: 288 VNLIFTLIGVYLIDRLGRRKLMIFGSLGYIFSLSMVAISF--------YLSWTGMAVPIF 339

Query: 373 LVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDT 432
           L    +++ S     G ++WV + E+F N +RA+  S  + V W+   II +  P L   
Sbjct: 340 LF---VFIASHAIGQGAVIWVFISEIFPNHLRASGQSFGSSVHWVLAAIIPSMVPILFSN 396

Query: 433 VGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
            G+G  +  +A      + F+ F + ETKG +LE M
Sbjct: 397 FGVGNVFSFFAIMMVFQLVFVLFMMPETKGVSLESM 432


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: 559
Number of extensions: 33
Number of successful extensions: 6
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: 439
Length adjustment: 33
Effective length of query: 435
Effective length of database: 406
Effective search space:   176610
Effective search space used:   176610
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