GapMind for catabolism of small carbon sources

 

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

Align The major glucose (or 2-deoxyglucose) uptake transporter, GlcP (characterized)
to candidate WP_066326777.1 BLR17_RS06000 sugar porter family MFS transporter

Query= TCDB::Q7BEC4
         (472 letters)



>NCBI__GCF_900100165.1:WP_066326777.1
          Length = 439

 Score =  239 bits (611), Expect = 1e-67
 Identities = 155/459 (33%), Positives = 249/459 (54%), Gaps = 41/459 (8%)

Query: 24  IFI-AAAAAMGGFLFGYDSSVINGAVEAIRDRYDVGSAVLAQVI-AVALIGCAIGAATAG 81
           IFI A  A++ GFLFG+D+ VI+GA + ++  ++   A    V+  +AL G  IGA   G
Sbjct: 4   IFIWALVASLAGFLFGFDTVVISGADKKLQTLWNSSDAFHGTVVMGMALWGTVIGAIFGG 63

Query: 82  RIADRIGRIRCMQIAAVLFTVSAVGSALPFALWDLAMWRIIGGFAIGMASVIGPAYIAEV 141
              +RIGR   +    +LF  SA+GSAL    +  A +R +GG  +G +++  PAYI+E+
Sbjct: 64  IPTNRIGRKNTLLWIGILFFFSAIGSALANGPYVFAAFRFVGGLGVGASTIAAPAYISEI 123

Query: 142 SPPAYRGRLGSFQQAAIVIGIAVSQLVNWGLLNAAGGDQRGELMGLEAWQVMLGVMVIPA 201
           +P   RG+L +F Q  IV+GI ++ L N+ L N          +G  +W+ M+GV   P+
Sbjct: 124 APAKDRGKLVAFYQFNIVLGILIAFLSNYLLRN----------VGENSWRWMMGVQAFPS 173

Query: 202 VLYGLLSFAIPESPRFLISVGKRERAKKILEEVEGKDVDFDARVTEIEHAMHREEKSSFK 261
            +Y +L F+IP+SPR+L+S  + E AK +L+ + G + DF+    +I      +  ++  
Sbjct: 174 FIYSVLIFSIPKSPRWLLSKNRDEEAKSVLQRM-GLEADFEEMKKDI------DADNANA 226

Query: 262 DLLGGSFFFK----PIVWIGIGLSVFQQFVGINVAFYYSSTLWQSVGVDPADSFFYSFTT 317
            L   S F K    P++ +   ++ F Q  GIN   YYS+ ++Q  G+  + +   S   
Sbjct: 227 ALANDSIFLKKYRTPLI-LAFLIAFFNQLSGINAFLYYSNRIFQEAGLGESTALLSSIGI 285

Query: 318 SIINIVGTVIAMIFVDRVGRKPLALIGSVGMVIGLALEAWAFSFDLVDGKLPATQGWVAL 377
            ++N+V T++ +  +DR+GRK L  IGSVG +I L L A AF            QG +  
Sbjct: 286 GVVNLVFTLLGVFLIDRLGRKILMYIGSVGYIISLTLVAMAFFLH--------WQGIMVP 337

Query: 378 IAAHVFVLFFALSWGVVVWVFLGEMFPNRIRAAALGVAASAQWIANWAITASFPSLADWN 437
           +   +F+   A+  G V+WVF+ E+FPN +RA+     ++  WI    + A  PSL  + 
Sbjct: 338 VFLFLFIAAHAIGQGAVIWVFISEIFPNHLRASGQAFGSTTHWI----LAAIIPSLIPFL 393

Query: 438 LS--GTYVIYTIFAAL---SIPFVLKFVKETKGKALEEM 471
            S  G  V++  FA +    + FV   + ETKG +LEE+
Sbjct: 394 FSTIGAGVVFLFFAIMMVFQLFFVAFLMPETKGISLEEL 432


Lambda     K      H
   0.326    0.139    0.426 

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: 655
Number of extensions: 41
Number of successful extensions: 7
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: 472
Length of database: 439
Length adjustment: 33
Effective length of query: 439
Effective length of database: 406
Effective search space:   178234
Effective search space used:   178234
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