GapMind for catabolism of small carbon sources

 

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

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_066329840.1 BLR17_RS08985 sugar porter family MFS transporter

Query= SwissProt::P0AEP1
         (464 letters)



>NCBI__GCF_900100165.1:WP_066329840.1
          Length = 452

 Score =  233 bits (595), Expect = 8e-66
 Identities = 142/437 (32%), Positives = 237/437 (54%), Gaps = 21/437 (4%)

Query: 22  AALAGLLFGLDIGVIAGALPFIADEFQITSHTQEW-----VVSSMMFGAAVGAVGSGWLS 76
           AALAG LFG D  VI+GA      + Q+  H+ +      V++  ++G  +GA+     +
Sbjct: 11  AALAGFLFGFDTVVISGA----DKQLQLLWHSSDAFHGLIVMAMALWGTVIGAIFGAIPT 66

Query: 77  FKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLSEIAPE 136
            KLGRKK+L    IL+   ++ +A A +  V    R + GL VG ++  AP Y+SEIAP 
Sbjct: 67  NKLGRKKTLFWIGILYFVSAIGAAFANDPYVFAAFRFIGGLGVGASTIAAPAYVSEIAPA 126

Query: 137 KIRGSMISMYQLMITIGILGAYLSDTAFSYTG--AWRWMLGVIIIPAILLLIGVFFLPDS 194
             RG ++++YQ  I +GIL A++S+      G  AWRWM+GV  IP+++ ++ +  +P+S
Sbjct: 127 DKRGRLVALYQFNIVLGILIAFISNYFLKDIGENAWRWMIGVQAIPSLIYILFIITIPES 186

Query: 195 PRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNFRRAVFL 254
           PRW  ++ R  +A +VL  + D  A  +  +D+ RE+   K     + K    +R  + L
Sbjct: 187 PRWLLSRNRDTEAGKVLFEI-DPLASIEDLIDDSRENGVTKHENIFMKK----YRFPLML 241

Query: 255 GVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLVDRW 314
             L+    QF+G+N  +YYAP+IFE AG    T  +  ++ +G+TN++ T + + L+D+ 
Sbjct: 242 AFLMAFFNQFSGINAFLYYAPRIFEEAGLGQNT-ALLSSIGIGITNLIFTLVGVSLIDKL 300

Query: 315 GRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLC 374
           GRK  + +G L     +G++    +      S   F    L +FI   A+  G +IWV  
Sbjct: 301 GRKVLMYIGSLGYIISLGLVSASFYFNWGGLSVPVF----LFLFIASHAIGQGAVIWVFI 356

Query: 375 SEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNVLFILLTLW 434
           SEI P   R  G    ++ +W+   I+ +    + + +G +  F ++  + VL +L  ++
Sbjct: 357 SEIFPNHIRAAGQAFGSSVHWVLAAIIPSLIPMLFSEIGPSVVFLIFTLMMVLQLLFVMF 416

Query: 435 LVPETKHVSLEHIERNL 451
           L+PETK +SLE +  NL
Sbjct: 417 LMPETKGISLETLSENL 433


Lambda     K      H
   0.327    0.140    0.425 

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: 615
Number of extensions: 26
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: 464
Length of database: 452
Length adjustment: 33
Effective length of query: 431
Effective length of database: 419
Effective search space:   180589
Effective search space used:   180589
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 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