GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Sphingobium czechense LL01

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_082679223.1 V473_RS17505 L-fucose:H+ symporter permease

Query= uniprot:A0A1I2JXG1
         (442 letters)



>NCBI__GCF_001046645.1:WP_082679223.1
          Length = 392

 Score =  257 bits (656), Expect = 5e-73
 Identities = 158/400 (39%), Positives = 226/400 (56%), Gaps = 21/400 (5%)

Query: 29  MGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVAR 88
           M + T +FF+WG    LND+LI H + VF L+  ++ LVQ  F+  YF  ++PA L   R
Sbjct: 1   MVLTTGLFFLWGVANNLNDVLIAHFRHVFSLSDFQSGLVQSAFYLGYFCFAIPAALAAER 60

Query: 89  LGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGP 148
           LGYK  ++ GL + G GA  F PA+    Y  FL ALFV+A+G+  L+ AAN  VA +GP
Sbjct: 61  LGYKATVILGLLLFGGGALLFLPASIQLSYGFFLVALFVIASGLAFLETAANPMVAAMGP 120

Query: 149 EKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTV 208
            + A+ RL LAQA N LG+      G  LILS A           P + VA     A  V
Sbjct: 121 AEGAAQRLNLAQAFNPLGSIAGVALGATLILSDA-----------PQQGVA----GAAAV 165

Query: 209 QGPYLGLAIVLFLLAVFVYLFRLP-ALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFY 267
           Q PYLG+A+V+ + A  +   R P A T+             + LR P  + GV A FFY
Sbjct: 166 QLPYLGIALVVLVWAAVLTFTRFPRAATQADGSGGSALAGYGALLRRPRYMAGVAAQFFY 225

Query: 268 VGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGA-MIGRFIGSALLAKLSPRKLL 326
           VG +V I S+L+ Y      G  +++AA  W+    L   M+GRFIG+ALL++    +L+
Sbjct: 226 VGAQVGIWSYLIRYAESVVPGIGAQKAA--WLLTLSLALFMVGRFIGAALLSRSDGARLM 283

Query: 327 AIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLI 386
           A+FA IN+ L L   +  G V + +VV+   F SIM+PTIF L +  +GP+T   +S+++
Sbjct: 284 ALFAGINIILSLVA-VAGGIVGLAAVVATSFFMSIMYPTIFVLSLRGLGPLTKAGASMIV 342

Query: 387 MAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFY 425
           MAI+GGA++    GL +D  G ++ A  +P LC+A +  Y
Sbjct: 343 MAIIGGAVLTMAMGLLSDLTGTIRAAMLVPALCFAVVTLY 382


Lambda     K      H
   0.327    0.140    0.414 

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: 455
Number of extensions: 24
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: 442
Length of database: 392
Length adjustment: 31
Effective length of query: 411
Effective length of database: 361
Effective search space:   148371
Effective search space used:   148371
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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