GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Escherichia coli BW25113

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 16885 b2801 L-fucose transporter (NCBI)

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__Keio:16885
          Length = 438

 Score =  271 bits (694), Expect = 2e-77
 Identities = 158/413 (38%), Positives = 237/413 (57%), Gaps = 8/413 (1%)

Query: 25  YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84
           Y +   +L S+FF+W     LNDIL+P  +  F L   +A L+Q  F+  YF++ +PAG+
Sbjct: 24  YIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGI 83

Query: 85  LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144
           L+ +L YK GI+ GL +  +GAA FWPAA +  Y  FL  LF++A G+  L+ AAN +V 
Sbjct: 84  LMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVT 143

Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIA-KLSPAEQVAYRVQ 203
           +LGPE S   RL LAQ  NS G  +A  FG  LILS     ++ +  K+SP +  AY+  
Sbjct: 144 VLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHS 203

Query: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPL----RHPHVLF 259
              +VQ PY+ +  ++ L+A+ + L + PAL +    +  KQ S  + L    R  H  +
Sbjct: 204 LVLSVQTPYMIIVAIVLLVALLIMLTKFPAL-QSDNHSDAKQGSFSASLSRLARIRHWRW 262

Query: 260 GVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAK 319
            VLA F YVG + A  S+L+ Y ++ +I  M+   AAN++    +   IGRF G+ L+++
Sbjct: 263 AVLAQFCYVGAQTACWSYLIRY-AVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISR 321

Query: 320 LSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTG 379
            +P K+LA +A I MAL L +    G V + ++     F SI +PTIFSLGI+ +G  T 
Sbjct: 322 FAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTK 381

Query: 380 EASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFYGLYGSR 431
             SS ++M I+GG IV  V G  +D  G +  A  +P LC+A I  +  + S+
Sbjct: 382 YGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFARFRSQ 434


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: 493
Number of extensions: 32
Number of successful extensions: 4
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: 438
Length adjustment: 32
Effective length of query: 410
Effective length of database: 406
Effective search space:   166460
Effective search space used:   166460
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 17 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