GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Escherichia coli BW25113

Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate 17988 b3949 predicted enzyme IIC component of PTS (NCBI)

Query= SwissProt::P23355
         (580 letters)



>FitnessBrowser__Keio:17988
          Length = 359

 Score =  270 bits (690), Expect = 7e-77
 Identities = 155/328 (47%), Positives = 204/328 (62%), Gaps = 5/328 (1%)

Query: 245 KHLMTGVSFMLPFVTAGGLLIALAFALGGIYAGDDAHQGTLAWSLFQIGAKAGFTLMVPA 304
           +HLMTGVS M+PFV +GG+L+A++  L G  A  DA        LF IG  AG TLMVP 
Sbjct: 13  QHLMTGVSHMIPFVVSGGILLAVSVMLYGKGAVPDAVADPNLKKLFDIGV-AGLTLMVPF 71

Query: 305 LAGYIAYSIADRPGIAPGMIGGLVAANLNAGFLGGIIAGFIAGYGVAALNRYIKLPRNLE 364
           LA YI YSIA+R  +AP  IG  V  +  AGF G +IAG I G  V  L + I + + L 
Sbjct: 72  LAAYIGYSIAERSALAPCAIGAWVGNSFGAGFFGALIAGIIGGIVVHYLKK-IPVHKVLR 130

Query: 365 GLKPVLILPVLGTLLVGLAMMYVFGQPVADLLAWLTAWLRGMQGSSALLLGLLLGGMMAF 424
            + P+ I+P++GTL+    MM+  G+PV  L   LT WL+GMQ  S ++L +++G M+AF
Sbjct: 131 SVMPIFIIPIVGTLITAGIMMWGLGEPVGALTNSLTQWLQGMQQGSIVMLAVIMGLMLAF 190

Query: 425 DMGGPVNKAAYAFSTGLIASQVYTPMAAAMVAGMTPPLGIALATWVFRNRFTVEERGSAT 484
           DMGGPVNK AYAF    +A  VYT +A A V    PPLG+ LAT + R  F+ EER +  
Sbjct: 191 DMGGPVNKVAYAFMLICVAQGVYTVVAIAAVGICIPPLGMGLATLIGRKNFSAEERETGK 250

Query: 485 AAGVLGLAFVTEGAIPYAARDPLRTIPALVIGSAVAGAISMTAGAELKAPHGGIFVLLIP 544
           AA V+G   VTEGAIP+AA DPLR IP++++GS      +   GA+  A  GG+ VL + 
Sbjct: 251 AALVMGCVGVTEGAIPFAAADPLRVIPSIMVGSVCGAVTAALVGAQCYAGWGGLIVLPV- 309

Query: 545 NAVTHLLNYVLALVVGVVVTAVALRLLK 572
             V   L Y+ A+ VG VVTAV + +LK
Sbjct: 310 --VEGKLGYIAAVAVGAVVTAVCVNVLK 335


Lambda     K      H
   0.320    0.135    0.386 

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: 451
Number of extensions: 17
Number of successful extensions: 3
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: 580
Length of database: 359
Length adjustment: 33
Effective length of query: 547
Effective length of database: 326
Effective search space:   178322
Effective search space used:   178322
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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