GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pseudomonas fluorescens GW456-L13

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate PfGW456L13_1301 UDP-glucose 4-epimerase (EC 5.1.3.2)

Query= BRENDA::F6DEY6
         (311 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1301
          Length = 309

 Score =  209 bits (532), Expect = 7e-59
 Identities = 124/291 (42%), Positives = 177/291 (60%), Gaps = 15/291 (5%)

Query: 3   VLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVPFFQV---DLRDKEEVE 59
           VL+TGGAGFIGSH+ + LLARG  V +LD+L+TGK  N+P   P  ++   D+ D   V 
Sbjct: 6   VLITGGAGFIGSHLTDALLARGHAVRILDDLSTGKHSNLPLDNPRVELIVGDVADAALVA 65

Query: 60  RAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTGG 119
           +A      + V+H AA ASV+ SV+DPV   + N +G LN+ EA RQ GV++++FAS+  
Sbjct: 66  QAMAGC--SAVAHLAAVASVQASVDDPVRTHQSNFIGTLNVCEAMRQTGVKRVLFASSA- 122

Query: 120 AIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQD 179
           A+YG   EGE  +E  P  P +PYA  K A E Y   Y + +GL+ V  R+ N+YGPRQD
Sbjct: 123 AVYGNNGEGESIDEDTPKAPLTPYAVDKLASEQYFDFYHRQHGLEPVIFRFFNIYGPRQD 182

Query: 180 PHGE-AGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAE--AHALALFSLE- 235
           P    +GV++IF+ER L GLP+T++     GD    RD+VYV D+ +    A+ +  +E 
Sbjct: 183 PSSPYSGVISIFSERALKGLPITVF-----GDGEQTRDFVYVEDLVDLLVQAIEMPQVEV 237

Query: 236 GIYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPPRPGDLERSVLSPLKLM 286
           G  NVG  +  T +++LEA+    GK P V   P R GD+  S  +  +L+
Sbjct: 238 GAVNVGWNQATTLKQMLEALEAVVGKLPPVSYGPARSGDIRHSRANNRRLL 288


Lambda     K      H
   0.318    0.138    0.411 

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: 288
Number of extensions: 15
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: 311
Length of database: 309
Length adjustment: 27
Effective length of query: 284
Effective length of database: 282
Effective search space:    80088
Effective search space used:    80088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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