GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pseudomonas fluorescens FW300-N2E3

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate AO353_06770 AO353_06770 NAD-dependent dehydratase

Query= BRENDA::F6DEY6
         (311 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_06770
          Length = 309

 Score =  204 bits (520), Expect = 2e-57
 Identities = 120/291 (41%), Positives = 179/291 (61%), Gaps = 15/291 (5%)

Query: 3   VLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVPFFQV---DLRDKEEVE 59
           VL+TGGAGFIGSH+ + LLA+G  V +LD+L+TGKR N+P   P  ++   D+ D   V 
Sbjct: 6   VLITGGAGFIGSHLADALLAKGHSVRILDDLSTGKRSNLPLDNPRVELIEGDVADAALVA 65

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

Query: 120 AIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQD 179
           A+YG   EGE  +E     P +PYAA K A E+YL  Y + +GL+    R+ N++GPRQD
Sbjct: 123 AVYGNNGEGESIDEETAKAPLTPYAADKLAGEYYLDFYRRQHGLEPAIFRFFNIFGPRQD 182

Query: 180 PHGE-AGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAE--AHALALFSLE- 235
           P    +GV++IF+ER   GLP+T++     GD    RD+VYV D+ +    A+ + +LE 
Sbjct: 183 PSSPYSGVISIFSERAQKGLPITVF-----GDGEQTRDFVYVEDLVDLLVQAIEMPTLEV 237

Query: 236 GIYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPPRPGDLERSVLSPLKLM 286
           G  NVG  +  T +++L+A+ E  G+ P +   P R GD+  S  +  +L+
Sbjct: 238 GAVNVGWNQATTLKQMLQALEEVVGQLPPIAYGPARSGDIRHSRANNQRLL 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: 267
Number of extensions: 16
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