GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pseudomonas simiae WCS417

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate GFF453 PS417_02315 NAD-dependent dehydratase

Query= BRENDA::F6DEY6
         (311 letters)



>FitnessBrowser__WCS417:GFF453
          Length = 308

 Score =  209 bits (532), Expect = 7e-59
 Identities = 125/293 (42%), Positives = 177/293 (60%), Gaps = 15/293 (5%)

Query: 2   RVLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVP---FFQVDLRDKEEV 58
           RVL+TGGAGFIGSH+V+ LLA+G  V VLDNL+TGKR N+P   P     + D+ D E V
Sbjct: 4   RVLITGGAGFIGSHLVDALLAKGYGVRVLDNLSTGKRSNLPLDNPRVELLEGDVADAELV 63

Query: 59  ERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTG 118
            RA  +   T V H AA ASV+ SV+DPV   + N +G LN+ EA R+ GV+++V+AS+ 
Sbjct: 64  ARAAVD--TTAVVHLAAVASVQASVDDPVSTHQSNFVGTLNVCEAMRKAGVKRVVYASS- 120

Query: 119 GAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQ 178
            A+YG   EG   +E     P +PYA+ K A EHY   Y + +GL+ V  R+ N++GPRQ
Sbjct: 121 AAVYGNNGEGASIDEETTKAPLTPYASDKLAGEHYFDFYRRQHGLEPVIFRFFNIFGPRQ 180

Query: 179 DPHGE-AGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAEAHALALFSLE-- 235
           DP    +GV++IF+ER   G+P+ ++     GD    RD++YV D+ +    A+ +    
Sbjct: 181 DPSSPYSGVISIFSERAQQGVPIAVF-----GDGEQTRDFMYVEDLVDVLVQAIEAPSAP 235

Query: 236 -GIYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPPRPGDLERSVLSPLKLMA 287
            G  NVG     T ++VL+A+ E  GK P V   P R GD+  S  +  +L+A
Sbjct: 236 LGAINVGWNRTTTLKQVLQALEEIVGKLPTVTYGPARSGDIRHSRANNQRLLA 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: 287
Number of extensions: 18
Number of successful extensions: 5
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: 308
Length adjustment: 27
Effective length of query: 284
Effective length of database: 281
Effective search space:    79804
Effective search space used:    79804
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