GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pseudomonas putida KT2440

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate PP_1803 PP_1803 UDP-sugar epimerase

Query= curated2:Q56623
         (328 letters)



>FitnessBrowser__Putida:PP_1803
          Length = 323

 Score =  305 bits (781), Expect = 1e-87
 Identities = 159/318 (50%), Positives = 217/318 (68%), Gaps = 3/318 (0%)

Query: 10  KSILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLL--FEVGDINASTDFELP 67
           ++IL+TG++GFVG  L + L     + +++A R         +    V D++A+TD+   
Sbjct: 4   RTILVTGASGFVGGALCRQLATLGSFAIRAASRDLGGASVAGIQAVTVADLSATTDWARA 63

Query: 68  LKNTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVN 127
           L    +VVH AAR HVM +  ++ L  +R VN  GT+NLA+QA  +GV+RFIFISSIKVN
Sbjct: 64  LSGVDLVVHAAARVHVMKETASDSLAEFRRVNVDGTLNLARQAAAAGVRRFIFISSIKVN 123

Query: 128 GEGTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKAN 187
           GE +  G P + +D+ AP+D YG+SK EAE+ L  LA  + MEVV+IRP +VYGPGVKAN
Sbjct: 124 GESSQPGQPLRADDSPAPQDAYGVSKHEAEQGLRQLAAATGMEVVVIRPVLVYGPGVKAN 183

Query: 188 FASLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVST 247
           F S+MR + +G+PLPFG++  N+RSLVS+ NLVDL+VTCIDHP+AANQ FL SDG DVS 
Sbjct: 184 FHSMMRWLQRGVPLPFGAVC-NRRSLVSLANLVDLVVTCIDHPRAANQTFLASDGDDVSL 242

Query: 248 AEMVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKP 307
            +++R L +AL +P   LPVP    +    L G+ D+  RL GTLQVDI   ++ LGW P
Sbjct: 243 TQLLRALGLALGRPARLLPVPAGLLRGAVLLIGRRDLAQRLFGTLQVDIEKNRQLLGWYP 302

Query: 308 PQTLQEGFKQTAQAFLQA 325
           P TL++G   TA++FL A
Sbjct: 303 PCTLEQGLNMTARSFLGA 320


Lambda     K      H
   0.318    0.134    0.388 

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: 249
Number of extensions: 7
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: 328
Length of database: 323
Length adjustment: 28
Effective length of query: 300
Effective length of database: 295
Effective search space:    88500
Effective search space used:    88500
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