GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Shewanella amazonensis SB2B

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 6938123 Sama_2244 polysaccharide biosynthesis protein (RefSeq)

Query= SwissProt::Q9ZDJ5
         (341 letters)



>FitnessBrowser__SB2B:6938123
          Length = 644

 Score =  135 bits (341), Expect = 2e-36
 Identities = 108/345 (31%), Positives = 173/345 (50%), Gaps = 36/345 (10%)

Query: 5   KTLMITGGTGSFGNAVLSRFLK----SNIINDIKEIRIFSRDEKKQEDMRIALN-NSKLK 59
           K +M+TG  GS G+ +  + L+      ++ ++ E  ++S  E++ + +R  L  + +L 
Sbjct: 281 KVVMVTGAGGSIGSELCRQILRLAPRKLVLFELSEFGLYSI-ERELQAIRAELGLDVELF 339

Query: 60  FYIGDVRNYQSIDDAMHG--VDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAIN 117
             +G V+    +   M    V  V+HAAA K VP  E   +E +  NV G      AAI 
Sbjct: 340 PMMGSVQRQNRVQAVMEAFKVQTVYHAAAYKHVPLVEHNVVEGVRNNVFGTLYTAQAAIA 399

Query: 118 NKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGS 177
             V   +++STDKAV P N MG +K + E +  A +++ S   T  C+ R+GNV+ S GS
Sbjct: 400 TGVETFVLISTDKAVRPTNVMGTTKRMAELVLQALSKLNSG--TRFCMVRFGNVLGSSGS 457

Query: 178 VIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPAST-IE 236
           V+PLF  QI  G  +T+T P +TRF M++ ++  LV+ A   G  GD+FV     S  I 
Sbjct: 458 VVPLFRKQIANGGPVTVTHPEITRFFMTIPEASQLVIQAGAMGIGGDVFVLDMGQSVKIV 517

Query: 237 VLAKALQEIFG----------SKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIP 286
            LA+ +  + G              I+F G R GEK YE L+  +++       G+ RI 
Sbjct: 518 DLARKMIRLSGFEVKDEHNPDGDIEIQFSGLRPGEKLYEELLIGDNVEGT----GHERI- 572

Query: 287 MDGRDLNYAKYFVTGEKKVALLD--DYTSHNTKRLNLKEVKELLL 329
                +   + F+T E+   +LD  D   H     + + ++EL+L
Sbjct: 573 -----MTAHEVFLTWEELKPVLDKLDMACH---AFDHESIRELML 609


Lambda     K      H
   0.319    0.135    0.373 

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: 417
Number of extensions: 23
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: 341
Length of database: 644
Length adjustment: 33
Effective length of query: 308
Effective length of database: 611
Effective search space:   188188
Effective search space used:   188188
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