GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6938123 Sama_2244 polysaccharide
           biosynthesis protein (RefSeq)
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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