GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Stenotrophomonas chelatiphaga DSM 21508

Align UTP--glucose-1-phosphate uridylyltransferase; EC 2.7.7.9; Alpha-D-glucosyl-1-phosphate uridylyltransferase; UDP-glucose pyrophosphorylase; UDPGP; Uridine diphosphoglucose pyrophosphorylase (uncharacterized)
to candidate WP_057508393.1 ABB28_RS09480 glucose-1-phosphate thymidylyltransferase

Query= curated2:P75124
         (291 letters)



>NCBI__GCF_001431535.1:WP_057508393.1
          Length = 297

 Score = 78.2 bits (191), Expect = 2e-19
 Identities = 84/277 (30%), Positives = 123/277 (44%), Gaps = 56/277 (20%)

Query: 5   RKAVIPAAGLGTRLLPATKAIPKEMLPLVNKPTIQYIVEEAVASGIKEILVIVSSKKEAI 64
           RK +I A G GTRL P TK I K++LP+ +KP I Y +   + +GI+E+L+I +      
Sbjct: 6   RKGIILAGGSGTRLYPITKGIGKQLLPVYDKPMIYYPLSVLMLAGIREVLIINAPH---- 61

Query: 65  IDHFDYDFILENALLQKHKDQEHQEIKDIANLAHIYFVRQKHQHGLGDAILHAKSFVGNE 124
                     E AL Q+      Q   D      I +  Q    GL  A L  + F+  +
Sbjct: 62  ----------EQALFQQLLGDGSQWGMD------IQYAAQPSPDGLAQAYLIGREFLDGK 105

Query: 125 DFAVLLGDDVVFGEQPALAQCIQAYEQTDCQVIGVQEVPHDQVNKYG--IVTPE----AN 178
              ++LGD+V  G           +  TD  V+   +  HD    +G  +  PE    A 
Sbjct: 106 PSCLVLGDNVFHG-----------HGLTD--VLKRADARHDGATVFGYWVSDPERYGVAE 152

Query: 179 WQKQALVKILGMVEKPAVNEAKSNLAILSRYIL--KPSIFTA-LKQVPFGVGGELQLTDG 235
           + K    K++G+VEKPA  + +SN A+   Y    K S + A LK  P    GEL++TD 
Sbjct: 153 FDKDG--KVIGLVEKPA--KPRSNYAVTGLYFYDGKASEYAADLKPSP---RGELEITDL 205

Query: 236 LNYCLQQG----EPFFAKHFGGTRFDVGTKNGFIKAN 268
               L +G    EP      G    D GT    ++A+
Sbjct: 206 NQRYLDEGALHLEPLGR---GYAWLDTGTHQSLLEAS 239


Lambda     K      H
   0.320    0.138    0.396 

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: 213
Number of extensions: 22
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: 291
Length of database: 297
Length adjustment: 26
Effective length of query: 265
Effective length of database: 271
Effective search space:    71815
Effective search space used:    71815
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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