GapMind for catabolism of small carbon sources

 

Alignments for a candidate for udh in Paraburkholderia bryophila 376MFSha3.1

Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate H281DRAFT_05321 H281DRAFT_05321 uronate dehydrogenase

Query= BRENDA::Q88NN6
         (268 letters)



>FitnessBrowser__Burk376:H281DRAFT_05321
          Length = 280

 Score =  299 bits (766), Expect = 4e-86
 Identities = 147/263 (55%), Positives = 192/263 (73%), Gaps = 2/263 (0%)

Query: 5   PFNRLLLTGAAGGLGKVLRERLKGYAEVLRLSDISPMAPAAGPHEEVITCDLADKAAVHT 64
           PF RLLLTGAAG LG  LR+ L  +A+V+R++DI+P+   A  HEE    DLAD+AAVH 
Sbjct: 14  PFRRLLLTGAAGNLGTQLRDALAAWADVVRVTDIAPLGEVAD-HEEAAIVDLADEAAVHA 72

Query: 65  LVEGVDAIIHFGGVSTEHAFEEILGPNICGVFHVYEAARKHGVKRIIFASSNHTIGFYRQ 124
           L+EGVDA+IH GG+S E  FE++L  NI G++++Y AA+K GVKR+++ASSNHT+GF+  
Sbjct: 73  LLEGVDAVIHLGGISVEAPFEDLLEANIRGLYNLYSAAQKQGVKRVVYASSNHTVGFHPV 132

Query: 125 DERIDAHAPRRPDSYYGLSKCYGEDVASFYFDRYGIETVSIRIGSSFPQPQNLRMLCTWL 184
            E +D  AP RPDS YG++KC+GE ++ +YFDR+G+ETV +RIGSSF QP+N RML T+L
Sbjct: 133 TEVVDIDAPLRPDSLYGVTKCFGESLSRYYFDRFGLETVCLRIGSSFEQPKNPRMLVTYL 192

Query: 185 SYDDLVQLIERGLFTPGVGHTIVYGASDNRTVWWDNRHAAHLGYVPKDSSETFRAAVEAQ 244
           SY D ++L+   LFT  VGH IVYG SDNRT W DN  AA LG+ P+DSS  F       
Sbjct: 193 SYRDFIELVRCSLFTNRVGHAIVYGVSDNRTKWVDNTKAAFLGFRPQDSSVQFEHLFPVA 252

Query: 245 PAPA-ADDPSMVYQGGAFAVAGP 266
            + A  DDP+  +QGGAF +AGP
Sbjct: 253 ASTADLDDPTQRFQGGAFVLAGP 275


Lambda     K      H
   0.321    0.138    0.427 

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: 255
Number of extensions: 12
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: 268
Length of database: 280
Length adjustment: 25
Effective length of query: 243
Effective length of database: 255
Effective search space:    61965
Effective search space used:    61965
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: 47 (22.7 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