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_05310 H281DRAFT_05310 uronate dehydrogenase

Query= BRENDA::Q7CRQ0
         (265 letters)



>FitnessBrowser__Burk376:H281DRAFT_05310
          Length = 280

 Score =  229 bits (583), Expect = 6e-65
 Identities = 125/259 (48%), Positives = 154/259 (59%), Gaps = 5/259 (1%)

Query: 1   MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLS-PLDPAGPNEECVQCDLADANAVNAM 59
           MK++ ++GA GQLG V+R       + LR A  S PL P    E+ +  DL D   V+ +
Sbjct: 1   MKKIALSGAGGQLGSVVRAAFIARGKPLRSAAGSKPLTPLVEGEDVMHGDLRDPAVVDRL 60

Query: 60  VAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQT 119
           + G D ++H  G SVE+P  +I++ N+ GL  +YE AR HG  RIVFASSNH IG YP T
Sbjct: 61  LDGVDVLIHFAGTSVERPLPEIIENNLRGLVEVYEGARRHGVKRIVFASSNHAIGMYPVT 120

Query: 120 ERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFS 179
           ERL  D   RPDG YG+SK +GE LARMY+DK G E+  VRIGSC   P   R LSTWF 
Sbjct: 121 ERLSLDCELRPDGFYGLSKVWGEALARMYWDKHGIESVCVRIGSCLERPTEPRHLSTWFG 180

Query: 180 HDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETT 239
           H D +  ++    A  LG   VWG SAN   WWDNS    LG+ PK NAE +     E  
Sbjct: 181 HADLMHFLDRCIEAEDLGFITVWGVSANTRSWWDNSGAERLGYMPKQNAEDY---ADEVL 237

Query: 240 PPPDPNDAL-VRFQGGTFV 257
             P+P DA   RFQGG FV
Sbjct: 238 ARPNPLDAFGQRFQGGGFV 256


Lambda     K      H
   0.321    0.139    0.443 

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: 274
Number of extensions: 12
Number of successful extensions: 2
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: 265
Length of database: 280
Length adjustment: 25
Effective length of query: 240
Effective length of database: 255
Effective search space:    61200
Effective search space used:    61200
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.

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:

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