GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pedobacter sp. GW460-11-11-14-LB5

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate CA265_RS09125 CA265_RS09125 methylglutaconyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Pedo557:CA265_RS09125
          Length = 258

 Score =  117 bits (293), Expect = 2e-31
 Identities = 81/242 (33%), Positives = 125/242 (51%), Gaps = 7/242 (2%)

Query: 17  ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQL--- 73
           IT+NRP+K NALN +L+ EL  A  +A  D  ++V+I+   G AF AGAD+    QL   
Sbjct: 16  ITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGDAFSAGADLAYLQQLQYN 75

Query: 74  TPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPE 133
           T  E    S   +++   I  L K  IA + G+A+ GG  LA  CDI  A  E+  G  E
Sbjct: 76  TFEENVADSNHLKKLFTTIYYLPKVVIAQVEGHAIAGGCGLATICDIVFATPESNFGYTE 135

Query: 134 INLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRK 193
           + +G  P       L   + +  A E+++TG     ++A KY L+N V   +++ Q  R+
Sbjct: 136 VKIGFVPAIVSC-FLKEKVSESIAKEILLTGKIFSAEEALKYNLINFVTNSSDIHQIVRE 194

Query: 194 LAEKIAK-KSPISLALIKEVVNRGLDSPLLSGLALESVGWGV-VFSTEDKKEGVSAFLEK 251
            A  +    S  SL + K+++ +   +PLL      +V     V  +ED K+G+S+FL K
Sbjct: 195 FALSLCSGSSGNSLMITKQLITQ-TTNPLLEKCLETAVQINARVRESEDFKKGISSFLNK 253

Query: 252 RE 253
            +
Sbjct: 254 EK 255


Lambda     K      H
   0.315    0.135    0.382 

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: 107
Number of extensions: 7
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: 259
Length of database: 258
Length adjustment: 24
Effective length of query: 235
Effective length of database: 234
Effective search space:    54990
Effective search space used:    54990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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