GapMind for catabolism of small carbon sources

 

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

Align 2-keto-4-pentenoate hydratase 3; EC 4.2.1.80; 2-hydroxypentadienoic acid hydratase 3 (uncharacterized)
to candidate H281DRAFT_05455 H281DRAFT_05455 2-keto-4-pentenoate hydratase

Query= curated2:Q706S1
         (269 letters)



>FitnessBrowser__Burk376:H281DRAFT_05455
          Length = 267

 Score =  159 bits (402), Expect = 6e-44
 Identities = 100/255 (39%), Positives = 145/255 (56%), Gaps = 7/255 (2%)

Query: 10  AQSLYQAMQSGKPIAPLRDTFPDMNVDDAYAIQS-INTQRRISLGRRVVGRKIGLTSVVV 68
           A+ LY A      +  +    P+ ++D AYAI +     R  +LG R VGRK+GLT+  V
Sbjct: 15  ARELYDARVGVYTVPYVSPRLPERDLDAAYAISAEFAALRERNLGVRRVGRKVGLTNPNV 74

Query: 69  QQQLGVDEPDFGALFDDMSFGDAETIPLSILHQPKVEAEIGFVLGRDLDTEQPTHQEVLQ 128
           Q+++G+ EPD+G + DDM F     +P S  ++  +EAE+ FVL  D+     T + V  
Sbjct: 75  QKRVGISEPDYGVIHDDMVFQSGAVLPKSRYNRLLIEAEVAFVLKSDIF--DATLERVAA 132

Query: 129 AVDYVVPALEIVGSRIADWNIKFVDTVADNASSGVYVLGSTPISPRGLDLSLVGMCLSRR 188
           A+DYV PA E+V  R      + VDT+ADNA     V+G        +DL  V M ++  
Sbjct: 133 AIDYVTPAFEVVDFRFDGSVGQIVDTIADNAGCSGIVVGEEKHPYGSVDLKAVEMVITGG 192

Query: 189 GEPVSTGAGAACLGTPLNAVVWLARTMSRLGKPLRAGELILSGALGPMVAVKPGDVFEC- 247
           G+ ++ G G+  LG P+NAV+WLA T  R G+PLRAGE++LSG++G  +   P DV EC 
Sbjct: 193 GKEITRGVGSNVLGDPINAVLWLADTAIRTGQPLRAGEVLLSGSIG-YIEPWPVDV-ECV 250

Query: 248 -HINGVGSVRTEFES 261
             I G+G V    +S
Sbjct: 251 ATITGLGRVVASVDS 265


Lambda     K      H
   0.318    0.135    0.392 

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: 214
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: 269
Length of database: 267
Length adjustment: 25
Effective length of query: 244
Effective length of database: 242
Effective search space:    59048
Effective search space used:    59048
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: 41 (21.7 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