GapMind for catabolism of small carbon sources

 

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

Align 2-oxopent-4-enoate hydratase; 2-keto-4-pentenoate hydratase; EC 4.2.1.80 (characterized)
to candidate H281DRAFT_01663 H281DRAFT_01663 2-keto-4-pentenoate hydratase

Query= SwissProt::Q9KWS4
         (261 letters)



>FitnessBrowser__Burk376:H281DRAFT_01663
          Length = 269

 Score =  299 bits (766), Expect = 4e-86
 Identities = 157/254 (61%), Positives = 187/254 (73%), Gaps = 1/254 (0%)

Query: 9   AALLNEAELSEKPIEPVRGHIEG-GIAQAYAIQQINVQRQLAAGRRVTGRKIGLTSAAVQ 67
           AA L  A+ S K + P+R   +   I  AYAIQ++N +R+LA GRRV G KIGLTS AVQ
Sbjct: 10  AAALATAQRSGKYLAPLRETYDQLSIDDAYAIQRVNTERRLAEGRRVVGCKIGLTSVAVQ 69

Query: 68  KQLGVDQPDFGTLFDSMAVNDGEEIAWSRTLQPKCEAEVALVIERDLDHENITLIDLIGA 127
           KQLGVDQPDFG LFD M   DGE I  S   QPK E+EVA VI RD+  +N T +D++ A
Sbjct: 70  KQLGVDQPDFGMLFDDMGYGDGEPIPSSILTQPKVESEVAFVIGRDMTMDNPTQVDVLNA 129

Query: 128 TAYALPAIEVVGSRIANWDINILDTVADNASAGLYVLGHTPVKLEGLDLRLAGMVMERAG 187
             YALPA+E+VGSRIA+W+I I DT+ADNAS+  YVLG  P KL   DLRL GMVMER G
Sbjct: 130 IEYALPALEIVGSRIADWNIRITDTIADNASSSAYVLGTIPRKLSEFDLRLCGMVMERRG 189

Query: 188 QQVSLGVGAACLGHPLNAALWLARTLVKQGTPLKSGDVVLSGALGPLVAANPGDVFEARI 247
           + VS+G GAACLG+P+NA +WLART+   G PLK+GD+VLSGALGP+V+  PGDVFE RI
Sbjct: 190 EPVSVGAGAACLGNPVNAVVWLARTMASLGQPLKAGDLVLSGALGPMVSVVPGDVFETRI 249

Query: 248 QGLGSVRACFSPAS 261
            GLGSVRA F P S
Sbjct: 250 HGLGSVRAVFEPLS 263


Lambda     K      H
   0.317    0.134    0.384 

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: 230
Number of extensions: 7
Number of successful extensions: 1
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: 261
Length of database: 269
Length adjustment: 25
Effective length of query: 236
Effective length of database: 244
Effective search space:    57584
Effective search space used:    57584
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