GapMind for catabolism of small carbon sources

 

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

Align 4-oxalocrotonate decarboxylase; EC 4.1.1.77 (characterized)
to candidate H281DRAFT_01664 H281DRAFT_01664 2-oxo-3-hexenedioate decarboxylase

Query= SwissProt::Q9KWS3
         (256 letters)



>FitnessBrowser__Burk376:H281DRAFT_01664
          Length = 255

 Score =  275 bits (704), Expect = 5e-79
 Identities = 137/247 (55%), Positives = 189/247 (76%)

Query: 4   SRIAQRLDEAAVSGKATPQLTGDDAVTVREAAEIQRLLIAHRIERGARQVGLKMGFTSRA 63
           + +A+ LD+AA++     +   +  +++ EA  IQ   I  R++RG R+VG+KMGFTSRA
Sbjct: 5   AELAKLLDDAALNATEVTRFDREGRLSLDEAYRIQAESIRRRLDRGERRVGVKMGFTSRA 64

Query: 64  KMAQMGVSDLIWGRLTSDMWVEEGGEIDLAHYVHPRVEPEICYLLGKRLEGNVTPLEALA 123
           KM QMG+SD+IWGRLT  M +EEG  IDL+ ++H R EPEI ++L + LEGNVT  +ALA
Sbjct: 65  KMVQMGLSDVIWGRLTDAMQIEEGTAIDLSRFIHARCEPEIAFILKRPLEGNVTGPQALA 124

Query: 124 AVEAVAPAMEIIDSRYRDFKFSLPDVIADNASSSGFVVGAWHKPETDVSNLGMVMSFDGR 183
           AVEA+APA+EIIDSRY+DFKFSLP+VIADNASSSGFV+GAW  P+ D SNLG+ +S DGR
Sbjct: 125 AVEAIAPAIEIIDSRYKDFKFSLPEVIADNASSSGFVIGAWCDPKIDFSNLGLTVSIDGR 184

Query: 184 AVELGTSAAILGSPIRALVAAARLAAQQGEALEAGSLILAGAATAAVALRPGISVRCEVQ 243
            V++G++AA+LG P+R+LVAAARL+A+ GE L+AG +++AG AT A  ++ G     +++
Sbjct: 185 VVQVGSTAALLGHPLRSLVAAARLSAEAGEPLQAGWIVMAGGATPAEWIKLGQYTSVDME 244

Query: 244 NLGSLSF 250
            LGS+ F
Sbjct: 245 QLGSVGF 251


Lambda     K      H
   0.318    0.132    0.372 

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: 200
Number of extensions: 6
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: 256
Length of database: 255
Length adjustment: 24
Effective length of query: 232
Effective length of database: 231
Effective search space:    53592
Effective search space used:    53592
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