GapMind for catabolism of small carbon sources

 

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

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate H281DRAFT_02514 H281DRAFT_02514 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__Burk376:H281DRAFT_02514
          Length = 258

 Score =  278 bits (712), Expect = 6e-80
 Identities = 145/258 (56%), Positives = 184/258 (71%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60
           M+   I  E RGRV LV L     LN L DALMD+L   L   +AD  + A V+TGS KA
Sbjct: 1   MSAAMIRSERRGRVALVRLASDNPLNPLTDALMDQLIDVLLRNEADPQVHATVLTGSGKA 60

Query: 61  FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120
           FAAGADI  MS   Y + +  DYI R+W+ +R++RKPIIAAV G+ALGGGCELAMMCDI+
Sbjct: 61  FAAGADIVAMSKLDYANAFSDDYIGRSWDRIRTVRKPIIAAVGGYALGGGCELAMMCDIV 120

Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180
            AAD A FGQPEIKLGI+PGAGGTQRLPRAV K+ AM  CLT   + A EA   GLVS++
Sbjct: 121 IAADDALFGQPEIKLGIVPGAGGTQRLPRAVGKSTAMLACLTGEPLGAQEALAYGLVSKI 180

Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240
           +    L+DEA+     IA    P ++ +KE+V+RA+E++L+EG+ FERRLFH+ F+  DQ
Sbjct: 181 VARERLIDEAMRVGEQIARHSLPVIVAIKEAVDRAFESSLSEGLLFERRLFHAGFSLADQ 240

Query: 241 KEGMAAFVEKRKPVFKHR 258
           KEGMAAF+E+R+  F++R
Sbjct: 241 KEGMAAFLERRQAAFQNR 258


Lambda     K      H
   0.321    0.134    0.380 

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: 198
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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 (21.9 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