GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pseudomonas putida KT2440

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate PP_3283 PP_3283 1,2-epoxyphenylacetyl-CoA isomerase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Putida:PP_3283
          Length = 263

 Score =  154 bits (388), Expect = 2e-42
 Identities = 90/263 (34%), Positives = 138/263 (52%), Gaps = 4/263 (1%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           M F+ I    E  + +++LNRP++LN+ N  +  E+  A+ Q     + RV+++T +G+ 
Sbjct: 1   MTFQHILFSIEDGVAFLSLNRPEQLNSFNTAMHLEVREALRQVRQSSDARVLLLTAEGRG 60

Query: 61  FCAGADITQFNQLTPAE----AWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELAL 116
           FCAG D++  N    AE         K    ++  +  L  P I  +NG A G G  + L
Sbjct: 61  FCAGQDLSDRNVAPGAEMPDLGQSIDKFYNPLVRTLRDLPLPVICAVNGVAAGAGANIPL 120

Query: 117 ACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYG 176
           ACD+ +AA  A        +G+ P  GGT  L R++G  RA  + M G+R+  + AE++G
Sbjct: 121 ACDLVLAARSASFIQAFCKIGLVPDSGGTWLLPRLVGMARAKALAMLGERLGAEQAEQWG 180

Query: 177 LVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVF 236
           L+ RVV  A L  E   LA  +A +    L LIK  +N   D+   + L LE     +  
Sbjct: 181 LIYRVVDDAALRDEALTLARHLAAQPTYGLTLIKRSLNASFDNGFEAQLELERDLQRLAG 240

Query: 237 STEDKKEGVSAFLEKREPTFKGK 259
            +ED +EGV+AF+ KR P FKG+
Sbjct: 241 RSEDYREGVNAFMNKRTPAFKGR 263


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: 144
Number of extensions: 5
Number of successful extensions: 2
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: 263
Length adjustment: 25
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
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