GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pseudomonas fluorescens GW456-L13

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate PfGW456L13_3427 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3427
          Length = 272

 Score =  204 bits (520), Expect = 1e-57
 Identities = 105/260 (40%), Positives = 169/260 (65%), Gaps = 6/260 (2%)

Query: 4   ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFC 62
           + +  +++  + W+ L RP ++NA+N ++ + + +A++  + DP+IRVI+I G+G + FC
Sbjct: 15  DAVRLERDAMVGWVVLTRPRQINAINDEIRQGVPQALALLQQDPDIRVIVIRGEGDRGFC 74

Query: 63  AGADITQFNQLTPAEAWKFSKKGREI--MDKIEALSKPTIAMINGYALGGGLELALACDI 120
           AGADI +  +  P  + +  ++   +  ++ ++ ++KP IA I+GY +GGGLEL LACDI
Sbjct: 75  AGADIKE--RRGPESSLQVRQRMENVRWIETLDGITKPVIAAIHGYCMGGGLELVLACDI 132

Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180
           R AA +A   LPE  LG+ PG GGTQRL+RV+  G+AL+M++TGDR+  + A++ GLV+R
Sbjct: 133 RFAAPDAVFALPETGLGLIPGGGGTQRLSRVVAPGQALDMLLTGDRVGAEQAQRIGLVSR 192

Query: 181 VV-PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239
           +    ANL QE R  A++IA K P + A +K+     L+  L  GL LE   + ++  T+
Sbjct: 193 LASDSANLVQEVRAFAQRIASKPPTASAFVKQAARAALEMDLKRGLDLELDLFALLAPTK 252

Query: 240 DKKEGVSAFLEKREPTFKGK 259
           D +E   AF E+REP F G+
Sbjct: 253 DAREAAQAFSERREPRFTGE 272


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: 169
Number of extensions: 7
Number of successful extensions: 4
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: 272
Length adjustment: 25
Effective length of query: 234
Effective length of database: 247
Effective search space:    57798
Effective search space used:    57798
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