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_2433 Phenylacetate degradation enoyl-CoA hydratase PaaB (EC 4.2.1.17)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2433
          Length = 263

 Score =  166 bits (420), Expect = 5e-46
 Identities = 92/263 (34%), Positives = 143/263 (54%), Gaps = 4/263 (1%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           M FE I    E  +  ++LNRPD+LN+ N ++  E+  A+ Q   +P++RV+++TG+G+ 
Sbjct: 1   MNFEHILFSIEAGVALLSLNRPDQLNSFNTQMHGEVKEALKQVRQNPDVRVLLLTGEGRG 60

Query: 61  FCAGADITQFN----QLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELAL 116
           FCAG D++  N       P       K    ++ ++  L  P I  +NG A G G  + L
Sbjct: 61  FCAGQDLSDRNVAPGSAVPDLGESIEKFYNPLIRQLRDLPMPVICAVNGVAAGAGANIPL 120

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

Query: 177 LVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVF 236
           L+ + V  A L  E  KLA  +A +    LALIK  +N  + +     L LE     +  
Sbjct: 181 LIYQCVEDAELRDEALKLARHLATQPTYGLALIKRSLNASMSNSFDEQLELEKDLQRLAG 240

Query: 237 STEDKKEGVSAFLEKREPTFKGK 259
            +ED +EGV AF+EKR P+FKG+
Sbjct: 241 RSEDYREGVGAFMEKRTPSFKGR 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: 158
Number of extensions: 4
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