GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pedobacter sp. GW460-11-11-14-LB5

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Pedo557:CA265_RS20005
          Length = 259

 Score =  218 bits (554), Expect = 1e-61
 Identities = 118/261 (45%), Positives = 177/261 (67%), Gaps = 4/261 (1%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-K 59
           M ++ + ++ + N+ ++T+NR   LNALN   L EL   ++ A    E+R +I+TG G K
Sbjct: 1   MAYQNLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEK 60

Query: 60  AFCAGADITQFNQLTPAEAWKFSKKGREIM-DKIEALSKPTIAMINGYALGGGLELALAC 118
           AF AGADI +F+  +  +  + +K+G E++ + IE  SKP IA ING+ALGGGLELA+AC
Sbjct: 61  AFVAGADIKEFSDYSGKQGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELAMAC 120

Query: 119 DIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLV 178
            IRIA++ A+LGLPE+ LG+ PGYGGTQRLT+++GKG+A+EM+ T + I   DAEK GLV
Sbjct: 121 HIRIASDNAKLGLPEVTLGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKIGLV 180

Query: 179 NRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238
           N VVP A+L  +  ++   I +++P++++   + V   +++   +G A E   +G  F T
Sbjct: 181 NVVVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIASINN--TNGYATEIEEFGKCFET 238

Query: 239 EDKKEGVSAFLEKREPTFKGK 259
            D KEGV+AF+EKR+  F GK
Sbjct: 239 ADFKEGVTAFVEKRKAIFTGK 259


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: 170
Number of extensions: 9
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: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
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.

Links

Downloads

Related tools

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