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_2984 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2984
          Length = 257

 Score =  217 bits (553), Expect = 2e-61
 Identities = 119/262 (45%), Positives = 166/262 (63%), Gaps = 8/262 (3%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           + +ETI  +  G +  ITLNRP  LNALNA+++ EL++A+   E+D  I  I++TG  KA
Sbjct: 1   VSYETILLETHGRVGLITLNRPQALNALNAQIVSELNQALDGFEADSNIGCIVLTGSKKA 60

Query: 61  FCAGADITQFNQLTPAEAW---KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALA 117
           F AGADI +  +LT  + +    FS       D++    KP IA +NG+ALGGG ELAL 
Sbjct: 61  FAAGADIKEMAELTYPQIYIDDLFSDS-----DRVANRRKPIIAAVNGFALGGGCELALM 115

Query: 118 CDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGL 177
           CD  +A + A+ G PEINLG+ PG GGTQRLTR +GK +A+EM ++G  I   +AE+ G+
Sbjct: 116 CDFILAGDNARFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGI 175

Query: 178 VNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFS 237
           V R+VP   L  E  K+A  IAKKS     ++KE VNR  +  L  G+  E   +   F+
Sbjct: 176 VARIVPSDELLDEALKVAALIAKKSLPIAMMVKESVNRAFEVSLAEGVRFERRVFHAAFA 235

Query: 238 TEDKKEGVSAFLEKREPTFKGK 259
           T+D+KEG++AF+ KRE  F+GK
Sbjct: 236 TQDQKEGMAAFIAKREAEFQGK 257


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: 178
Number of extensions: 9
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: 257
Length adjustment: 24
Effective length of query: 235
Effective length of database: 233
Effective search space:    54755
Effective search space used:    54755
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