GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Pseudomonas fluorescens FW300-N2C3

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30355
          Length = 264

 Score =  164 bits (415), Expect = 2e-45
 Identities = 95/261 (36%), Positives = 145/261 (55%), Gaps = 7/261 (2%)

Query: 6   IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGA 65
           +E    G +    LNRP+K NAL+  +L+ L  A+  A+ + +I   +ITG G AFC+G 
Sbjct: 4   LEVSTVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGG 63

Query: 66  DI------TQFNQLTPAEAW-KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALAC 118
           D+      +     TP E   +  K   ++   IE   KP IA +NG A+G G++L+L C
Sbjct: 64  DLGRRAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQC 123

Query: 119 DIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLV 178
           D+R A+E A+     I +G+ PG GG   L R++G  +ALE++ TGD +  ++A   G+V
Sbjct: 124 DMRFASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIV 183

Query: 179 NRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238
           NRV     L Q+T   A ++A   PI    IK+++ + L + L + L   +    VV ST
Sbjct: 184 NRVFSDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQST 243

Query: 239 EDKKEGVSAFLEKREPTFKGK 259
           +D KE + A+ EKR+P F GK
Sbjct: 244 DDYKEAIKAYKEKRKPRFIGK 264


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: 139
Number of extensions: 7
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: 264
Length adjustment: 25
Effective length of query: 234
Effective length of database: 239
Effective search space:    55926
Effective search space used:    55926
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