GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hpcD in Herbaspirillum seropedicae SmR1

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19405 HSERO_RS19405 enoyl-CoA
           hydratase
          Length = 258

 Score =  187 bits (476), Expect = 1e-52
 Identities = 109/259 (42%), Positives = 154/259 (59%), Gaps = 5/259 (1%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           M +E I+ +    +  I L+RP  LNAL+  L+ EL  A+   ++  EI  IIITG  KA
Sbjct: 1   MSYENIQVETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIITGSEKA 60

Query: 61  FCAGADITQFNQLTPAEAWK--FSKKGREIMDKIEALSKPTIAMINGYALGGGLELALAC 118
           F AGADI+        + +K  F  +  E + +I    KP IA + GYALGGG ELA+ C
Sbjct: 61  FAAGADISAMAGYDYMDVFKGEFITRNWETLRRIR---KPVIAAVAGYALGGGCELAMMC 117

Query: 119 DIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLV 178
           D  IAA+ A+ G PEI LGI PG GGTQRL R + K +A+++ +TG  +  ++AE+ GLV
Sbjct: 118 DFIIAADNAKFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGLV 177

Query: 179 NRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238
           +R+V    L +E    A  IA+       ++K+ VNR  ++ L  G+  E   +   F+T
Sbjct: 178 SRIVAADKLLEEAMAAAIIIAEMPRQVAMMVKDSVNRAYETTLSEGMKYERALFYSCFAT 237

Query: 239 EDKKEGVSAFLEKREPTFK 257
           ED+KEG+ AFLEKR+P FK
Sbjct: 238 EDQKEGMKAFLEKRQPVFK 256


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: 153
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: 258
Length adjustment: 24
Effective length of query: 235
Effective length of database: 234
Effective search space:    54990
Effective search space used:    54990
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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