GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS19405
          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 (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