GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Rhodobacter ovatus JA234

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_097029986.1 CRO07_RS07050 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_900207575.1:WP_097029986.1
          Length = 258

 Score =  214 bits (545), Expect = 1e-60
 Identities = 116/259 (44%), Positives = 168/259 (64%), Gaps = 1/259 (0%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           M +ET+  + E  +  I LNRPD LNALN +L+ EL  A+  A+ + ++R I++TG  KA
Sbjct: 1   MAYETLIVEIEDYVALIRLNRPDALNALNNRLMTELADALGAADRNDKVRCIVLTGSDKA 60

Query: 61  FCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDI 120
           F AGADI + ++    + +       E  + I  + KP +A + GYALGGG ELA+ CD 
Sbjct: 61  FAAGADIKEMSEKGFVDMFGGDFFTPET-EAILRVRKPIVAAVAGYALGGGCELAMMCDF 119

Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180
            IAA+ A+ G PEINLG+  G GGTQRLTR +GK ++++M +TG  +   +AE+ GLV+R
Sbjct: 120 IIAADTAKFGQPEINLGVVAGMGGTQRLTRYVGKSKSMDMHLTGRFMDAAEAERCGLVSR 179

Query: 181 VVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTED 240
           VVP  NL +E  K A KI++KS ++   +KE VNR  ++ L  G+  E   +  +F+TED
Sbjct: 180 VVPAKNLMEEVMKAAAKISEKSLLTAMAVKEAVNRSYETTLREGVLFERRLFHALFATED 239

Query: 241 KKEGVSAFLEKREPTFKGK 259
           +KEG++AFLEKR P F+ K
Sbjct: 240 QKEGMAAFLEKRTPQFRDK 258


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: 157
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 24 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