GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate H281DRAFT_05516 H281DRAFT_05516 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Burk376:H281DRAFT_05516
          Length = 264

 Score =  162 bits (409), Expect = 9e-45
 Identities = 92/258 (35%), Positives = 148/258 (57%), Gaps = 7/258 (2%)

Query: 9   KKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADI 67
           +  G++  I +NR +++N+LN +  +EL  A      D +  V ++TG G KAFCAGAD+
Sbjct: 7   ESHGHVRLIIINRAERMNSLNFEANDELVGAFESFNDDDDAYVAVVTGAGEKAFCAGADL 66

Query: 68  TQFN-QLTPAEAWKFSKK-----GREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121
             +      + A  F +K     G   + +   + KP +A +NG+A+ GG ELALA D+R
Sbjct: 67  KTYTVNFARSPAPDFRRKYTNGPGFAGITRNMDIFKPVVAAVNGFAISGGFELALAADLR 126

Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181
             +  A+  L +   G +   GG  RL +++G G A+E++++G+R+  + A + GLVNR+
Sbjct: 127 FCSPNAEFALQDAKWGFHACDGGLIRLPQIVGLGHAMEIILSGERLNAEHAYRIGLVNRI 186

Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDK 241
           VP  +L +ET + A+ +A +SP+S    KEV+ R +  P+   L LES  +     TED 
Sbjct: 187 VPAESLLEETMRYAQMLASRSPLSHRFAKEVMKRAIGMPMDEALRLESRSFYDFGMTEDL 246

Query: 242 KEGVSAFLEKREPTFKGK 259
            EG ++F E+R   FKGK
Sbjct: 247 VEGTTSFRERRPANFKGK 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: 138
Number of extensions: 5
Number of successful extensions: 3
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