GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Dinoroseobacter shibae DFL-12

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 3607639 Dshi_1048 Enoyl-CoA hydratase/isomerase (RefSeq)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Dino:3607639
          Length = 265

 Score =  148 bits (374), Expect = 1e-40
 Identities = 96/258 (37%), Positives = 142/258 (55%), Gaps = 14/258 (5%)

Query: 10  KEGNLFWITLNRPDKLNALNAKLLEEL-DRAVSQAESDPEIRVIIITGKG-KAFCAGADI 67
           +EG +  ITLN PD+LNA+   + + L D AV  A SD   RV+++ G G +AFCAGADI
Sbjct: 14  REGPVARITLNNPDRLNAMRLAMWQGLGDLAVELAASDA--RVVVLRGAGDRAFCAGADI 71

Query: 68  TQFNQL--TPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAE 125
           ++F Q+  TP     +++     ++ + AL  P +A I G+ +GGGLE+A+ CD+R+A+E
Sbjct: 72  SEFPQVRATPEGVAAYNRTVARALEGLAALPMPVLAAIRGHCIGGGLEIAVRCDLRLASE 131

Query: 126 EAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLA 185
            A++      LG+  G      L R+ G   A E++ T   +    AE++GLVNR VP  
Sbjct: 132 TARIAFTPAKLGLAIGADEVAALARIAGPAAAAELLYTAQPVDAARAERWGLVNRRVPED 191

Query: 186 NLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVV----FSTEDK 241
            L  E   LA  IA  +P++L  +K     GL +    G A  +     +    F + D 
Sbjct: 192 MLMDEADALARTIAANAPLTLRAVK----AGLAAFARPGDAAAASHADALVKTCFDSADY 247

Query: 242 KEGVSAFLEKREPTFKGK 259
           +EG  AF EKR P FKG+
Sbjct: 248 REGQRAFAEKRRPEFKGQ 265


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: 137
Number of extensions: 8
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: 265
Length adjustment: 25
Effective length of query: 234
Effective length of database: 240
Effective search space:    56160
Effective search space used:    56160
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.

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