GapMind for catabolism of small carbon sources

 

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

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 3608351 Dshi_1753 Enoyl-CoA hydratase/isomerase (RefSeq)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Dino:3608351
          Length = 258

 Score =  134 bits (336), Expect = 2e-36
 Identities = 94/246 (38%), Positives = 131/246 (53%), Gaps = 7/246 (2%)

Query: 14  LLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAEK-- 71
           +LTLNRP   NALN+ +  ++ + ++ A  +    V V+TG  R F +G DL + A    
Sbjct: 16  VLTLNRPDVMNALNSQMRAEITDAVKLAGAEAR--VLVMTGAGRAFCSGQDLGDRANAAN 73

Query: 72  -DLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPEI 130
            DL  TL D    +   +     P IAAVNG A GAG  LAL  DVV+A E+A F     
Sbjct: 74  LDLERTLRDEYVPMLRAIFDCPVPTIAAVNGPAAGAGANLALAADVVIATESAVFLQAFT 133

Query: 131 TLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQL 190
            +G++P AGGT  L R +G + A    L  + ITA+QA   G++ +  P D   E   + 
Sbjct: 134 RIGLIPDAGGTYWLPRQMGFAKAMGAALFADKITARQADAWGMIWEAVP-DAEFEAVWRA 192

Query: 191 -ASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRT 249
            A+ +A+    A +A KQALR S    L   LA E +L   +  T D  EG+ AFL+KR+
Sbjct: 193 RAAHLAKGPTAAYEAVKQALRDSFNNDLDGQLALEAKLQGKMGETRDFKEGVLAFLEKRS 252

Query: 250 PDFKGR 255
             F+GR
Sbjct: 253 ASFEGR 258


Lambda     K      H
   0.318    0.130    0.356 

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: 103
Number of extensions: 7
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: 255
Length of database: 258
Length adjustment: 24
Effective length of query: 231
Effective length of database: 234
Effective search space:    54054
Effective search space used:    54054
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: 41 (21.8 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