GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Dechlorosoma suillum PS

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Dsui_0325 Dsui_0325 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__PS:Dsui_0325
          Length = 432

 Score =  235 bits (599), Expect = 2e-66
 Identities = 161/429 (37%), Positives = 236/429 (55%), Gaps = 43/429 (10%)

Query: 5   FICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDN 64
           ++ DG RTP  +         A DLA    R LL R P    E +D+V+LGCA+ +  D 
Sbjct: 11  YVVDGARTPFLKAKNGPGPFSAADLAVQAGRALLARQP-FAPEDLDEVVLGCASPS-PDE 68

Query: 65  RNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAP 124
            N+ R+A L  G    V+G T+ R C SG+ AL  A   I++G  +L++AGGV+++SRAP
Sbjct: 69  VNIGRVAALRLGCGNKVTGWTVMRNCASGMQALDSAMANIQSGRSELVLAGGVDALSRAP 128

Query: 125 FVMGKAASA-FSRQAEMFDTTIGWR-----------FVNPLMAQQFG-TDS-----MPET 166
            +   A    F+   +M   T+G +            +NP++    G TD      M +T
Sbjct: 129 LLYNDAMVLWFAGMMQM--KTLGQKAGHFLKLRPSVLLNPVIGLMKGLTDPVVGLLMGQT 186

Query: 167 AENVAELLKISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHL 226
           AEN+A    ISRE+ D+F++RS QR    ++     E IVP+V  +     T    D+ +
Sbjct: 187 AENLAWRFGISREEMDAFSVRSHQRVMAGRAKQAFGE-IVPLVGNDG----TVYAEDDGV 241

Query: 227 RPETTLEQLRGLKAPF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAM 285
           R + +++ ++ LK  F +  G +T  N+S + DG A L++ASE       L P  RIV  
Sbjct: 242 RVDASMDGMKKLKPFFDKKYGRVTPANSSQITDGGAWLLLASESAVKRWKLEPLGRIVDA 301

Query: 286 ATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLR---------- 335
             AG++P  MGLGPV A   +L+R GL ++D+D++E+NEAFAAQ LG L+          
Sbjct: 302 QWAGLDPSQMGLGPVHAVTPILQRHGLGLNDVDLMEINEAFAAQVLGCLKAWEDDAYCRE 361

Query: 336 ELGLPD-----DAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGV 390
           ELGLP      D   +N +GGA+A GHP+G SGAR+ L   H L  R G+  + ++CIG 
Sbjct: 362 ELGLPGALGSLDQDKLNVDGGAVAQGHPVGASGARIVLHLLHALKARGGKRGVASICIGG 421

Query: 391 GQGIAMILE 399
           GQG AM++E
Sbjct: 422 GQGGAMLVE 430


Lambda     K      H
   0.319    0.135    0.384 

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: 491
Number of extensions: 24
Number of successful extensions: 6
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: 401
Length of database: 432
Length adjustment: 31
Effective length of query: 370
Effective length of database: 401
Effective search space:   148370
Effective search space used:   148370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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