GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Dechlorosoma suillum PS

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate Dsui_0325 Dsui_0325 acetyl-CoA acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__PS:Dsui_0325
          Length = 432

 Score =  241 bits (615), Expect = 3e-68
 Identities = 168/432 (38%), Positives = 244/432 (56%), Gaps = 48/432 (11%)

Query: 5   VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64
           VY+ D  RTP  +         A DLA    +AL+ R P      LDEV LGCA+ +  D
Sbjct: 10  VYVVDGARTPFLKAKNGPGPFSAADLAVQAGRALLARQPFAP-EDLDEVVLGCASPS-PD 67

Query: 65  NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124
             N+ R+A L  G  + V G T+ R CASGM A+ +A   I SG +ELV+AGGV+++SRA
Sbjct: 68  EVNIGRVAALRLGCGNKVTGWTVMRNCASGMQALDSAMANIQSGRSELVLAGGVDALSRA 127

Query: 125 PYVMGKADSAFGRGQKIEDTTIGWR-----------FINPLMKAQYGVD------AMPET 167
           P +   A   +  G  ++  T+G +            +NP++    G+        M +T
Sbjct: 128 PLLYNDAMVLWFAGM-MQMKTLGQKAGHFLKLRPSVLLNPVIGLMKGLTDPVVGLLMGQT 186

Query: 168 ADNVADDYKVSRADQDAFALRSQQ--LAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEH 225
           A+N+A  + +SR + DAF++RS Q  +AGRA+ A     EIVP+V  G  G TV   D+ 
Sbjct: 187 AENLAWRFGISREEMDAFSVRSHQRVMAGRAKQA---FGEIVPLV--GNDG-TVYAEDDG 240

Query: 226 LRPDTTLEALAKLKPVNGPDKT---VTAGNASGVNDGSVALILASAEAVKKHGLKARAKV 282
           +R D +++ + KLKP    DK    VT  N+S + DG   L+LAS  AVK+  L+   ++
Sbjct: 241 VRVDASMDGMKKLKPFF--DKKYGRVTPANSSQITDGGAWLLLASESAVKRWKLEPLGRI 298

Query: 283 LGMASAGVAPRVMGIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTR------- 335
           +    AG+ P  MG+GPV AV  +L+R  L + D D++E+NEAFAAQ L   +       
Sbjct: 299 VDAQWAGLDPSQMGLGPVHAVTPILQRHGLGLNDVDLMEINEAFAAQVLGCLKAWEDDAY 358

Query: 336 ---ELGIAD-----DDARVNPNGGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMC 387
              ELG+       D  ++N +GGA+A GHP+GASGAR+VL  +H L+  GG+RG+ ++C
Sbjct: 359 CREELGLPGALGSLDQDKLNVDGGAVAQGHPVGASGARIVLHLLHALKARGGKRGVASIC 418

Query: 388 VGVGQGVALAVE 399
           +G GQG A+ VE
Sbjct: 419 IGGGQGGAMLVE 430


Lambda     K      H
   0.317    0.134    0.379 

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: 494
Number of extensions: 32
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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