GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ2 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)



>lcl|FitnessBrowser__PS:Dsui_0325 Dsui_0325 acetyl-CoA
           acetyltransferase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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