GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Dechlorosoma suillum PS

Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Dsui_3239 Dsui_3239 acetyl-CoA acetyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411
         (393 letters)



>lcl|FitnessBrowser__PS:Dsui_3239 Dsui_3239 acetyl-CoA
           acetyltransferase
          Length = 392

 Score =  443 bits (1139), Expect = e-129
 Identities = 225/389 (57%), Positives = 282/389 (72%)

Query: 5   EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTETR 64
           EI V+SA R+A+G FGGSL  +  A+L    VK A+ RA VDP  V    +GN IPTETR
Sbjct: 4   EIVVLSAVRSAVGGFGGSLAGMEPAELGGLVVKEAIARAGVDPKAVTFATVGNCIPTETR 63

Query: 65  DAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSRG 124
            AY++R+A +  G+  ++ A+ VNRLCGS +QAI+++AQ +MLGDAD  +G G E MSRG
Sbjct: 64  YAYVARLATIQGGMSMDSVAFAVNRLCGSAMQAIVSSAQAIMLGDADYAIGGGVEVMSRG 123

Query: 125 PYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDALAFED 184
            YL+PA R G+RMG+ + ID M+ +L DPF   HMGITAEN+  + G+TRE QDA A E 
Sbjct: 124 AYLLPALRSGARMGDTKAIDAMVSVLTDPFGVGHMGITAENLVTKWGLTREEQDAFALES 183

Query: 185 QQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRATSLEQLAAMKPAFKKDGSVTA 244
           Q RAA AIA G F  QI  +  Q +KG  +F  DEHPRAT++E LA MK AFKKDGSVTA
Sbjct: 184 QNRAAKAIAEGRFKSQIVPITFQTKKGDVVFDTDEHPRATTMEALAKMKAAFKKDGSVTA 243

Query: 245 GNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRLALKRA 304
           GNASG+ND AA LV+A      A   KP+ARLVSYA AGV  E MG GPIP+++LAL++A
Sbjct: 244 GNASGINDAAAFLVLADAAKAAAAGHKPIARLVSYAIAGVPNEIMGEGPIPSSKLALQKA 303

Query: 305 GLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIATKAIH 364
           GLT+  +D++E+N AFAAQ+ AV++ L LDPAK N NG  IALGHPVGATG +I TK +H
Sbjct: 304 GLTLDQIDLVESNEAFAAQSLAVAKGLGLDPAKTNVNGGAIALGHPVGATGGVIVTKLLH 363

Query: 365 ELHRTGGRYALVTMCIGGGQGIAAIFERV 393
           E+ RTG RY + TMCIGGGQGI  I+ER+
Sbjct: 364 EMQRTGARYGMATMCIGGGQGITTIYERI 392


Lambda     K      H
   0.318    0.133    0.378 

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: 438
Number of extensions: 17
Number of successful extensions: 2
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 (21.7 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 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