GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_3239
          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.

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