GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Dechlorosoma suillum PS

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Dsui_0317 Dsui_0317 acetyl-CoA acetyltransferase

Query= BRENDA::Q8VCH0
         (424 letters)



>FitnessBrowser__PS:Dsui_0317
          Length = 399

 Score =  311 bits (796), Expect = 3e-89
 Identities = 175/393 (44%), Positives = 250/393 (63%), Gaps = 11/393 (2%)

Query: 37  DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDV-KLKPEQLGDISVGNVL-QP 94
           D  +V   R P+ + + G FK T PD++L+  L +V+  V +L P  + D+ VG  + + 
Sbjct: 7   DAYIVAATRLPVAKRN-GMFKTTRPDDMLAHALKSVMAQVPQLDPALVEDVIVGCAMPEA 65

Query: 95  GAGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154
             G  +ARI   L+G+P+TVP  T+NR CSSG+QAVA+ A  IR G  D+ +A G E+M+
Sbjct: 66  EQGMNVARIGLLLAGLPDTVPGLTINRFCSSGVQAVADAAARIRLGEADVMLAAGTETMS 125

Query: 155 LSQR--GNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAAS 212
           L  +  GN  +++  + E ++       MG+T+E VA+++G+SR  QDAFA+AS QKA +
Sbjct: 126 LMSQMMGNKVSLNPAIFEKDENVAIAYGMGLTAEKVAQKWGISRDDQDAFAVASHQKAVA 185

Query: 213 AQSRGCFHAEIVPVTTTVLNDKGDKKTITVSQ-----DEGVRPSTTMQGLAKLKPAFKDG 267
           A + G F  EI P T           T+ + +     DEG RP +++QGLAKLKP F   
Sbjct: 186 AIAAGKFKDEISPYTVRAHLPDLKSGTVRIVEKVCDTDEGPRPDSSLQGLAKLKPVFNAR 245

Query: 268 GSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPA 327
           GS TAGNSSQ+SDGA AVLL      ++  L  L     ++V GVPP++MGIGP  AIP 
Sbjct: 246 GSVTAGNSSQMSDGAGAVLLVSEKILKQFNLQPLARFAGFSVAGVPPEIMGIGPIAAIPK 305

Query: 328 ALQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQV 387
            L +AG+  +D+D  E+NEAFA+QA+    +LG+   K+NP GGAIALGHPLG TGA + 
Sbjct: 306 VLAQAGIKQDDLDWIELNEAFAAQALAVTRELGLDPAKINPQGGAIALGHPLGATGAIRT 365

Query: 388 VTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
            TL++ ++R  ++ +G+V+MCIGTGMGAA +FE
Sbjct: 366 ATLVHGMRRENKK-WGMVTMCIGTGMGAAGLFE 397


Lambda     K      H
   0.317    0.133    0.377 

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: 433
Number of extensions: 15
Number of successful extensions: 5
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: 424
Length of database: 399
Length adjustment: 31
Effective length of query: 393
Effective length of database: 368
Effective search space:   144624
Effective search space used:   144624
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