GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Caulobacter crescentus NA1000

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02490 CCNA_02490 3-ketoacyl-CoA
           thiolase
          Length = 399

 Score =  335 bits (860), Expect = 1e-96
 Identities = 177/390 (45%), Positives = 246/390 (63%), Gaps = 10/390 (2%)

Query: 12  RTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL-GQNVARQ 69
           RTP+G +GG+L  V +  L AI +   + R   +    IDE++ G   QAG   +NVAR 
Sbjct: 11  RTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQAGEDNRNVARM 70

Query: 70  CMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKAPFILPNA 129
            ++ AG P  V   T+N++C SGL AV  AA+ I +G  D+++AGG E+M +APF++  A
Sbjct: 71  ALLLAGYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESMSRAPFVMGKA 130

Query: 130 RWGYRMSMPKGDLIDEMV-WG----GLTDVFNGYHMGITAENINDMYGITREEQDAFGFR 184
              +  S    ++ D  + W      +  ++    M  TAEN+   YG+ RE+QDAF  R
Sbjct: 131 DSAFSRS---AEIFDTTIGWRFVNPAMRKLYGVDSMPETAENVATDYGVNREDQDAFALR 187

Query: 185 SQTLAAQAIESGRFKDEIVPVVIKGKKGDIVFDTDEHPRKSTPEAMAKLAPAFKKGGSVT 244
           SQ   A A  +G    EI PV I GK G  + D DEHPR++T EA+AKL P  ++GG+VT
Sbjct: 188 SQARTAAAQANGFLAGEITPVEIPGKAGPTIVDRDEHPRETTMEALAKLKPIVREGGTVT 247

Query: 245 AGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPASRKALEK 304
           AGNASG+ND A A+++ S++     G+ P A++  YAS GV+P VMG+GP+PA RK + K
Sbjct: 248 AGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASAGVEPRVMGIGPVPAVRKLMAK 307

Query: 305 AGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSSGARILVT 364
            GL I D D++E NEAFAAQ +AV R LG  D    VN NGGAIA+GHP+G+SGAR+++T
Sbjct: 308 TGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGASGARLVLT 367

Query: 365 LLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
            L +++  G ++GLATLCIG G G AL  E
Sbjct: 368 ALRQLEASGGQRGLATLCIGVGQGAALAFE 397


Lambda     K      H
   0.317    0.135    0.387 

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: 474
Number of extensions: 23
Number of successful extensions: 3
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: 396
Length of database: 399
Length adjustment: 31
Effective length of query: 365
Effective length of database: 368
Effective search space:   134320
Effective search space used:   134320
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 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