GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_02490
          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 (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