GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Caulobacter crescentus NA1000

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate CCNA_00544 CCNA_00544 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Caulo:CCNA_00544
          Length = 391

 Score =  320 bits (819), Expect = 6e-92
 Identities = 185/406 (45%), Positives = 261/406 (64%), Gaps = 20/406 (4%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M+E +I+ A RTP+G + GALAS+ A +LG   ++A ++R   +  S VD+VI G   QA
Sbjct: 1   MSEIVIVSAARTPVGSFNGALASLPASELGKAVIEAAVSR-AGIAPSDVDEVILGQVLQA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
               +  AR A++ AG+PV  P  +LN+LCGSGL AV  AA+ +  G A +++AGG ESM
Sbjct: 60  AA-GQGPARQASVKAGIPVEAPAWSLNQLCGSGLRAVALAAQQIADGSAKVVVAGGQESM 118

Query: 121 SRAPFVMG-KSEQAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQFN 175
           S+AP     +  Q  G            +FV+ +++ G    F    M +TAEN+A+++ 
Sbjct: 119 SQAPHAQNLRGGQKMG----------DLQFVDTMIKDGLWDAFHGYHMGQTAENIASRWQ 168

Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235
           I+R DQD FA+ SQ++A AA   G+   EIV + I  RKG   IV+ DE  R   T+E +
Sbjct: 169 ITREDQDKFAVTSQNRAEAAQKAGKFDDEIVPITIKGRKGDT-IVDKDEFIRHGATIESV 227

Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295
             L   F + GSVTA NASG+NDGA AL+L S+E A + GLK  AR+   A AGVEP IM
Sbjct: 228 QGLKPVFNKEGSVTAANASGLNDGAAALVLMSAEEAAKRGLKPLARIASWANAGVEPEIM 287

Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355
           G GP+PA++K LE  G +++D+D++E NEAFAAQ L V+RELGL  D  +VN NGGAIA+
Sbjct: 288 GTGPIPASKKALEKAGWSVSDLDLVESNEAFAAQALCVVRELGL--DPAKVNVNGGAIAI 345

Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           GHP+G SGAR++TT +HE++    +  L T+C+G G G+A+ +E +
Sbjct: 346 GHPIGASGARILTTLVHEMKRSGAKKGLATLCVGGGMGVAMCVEAV 391


Lambda     K      H
   0.319    0.134    0.384 

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: 419
Number of extensions: 17
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: 401
Length of database: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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