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_00075 CCNA_00075 3-ketoacyl-CoA thiolase

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



>FitnessBrowser__Caulo:CCNA_00075
          Length = 401

 Score =  260 bits (664), Expect = 6e-74
 Identities = 168/423 (39%), Positives = 230/423 (54%), Gaps = 44/423 (10%)

Query: 1   MNEALIIDAVRTPIGRYA--GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCAN 58
           M +A I DAVRTP G+    G+L    A  L    L+AL  R+  LD S VDDV+ GC +
Sbjct: 1   MADAYIFDAVRTPRGKGKKDGSLHETTALSLATQVLEALRDRNG-LDTSKVDDVVLGCVS 59

Query: 59  QAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVE 118
             GE   ++AR A L A    SV G  +NR C SGL+AV  AA  +  GEAGL + GGVE
Sbjct: 60  PVGEQGSDIARTAVLTADYAESVAGVQINRFCASGLEAVNMAAAKVASGEAGLAIGGGVE 119

Query: 119 SMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
           SMSR P          G     + T     F      QG        +A+ +A  +  SR
Sbjct: 120 SMSRVP---------MGSDGGAWPTDPSSAFKTYFAPQGV-------SADLIATLYGFSR 163

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238
            D DA+A+ SQ +AAAA A+ R  K ++ V+   + G   +++HDE  RG TT++ LA L
Sbjct: 164 DDVDAYAVESQKRAAAAWADNRFKKSVIPVK--DQLG-LTLLDHDETVRGSTTMQTLASL 220

Query: 239 GTPFRQGGSVT--------------------AGNASGVNDGACALLLASSEAAQRHGLKA 278
              F   G +                     AGN+SG+ DGA  +L+ + E  +  GLKA
Sbjct: 221 NPSFTGMGEMAFDAVVTQRYPQVERVNHVHHAGNSSGIVDGAAGVLIGTKEMGEALGLKA 280

Query: 279 RARVVGMATAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELG 338
           RAR+ G A+ G EP IM  GP   + K+L+  G+ + D+D+ ELNEAFA+  L +++ L 
Sbjct: 281 RARIKGAASIGSEPSIMLTGPALVSEKLLKKLGMEVKDIDLYELNEAFASVVLRMMQALD 340

Query: 339 LADDDERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALII 398
           +  D  ++N NGGAIA+GHPLG +GA ++ T L ELE      AL T+C+G G G A +I
Sbjct: 341 IPHD--KMNVNGGAIAMGHPLGATGAMILGTVLDELERSDKETALITLCVGAGMGTATVI 398

Query: 399 ERI 401
           ER+
Sbjct: 399 ERV 401


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: 431
Number of extensions: 25
Number of successful extensions: 6
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: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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