GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Caulobacter crescentus NA1000

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate CCNA_00075 CCNA_00075 3-ketoacyl-CoA thiolase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__Caulo:CCNA_00075
          Length = 401

 Score =  259 bits (661), Expect = 1e-73
 Identities = 171/420 (40%), Positives = 235/420 (55%), Gaps = 43/420 (10%)

Query: 4   EVYICDAVRTPIGRF--GGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61
           + YI DAVRTP G+    GSL    A  LA   ++AL +RN  +D S++D+V LGC +  
Sbjct: 3   DAYIFDAVRTPRGKGKKDGSLHETTALSLATQVLEALRDRNG-LDTSKVDDVVLGCVSPV 61

Query: 62  GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121
           GE   ++AR A+L A   +SV GV +NR CASG++AV  A   +ASGEA L I GGVESM
Sbjct: 62  GEQGSDIARTAVLTADYAESVAGVQINRFCASGLEAVNMAAAKVASGEAGLAIGGGVESM 121

Query: 122 SRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRAD 181
           SR P  MG    A+         T           A  GV     +AD +A  Y  SR D
Sbjct: 122 SRVP--MGSDGGAWPTDPSSAFKT---------YFAPQGV-----SADLIATLYGFSRDD 165

Query: 182 QDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP- 240
            DA+A+ SQ+ A  A A   F + ++PV  K + G T++D DE +R  TT++ LA L P 
Sbjct: 166 VDAYAVESQKRAAAAWADNRFKKSVIPV--KDQLGLTLLDHDETVRGSTTMQTLASLNPS 223

Query: 241 -------------------VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAK 281
                              V   +    AGN+SG+ DG+  +++ + E  +  GLKARA+
Sbjct: 224 FTGMGEMAFDAVVTQRYPQVERVNHVHHAGNSSGIVDGAAGVLIGTKEMGEALGLKARAR 283

Query: 282 VLGMASAGVAPRVMGIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIAD 341
           + G AS G  P +M  GP     KLL++L + V D D+ ELNEAFA+  L + + L I  
Sbjct: 284 IKGAASIGSEPSIMLTGPALVSEKLLKKLGMEVKDIDLYELNEAFASVVLRMMQALDIPH 343

Query: 342 DDARVNPNGGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           D  ++N NGGAIA+GHPLGA+GA ++ T + +LE+S  +  L T+CVG G G A  +ERV
Sbjct: 344 D--KMNVNGGAIAMGHPLGATGAMILGTVLDELERSDKETALITLCVGAGMGTATVIERV 401


Lambda     K      H
   0.317    0.134    0.379 

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: 440
Number of extensions: 27
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 ( 7.3 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