GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Escherichia coli BW25113

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate 1937156 b3845 acetyl-CoA acetyltransferase (NCBI)

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Keio:1937156
          Length = 387

 Score =  291 bits (744), Expect = 3e-83
 Identities = 174/406 (42%), Positives = 242/406 (59%), Gaps = 25/406 (6%)

Query: 1   MRDVFICDAIRTPIGRF-GGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQ 59
           M  V I DAIRTP+GR  GGA   VRA+DL+A  +++L+  NPA++   +D++++GC  Q
Sbjct: 1   MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60

Query: 60  AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119
             E   N+AR A LLA +P S+P VT+NRLC S M A+  A R I +G+ +  + GGVE 
Sbjct: 61  TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120

Query: 120 MSRAPFVMG-KAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178
           M   P   G     G SRN+      +G                   TA+ +A  + +SR
Sbjct: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGL------------------TAEMLARMHGISR 162

Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVE--RDEHLRPETTLEALTK 236
             QDAFA RS  +A AA  +  F  EI+P    H     + +   DE +RPETT+EAL  
Sbjct: 163 EMQDAFAARSHARAWAATQSAAFKNEIIPTG-GHDADGVLKQFNYDEVIRPETTVEALAT 221

Query: 237 LKPVNGP-DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295
           L+P   P +  VTAG +S ++DGAAA+++ S     + GL PRARV  MA  G  P +MG
Sbjct: 222 LRPAFDPVNGMVTAGTSSALSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMG 281

Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQ-VNPNGGAIAL 354
            GPVPA +   ++ G++ SD  V E+NEAFA+Q L  +++LG+ +   + +N NGGAIAL
Sbjct: 282 YGPVPASKLALKKAGLSASDIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIAL 341

Query: 355 GHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GHPLG SGAR+  T L+ +E+   + GLATMC+G+GQG+A   ERV
Sbjct: 342 GHPLGCSGARISTTLLNLMERKDVQFGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.318    0.134    0.383 

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: 378
Number of extensions: 18
Number of successful extensions: 7
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: 400
Length of database: 387
Length adjustment: 31
Effective length of query: 369
Effective length of database: 356
Effective search space:   131364
Effective search space used:   131364
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