GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Marinobacter guineae M3B

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_099619682.1 CLH62_RS18535 acetyl-CoA C-acyltransferase FadA

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_002744735.1:WP_099619682.1
          Length = 391

 Score =  306 bits (784), Expect = 7e-88
 Identities = 176/407 (43%), Positives = 246/407 (60%), Gaps = 28/407 (6%)

Query: 2   REAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           R+  + D +RTP+GR   G   +VRA+ L+A  +  L  RNP+LD + ++DVI GC NQ 
Sbjct: 6   RDVVVVDCVRTPMGRAKNGCFRNVRAETLSAALIEALFERNPKLDPKEVEDVIWGCVNQT 65

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
            E   NVAR  +LL  +P   +  T+NRLCGS + A+  AA+AI  G+GD+ + GGVE M
Sbjct: 66  KEQGFNVARQISLLTRIPHESAAQTVNRLCGSSMSAIHTAAQAIMTGNGDVFVVGGVEHM 125

Query: 121 SRAPFVMG----KAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKI 176
              P   G     AAS ++ +A                     ++ M  TAE +A++  I
Sbjct: 126 GHVPMTEGFDHNPAASKYTAKA---------------------SNMMGLTAEMLAKMHGI 164

Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236
           +R+ QD F  RS +   +A   G    EIVP+   ++ G V  I+ DE +RP+TT+E L 
Sbjct: 165 TRKQQDEFGARSHRLAHEATLEGRFNNEIVPIEGHDENGFVKLIEEDETIRPDTTVESLG 224

Query: 237 GLKAPFRA-NGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLM 295
            LK  F   NG +TAG +S + DGAAA+++ S + A A GL P AR+ +MA AG +P +M
Sbjct: 225 QLKPAFDPKNGTVTAGTSSQLTDGAAAMVLMSAERAEALGLKPIARVRSMAVAGCDPAIM 284

Query: 296 GLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPD-DAPHVNPNGGAIA 354
           G GPVPAT++ L+RAGL + D+D  ELNEAFA Q+L VL++L L    A  VN NGGAIA
Sbjct: 285 GYGPVPATKKALKRAGLKVEDIDFWELNEAFAGQSLPVLKDLKLLGVMAEKVNLNGGAIA 344

Query: 355 LGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           LGHPLG SGAR++    + +  + G+  + TMCIG+GQGIA + ER+
Sbjct: 345 LGHPLGCSGARISTTLLNVMQAKGGKLGVSTMCIGLGQGIATVWERL 391


Lambda     K      H
   0.319    0.135    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: 400
Number of extensions: 15
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 24 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