GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Cola:Echvi_1071
          Length = 391

 Score =  281 bits (720), Expect = 2e-80
 Identities = 167/406 (41%), Positives = 238/406 (58%), Gaps = 28/406 (6%)

Query: 3   EAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61
           +A+I  G RT +G+   G     R DDLA   +++L+   P L+AE +DD+I+G A    
Sbjct: 2   DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61

Query: 62  EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121
           E    + RM +L+A L + V G  INR CGSGL+A+  A   IK+G  D +IAGG ESMS
Sbjct: 62  EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120

Query: 122 RAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQ 181
             P +MG            + T + W+  +          SM  TAE +A+   ISRED 
Sbjct: 121 MVP-MMG------------YKTALNWKIASEHPDYYL---SMGLTAEELAKDYDISREDS 164

Query: 182 DSFALRSQQRTAKAQSSGILAEEIVPVVLKN--------KKGVVTEIQHDEHLRPETTLE 233
           D FA+ S +R   A   G   EEIVP+ ++         ++     +  DE  RP T ++
Sbjct: 165 DQFAVTSHERAISAIKEGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMD 224

Query: 234 QLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPR 293
            L GLK  F+  G +TAGN+S  +DGAA  ++ SE+M     L P AR+V+ + AGV+PR
Sbjct: 225 VLGGLKPAFKQGGQVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPR 284

Query: 294 LMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAI 353
           +MG+GP  A  + L++AG+ + D+ ++ELNEAFAAQAL V+R L +  D   VN NGGA+
Sbjct: 285 IMGIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALDM--DPNTVNVNGGAV 342

Query: 354 ALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399
           ALGHPLG +GA+L +   +EL RRN +Y + T C+G GQG+A ++E
Sbjct: 343 ALGHPLGCTGAKLTVQMINELRRRNQKYGMVTACVGGGQGVAGVVE 388


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: 411
Number of extensions: 18
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