GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ2 in Phaeobacter inhibens BS107

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF3382 PGA1_c34350 acetyl-CoA acetyltransferase PhbA

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



>lcl|FitnessBrowser__Phaeo:GFF3382 PGA1_c34350 acetyl-CoA
           acetyltransferase PhbA
          Length = 391

 Score =  346 bits (888), Expect = e-100
 Identities = 191/401 (47%), Positives = 262/401 (65%), Gaps = 11/401 (2%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M D+ I D  RT IG FGG+LAG    DLA V  KA +E +  V  +Q+  V FG     
Sbjct: 1   MTDIVILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERS-GVAPEQIGNVVFGHVINT 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
              +  ++R+A + AG+P   P + +NRLC SG  AI +  +++  G+ E A+ GG E+M
Sbjct: 60  EPRDMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENM 119

Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRA 179
           SR+PF++  A  G    + +  D  +G       +   +G   M  TA+NVAD++ ++RA
Sbjct: 120 SRSPFIVPSARWGQKMGDARALDMMLG------ALNCPFGTGHMGVTAENVADEHDITRA 173

Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKP 239
             D FAL SQ +AAAA  AG+FA +I PV +  K+     + DEH +  +TLE L  LK 
Sbjct: 174 QMDEFALASQTRAAAAIEAGYFASQITPVEVKVKRDMVPFDVDEHPKA-STLETLGGLKA 232

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
           V   D  VTAGNASG+NDGAAA+++A+A+A ++ GL P+AR+LG A  GV P VMGIGPV
Sbjct: 233 VFKKDGRVTAGNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPV 292

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PAV+ L ++ G++ SDFDV+E NEAFA+Q LAV +ELG+  D  +VNPNGGAIALGHP+G
Sbjct: 293 PAVQNLLKKTGLSASDFDVVESNEAFAAQALAVNKELGL--DPAKVNPNGGAIALGHPVG 350

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
            +GA + L  L++LE+ GG KGL TMC+G GQG+ALAIER+
Sbjct: 351 ATGAIITLKTLYELERIGGSKGLITMCIGGGQGIALAIERL 391


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: 421
Number of extensions: 14
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: 400
Length of database: 391
Length adjustment: 31
Effective length of query: 369
Effective length of database: 360
Effective search space:   132840
Effective search space used:   132840
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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