GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Paraburkholderia bryophila 376MFSha3.1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate H281DRAFT_00857 H281DRAFT_00857 acetyl-CoA acetyltransferase /3-ketoacyl-CoA thiolase

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



>FitnessBrowser__Burk376:H281DRAFT_00857
          Length = 394

 Score =  317 bits (811), Expect = 5e-91
 Identities = 181/402 (45%), Positives = 247/402 (61%), Gaps = 13/402 (3%)

Query: 2   RDVFICDAIRTPIGRFGGALAGVRADDLAA-VPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           RDV +   +RT IG FGG+L      DL A V  +AL   N  V  D+V  V FG     
Sbjct: 3   RDVVVVSGVRTAIGGFGGSLKDFPPTDLGARVVREALARAN--VSGDEVGHVVFGNVVHT 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
              +  +AR+A +  G+ +  P +T+NRLC SG+ AI +A +++  G+ ++AI GG E+M
Sbjct: 61  EPKDMYLARVAAINGGVAQHTPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENM 120

Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRA 179
           SRAP+ M  A  G    + +L D  +G    +P      GV     TA+NVA  Y VSR 
Sbjct: 121 SRAPYSMPAARFGQRMGDARLVDMMVG-ALNDPFQSIHMGV-----TAENVARKYDVSRE 174

Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKP 239
            QDA AL S ++AA A  +G+F E+I+P+ I  KKG+T+ + DEH R   + E  +KLKP
Sbjct: 175 AQDALALESHRRAANAITSGYFKEQILPITIPSKKGDTVFDTDEHARMNASAEDFSKLKP 234

Query: 240 VNGPDK-TVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
           V   +  TVTAGNASG+ND AAA++L      ++ G+ P AR++  A  GV P  MGIGP
Sbjct: 235 VFAKENGTVTAGNASGINDAAAAVVLMERSVAEQRGIKPLARLVSYAHAGVDPAYMGIGP 294

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           VPA RK  ER G+ V+D DVIE NEAFA+Q  AV +ELG   D  +VNPNG  I+LGHP+
Sbjct: 295 VPASRKALERAGLTVADLDVIEANEAFAAQACAVSKELGF--DPAKVNPNGSGISLGHPI 352

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           G +GA + + AL++L++ GGR  L TMC+G GQG+A   ER+
Sbjct: 353 GATGALITVKALYELQRIGGRYALVTMCIGGGQGIAAIFERI 394


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: 379
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: 400
Length of database: 394
Length adjustment: 31
Effective length of query: 369
Effective length of database: 363
Effective search space:   133947
Effective search space used:   133947
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