GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Burkholderia phytofirmans PsJN

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate BPHYT_RS09180 BPHYT_RS09180 3-ketoacyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS09180 BPHYT_RS09180
           3-ketoacyl-CoA thiolase
          Length = 394

 Score =  321 bits (822), Expect = 3e-92
 Identities = 184/404 (45%), Positives = 248/404 (61%), Gaps = 16/404 (3%)

Query: 2   REAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61
           R+  +  G+RT IG +GG+L      DL A  +RE+L R   +  + +  V+ G      
Sbjct: 3   RDVVVVSGVRTAIGGFGGSLKDFSPTDLGARVVREVLAR-ANVSGDEVGHVVFGNVVHTE 61

Query: 62  EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121
             +  +AR+A +  G+ Q     T+NRLCGSGL A+  AA+++  GD D+ I GG E+MS
Sbjct: 62  PKDMYLARVAAINGGVAQHAPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENMS 121

Query: 122 RAPFVMGKAASAFSRQ---AEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178
           RAP+ M   A+ F ++   A + D  +G       +   F +  M  TAENVA    ISR
Sbjct: 122 RAPYSM--PAARFGQRMGDARLVDMMVG------ALNDPFQSIHMGVTAENVARKYDISR 173

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
           E QD+ AL S +R A A +SG   E+I+P+ + +KKG V     DEH R   + E    L
Sbjct: 174 EAQDALALESHRRAANAITSGYFKEQILPITIPSKKGDVV-FDTDEHTRMSASPEDFSKL 232

Query: 239 KAPF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGL 297
           K  F + NG +TAGNASG+ND AAA+++    +A  +G+ P AR+V+ A AGV+P  MG+
Sbjct: 233 KPVFAKENGTVTAGNASGINDAAAAVVLMERSLAEQRGIKPLARLVSYAHAGVDPAYMGI 292

Query: 298 GPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGH 357
           GPVPATRR LERAGL++ D+DVIE NEAFAAQA  V +ELG   D   VNPNG  I+LGH
Sbjct: 293 GPVPATRRALERAGLTVADLDVIEANEAFAAQACAVSKELGF--DPAKVNPNGSGISLGH 350

Query: 358 PLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           P+G +GA + + A +EL R  GRYAL TMCIG GQGIA I ER+
Sbjct: 351 PIGATGALITVKALYELQRIGGRYALVTMCIGGGQGIAAIFERI 394


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: 420
Number of extensions: 19
Number of successful extensions: 6
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: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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