GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF 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)



>FitnessBrowser__BFirm:BPHYT_RS09180
          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:

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