GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Burkholderia phytofirmans PsJN

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase

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



>FitnessBrowser__BFirm:BPHYT_RS09150
          Length = 393

 Score =  323 bits (827), Expect = 7e-93
 Identities = 183/404 (45%), Positives = 263/404 (65%), Gaps = 17/404 (4%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M DV I  A RT +G+FGG+LA + A +L A  ++A++E    ++ +QV EV  G    A
Sbjct: 1   MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLE-RAGLKPEQVSEVILGQVLTA 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           G   +N AR A++ AGLP ++PG+T+N +C SG+ A+  A  AI +G+ ++ +AGG E+M
Sbjct: 60  GS-GQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENM 118

Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQV 176
           S AP V+  +  G+   + KL D+ I    W   N     QY    M  TA+NVA +Y +
Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYN-----QY---HMGVTAENVAKEYGI 170

Query: 177 SRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALT 235
           +R  QDAFA  SQ KA AAQ AG F +EIVPV I  +KGE +    DE +R   T E+L 
Sbjct: 171 TREQQDAFAALSQNKAEAAQKAGRFDDEIVPVEIPQRKGEPLRFATDEFVRHGVTAESLA 230

Query: 236 KLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295
            LKP    + +VTA NASG+NDGAAA+++ SA+  +  GL P AR+   A+ G+ P+VMG
Sbjct: 231 GLKPAFSKEGSVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVMG 290

Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALG 355
           +GPVPA R+  ER G   +D D++E+NEAFA+Q  AV +++G   D  ++N NGGAIA+G
Sbjct: 291 MGPVPASRRCLERAGWTPADLDLMEINEAFAAQACAVNQQMGW--DTSKINVNGGAIAIG 348

Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           HP+G SG R+++T LH+++K   +KGLA++C+G G G+ALA+ER
Sbjct: 349 HPIGASGCRILVTLLHEMQKRDAKKGLASLCIGGGMGVALALER 392


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: 402
Number of extensions: 16
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: 393
Length adjustment: 31
Effective length of query: 369
Effective length of database: 362
Effective search space:   133578
Effective search space used:   133578
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