GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Burkholderia phytofirmans PsJN

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__BFirm:BPHYT_RS09150
          Length = 393

 Score =  321 bits (822), Expect = 3e-92
 Identities = 184/401 (45%), Positives = 256/401 (63%), Gaps = 10/401 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M + +I+ A RT +G++ G+LA + A +LGA  ++A++ R   L    V +VI G    A
Sbjct: 1   MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLER-AGLKPEQVSEVILGQVLTA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR A + AGLP +VPG T+N +CGSGL AV  AA A+  G+A +++AGG E+M
Sbjct: 60  GS-GQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENM 118

Query: 121 SRAPFVMGKSEQAFGRS-AEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179
           S AP V+  S   F    A++ D+ I     +   Q   G+     TAENVA ++ I+R 
Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGV-----TAENVAKEYGITRE 173

Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239
            QDAFA  SQ+KA AA   GR   EIV VEI QRKG       DE  R   T E LA L 
Sbjct: 174 QQDAFAALSQNKAEAAQKAGRFDDEIVPVEIPQRKGEPLRFATDEFVRHGVTAESLAGLK 233

Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
             F + GSVTA NASG+NDGA A+L+ S++ A+  GLK  AR+   AT+G++P++MG+GP
Sbjct: 234 PAFSKEGSVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVMGMGP 293

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359
           VPA+R+ LE  G   AD+D++E+NEAFAAQ  AV +++G   D  ++N NGGAIA+GHP+
Sbjct: 294 VPASRRCLERAGWTPADLDLMEINEAFAAQACAVNQQMGW--DTSKINVNGGAIAIGHPI 351

Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           G SG R++ T LHE+++R  +  L ++CIG G G+AL +ER
Sbjct: 352 GASGCRILVTLLHEMQKRDAKKGLASLCIGGGMGVALALER 392


Lambda     K      H
   0.319    0.134    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: 421
Number of extensions: 17
Number of successful extensions: 4
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: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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