GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas simiae WCS417

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF2062 PS417_10515 acetyl-CoA acetyltransferase

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



>FitnessBrowser__WCS417:GFF2062
          Length = 393

 Score =  337 bits (865), Expect = 3e-97
 Identities = 194/401 (48%), Positives = 260/401 (64%), Gaps = 10/401 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M + +I+ A RT +G + G+LAS+ A +LGA  ++ L+ +   LD + VD+VI G    A
Sbjct: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQ-TGLDPAQVDEVILGQVLTA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR A++LAGLP +VP  TLN++CGSGL A+   A+A+RCG+A +++AGG+E+M
Sbjct: 60  GS-GQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118

Query: 121 SRAPFVMGKSEQAFGRS-AEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179
           S AP+V+  +        A++ D+ I     +       GI     TAEN+  ++ ISR 
Sbjct: 119 SLAPYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGI-----TAENLVDKYGISRE 173

Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239
            QDAFA  SQ KA AAI  GR   EI  + I QRKG       DE PR  TT E LAKL 
Sbjct: 174 AQDAFAAASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLK 233

Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
             F++ GSVTAGNAS +NDGA A+LL S++ A+  GL   AR+   A AGV+P IMGIGP
Sbjct: 234 PAFKKDGSVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGP 293

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359
           V ATR+ L+  G +L D+D+IE NEAFAAQ LAV +EL    D E+VN NGGAIA+GHP+
Sbjct: 294 VSATRRCLDKAGWSLGDLDLIEANEAFAAQSLAVGKELEW--DAEKVNVNGGAIAIGHPI 351

Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           G SG R++ T LHE+ +R  +  L T+CIG GQG+AL +ER
Sbjct: 352 GASGCRVLVTLLHEMIKRDAKKGLATLCIGGGQGVALALER 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: 390
Number of extensions: 13
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