GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pseudomonas putida KT2440

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Putida:PP_4636
          Length = 392

 Score =  345 bits (886), Expect = 1e-99
 Identities = 202/402 (50%), Positives = 263/402 (65%), Gaps = 12/402 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+ +I+ A RT IG + GALA+V A DLGA  +K L+ +   LD + VD+VI G    A
Sbjct: 1   MNDVVIVAATRTAIGSFQGALATVPAVDLGAAVIKQLL-KQTGLDPAQVDEVILGQVLTA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR AA+ AGLP SVP  TLN++CGSGL A+  AA+A+RCG+A +++AGG E+M
Sbjct: 60  GA-GQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENM 118

Query: 121 SRAPFVM--GKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
           S AP+VM   ++ Q  G   ++ D+ I     +       GI     TAEN+  ++ +SR
Sbjct: 119 SLAPYVMPSARTGQRMGHG-QLIDSMITDGLWDAFNDYHMGI-----TAENLVDKYGLSR 172

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238
             QDAFA  SQ KA AAI  GR   EI  + + Q+KG  K+   DE PR DTT E LAKL
Sbjct: 173 EQQDAFAAESQRKAVAAIEAGRFDAEITPIVLPQKKGEPKVFARDEQPRPDTTAESLAKL 232

Query: 239 GTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIG 298
              F++ GSVTAGNAS +NDGA A+LL S+  A+  GL   A++   A+AGV+P IMGIG
Sbjct: 233 RPAFKKDGSVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIG 292

Query: 299 PVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHP 358
           PV AT++ L+  G  LA++D+IE NEAFAAQ LAV     LA D  RVN NGGAIALGHP
Sbjct: 293 PVSATQRCLDKAGWQLAELDLIEANEAFAAQALAVGN--ALAWDAARVNVNGGAIALGHP 350

Query: 359 LGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           +G SG R++ T LHE+ +R  +  L T+CIG GQG+AL IER
Sbjct: 351 IGASGCRVLVTLLHEMIKRDVKKGLATLCIGGGQGVALAIER 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: 398
Number of extensions: 16
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: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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