GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas fluorescens FW300-N1B4

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835
          Length = 393

 Score =  336 bits (862), Expect = 6e-97
 Identities = 195/401 (48%), Positives = 260/401 (64%), Gaps = 10/401 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M E +I+ A RT IG + G+LA+V A DLGA  ++ L+A+   LD + VD+VI G    A
Sbjct: 1   MQEVVIVAATRTAIGSFQGSLANVSAVDLGAAVIRQLLAQ-TGLDPAQVDEVIMGQVLTA 59

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

Query: 121 SRAPFVMGKSEQAFGRS-AEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179
           S + +VM  +        A+I DT I     +       GI     TAEN+A +++++R 
Sbjct: 119 SLSNYVMPGARTGLRMGHAQIVDTMISDGLWDAFNDYHMGI-----TAENLAEKYSLTRE 173

Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239
            QDAFA  SQ KA AAI  GR A EI  + I QRKG       DE PR  TT + L KL 
Sbjct: 174 QQDAFAAASQQKAVAAIEAGRFADEITPILIPQRKGDPLSFATDEQPRAGTTADSLGKLK 233

Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
             F++ GSVTAGNAS +NDGA A++L S+E A+  GL   A++   A AGV+P IMGIGP
Sbjct: 234 AAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKIAAYANAGVDPAIMGIGP 293

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359
           V ATR+ L+ TG ++  +D+IE NEAFAAQ LAV ++L    D  +VN NGGAIALGHP+
Sbjct: 294 VSATRRCLDKTGWSIGQLDLIEANEAFAAQSLAVAKDLEW--DLNKVNVNGGAIALGHPI 351

Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           G SG R++ T LHE+ ++  +  L T+CIG GQG+AL IER
Sbjct: 352 GASGCRVLVTLLHEMIKQDAKKGLATLCIGGGQGVALAIER 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: 395
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