GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas fluorescens FW300-N2E3

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate AO353_27530 AO353_27530 acetyl-CoA acetyltransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_27530
          Length = 394

 Score =  327 bits (839), Expect = 3e-94
 Identities = 187/400 (46%), Positives = 250/400 (62%), Gaps = 9/400 (2%)

Query: 2   NEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAG 61
           ++  ++ AVR+ IG + G+L  V    L     +A I R   L    +   + G      
Sbjct: 4   SDIFVVSAVRSAIGSFGGSLKDVPPIQLATDVCRAAIERSG-LAPEHIGHAVMGHVIPTE 62

Query: 62  EDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMS 121
             +  ++R  A+ AGLP   P   +NRLCGSGL A+ SAA++L  G+ G  LAGGVESMS
Sbjct: 63  ARDAYISRAVAMNAGLPKETPAFNVNRLCGSGLQAIVSAAQSLMLGDTGAALAGGVESMS 122

Query: 122 RAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQ 181
           R  +++ ++     R  +I     G  ++  ++Q  F    M  TAEN+A  + ISR  Q
Sbjct: 123 RGAYLLPQARWG-ARMGDIQ----GIDYMLGVLQDPFAGFHMGITAENIAEHYGISRQTQ 177

Query: 182 DAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTP 241
           D  AL SQ +AA AIA GR   +IV +E+A RKG       DEH R + + EQL+ +   
Sbjct: 178 DQLALLSQQRAARAIAEGRFTGQIVPIEVASRKGTVSFAT-DEHVRAEVSFEQLSGMKPA 236

Query: 242 FRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVP 301
           F++ GSVTAGNASG+NDGA AL++A+ +  Q  GLK  AR+VG A AGVEP +MG+GP+P
Sbjct: 237 FKKDGSVTAGNASGLNDGAGALIMATGQVVQEQGLKPMARLVGYAHAGVEPSMMGLGPIP 296

Query: 302 ATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGM 361
           ATR VL+  GL +AD+DVIE NEAFAAQ  AV +ELG   D E+VNPNG  I+LGHP+G 
Sbjct: 297 ATRLVLKRAGLTVADLDVIESNEAFAAQACAVAQELGF--DPEKVNPNGSGISLGHPVGA 354

Query: 362 SGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           +GA + T A+HEL   QGRYAL TMCIG GQGIA++ ER+
Sbjct: 355 TGAIIATKAIHELHRIQGRYALATMCIGGGQGIAVLFERV 394


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: 416
Number of extensions: 20
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: 401
Length of database: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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