GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Dyella japonica UNC79MFTsu3.2

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3009
          Length = 427

 Score =  178 bits (452), Expect = 2e-49
 Identities = 140/435 (32%), Positives = 216/435 (49%), Gaps = 54/435 (12%)

Query: 4   VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63
           V +   IR P  R   A A V    ++   L AL+E    +  +++ EV  G   +   +
Sbjct: 8   VGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVE-RFRLHGEELGEVAMGAVIKHSSE 66

Query: 64  NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123
             N+AR A+L +GL  + PG+T  R C + +D        IA+G++E  IAGG ++ S  
Sbjct: 67  -WNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDV 125

Query: 124 PFVMGKAESGYSRNMKLEDTTIGWR----------FINPLMKSQYGVD------SMPETA 167
           P V+G+    + + +   +   GW+           +  L  S  GV       SM +  
Sbjct: 126 PIVLGER---FRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHC 182

Query: 168 DNVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRP 227
           + +A ++ + R  QD  AL S QK AAA  AGFF + +VP R         ++RD  LR 
Sbjct: 183 ERMAKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVPFR--------GLKRDGFLRA 234

Query: 228 ETTLEALTKLKP----VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLG 283
           ++++E L  LKP    ++G   T+TAGN++G++DGAAA++L S E   + GL  +A  L 
Sbjct: 235 DSSMEKLGTLKPAFDKISG-HGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLD 293

Query: 284 MASGGVAPRVMGIG----PVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLR----- 334
            A       V G G    P  AV ++  R G+ + DFD  E++EAFA+Q L  LR     
Sbjct: 294 -AEVAAVDFVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESE 352

Query: 335 -----ELGVAD-----DAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLAT 384
                 LG+       D  ++N +G ++A GHP   +GAR+V T    LE+ G  +GL +
Sbjct: 353 TYCRNRLGLEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLIS 412

Query: 385 MCVGVGQGLALAIER 399
           +C   G G+   +ER
Sbjct: 413 ICTAGGMGVTAILER 427


Lambda     K      H
   0.318    0.134    0.383 

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: 396
Number of extensions: 17
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: 400
Length of database: 427
Length adjustment: 31
Effective length of query: 369
Effective length of database: 396
Effective search space:   146124
Effective search space used:   146124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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