GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Dyella japonica UNC79MFTsu3.2

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3009
          Length = 427

 Score =  166 bits (421), Expect = 9e-46
 Identities = 135/429 (31%), Positives = 206/429 (48%), Gaps = 45/429 (10%)

Query: 6   ICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNR 65
           +  GIR P  R   A + V    ++ + +   LV   RL  E + +V +G   +   +  
Sbjct: 10  VIGGIRIPFCRNNTAYADVGNFGMS-VKVLGALVERFRLHGEELGEVAMGAVIKHSSE-W 67

Query: 66  NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125
           N+AR A L +GL  +  G T  R CG+ LD     A  I AG  +  IAGG ++ S  P 
Sbjct: 68  NLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDVPI 127

Query: 126 VMG----KAASAFSR----QAEMFDTTIGWRFVN-----PLMAQQFGTDSMPETAENVAE 172
           V+G    K   A +R    Q +M   T G+         P +A+     SM +  E +A+
Sbjct: 128 VLGERFRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHCERMAK 187

Query: 173 LLKISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTL 232
              I RE QD  AL S Q+ A A  +G   + +VP            ++ D  LR ++++
Sbjct: 188 EWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVP---------FRGLKRDGFLRADSSM 238

Query: 233 EQLRGLKAPF---RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAG 289
           E+L  LK  F     +G +TAGN++G++DGAAA+++ S++ AA +GL  +A  +    A 
Sbjct: 239 EKLGTLKPAFDKISGHGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLDAEVAA 298

Query: 290 VE---PRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLR----------E 336
           V+      + + P  A  R+L R GL++ D D  E++EAFAAQ L  LR           
Sbjct: 299 VDFVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESETYCRNR 358

Query: 337 LGLPD-----DAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVG 391
           LGL       D   +N +G ++A GHP   +GAR+    +  L  +     L ++C   G
Sbjct: 359 LGLEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLISICTAGG 418

Query: 392 QGIAMILER 400
            G+  ILER
Sbjct: 419 MGVTAILER 427


Lambda     K      H
   0.319    0.135    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: 381
Number of extensions: 20
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: 427
Length adjustment: 31
Effective length of query: 370
Effective length of database: 396
Effective search space:   146520
Effective search space used:   146520
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