GapMind for catabolism of small carbon sources

 

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

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase

Query= reanno::Marino:GFF2751
         (415 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0938
          Length = 394

 Score =  252 bits (644), Expect = 1e-71
 Identities = 160/399 (40%), Positives = 223/399 (55%), Gaps = 16/399 (4%)

Query: 12  IVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNR 71
           I  A RT IG + G  + V    LGA  IKA  E+   +    +++VL GC   A     
Sbjct: 8   IAGAKRTAIGSFLGQFTGVPTPVLGATAIKAALEQ-AGIAAQDVNEVLMGCVLPANLGQA 66

Query: 72  DVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPF 131
             AR + L AGLP  V  +T+N++CGSGM A+      I+ G   +++AGG+ESM+ AP 
Sbjct: 67  P-ARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESMTNAPH 125

Query: 132 VMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQDAFA 191
           ++           ++ D        NP   K  G+       E  A  +  +RE+QDAFA
Sbjct: 126 MVNARTGIRYGDGQLVDHMAWDGLTNPYDGKAMGV-----FGELCADKYHFTREEQDAFA 180

Query: 192 LRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTPFR-EN 250
           + S +R  AAQ+ G  A EI PVT+  RK D +VVDTDE P  + + K+ SL   FR EN
Sbjct: 181 IESVKRAQAAQQNGAFAGEIVPVTVAGRKGD-VVVDTDEQPGRSDIAKVPSLKPAFRKEN 239

Query: 251 GTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAPATRK 310
           GT+TA ++S ++DGA A++L  AD  K   L+P AR+VA AT   EP      P  A +K
Sbjct: 240 GTITAASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPEWFTTAPVSAIQK 299

Query: 311 VLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGAR 370
           VL  AG ++ D+D+ E+NEAFA  A+A  R+LG+P     +N NGGA ALGHP+G SG R
Sbjct: 300 VLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELGIPH--AKLNVNGGACALGHPIGASGTR 357

Query: 371 LVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIE 409
           LV T LN L+ R       +  + ++CIG G+  A+ +E
Sbjct: 358 LVVTLLNALQTR-----GLKRGVASLCIGGGEATAIAVE 391


Lambda     K      H
   0.318    0.133    0.382 

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: 379
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: 415
Length of database: 394
Length adjustment: 31
Effective length of query: 384
Effective length of database: 363
Effective search space:   139392
Effective search space used:   139392
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