GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0938
          Length = 394

 Score =  442 bits (1138), Expect = e-129
 Identities = 232/395 (58%), Positives = 298/395 (75%), Gaps = 3/395 (0%)

Query: 3   MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLS 62
           MS   +VI  A RT +G F G+   +  P LGA AI+AA+E+AG+AA  V EVL GCVL 
Sbjct: 1   MSDVSVVIAGAKRTAIGSFLGQFTGVPTPVLGATAIKAALEQAGIAAQDVNEVLMGCVLP 60

Query: 63  AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122
           A LGQAPARQAAL AGL  +  CTT+NK+CGSGM+A +L HD++ AGSA VVVAGGMESM
Sbjct: 61  ANLGQAPARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESM 120

Query: 123 SNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDE 182
           +NAP++++ AR+G R G G+++DHM  DGL + YD G+ MG F E CA+   FTRE QD 
Sbjct: 121 TNAPHMVN-ARTGIRYGDGQLVDHMAWDGLTNPYD-GKAMGVFGELCADKYHFTREEQDA 178

Query: 183 FAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFR-D 241
           FAI S  RAQ A ++G+F  EIVP+ V   K   ++  DEQP ++ + K+ SLKPAFR +
Sbjct: 179 FAIESVKRAQAAQQNGAFAGEIVPVTVAGRKGDVVVDTDEQPGRSDIAKVPSLKPAFRKE 238

Query: 242 GGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIK 301
            GT+TAA+SSSISDGAAA++L+   +A+ RGL+PLA I  HA  +  P  F  APV AI+
Sbjct: 239 NGTITAASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPEWFTTAPVSAIQ 298

Query: 302 KLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARI 361
           K+L K GW +D+V+LFEVNEAFAVV++  M +L IPH+K+NV+GGACALGHPIGASG R+
Sbjct: 299 KVLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELGIPHAKLNVNGGACALGHPIGASGTRL 358

Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVECL 396
           +VTLL+AL+ +GLKRGVA++CIGGGEATA+AVE L
Sbjct: 359 VVTLLNALQTRGLKRGVASLCIGGGEATAIAVELL 393


Lambda     K      H
   0.318    0.133    0.378 

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: 466
Number of extensions: 15
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: 397
Length of database: 394
Length adjustment: 31
Effective length of query: 366
Effective length of database: 363
Effective search space:   132858
Effective search space used:   132858
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