GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Phaeobacter inhibens BS107

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 GFF3267 PGA1_c33180 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Phaeo:GFF3267
          Length = 390

 Score =  473 bits (1216), Expect = e-138
 Identities = 240/387 (62%), Positives = 296/387 (76%), Gaps = 2/387 (0%)

Query: 8   IVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQ 67
           +VI  A RTPMGGFQG    ++A +LG +AIRAA+  AG  A  V+E+L GCVL AG GQ
Sbjct: 4   VVIAGAARTPMGGFQGMYDGVAAAELGGSAIRAAL--AGAGATTVDEILMGCVLPAGQGQ 61

Query: 68  APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127
           APARQA   AGL +    TTLNKMCGSGM+AA++A+D +  G AD ++AGGMESM+NAPY
Sbjct: 62  APARQAGFAAGLGEEVPATTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESMTNAPY 121

Query: 128 LLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIAS 187
           LL + R+G R+GHG+V+DHMFLDGLEDAYDKGRLMGTFAEDCAE   FTREAQDE+A+ S
Sbjct: 122 LLPKMRNGARLGHGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAETYQFTREAQDEYALTS 181

Query: 188 TTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTA 247
            + A  A + G+F+AEI P+ V   K + +   DEQP  A+ DKI +LKPAFR  GTVTA
Sbjct: 182 LSNALAAQESGAFDAEIAPVTVKTRKGETVTNADEQPKSARPDKIPTLKPAFRKDGTVTA 241

Query: 248 ANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKT 307
           AN+SSISDGAAAL+L     AE +GL   A I GHA+ A  PGLF  APV A KKL+ + 
Sbjct: 242 ANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVPAAKKLMAQL 301

Query: 308 GWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLS 367
           GW++ +V+L+EVNEAFAVV +  M ++ +P  KVNV+GGACALGHPIGASGARI+VTLL+
Sbjct: 302 GWTVSDVDLWEVNEAFAVVPMAFMHEMGLPRDKVNVNGGACALGHPIGASGARIMVTLLN 361

Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394
           AL ++ LKRG+AAICIGGGE TA+A+E
Sbjct: 362 ALEKRNLKRGIAAICIGGGEGTAIAIE 388


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: 488
Number of extensions: 15
Number of successful extensions: 2
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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