GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas simiae WCS417

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 GFF2716 PS417_13855 acetyl-CoA acetyltransferase

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



>FitnessBrowser__WCS417:GFF2716
          Length = 394

 Score =  686 bits (1769), Expect = 0.0
 Identities = 346/392 (88%), Positives = 370/392 (94%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DPIVIVSAVRTPMGGFQG+LK L+APQLG+AAIRAAVERAG+A DAV+EVLFGCVL AGL
Sbjct: 3   DPIVIVSAVRTPMGGFQGDLKGLTAPQLGSAAIRAAVERAGIATDAVDEVLFGCVLPAGL 62

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAALGAGLDK+TRCTTLNKMCGSGMEAAILAHD LLAGS DVV+AGGMESMSNA
Sbjct: 63  GQAPARQAALGAGLDKATRCTTLNKMCGSGMEAAILAHDSLLAGSVDVVIAGGMESMSNA 122

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLLDRARSGYRMGH KVLDHMFLDGLEDAYDKGRLMGTFAEDCA  NGFTREAQD FAI
Sbjct: 123 PYLLDRARSGYRMGHSKVLDHMFLDGLEDAYDKGRLMGTFAEDCALHNGFTREAQDAFAI 182

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
           AS TRAQ+AI  G+F AEIVP+QV VGKEQK I  DEQPPKAKLDKI+SLK AFRDGGTV
Sbjct: 183 ASLTRAQEAISHGNFAAEIVPVQVTVGKEQKTILHDEQPPKAKLDKISSLKAAFRDGGTV 242

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAAN+SSISDGAAALLLMR+SEA+KRGLKPLAVIHGHAAFAD PGLFPVAPVGAI+KL+ 
Sbjct: 243 TAANASSISDGAAALLLMRQSEAQKRGLKPLAVIHGHAAFADEPGLFPVAPVGAIRKLMT 302

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           KTGW++ EV+LFE+NEAFAVVSLVTM+KL+IPH+KVN+HGGACALGHPIGASGARILVTL
Sbjct: 303 KTGWNVGEVDLFEINEAFAVVSLVTMSKLDIPHAKVNIHGGACALGHPIGASGARILVTL 362

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVECLY 397
           LSALRQ GLKRGVAAICIGGGEATAMAVECLY
Sbjct: 363 LSALRQNGLKRGVAAICIGGGEATAMAVECLY 394


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: 593
Number of extensions: 10
Number of successful extensions: 1
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