GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF2716 PS417_13855 acetyl-CoA
           acetyltransferase
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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