GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Shewanella sp. ANA-3

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 7025620 Shewana3_2771 acetyl-CoA acetyltransferases (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7025620 Shewana3_2771 acetyl-CoA
           acetyltransferases (RefSeq)
          Length = 396

 Score =  470 bits (1210), Expect = e-137
 Identities = 243/387 (62%), Positives = 294/387 (75%), Gaps = 1/387 (0%)

Query: 8   IVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQ 67
           IVIV+A RTPMGGFQG L  + +P L A AI+A +    VA D V+EVL GCVL AGLGQ
Sbjct: 10  IVIVAAKRTPMGGFQGSLSGVMSPSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQ 69

Query: 68  APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127
           APARQA LGAGL  S   TT+NK+CGSGM+  +LAHD+L AGSA +VVAGGMESMS APY
Sbjct: 70  APARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLLKAGSAKLVVAGGMESMSQAPY 129

Query: 128 LLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIAS 187
           LLD+AR+G RMGHGKVLDHMFLDGLEDAY  G  MGTFA+  A+  G TRE  D FA++S
Sbjct: 130 LLDKARAGMRMGHGKVLDHMFLDGLEDAYTGGA-MGTFAQKTADEYGLTREQMDAFALSS 188

Query: 188 TTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTA 247
             +A  AI  G+F AEIVP+ V   +    +  DEQP  A+ +KI +L+PAF   GT+TA
Sbjct: 189 LEKANAAINSGAFKAEIVPVTVSDRRGDVTVDTDEQPGNARPEKIPALRPAFAKDGTITA 248

Query: 248 ANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKT 307
           ANSSSISDGAAAL+L  R+ AE+ GL  LA I GH   A  P LF  APVGA+ KLL   
Sbjct: 249 ANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPSLFTTAPVGAMAKLLSNV 308

Query: 308 GWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLS 367
           GWS DEV+LFE+NEAFA+V+++ +++L +  +KVNV+GGACALGHPIG SGAR+LVTL+ 
Sbjct: 309 GWSKDEVDLFEINEAFAMVTMLAVSELGLDMAKVNVNGGACALGHPIGCSGARLLVTLIH 368

Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394
           AL+ +GLKRGVA++CIGGGEATAMA+E
Sbjct: 369 ALKARGLKRGVASLCIGGGEATAMAIE 395


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: 486
Number of extensions: 17
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: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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 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