GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Shewanella amazonensis SB2B

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 6937205 Sama_1375 Acetyl-CoA C-acetyltransferase (RefSeq)

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



>FitnessBrowser__SB2B:6937205
          Length = 392

 Score =  470 bits (1210), Expect = e-137
 Identities = 240/392 (61%), Positives = 299/392 (76%), Gaps = 1/392 (0%)

Query: 3   MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLS 62
           MS   IVIV+A RT MGGFQG L  + +P+L A A++A ++  G+    V+E+L GCVL 
Sbjct: 1   MSVSDIVIVAAKRTAMGGFQGSLSEVPSPKLAATAVKALLDDTGLDGARVDELLMGCVLP 60

Query: 63  AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122
           AGLGQAPARQAALGAGL  S   TT+NK+CGSGM+  +LAHD++ AGSA VV+AGGMESM
Sbjct: 61  AGLGQAPARQAALGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESM 120

Query: 123 SNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDE 182
           S APYLLD+AR G RMGHGKVLDHMFLDGLEDAY  G  MGTFA+  A+  G TRE+ D 
Sbjct: 121 SQAPYLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGGA-MGTFAQKTADDYGLTRESMDA 179

Query: 183 FAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDG 242
           FA++S  +A  AI  G+F AEIVP+ V   K    +  DEQP  A+ +KI +L+PAF   
Sbjct: 180 FALSSLEKANAAINSGAFEAEIVPVTVSSRKGDVEVKVDEQPGNARPEKIPTLRPAFAKD 239

Query: 243 GTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKK 302
           GT+TAANSSSISDGAAAL+LM R +A+  GLK LA I GH   A  P +F  APVGA+ K
Sbjct: 240 GTITAANSSSISDGAAALMLMSRDQADALGLKVLATIKGHTTHAQEPAMFTTAPVGAMTK 299

Query: 303 LLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARIL 362
           LL   GWS DEV+LFE+NEAFA+V+++ +++L++  ++VNV+GGACALGHPIG SGAR+L
Sbjct: 300 LLSNVGWSKDEVDLFEINEAFAMVTMLAISELKLDAARVNVNGGACALGHPIGCSGARVL 359

Query: 363 VTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394
           VTL+ AL+ +GLKRGVA++CIGGGEATAMA+E
Sbjct: 360 VTLIHALKARGLKRGVASLCIGGGEATAMAIE 391


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: 508
Number of extensions: 14
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: 392
Length adjustment: 31
Effective length of query: 366
Effective length of database: 361
Effective search space:   132126
Effective search space used:   132126
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