GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Dechlorosoma suillum PS

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 Dsui_0976 Dsui_0976 acetyl-CoA acetyltransferase

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



>FitnessBrowser__PS:Dsui_0976
          Length = 393

 Score =  513 bits (1321), Expect = e-150
 Identities = 255/389 (65%), Positives = 317/389 (81%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DPIVIVS  RTPMGGFQG+  SL+APQLGA AI+AAVERAG+  + VEEV+FG VL AG+
Sbjct: 3   DPIVIVSVARTPMGGFQGDFNSLTAPQLGATAIKAAVERAGIKPEQVEEVVFGNVLQAGV 62

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAALGAGL  S  CTT++K+CGS +++ ++ HD LLAGS ++ VAGG ESMSNA
Sbjct: 63  GQAPARQAALGAGLPLSAGCTTIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQESMSNA 122

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLL +AR GYR+GHG++LDHMF DGLEDAY KGRLMGTFAE+CAE+ GFTREAQDE+AI
Sbjct: 123 PYLLPKARGGYRLGHGQLLDHMFFDGLEDAYQKGRLMGTFAEECAESYGFTREAQDEWAI 182

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
            ST RAQ+AIK+G F  EI P+ +   K   ++  DEQP KA+++KI +LKPAF+  GTV
Sbjct: 183 QSTVRAQKAIKEGLFKWEIAPVTIAGKKGDVVVDQDEQPLKAQIEKIPALKPAFKKDGTV 242

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAANSSSISDGAAAL+LM+ S+A+  GL P+A I GH   A  P LF  APV A++KL++
Sbjct: 243 TAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTAPVFAMEKLMQ 302

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           KTGW++ +V+L+E+NEAFAVV++  +  L++  +KVNVHGGACALGHPIGASGARILVTL
Sbjct: 303 KTGWNVADVDLWEINEAFAVVTMAAIKDLKLDPAKVNVHGGACALGHPIGASGARILVTL 362

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394
           + AL+Q G K+GVA++CIGGGEA A+ VE
Sbjct: 363 IGALKQYGKKKGVASLCIGGGEAVAVGVE 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: 494
Number of extensions: 11
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: 393
Length adjustment: 31
Effective length of query: 366
Effective length of database: 362
Effective search space:   132492
Effective search space used:   132492
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