GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Oscillibacter ruminantium GH1

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_040660027.1 ON16_RS04985 acetyl-CoA C-acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_000307265.1:WP_040660027.1
          Length = 418

 Score =  451 bits (1159), Expect = e-131
 Identities = 234/418 (55%), Positives = 299/418 (71%), Gaps = 27/418 (6%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M ++ +V+  RTA+G FGG+L   PA ELG++V+K AL RAGVKPEQV EV+ G +LTAG
Sbjct: 1   MKELYVVNCCRTAIGSFGGTLKNTPATELGSIVVKEALNRAGVKPEQVDEVMFGCILTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQN ARQ A+KAG+P  VPA T+  VCGSG+K+V+  A +I+AGDA+++V GG ENMSA
Sbjct: 61  LGQNVARQVAVKAGIPYSVPAYTVGMVCGSGMKSVIEGARSILAGDADVIVCGGTENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           AP+  P +R G RMGD KLVDTMI DGLWD +N YHMG TAEN+   +GITR+  DEFAV
Sbjct: 121 APYAAPDARWGARMGDKKLVDTMIKDGLWDAFNNYHMGTTAENICDVWGITRQELDEFAV 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAF---- 236
            SQ K EAAQ AGKFD+EIV V +  +K D V FK DEF R G TL+ +  +K AF    
Sbjct: 181 SSQQKCEAAQAAGKFDDEIVAVPVKVKK-DIVEFKKDEFPRAGTTLEGVGKMKGAFPVGP 239

Query: 237 -------------------DKAGT--VTAANASGLNDGAAAVVVMSAAKAKELGLTPLAT 275
                              D  GT  VTAA++SG+NDGAAA+V+ S     + GL P+A 
Sbjct: 240 ESPNPQVVHTFEVTGAKETDDKGTQRVTAASSSGINDGAAAIVLASGEAVAKYGLKPMAK 299

Query: 276 IKSYANAGVDPKVMGMGPVPASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDT 335
           +  +   GVDPK+MG+GPVPAS++A+ +A  T  D+DL+E NEAFAAQ++AV +++ +D 
Sbjct: 300 LIGWGQGGVDPKIMGVGPVPASQQAMKKAGVTIDDMDLVEANEAFAAQSIAVARELHFDM 359

Query: 336 SKVNVNGGAIAIGHPIGASGCRILVTLLHEM-KRRDAKKGLASLCIGGGMGVALAVER 392
           SKVNVNGGA+++GHP+G SG RI+VTLLHE+ KR DAKKGLA+LCIGGG GVA   E+
Sbjct: 360 SKVNVNGGALSLGHPVGCSGARIIVTLLHELQKRDDAKKGLATLCIGGGQGVATIFEK 417


Lambda     K      H
   0.315    0.131    0.369 

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: 459
Number of extensions: 22
Number of successful extensions: 4
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: 393
Length of database: 418
Length adjustment: 31
Effective length of query: 362
Effective length of database: 387
Effective search space:   140094
Effective search space used:   140094
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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