GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Acidovorax sp. GW101-3H11

Align 3-ketoacyl-CoA thiolase B, peroxisomal; Acetyl-CoA acyltransferase B; Beta-ketothiolase B; Peroxisomal 3-oxoacyl-CoA thiolase B; EC 2.3.1.155; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ac3H11_1916 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::P07871
         (424 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1916
          Length = 399

 Score =  303 bits (775), Expect = 8e-87
 Identities = 184/397 (46%), Positives = 244/397 (61%), Gaps = 10/397 (2%)

Query: 32  QASASDVVVVHGRRTPIGRAGRGGFKDTTPDELL-SAVLTAVLQDVKLKPECLGDISVGN 90
           Q    D  +V   RTPIGR+GRG FK+T PD+LL +A+ +A+LQ   L P+ + D  +G 
Sbjct: 3   QKQVQDAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGC 62

Query: 91  VLQPGA-GAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACG 149
               G  G  MARIA  L+     V    VNR C+SG+ A+   A  IR G  D+ +A G
Sbjct: 63  SFPEGEQGMNMARIAVGLA-FNHPVGGVTVNRFCASGITALQMAADRIRVGEADVLIAGG 121

Query: 150 VESMTLSERG-NPGNISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQ 208
            ESM+L   G N  + ++ +   ++       MG+T+E VA+++ ISR+ QDAFAL S  
Sbjct: 122 AESMSLVPMGGNKPSFNAEVFARDEDVGIAYGMGLTAEKVAQQWKISREAQDAFALESHL 181

Query: 209 KAASAQSKGCFRAEIVPV-----TTTVLDDKGDRKTITVSQDEGVRPSTTMEGLAKLKPA 263
           +A  AQ  G F  EI P      +  +   +   K  TVS DEG RP T++EGLAKLKP 
Sbjct: 182 RAIKAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRPDTSLEGLAKLKPV 241

Query: 264 FKDGGSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAY 323
           F   GS TAGNSSQ SDGA A+++A     ++ GL  L    SYA  GVPP+IMGIGP  
Sbjct: 242 FAARGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGVPPEIMGIGPIE 301

Query: 324 AIPAALQKAGLTVNDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLGCTG 383
           AIPAAL+ AGL  +DI  +E+NEAFA+Q+L  +  LG+    VNP+GGAIALGHPLG TG
Sbjct: 302 AIPAALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGLNPANVNPMGGAIALGHPLGATG 361

Query: 384 ARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
           A +  T+++ L RR +  YG+V+MC+GTG GAA + E
Sbjct: 362 AIRAATVVHAL-RRHKLKYGMVTMCVGTGQGAAGIIE 397


Lambda     K      H
   0.316    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: 451
Number of extensions: 24
Number of successful extensions: 5
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: 424
Length of database: 399
Length adjustment: 31
Effective length of query: 393
Effective length of database: 368
Effective search space:   144624
Effective search space used:   144624
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 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