GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Geobacter daltonii FRC-32

Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate WP_012647510.1 GEOB_RS12065 thiolase family protein

Query= BRENDA::I3R3D1
         (383 letters)



>NCBI__GCF_000022265.1:WP_012647510.1
          Length = 390

 Score =  169 bits (427), Expect = 2e-46
 Identities = 117/359 (32%), Positives = 182/359 (50%), Gaps = 12/359 (3%)

Query: 4   VAIIGASMTQFGQRDAWIRELLAEAGQAALADADVS-PDEIEHLYVSNMASGEFEGQTGV 62
           V I G   T+FG+       L  EA   A+  +++  PD ++  YV N  +    GQT V
Sbjct: 7   VYIAGVGETKFGKHTVDFDVLGREAALQAMRGSNIDRPDMVQSAYVGNGMNDMVTGQT-V 65

Query: 63  PNALAHDLAAMPAYTARIDQTSSSGGAGVYAAWQSVASGASDMTMLVGGEKMT-HRSTAE 121
              L      +P     +    S+G   V+ A + VA+G +D+++ VG E  T HR +  
Sbjct: 66  FRGLGMCGPNLPIIN--VQSACSAGAMAVFCAIKDVATGVTDLSIGVGCENHTMHRQSGA 123

Query: 122 ATDVIASLTHPVEYKHGVTLPSFAGLTARLYLDTYDAPRESLGKVAVKNHKNGLDNPHAQ 181
           A     S    +E  HG  +     + A  Y+    A  E L  + VKN K+   NPHA 
Sbjct: 124 AFSAARS---DIETMHGAVMTGKYAMRATRYMHETGATIEDLAMITVKNRKHATHNPHAW 180

Query: 182 FRKEVDLETVLDSPVVADPLRLYDFCPITDGSAALVFCSESVAREY-TDDYVVISGIGGA 240
           F+  + +E V++S +VA P+ L   C I DG+AA+V  S+ + ++      V ++G+   
Sbjct: 181 FKGPITIEEVVNSRMVAYPMTLQQCCGIADGAAAVVVGSKEMMKKLGIAKPVRVAGV--V 238

Query: 241 TDTHVVHERADPTTMGGVVNS-SDIAYEMADLEPDDIDVAELHDMFTILEFLQSEDLGFF 299
            ++   H R    T   +  + S+  YE + + PD++++ ELHD FTI E L  E +G  
Sbjct: 239 VESGPYHNRPRDITGDDITETTSEKLYEESGIGPDEVNILELHDAFTISELLYYECMGLC 298

Query: 300 EKGEGWKAVEEGVTDRDGELPINTSGGLKSKGHPLGASGVAQVYEIYKQLIGDAGDRQV 358
           +KGEG K + +G +   G+  ++  GG+ S GHP+GASG AQV +  KQL G+ G  QV
Sbjct: 299 KKGEGLKFLRDGQSTYGGKCVVSPRGGMLSYGHPIGASGAAQVAQNVKQLRGECGGHQV 357


Lambda     K      H
   0.315    0.132    0.384 

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: 393
Number of extensions: 25
Number of successful extensions: 3
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: 383
Length of database: 390
Length adjustment: 30
Effective length of query: 353
Effective length of database: 360
Effective search space:   127080
Effective search space used:   127080
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: 42 (22.0 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