GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Azospirillum brasilense Sp245

Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate AZOBR_RS24680 AZOBR_RS24680 hypothetical protein

Query= BRENDA::I3RA72
         (383 letters)



>FitnessBrowser__azobra:AZOBR_RS24680
          Length = 387

 Score =  152 bits (383), Expect = 2e-41
 Identities = 120/358 (33%), Positives = 176/358 (49%), Gaps = 19/358 (5%)

Query: 32  LEDAGVAPASVDHLYVSNMASGEFE--GQTGVMNALAHDLGVIPAYTQRIDQTSSSGGAG 89
           L+DAG+    VD L     ASG++   G T  +  LA  +G+ P Y   ++ T   G + 
Sbjct: 37  LDDAGLTLKDVDGLCA---ASGDWAEGGSTMDVVELAEYIGIAPTY---VNSTDVGGCSY 90

Query: 90  IYEAWQS---IASGVSEMTLL-VGGEKMTHKTTGESTDIIASCTHPEEYK--HGVTLPSF 143
           I +A Q+   IA+G++E+ ++           +  S D       P +Y+  +  TL S 
Sbjct: 91  ILQAGQAAAAIATGLAEVVVISYAACPRWWPLSSPSFDPFVFPAGPGQYEIPYAPTLIST 150

Query: 144 AGMTARNYLERFDAPRESLARVAVKNHRNGVDNPKAQFQKEIDIETALESPIIADPLRLY 203
            G+ AR +++ +    E LA+VAV    +   NP A+ +K I ++  L SP+IA PL   
Sbjct: 151 YGLFARRHMDLYGTTPEQLAQVAVTFREHAAKNPDARLRKPITVDDVLASPMIASPLHRL 210

Query: 204 DFCPITDGSAAMMFTTEERAQEITDEYAIVSGVGGA-TDTHVVHERDDPTVMGGVVESSK 262
           D C +TDG  A++ T+ ERA+++      V G G A   T      DD T    +  S  
Sbjct: 211 DCCVVTDGGGAVVMTSRERARDLKKPPVHVVGYGAAVARTQNSQIPDDLTTPAAL--SGP 268

Query: 263 QAYEMAGVGPDDLDVAELHDMFTILEFLQLEGIGVADHGAAWELAMDGVTAKDGGLPINT 322
           +A+ MAGV P ++DVA+++D FTI   L LE +G    G +     DG     G LP NT
Sbjct: 269 RAFAMAGVTPGEIDVAQIYDAFTITPMLALEDLGFCGRGESGAFVADGNLTLGGSLPTNT 328

Query: 323 SGGLKSKGHPLGASGVAQGVEIYEQLVGEAGPRQV-EADTALACNVGGFGNCVITTIM 379
            GG  S  HP G  G+   +E   QL GE    QV +A  ALA  +GG      T I+
Sbjct: 329 DGGGLSSNHP-GKRGIFTLIESVRQLRGEGPGVQVPDARIALAHGLGGTFCSAATAIL 385


Lambda     K      H
   0.314    0.131    0.379 

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: 440
Number of extensions: 26
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: 387
Length adjustment: 30
Effective length of query: 353
Effective length of database: 357
Effective search space:   126021
Effective search space used:   126021
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 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