GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Mesorhizobium ciceri WSM1271

Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate YP_004144074.1 Mesci_4919 propanoyl-CoA C-acyltransferase

Query= BRENDA::I3RA72
         (383 letters)



>NCBI__GCF_000185905.1:YP_004144074.1
          Length = 388

 Score =  181 bits (459), Expect = 3e-50
 Identities = 126/382 (32%), Positives = 200/382 (52%), Gaps = 21/382 (5%)

Query: 1   MEVAVIGSSMTKFGQ-RSAWIRELLSEAGQACLEDAGVAPASVDHLYVSNMASGEFEGQ- 58
           M   ++G + ++FG+     +  L+ +     L+ AG+ P  VD + + +  +G F  Q 
Sbjct: 1   MTACIVGWTHSRFGKLEGETLENLIVKVATDALDHAGIGPDEVDEIVLGHFNAG-FSAQD 59

Query: 59  -TGVMNALAHD-LGVIPAYTQRIDQTSSSGGAGIYEAWQSIASGVSEMTLLVGGEKMTHK 116
            T  +   A D L   PA   R++   ++G A + +  ++I +  + + L+VG E+MT  
Sbjct: 60  FTASLVLQADDRLRFKPA--TRVENACATGSAAVRQGIRAIDANAARIVLVVGAEQMTTT 117

Query: 117 TTGE-STDIIASCTHPEEYKHGVTLPSFAGM---TARNYLERFDAPRESLARVAVKNHRN 172
              E   +++ +   PE+   G T   FAG+    A+ Y +R+    ++LA +A KNH+N
Sbjct: 118 PGPEIGKNLLKASYLPED---GETPAGFAGVFGKIAQAYFQRYGDQSDALAMIAAKNHKN 174

Query: 173 GVDNPKAQFQKEIDIETALE----SPIIADPLRLYDFCPITDGSAAMMFTTEERAQEITD 228
           GVDNP AQ +K+   E   +    +P +A PL+  D   ++DG+AA++    + A  +  
Sbjct: 175 GVDNPYAQMRKDFGYEFCRQESEKNPFVAGPLKRTDCSLVSDGAAALILA--DTATALKM 232

Query: 229 EYAIVSGVGGATDTHVVHERDDPTVMGGVVESSKQAYEMAGVGPDDLDVAELHDMFTILE 288
             A+           +   + D     G  ++  +A + AGV  DDL   E HD FTI E
Sbjct: 233 RRAVAFRANEHVQDFLPMSKRDILTFEGCEQAWNRALKSAGVTLDDLSFVETHDCFTIAE 292

Query: 289 FLQLEGIGVADHGAAWELAMDGVTAKDGGLPINTSGGLKSKGHPLGASGVAQGVEIYEQL 348
            ++ E +G+A  G   +LA+DG TAKDG LP+N SGGLK+KGHP+GA+GV+  V    QL
Sbjct: 293 LIEYEAMGLAKPGEGAKLALDGTTAKDGRLPVNPSGGLKAKGHPIGATGVSMHVLTAMQL 352

Query: 349 VGEAGPRQVE-ADTALACNVGG 369
           VGEA   QV  A      N+GG
Sbjct: 353 VGEASGIQVPGAKLGGIFNMGG 374


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: 404
Number of extensions: 25
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: 383
Length of database: 388
Length adjustment: 30
Effective length of query: 353
Effective length of database: 358
Effective search space:   126374
Effective search space used:   126374
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