GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA2 in Echinicola vietnamensis KMM 6221, DSM 17526

Align acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate Echvi_0275 Echvi_0275 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= metacyc::MONOMER-13596
         (167 letters)



>FitnessBrowser__Cola:Echvi_0275
          Length = 164

 Score = 63.5 bits (153), Expect = 2e-15
 Identities = 42/131 (32%), Positives = 64/131 (48%), Gaps = 16/131 (12%)

Query: 34  FEIEYLGKGTRENEYLFKVNGKVHRAFIDNGYILLDNASVFRLERLTELPSKEGESIEEM 93
           + +E +     + E   K+N K     I + + LL       LE+L          +   
Sbjct: 48  YVVELVKLDAAKKELTLKINNKSAEVKIQDKFDLL-------LEKL---------GMNGQ 91

Query: 94  IKGKEGEVISPLQGRIVTIRVNEGDAVNKGQPLLSVEAMKSETIISAPIAGIVEKIIVKP 153
              K   + +P+ G I+ I V EGD V K QP++ +EAMK E II +P  GIV+KI+V  
Sbjct: 92  ANAKLTSITAPMPGLILEINVQEGDTVEKDQPMVILEAMKMENIIKSPGDGIVKKILVTT 151

Query: 154 GQGVKKGDTLL 164
           G+ V+K   L+
Sbjct: 152 GESVEKKQILI 162



 Score = 28.1 bits (61), Expect = 8e-05
 Identities = 21/89 (23%), Positives = 46/89 (51%), Gaps = 13/89 (14%)

Query: 92  EMIKGKEGEVISPLQ----GRIVTIRVNEGDAVNKGQPLLSV---------EAMKSETII 138
           ++IKG++  V+  ++     + +T+++N   A  K Q    +         +A    T I
Sbjct: 40  QIIKGQKSYVVELVKLDAAKKELTLKINNKSAEVKIQDKFDLLLEKLGMNGQANAKLTSI 99

Query: 139 SAPIAGIVEKIIVKPGQGVKKGDTLLIIK 167
           +AP+ G++ +I V+ G  V+K   ++I++
Sbjct: 100 TAPMPGLILEINVQEGDTVEKDQPMVILE 128


Lambda     K      H
   0.313    0.136    0.368 

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: 100
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 167
Length of database: 164
Length adjustment: 18
Effective length of query: 149
Effective length of database: 146
Effective search space:    21754
Effective search space used:    21754
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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