GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Sinorhizobium meliloti 1021

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__Smeli:SMc01669
          Length = 263

 Score =  109 bits (272), Expect = 7e-29
 Identities = 81/258 (31%), Positives = 130/258 (50%), Gaps = 12/258 (4%)

Query: 4   NTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFC 62
           +T+L E    +A +TLN P   N L   ++  +   L  ++ D T+Q ++   AGD+AF 
Sbjct: 3   DTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFS 62

Query: 63  DGVD-------VADHVPEKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFC 115
            G D       VA  V     + +     +   + A     +  VNG + GGGCE+    
Sbjct: 63  AGGDIHEFSGSVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEAV 122

Query: 116 DIVIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLV 174
            + IASE+A+  +PEI LA+ P        P++ G K+A+EL+LTG   S + A  +GLV
Sbjct: 123 HLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGLV 182

Query: 175 NVVLPVEGFREAAQKFMADFTSKSRPVAMWA-RRAIMAGLNLDFLQALKASEIIYMQGCM 233
           N V+P E    A+ + +A  T +  P+A  A   A+  GLN+   + L      + +  +
Sbjct: 183 NAVVPHEQL-IASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFAR-MV 240

Query: 234 ATEDANEGLASFLEKRKP 251
            + D  EGLA++ E+R+P
Sbjct: 241 PSHDLKEGLAAWKERREP 258


Lambda     K      H
   0.322    0.136    0.401 

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: 138
Number of extensions: 11
Number of successful extensions: 4
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: 256
Length of database: 263
Length adjustment: 24
Effective length of query: 232
Effective length of database: 239
Effective search space:    55448
Effective search space used:    55448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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