GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sinorhizobium meliloti 1021

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase

Query= SwissProt::P94549
         (258 letters)



>FitnessBrowser__Smeli:SMc01669
          Length = 263

 Score =  173 bits (439), Expect = 3e-48
 Identities = 101/261 (38%), Positives = 157/261 (60%), Gaps = 6/261 (2%)

Query: 2   NAISLAVDQFVAVLTIHNPPA-NALSSRILEELSSCLDQCETDAGVRSIIIHGEG-RFFS 59
           + + + +   +A+LT++ P   NAL+  +++ L + LD+ E D  V+++I+ G G R FS
Sbjct: 3   DTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFS 62

Query: 60  AGADIKEFTS--LKG-NEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMAC 116
           AG DI EF+    KG N  +     RGQQL  R+E+FPKP+IAA++G A GGG E+  A 
Sbjct: 63  AGGDIHEFSGSVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEAV 122

Query: 117 HIRIAAEDAKLGLPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLV 176
           H+ IA+E A+   PE+ L + P F GTQRLPR  G  +ALEL+ +G+  S + ALD+GLV
Sbjct: 123 HLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGLV 182

Query: 177 SIGAKDEAEVIEKAKALAAKFAEKSPQTLASLLELLYSNKVYSYEGSLKLEAKRFGEAFE 236
           +     E ++I  A+ALA +    SP   A+++  +      +    L  E+++F     
Sbjct: 183 NAVVPHE-QLIASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFARMVP 241

Query: 237 SEDAKEGIQAFLEKRKPQFKG 257
           S D KEG+ A+ E+R+P++ G
Sbjct: 242 SHDLKEGLAAWKERREPRYAG 262


Lambda     K      H
   0.315    0.134    0.366 

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: 140
Number of extensions: 6
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: 258
Length of database: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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: 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