GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sinorhizobium meliloti 1021

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Smeli:SMc01669
          Length = 263

 Score =  181 bits (459), Expect = 1e-50
 Identities = 103/256 (40%), Positives = 149/256 (58%), Gaps = 6/256 (2%)

Query: 4   NNVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFV 63
           + V++E    +A++T+NRP+ LNALN + +  +  ++  IE D  V AVILTGAG+++F 
Sbjct: 3   DTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFS 62

Query: 64  AGADISEM-----KEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMS 118
           AG DI E      K +N    R F   G ++  RLE   KPVIAAVNG A GGGCE+  +
Sbjct: 63  AGGDIHEFSGSVAKGVNAAT-RDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEA 121

Query: 119 CDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGL 178
             + IAS  ARF +PE+ L + P FGGTQRL RL G   A +L+ T        AL +GL
Sbjct: 122 VHLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGL 181

Query: 179 VNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFS 238
           VN VV   +L+ +A+ +A + + ++P+A      A+ RG+   I   L  ESE F     
Sbjct: 182 VNAVVPHEQLIASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFARMVP 241

Query: 239 TEDQKDAMTAFIEKRK 254
           + D K+ + A+ E+R+
Sbjct: 242 SHDLKEGLAAWKERRE 257


Lambda     K      H
   0.317    0.134    0.365 

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: 161
Number of extensions: 4
Number of successful extensions: 2
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: 261
Length of database: 263
Length adjustment: 25
Effective length of query: 236
Effective length of database: 238
Effective search space:    56168
Effective search space used:    56168
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: 41 (21.6 bits)
S2: 47 (22.7 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