GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Sinorhizobium meliloti 1021

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate SMc01153 SMc01153 enoyl-CoA hydratase

Query= BRENDA::Q1D5Y4
         (258 letters)



>FitnessBrowser__Smeli:SMc01153
          Length = 257

 Score =  161 bits (408), Expect = 1e-44
 Identities = 95/253 (37%), Positives = 143/253 (56%), Gaps = 3/253 (1%)

Query: 6   VDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65
           V+ +G + + T++     NA++  +++EL   +    + R V A+V+ G+ +KAF AGAD
Sbjct: 8   VETQGRVGLITLNRPQALNALNAVLMRELDAALKAFDADRAVGAIVLAGS-EKAFAAGAD 66

Query: 66  LKERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPA 125
           +KE   +  D V  +L      +  +  +    IAA++G ALGGG ELA+ CD  +A+  
Sbjct: 67  IKEMQGL--DFVDGYLADFLGGWEHVANARKPMIAAVSGFALGGGCELAMMCDFIIASET 124

Query: 126 AELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGH 185
           A+ G  E+ LG+IPG GG+QRL R VG  +A DLILT R ++AAEA   GL +R+     
Sbjct: 125 AKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLILTGRMMDAAEAERSGLVSRVVAPDR 184

Query: 186 LLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLR 245
           LL  A G AE +   +  A   AK A++    L L + L  E R ++ +  TED+ EG+ 
Sbjct: 185 LLEEALGAAEKIASFSLPAAMMAKEAVNRSLELTLAEGLRFERRLFQSLFATEDQKEGMA 244

Query: 246 AFAEKRAPVYKGR 258
           AF  KR   +K R
Sbjct: 245 AFVAKRKAEFKHR 257


Lambda     K      H
   0.319    0.136    0.380 

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: 135
Number of extensions: 5
Number of successful extensions: 3
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: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
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 (21.7 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