GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fumD in Methanospirillum lacunae Ki8-1

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_109968318.1 DK846_RS07605 fumarate hydratase

Query= BRENDA::Q141Z6
         (520 letters)



>NCBI__GCF_003173355.1:WP_109968318.1
          Length = 279

 Score =  151 bits (382), Expect = 3e-41
 Identities = 102/275 (37%), Positives = 150/275 (54%), Gaps = 25/275 (9%)

Query: 27  ADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEGKRPICQDTGIVT 86
           A++++      P D ++ +  A E E SP A+  +  IL N R+  E + PICQDTGI  
Sbjct: 18  ANAIRIAEITLPPDVLERIVAASEDETSPVARRELMHILENIRLADERQAPICQDTGIPV 77

Query: 87  VFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEGGRKNTKDNTPA-- 144
           +++ +   + +      + D + +GVR   +     LR ++V P    R NT  NT A  
Sbjct: 78  IYLTLPPQIPFSSE---IVDAVRKGVREATVTIP--LRPNLVDPIT--RHNTGTNTSADM 130

Query: 145 -VIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPS--DSIVDWILKTVPTMGAGWCPPG 201
             +H  I+PG+ + V V  KG GSEN S+  M  P+  D I ++I++T    G   CPP 
Sbjct: 131 PAVH--ILPGDRMQVTVLPKGAGSENVSRLKMFTPTEKDRIPEFIVETALLAGGRPCPPI 188

Query: 202 MLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNALGIGAQGL 261
           +LG+GIGGT + A  +AKE+L++P+D        P++      +E+ +KVN LGIG  GL
Sbjct: 189 ILGVGIGGTFDGAASLAKEALLEPLDQMT-----PEE------MEICQKVNDLGIGPMGL 237

Query: 262 GGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHA 296
           GG  T L VKI +A  H AS PVA+   C A R A
Sbjct: 238 GGKTTCLGVKIKSAGCHTASLPVAVNIQCWAARRA 272


Lambda     K      H
   0.316    0.133    0.392 

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: 355
Number of extensions: 24
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: 520
Length of database: 279
Length adjustment: 30
Effective length of query: 490
Effective length of database: 249
Effective search space:   122010
Effective search space used:   122010
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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