GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Sinorhizobium meliloti 1021

Align glutathione transferase (EC 2.5.1.18); maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate SM_b20005 SM_b20005 glutathione S-transferase

Query= BRENDA::O43708
         (216 letters)



>FitnessBrowser__Smeli:SM_b20005
          Length = 203

 Score = 68.6 bits (166), Expect = 8e-17
 Identities = 63/196 (32%), Positives = 91/196 (46%), Gaps = 11/196 (5%)

Query: 8   LYSYFRSSCSWRVRIALALKGIDYKTVPINLIKDRGQQFSKDFQALNPMKQVPTLKIDGI 67
           LY +  S  + R R+ L+L GI+++ V ++  +   +Q   DF  LN   QVP L   G 
Sbjct: 3   LYHHPLSGHAHRARLFLSLLGIEHELVVVDFARREHKQ--ADFLKLNSFGQVPVLDDAGT 60

Query: 68  TIHQSLAIIEYLEEMRPTPRLLPQDPKKRASVRMISDLIAGGIQ--PLQN--LSVLKQVG 123
            I  S AI+ YL +    P  LP+D    A+V+    + AG I   P Q   ++V K   
Sbjct: 61  IISDSNAILVYLAKKTGRPDWLPEDAVGAAAVQRWLSVAAGQIAHGPAQARLINVFKAPY 120

Query: 124 EEMQLTWAQNAITCGFNALEQILQSTAGIYCVGDEVTMADLCLVPQVANAERFKVDLTPY 183
              ++    +AI      +EQ L+    I    D  T+AD+ L   VA A    VDL PY
Sbjct: 121 RPEEVIPRSHAILA---LIEQELEGRGWI--AADRPTIADVALYSYVARAPEGDVDLQPY 175

Query: 184 PTISSINKRLLVLEAF 199
           P I +   R+  L  F
Sbjct: 176 PEIRAWLARIEALPGF 191


Lambda     K      H
   0.321    0.136    0.400 

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: 89
Number of extensions: 5
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: 216
Length of database: 203
Length adjustment: 21
Effective length of query: 195
Effective length of database: 182
Effective search space:    35490
Effective search space used:    35490
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: 45 (21.9 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