GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-med in Sinorhizobium meliloti 1021

Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate SM_b21011 SM_b21011 xanthine dehydrogenase

Query= SwissProt::Q4J6M6
         (281 letters)



>FitnessBrowser__Smeli:SM_b21011
          Length = 495

 Score =  118 bits (296), Expect = 2e-31
 Identities = 81/241 (33%), Positives = 119/241 (49%), Gaps = 6/241 (2%)

Query: 41  KLRVLSPDYILDINRLNELNYVKTSLNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTI 100
           ++R L+P  ++ IN + EL  +++S  G++IGA   Y    +++ + S  P        I
Sbjct: 244 QMRSLNP--VVFINGIAELQRIESSTAGLTIGAGVSY--TAAHEALSSAYPSFGRLLDRI 299

Query: 101 GDMQVRNMGTIGGAISNADPASDMPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDT 160
           G  QVRNMGTIGG I+N  P  D P  L  L AT+ L S  G R++   DFF      D 
Sbjct: 300 GGDQVRNMGTIGGNIANGSPIGDSPPPLIVLGATVTLRSKDGQRTLPLEDFFIAYGKQDR 359

Query: 161 NKGELVTQIEVPVL--DGYKTVYKKVVRRAGDYALASVALAIKLKGNEIEDIKLAYGGVH 218
             GE V  + VP L  D     YK   RR  D +    A  I L G+ ++  ++A+GG+ 
Sbjct: 360 RPGEFVESLFVPALPADERFAAYKISKRRDEDISALLGAFRISLDGDRVKTARIAFGGMA 419

Query: 219 DKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINPPSDHRGSSWYRREVVKVLTMKAFK 278
             P RA  VE  +IG+   ++ V+   +   +   P +D R +  YR    K L M+ F 
Sbjct: 420 ATPKRAKTVEAALIGQAWTEETVRTAQAAFETDYQPITDWRATGAYRMLAAKNLLMRFFL 479

Query: 279 E 279
           E
Sbjct: 480 E 480


Lambda     K      H
   0.316    0.134    0.372 

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: 252
Number of extensions: 12
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: 281
Length of database: 495
Length adjustment: 30
Effective length of query: 251
Effective length of database: 465
Effective search space:   116715
Effective search space used:   116715
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: 49 (23.5 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