GapMind for catabolism of small carbon sources

 

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

Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate SM_b20130 SM_b20130 dehydrogenase

Query= metacyc::MONOMER-18072
         (282 letters)



>FitnessBrowser__Smeli:SM_b20130
          Length = 287

 Score =  120 bits (300), Expect = 4e-32
 Identities = 88/281 (31%), Positives = 137/281 (48%), Gaps = 4/281 (1%)

Query: 6   FTYVRVSSSEEATKFLES-HDDARPLAGGQSLIPMLKLRVISPNYIVDLNPITSL-SYVR 63
           F Y   +S  EA+  L     DA  +AGG  L+  +K  + S  ++V++  I +L  +  
Sbjct: 4   FEYYEPASLAEASDLLRRLGKDASIIAGGTDLLVEMKEELRSVLHLVNIKKIPNLRDFTY 63

Query: 64  SSFNSTKIGALTRYNEILKNDLVRVNVPLLHQAVRVVGDMQVRNLGTIGGSAANADPSAD 123
                 + GAL    EI  +  V  N P L +AV ++G +QVRN  TI G+   A PSAD
Sbjct: 64  DPAAGLRFGALVTVREIETSPHVIGNYPNLAKAVSLLGSVQVRNRATIVGNICRASPSAD 123

Query: 124 IPTVLTALNAEIILSSASGNRSVNALDFFKGAFATDLRKGEIISEIVL--PNLEGYRTIY 181
               L A  A + + +    R++   DFF G   T L  G+I++ I L  P     R   
Sbjct: 124 TIPPLIADGASLSVYNGGTERTILLEDFFTGPGRTVLSPGDIVTGISLPAPRPTSGRAYI 183

Query: 182 KKVVRRAGDFALVSLALAIKLRQNEIEDIRLAYGGVGERPFRALEVEKSVMGKRLNDELV 241
           K   R+A + A V +A++I+    +  DIR+A G V     RA   E  + G+R++  L+
Sbjct: 184 KHGRRKAMELATVGVAVSIEHVAGQCSDIRIALGAVAPTVIRARRTEDLIRGRRIDAALL 243

Query: 242 EEIVSKVSSQVNPPSDTRGSSWYRREVMKVITRKALKEVSG 282
            E       +  P  + R S+ YRR+++ V+TR+A+    G
Sbjct: 244 AEAAESAMQEATPIGNVRASAAYRRDMVGVLTRRAIGYAMG 284


Lambda     K      H
   0.317    0.134    0.367 

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: 178
Number of extensions: 6
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: 282
Length of database: 287
Length adjustment: 26
Effective length of query: 256
Effective length of database: 261
Effective search space:    66816
Effective search space used:    66816
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