GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Amantichitinum ursilacus IGB-41

Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate WP_053936590.1 WG78_RS04575 3-oxoacyl-ACP reductase FabG

Query= SwissProt::A9CES4
         (256 letters)



>NCBI__GCF_001294205.1:WP_053936590.1
          Length = 246

 Score =  149 bits (377), Expect = 4e-41
 Identities = 96/255 (37%), Positives = 140/255 (54%), Gaps = 15/255 (5%)

Query: 1   MRLNNKVALITGAARGIGLGFAQAFAAEGAKVIIADIDIA---RATTSAAAIGPAAKAVK 57
           M+L NKVA+ITGAA GIG   A+ F  EGA+V++ D++ A      +   A G  A   +
Sbjct: 1   MKLKNKVAIITGAASGIGHATARKFVTEGARVVVCDVNRAGVDAVVSELIAQGGQALGFE 60

Query: 58  LDVTDLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFM 117
           +DVT+ AQI A+V    ++FG IDILVNNA I   A ++ +TE+ ++RV DINLKG    
Sbjct: 61  VDVTNKAQIAAMVAGTQQQFGRIDILVNNAGIVADAQLSKMTEDQFDRVIDINLKGVYNC 120

Query: 118 MKAVSNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHGINV 177
            +AV ++MI + + G I+N +S  G  G    T Y A+K  +I   ++ A  L K GI  
Sbjct: 121 TRAVVDIMIEQ-QSGVILNASSVVGLYGNFGQTNYAAAKFGVIGMVKTWARELGKKGIRA 179

Query: 178 NAIAPGVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLASA 237
           NA+ PG V     + +           P +    + + VP+ R A P++I  +  FLAS 
Sbjct: 180 NAVCPGFVATPILKDM-----------PDKVIQGMEERVPLRRMAQPEEIANVYAFLASD 228

Query: 238 DSDYILAQTYNVDGG 252
           ++ YI      V GG
Sbjct: 229 EASYISGAAIEVTGG 243


Lambda     K      H
   0.319    0.133    0.376 

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: 148
Number of extensions: 10
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: 256
Length of database: 246
Length adjustment: 24
Effective length of query: 232
Effective length of database: 222
Effective search space:    51504
Effective search space used:    51504
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 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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