GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Herbaspirillum seropedicae SmR1

Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate HSERO_RS02535 HSERO_RS02535 short-chain dehydrogenase

Query= SwissProt::A9CES4
         (256 letters)



>FitnessBrowser__HerbieS:HSERO_RS02535
          Length = 249

 Score =  158 bits (399), Expect = 1e-43
 Identities = 96/257 (37%), Positives = 152/257 (59%), Gaps = 17/257 (6%)

Query: 1   MRLNNKVALITGAARGIGLGFAQA--FAAEGAKVIIADIDIARATTSAAAIGPAAKAVKL 58
           M L +KVA+ITG A   GLGF+ A   AA+GA+++I D++ A    +AA +G     +  
Sbjct: 1   MLLKDKVAIITGGAGQNGLGFSTARLMAAQGARIVILDLERAEPAGAAARLGAQHLGLVA 60

Query: 59  DVTDLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFMM 118
           DVTD A  +A   AV ++FG IDILVNNA +   A +  IT + Y+R+ D++L+G ++M 
Sbjct: 61  DVTDKAACEAAAAAVLKQFGRIDILVNNAGVTQPAKLLEITGKDYDRILDVSLRGTLYMS 120

Query: 119 KAVSNVMIARARGGKIINMASQAGRRGEALV--TLYCASKAAIISATQSAALALVKHGIN 176
           +AV   M A+ + G I+ ++S + +RG  ++    Y A+KA ++   ++ A      GI 
Sbjct: 121 QAVLPAMQAQ-QSGSIVCISSVSAQRGGGILGGPHYSAAKAGVLGLARAMAREFGPQGIR 179

Query: 177 VNAIAPGVVDGE-HWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLA 235
           VN I PG++  + + +++ A           EKKA +A+++P+GR   PDD+ G+ VFLA
Sbjct: 180 VNCITPGLISTDINKDILSA-----------EKKAEIAQTIPLGRLGGPDDVGGVCVFLA 228

Query: 236 SADSDYILAQTYNVDGG 252
           S  S Y    T +V+GG
Sbjct: 229 SDLSQYCTGVTLDVNGG 245


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: 135
Number of extensions: 7
Number of successful extensions: 3
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: 249
Length adjustment: 24
Effective length of query: 232
Effective length of database: 225
Effective search space:    52200
Effective search space used:    52200
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 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