GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Dechlorosoma suillum PS

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate Dsui_3259 Dsui_3259 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein

Query= SwissProt::O93868
         (262 letters)



>FitnessBrowser__PS:Dsui_3259
          Length = 256

 Score =  115 bits (289), Expect = 7e-31
 Identities = 85/261 (32%), Positives = 131/261 (50%), Gaps = 16/261 (6%)

Query: 10  VNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAV-----EVTEKVGKEFG---V 61
           ++KT+++TGG+RGIG A  R  A AG  V   YR    A      EVT +  ++ G    
Sbjct: 1   MHKTLLITGGSRGIGAATVRLAARAGYAVCFSYRQDAAAAQQLVAEVTRESSRDSGREGA 60

Query: 62  KTKAYQCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATE-LTHEDFKFVYDVN 120
              A+Q D+S  + +       +   G I+ L+ NAG+  ++   E +  +  + ++  N
Sbjct: 61  PILAFQADISREEEIRALFAAAEQRFGPITALVNNAGILELQTRVEDMDGDRLQRIFATN 120

Query: 121 VFGVFNTCR-AVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNL 179
           V G F  CR AV +L  +    G  +V  S  +     + L  +   V Y +SKAA   L
Sbjct: 121 VIGTFLCCREAVRRLSTRHGGHGGAIVNLSSRA-----ARLGAAGEYVDYAASKAAIDTL 175

Query: 180 VKGLAAEWASAGIRVNALSPGYVNTDQTAHMDKKIR-DHQASNIPLNRFAQPEEMTGQAI 238
             GLA E A+ GIRVNA++PG ++TD  A   +  R +   + IP+ R   PEE+    +
Sbjct: 176 TLGLAREVAAEGIRVNAVAPGLIDTDIHASGGEPGRVERLRTGIPMQRGGTPEEVAKAIL 235

Query: 239 LLLSDHATYMTGGEYFIDGGQ 259
            LLS+ A+Y TG    + GG+
Sbjct: 236 WLLSEDASYTTGAILDVAGGR 256


Lambda     K      H
   0.317    0.130    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: 151
Number of extensions: 9
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: 262
Length of database: 256
Length adjustment: 24
Effective length of query: 238
Effective length of database: 232
Effective search space:    55216
Effective search space used:    55216
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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