GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudomonas putida KT2440

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate PP_1951 PP_1951 Oxidoreductase, short chain dehydrogenase/reductase family

Query= SwissProt::O93868
         (262 letters)



>FitnessBrowser__Putida:PP_1951
          Length = 275

 Score =  116 bits (291), Expect = 4e-31
 Identities = 82/263 (31%), Positives = 143/263 (54%), Gaps = 27/263 (10%)

Query: 14  IIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVSNT 73
           +IVTG   G+GLAFT A+A +GA VA++  + ++A++   +  +  G   +++  DV++ 
Sbjct: 14  VIVTGAASGLGLAFTEAMAESGAQVAMLDLN-REALDAQFRRLRSLGYSVRSHVLDVTDR 72

Query: 74  DIVTKTIQQIDADLGAISGLIANAGVSVV------------KPAT---ELTHEDFKFVYD 118
           D V  T   + A  G +  + ANAG+               +PA    E +   ++ V  
Sbjct: 73  DAVDDTFNAVAAGFGGLDIVFANAGIDPGPGFAALNAAGEREPANMLEEYSDHRWRKVIS 132

Query: 119 VNVFGVFNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQ-VFYNSSKAACS 177
           V++  VF + RA A+  ++  + GSI+VT+S+S+       L  ++T    Y ++KA  +
Sbjct: 133 VSLDAVFYSIRAAAR-HMRANRSGSIIVTTSVSA-------LRPAVTLGAAYAAAKAGAA 184

Query: 178 NLVKGLAAEWASAGIRVNALSPGYVNTDQTAHM--DKKIRDHQASNIPLNRFAQPEEMTG 235
            LV+  A E AS G+RVNA++PG   TD       + ++R   A+ +P+ R A+ EE+  
Sbjct: 185 QLVRATALELASDGVRVNAIAPGPFETDIGGGFMHNSEVRAKMAAGVPMGRIAEVEEIKP 244

Query: 236 QAILLLSDHATYMTGGEYFIDGG 258
            A+ L S  ++++TG ++ IDGG
Sbjct: 245 LALYLASKASSFVTGQQFVIDGG 267


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: 136
Number of extensions: 7
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: 275
Length adjustment: 25
Effective length of query: 237
Effective length of database: 250
Effective search space:    59250
Effective search space used:    59250
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