GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudomonas simiae WCS417

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate GFF2363 PS417_12050 short-chain dehydrogenase

Query= SwissProt::O93868
         (262 letters)



>FitnessBrowser__WCS417:GFF2363
          Length = 251

 Score =  100 bits (250), Expect = 2e-26
 Identities = 85/253 (33%), Positives = 121/253 (47%), Gaps = 25/253 (9%)

Query: 15  IVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGK-EFGVKTKAYQCDVSNT 73
           ++TGG  GIGLA    +   GA VA++ R     VEV   +G    G+       D+   
Sbjct: 17  VITGGAAGIGLACASLLVERGARVALLDRDPA-VVEVAAGLGAGHLGIAV-----DLGQI 70

Query: 74  DIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAVAK 133
             +  TI  + A    +  LI +AGV ++  A +++   +    D+N+   F   +A A+
Sbjct: 71  GQIQHTIDTVFAHFQRLDYLINSAGVVLLDKAVDVSESAWDTTLDINLKASFFVAQACAR 130

Query: 134 LWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASAGIR 193
             L  Q  G IV        + +Q+++ G    V Y +SKAA   + K LA EWA   I 
Sbjct: 131 HMLA-QGSGRIV-------NLASQAAVIGLDRHVAYCASKAAIVGMTKVLAMEWAPQ-IN 181

Query: 194 VNALSPGYVNTDQTAHMDKK-----IRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYM 248
           VNA+SP  V T     + KK     + +     IP  RFAQPEE+ G A+ LLSD A  +
Sbjct: 182 VNAISPTIVETA----LGKKAWAGEVGEKAKLQIPAGRFAQPEEIAGLALYLLSDAAQMI 237

Query: 249 TGGEYFIDGGQLI 261
           TG    IDGG  I
Sbjct: 238 TGANMVIDGGYSI 250


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: 133
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: 251
Length adjustment: 24
Effective length of query: 238
Effective length of database: 227
Effective search space:    54026
Effective search space used:    54026
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.

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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