GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudomonas fluorescens GW456-L13

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate PfGW456L13_3262 Short-chain dehydrogenase/reductase SDR

Query= SwissProt::O93868
         (262 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3262
          Length = 248

 Score =  107 bits (266), Expect = 3e-28
 Identities = 86/256 (33%), Positives = 127/256 (49%), Gaps = 14/256 (5%)

Query: 10  VNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRS-AKDAVEVTEKVGKEFGVKTKAYQC 68
           ++K I++TGG+RGIG A     AA G  + + Y++  + A  V E+V +  G +  A + 
Sbjct: 1   MDKVIVITGGSRGIGAATALLAAAQGYRICINYQADEQSAFGVLEQV-RALGAQAIAVRA 59

Query: 69  DVSNTDIVTKTIQQIDADLGAISGLIANAG-VSVVKPATELTHEDFKFVYDVNVFGVFNT 127
           DVS  D V     ++D++LG ++ L+ NAG V       E++      +   NV      
Sbjct: 60  DVSIEDEVIALFNRVDSELGRVTALVNNAGTVGQKSRVDEMSEFRILKIMKTNVLAPM-L 118

Query: 128 CRAVAKLWLQKQ---QKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLA 184
           C   A L +  +   Q GSIV  SS++S+      L      V Y +SK A      GL+
Sbjct: 119 CAKHAILRMSPRHGGQGGSIVNVSSVASR------LGSPNEYVDYAASKGALDTFTIGLS 172

Query: 185 AEWASAGIRVNALSPGYVNTDQTAHMDKKIR-DHQASNIPLNRFAQPEEMTGQAILLLSD 243
            E A  GIRVNA+ PGY+ TD  A      R     S IP+ R  +P+E+    + LLSD
Sbjct: 173 KEVAGEGIRVNAVRPGYIYTDFHALSGDPDRVSKLESAIPMARGGRPDEVAEAIVWLLSD 232

Query: 244 HATYMTGGEYFIDGGQ 259
            A+Y TG    + GG+
Sbjct: 233 KASYATGTFVDLGGGR 248


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: 148
Number of extensions: 11
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: 262
Length of database: 248
Length adjustment: 24
Effective length of query: 238
Effective length of database: 224
Effective search space:    53312
Effective search space used:    53312
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