GapMind for catabolism of small carbon sources

 

Aligments 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_4129 Oxidoreductase, short chain dehydrogenase/reductase family

Query= SwissProt::O93868
         (262 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4129
           Oxidoreductase, short chain dehydrogenase/reductase
           family
          Length = 248

 Score =  104 bits (260), Expect = 2e-27
 Identities = 82/260 (31%), Positives = 113/260 (43%), Gaps = 24/260 (9%)

Query: 6   TISFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKA 65
           T +   K  ++ GG+RGIG A  + +AA GA VA  Y S+    E  +      G K  A
Sbjct: 3   TQNLSGKVALIQGGSRGIGAAIVKRLAAEGATVAFTYVSSTAKAEELQDSITAKGGKALA 62

Query: 66  YQCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVF 125
            + D ++ D +   +       G +  L+ NAGV  V P  E   EDF     +NV  VF
Sbjct: 63  IKADSADADAIRSAVSATVEAFGRLDILVNNAGVLAVAPLAEFKLEDFDQTLAINVRSVF 122

Query: 126 NTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVF----YNSSKAACSNLVK 181
              +A A+   +               +IIN  S N           Y  SK+A   L K
Sbjct: 123 IATQAAARHMTE-------------GGRIINIGSTNADRMPFAGGGPYAMSKSALVGLTK 169

Query: 182 GLAAEWASAGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPL---NRFAQPEEMTGQAI 238
           GLA +    GI +N + PG V+TD    M+    D   S IPL    R+ + EE+     
Sbjct: 170 GLARDLGPQGITINNVQPGPVDTD----MNPAEGDFAESLIPLMAVGRYGKAEEIASFVA 225

Query: 239 LLLSDHATYMTGGEYFIDGG 258
            L+S  A Y+TG    IDGG
Sbjct: 226 YLVSPEAGYITGASLTIDGG 245


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: 5
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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