GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Pseudomonas fluorescens FW300-N2E2

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate Pf6N2E2_3703 Oxidoreductase, short chain dehydrogenase/reductase family

Query= uniprot:A0A4R8NY47
         (263 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3703
          Length = 249

 Score =  111 bits (277), Expect = 2e-29
 Identities = 84/237 (35%), Positives = 123/237 (51%), Gaps = 12/237 (5%)

Query: 15  RSLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDA-AVAPRFF 73
           + L  +R VITG GSGIGAA+  A+  QGA+   L +A   +E L A+  D  A+A    
Sbjct: 2   QQLFNRRAVITGAGSGIGAAIARAYAEQGAR---LVLADRDAERLTATANDCRALAVEVH 58

Query: 74  PC--NLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQ 131
            C  ++  LE  +A         GG+DIL+NNA    + +  +++   W++ L V+L   
Sbjct: 59  ECVADVGTLEGAQAGVDACVEHFGGIDILVNNAGMLTQARCTELSIEMWNDMLRVDLTSV 118

Query: 132 FFCAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGV 191
           F  +Q  LP M  ++ G I+N  S     G  +L+ Y  AKAG+ G T  +A +   D V
Sbjct: 119 FIASQRALPHMLAQRWGRIINIASQLGIKGGAELSHYAAAKAGVIGFTKSLALEVAADNV 178

Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVD--PHDVAALALFLSSDSG 246
            VNAI PG I TP   L+    E   +  +A+ LP+R      +VA  A+ L+SD G
Sbjct: 179 LVNAIAPGPIETP---LVAGISESWKQAKSAE-LPLRRFGLATEVAPTAVLLASDPG 231


Lambda     K      H
   0.322    0.137    0.417 

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: 185
Number of extensions: 6
Number of successful extensions: 1
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: 263
Length of database: 249
Length adjustment: 24
Effective length of query: 239
Effective length of database: 225
Effective search space:    53775
Effective search space used:    53775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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