GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas fluorescens FW300-N2E3

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate AO353_24520 AO353_24520 short-chain dehydrogenase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24520
          Length = 249

 Score =  119 bits (298), Expect = 6e-32
 Identities = 84/254 (33%), Positives = 137/254 (53%), Gaps = 17/254 (6%)

Query: 12  GLRVLISGAAA--GIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGV-ADVSD 68
           G   +I+GAA+  GIG A A  F   GA V I D+D +A   A  +  + H G+ A+V+D
Sbjct: 5   GKVAIITGAASARGIGRATATTFAQQGARVVILDLDESAARDAAASLGEGHLGIGANVAD 64

Query: 69  CAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKA 128
             QV + +       G +D+LINNAGI  P   + D+ P+++++ +  +L       +  
Sbjct: 65  ELQVRQAVAKIIEHFGRIDILINNAGITQPLKTL-DIRPSDYDKVLDVSLRGTLLMSQAV 123

Query: 129 VPLLKETSANPGIIAMASV-AGRLGYAFRTP-YAASKWAIVGMVKSLAIELGPNNVRVNA 186
           +P +++ S+   I+ M+SV A R G  F  P Y+A+K  ++G+ K++A ELGP+ VRVN+
Sbjct: 124 IPTMRQQSSG-SIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLAKAMARELGPDKVRVNS 182

Query: 187 ILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAG 246
           I PG++  +             G+  D+ +   +  I L R+    DVA  ALFLAS   
Sbjct: 183 IAPGLIHTDITG----------GLMQDERRHAIIDGIPLGRLGEAQDVANAALFLASDLS 232

Query: 247 QNISGQAISVDGNV 260
             ++G  + V+G +
Sbjct: 233 SYLTGITLDVNGGM 246


Lambda     K      H
   0.320    0.136    0.391 

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: 139
Number of extensions: 6
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: 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 (21.8 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