GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Pseudomonas fluorescens FW300-N1B4

Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate Pf1N1B4_5813 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)

Query= SwissProt::P75682
         (302 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813
          Length = 291

 Score =  117 bits (292), Expect = 4e-31
 Identities = 96/299 (32%), Positives = 149/299 (49%), Gaps = 20/299 (6%)

Query: 7   FTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIAR 66
           F GI  P+ T F  DG +D  G   L+  L++ GVDG+   G+ GE + LG  E+ A+  
Sbjct: 4   FQGIWVPIVTPFH-DGAIDFAGLRRLVSHLLEKGVDGIVVCGTTGEAAALGKHEQLAV-- 60

Query: 67  FAIDHVDRRVP---VLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRY 123
             +D V   VP   V++G  G N  E ++      +    G++V  PYY + S+A L  +
Sbjct: 61  --LDAVLELVPPERVVMGLAGNNLAELLQFQSEILKRPLAGLLVPPPYYIRPSQAGLEAF 118

Query: 124 FEQVADSVTLPVMLYNFPALTGQDLTPA-LVKTLADSRSNIIGIKDTIDSVAHLRSMIHT 182
           F+ VAD+ ++PV+LY+ P  TG     A L++ +A  R  I+ IKD   + A   +++ +
Sbjct: 119 FKTVADASSVPVILYDIPYRTGIAFEQATLLRIVAHER--IVAIKDCGGNPATTLALLSS 176

Query: 183 VKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKA-AGY 241
            K       VLCG D  +F  L LG  GAI+AS +  P++ V L +  RD  +A   A +
Sbjct: 177 GK-----VDVLCGEDHQIFGALCLGATGAIAASAHVHPELFVALYQQIRDNQLAVGRATF 231

Query: 242 HQTLLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLK 300
            Q L  I  ++    P    +K A+ L G  +   +  P     E    +LK +L  L+
Sbjct: 232 FQLLPLIHSLFIEPNP--APVKTALALEGL-IRDELRSPMQRSSETTAVRLKEVLAVLE 287


Lambda     K      H
   0.320    0.138    0.407 

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: 194
Number of extensions: 12
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: 302
Length of database: 291
Length adjustment: 26
Effective length of query: 276
Effective length of database: 265
Effective search space:    73140
Effective search space used:    73140
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: 48 (23.1 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