GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Pseudomonas fluorescens FW300-N2E3

Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate AO353_14875 AO353_14875 4-hydroxy-tetrahydrodipicolinate synthase

Query= curated2:A4YNH1
         (314 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_14875
          Length = 305

 Score =  112 bits (280), Expect = 1e-29
 Identities = 86/292 (29%), Positives = 137/292 (46%), Gaps = 11/292 (3%)

Query: 15  SGLLSFPVTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKV 74
           SG+     T F  D+S D       +  L    V+GL   G  GE  SL+  E   +V+V
Sbjct: 8   SGVFPAVTTQFNPDFSIDYEGTHKVISGLVRDGVSGLVICGTVGENTSLSTEEKISLVEV 67

Query: 75  AVDETKGRVPVLAGTG-YGTAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAV 133
           A D   GRVPV++G   + +A A ++A   ++ GADG++L+P  +  ++    AAH  +V
Sbjct: 68  AKDAAAGRVPVISGVAEFTSANASKVAKEIQRVGADGIMLMPALVYSSKPFETAAHFRSV 127

Query: 134 CKSVKIGVIVYNRDNAI---LQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKMGDRL 190
             S+ + V+VYN        + PD L  L + C N+V +KD  GD      V  ++GDR 
Sbjct: 128 AASIDLPVMVYNNPPIYRNDVTPDILISLAD-CDNVVCFKDSSGDTRRFIDVRNEVGDRF 186

Query: 191 TYIGGLPTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIHAGLKDFIL 250
               GL   +   L  + +G   + S + N  P+     +   R          + ++ +
Sbjct: 187 VLFAGL---DDVVLESIAVGAVGWVSGMSNAFPKEGETLFRLARDGRFKEA-MPIYEWFM 242

Query: 251 PLIAIRNRKKGYAVSIIKAGMKVIGRDSGPVRLPLTDLTEAEMAELTALVKA 302
           PL+ +  R     V  IK   +++GR +   R P   L + E +E+ ALVKA
Sbjct: 243 PLLHLDARPD--LVQCIKLCEELMGRGTALTRPPRLGLLDHERSEVEALVKA 292


Lambda     K      H
   0.320    0.136    0.392 

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: 220
Number of extensions: 12
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: 314
Length of database: 305
Length adjustment: 27
Effective length of query: 287
Effective length of database: 278
Effective search space:    79786
Effective search space used:    79786
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.

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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