GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1276 Echvi_1276 Dihydrodipicolinate synthase/N-acetylneuraminate lyase

Query= SwissProt::P75682
         (302 letters)



>FitnessBrowser__Cola:Echvi_1276
          Length = 308

 Score =  158 bits (399), Expect = 2e-43
 Identities = 100/298 (33%), Positives = 162/298 (54%), Gaps = 10/298 (3%)

Query: 7   FTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIAR 66
           F GI+PP+ T    + QLD PG   LI+ +I  GV GLF LG+ GE + L  + R  + +
Sbjct: 11  FRGIVPPMITPLADENQLDIPGLERLINHIIAGGVHGLFILGTTGESTSLSYDIRHELVK 70

Query: 67  FAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQ 126
                V+ RVPVL+G   T A E++ L+  A + GA  +V   PYY+ + +  LI Y+E 
Sbjct: 71  RTCAIVNGRVPVLVGITDTAATESLRLADTAAKEGAAAVVAAPPYYFSLGQPELIEYYEY 130

Query: 127 VADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGA 186
           + + ++LP+ LYN P+ T   + P  VKTL+    NI+G+KD+  + A+   ++  +K  
Sbjct: 131 LVERLSLPLFLYNMPSHTKIVIEPDTVKTLS-QYDNIVGLKDSSANNAYFNKVMAKMKD- 188

Query: 187 HPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLL 246
              F++  G ++ +  T+LLG  G ++   N  P++ V L  A   GD+      H  ++
Sbjct: 189 RQDFSLFVGPEEIMAETVLLGAHGGVNGGANMFPELYVKLYAAAESGDLETVKRLHAIVM 248

Query: 247 QI-PQMY---QLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLK 300
           QI  +MY   Q  + ++  IK A+ L G  + +  +  ASPL   R+ + + L +QLK
Sbjct: 249 QISTKMYSLGQFGSSYLKGIKGALSLLG--ICSDYM--ASPLHRFREKEREILAEQLK 302


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: 199
Number of extensions: 10
Number of successful extensions: 2
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: 308
Length adjustment: 27
Effective length of query: 275
Effective length of database: 281
Effective search space:    77275
Effective search space used:    77275
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