GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Kocuria flava HO-9041

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 WP_083529352.1 AS188_RS08430 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::P75682
         (302 letters)



>NCBI__GCF_001482365.1:WP_083529352.1
          Length = 318

 Score =  129 bits (323), Expect = 1e-34
 Identities = 89/293 (30%), Positives = 138/293 (47%), Gaps = 8/293 (2%)

Query: 6   LFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIA 65
           LF  ++  + T+F  DG +D  GT  +   L+  G DGL   G+ GE+S +  EE  ++ 
Sbjct: 20  LFGTLLTAMITVFAEDGSVDLDGTVGVAQQLVDDGCDGLVVCGTTGEYSTMTDEENLSVF 79

Query: 66  RFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFE 125
           R   D +  RVP+L GTG  +   +  LS+ A++ G DG++++ PYY K ++A +  +F 
Sbjct: 80  RAVKDALGGRVPLLAGTGSNDTEHSRHLSREAEKIGMDGLLIVTPYYNKPTQAGVEAHFR 139

Query: 126 QVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDT-IDSVAHLRSMIHTVK 184
            +ADSV LP+MLY+ P  TG  L P  + +LA +  NI+ +KD   D  A  R +  T  
Sbjct: 140 SLADSVDLPIMLYDIPGRTGIPLEPETLISLA-AHPNIVAVKDAKADLFAATRVLAET-- 196

Query: 185 GAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQT 244
                     G D      + +G  G I  + + A      L+ A R GD+A A   +  
Sbjct: 197 ----DLLYYSGDDGLTLPWMAIGAAGLIGVTTHVATARYRELVDAVRAGDLATARRINFE 252

Query: 245 LLQIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQ 297
           L  + +      P     K  +   GR     V  P  PL     A ++  L+
Sbjct: 253 LEPVVRATMTRAPGAVAAKTILTWQGRLPHPTVRLPHVPLTPAEAALVRADLE 305


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: 241
Number of extensions: 12
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: 302
Length of database: 318
Length adjustment: 27
Effective length of query: 275
Effective length of database: 291
Effective search space:    80025
Effective search space used:    80025
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 24 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