GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Snodgrassella alvi wkB2

Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate WP_025330452.1 SALWKB2_RS04305 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::P39359
         (301 letters)



>NCBI__GCF_000600005.1:WP_025330452.1
          Length = 291

 Score =  150 bits (380), Expect = 3e-41
 Identities = 93/276 (33%), Positives = 152/276 (55%), Gaps = 6/276 (2%)

Query: 5   SGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAEE 64
           +G +  + +  H DG++D +  +++ D+ I  G D +  +GT GE + ++  + + + + 
Sbjct: 3   TGSLVAIVTPMHEDGSIDYEQYKQLIDWHIESGTDAIVAVGTTGESATLSVDEHLNVIKT 62

Query: 65  AVTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQI 124
           AV  V GRV V+ G G+ +T EA+ LAQ AQ  GAD  +++ PYY K     +  +++ I
Sbjct: 63  AVEHVAGRVKVIAGTGANNTHEAIYLAQEAQQAGADMTLSVVPYYNKPNQEGIYRHFKTI 122

Query: 125 ARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSVR 184
           A + ++P+ILYN P  T  D+ P+T  RLA + +NIVGIK+   ++G    +    K V 
Sbjct: 123 AEATSIPMILYNVPGRTVADMQPDTALRLA-EIDNIVGIKEATGNIGRACYLF---KHVP 178

Query: 185 PSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLLQ 244
            +F+V+ G D   L  +L GG G I+ +AN AP+L   +  A   GD+  A  LN KL +
Sbjct: 179 ENFAVYSGDDPTALAFLLCGGHGVISVTANVAPKLFADMCHAALRGDITGARALNDKLQR 238

Query: 245 LPAIYALETPFVSLIKYSMQCVGLPVETYCLPPILE 280
           L      E P  +  K+++  +G  +   C  PI E
Sbjct: 239 LHGDLFCE-PSPAPTKWALSKLG-KINPVCRLPITE 272


Lambda     K      H
   0.319    0.137    0.398 

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: 200
Number of extensions: 9
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: 301
Length of database: 291
Length adjustment: 26
Effective length of query: 275
Effective length of database: 265
Effective search space:    72875
Effective search space used:    72875
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