GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Cupriavidus basilensis 4G11

Align Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH; EC 4.1.2.28 (characterized)
to candidate RR42_RS36370 RR42_RS36370 dihydrodipicolinate synthase

Query= SwissProt::P39359
         (301 letters)



>FitnessBrowser__Cup4G11:RR42_RS36370
          Length = 308

 Score =  122 bits (307), Expect = 8e-33
 Identities = 79/242 (32%), Positives = 124/242 (51%), Gaps = 4/242 (1%)

Query: 4   FSGIIPPVSSTFHRDGTLDKKAMREVADFLINKGVDGLFYLGTGGEFSQMNTAQRMALAE 63
           +SG+ P VS+ F  D +LD +A  +V   L+  GV GL   GT GE + M+  +++A+ E
Sbjct: 8   WSGVFPAVSTQFKADYSLDIEATHKVMCNLVADGVCGLVVCGTVGENTSMSAREKLAVIE 67

Query: 64  EAVTIVDGRVPVLIGVGSPSTDEAVKLAQHAQAYGADGIVAINPYYWKVAPRNLDDYYQQ 123
            A     GRVPV+ G+   +T  A  +   A   G DG++ +    +   P     +++ 
Sbjct: 68  AAKDAARGRVPVIAGIAEFTTAFARDMVTEAARAGVDGVMVMPALVYSAKPHEAAAHFRD 127

Query: 124 IARSVTLPVILYNFPDLTGQDLTPETVTRLALQNENIVGIKDTIDSVGHLRTMINTVKSV 183
           IA +  LPV+LYN P +   D+TP+ +  LA   ENIV  K   DS G  R  I+   +V
Sbjct: 128 IATATDLPVMLYNNPPVYRSDITPDILVSLA-DCENIVCFK---DSSGDTRRFIDLRNAV 183

Query: 184 RPSFSVFCGYDDHLLNTMLLGGDGAITASANFAPELSVGIYRAWREGDLATAATLNKKLL 243
              F +F G DD +L ++ +G DG I+  +N  P+    ++R  R+     A  L +  +
Sbjct: 184 GDRFVLFAGLDDVVLESIAVGADGWISGMSNAFPKEGETLFRLARQRRFDEALALYRWFM 243

Query: 244 QL 245
            L
Sbjct: 244 PL 245


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: 209
Number of extensions: 15
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: 301
Length of database: 308
Length adjustment: 27
Effective length of query: 274
Effective length of database: 281
Effective search space:    76994
Effective search space used:    76994
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