GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuE in Cupriavidus basilensis 4G11

Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate RR42_RS13255 RR42_RS13255 hydroxymethylglutaryl-CoA lyase

Query= SwissProt::O34873
         (299 letters)



>FitnessBrowser__Cup4G11:RR42_RS13255
          Length = 322

 Score =  228 bits (582), Expect = 1e-64
 Identities = 122/271 (45%), Positives = 165/271 (60%)

Query: 4   PKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAI 63
           P ++ I EV PRDGLQ EP  + T+ K+ +++ LS  G + IE TSF   K IPAL DA 
Sbjct: 10  PARIEINEVAPRDGLQIEPAVVPTDAKVAFLDALSACGFARIEATSFTSAKAIPALADAE 69

Query: 64  DVAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHI 123
            V   + R  GV Y ALVPN RGLE AL    +E  + MSASETHNR N+  + ++S   
Sbjct: 70  AVMLRMQRGAGVRYTALVPNLRGLERALSCRPDELNLVMSASETHNRANLRMTRAQSQAQ 129

Query: 124 LKQVNNDAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTIGAA 183
           L  +   A  A +     LSTVFGCP+E +V  + V+ L+E+    G + ++L DT G A
Sbjct: 130 LLAMVEAANAAGVPVNVSLSTVFGCPFEGEVDADAVMALAESFAHAGAAGITLCDTTGMA 189

Query: 184 NPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLGGCPYA 243
            P QV  + E      P   + +H H+TRG  LAN + A Q G+T FD +AGGLGGCP+A
Sbjct: 190 YPTQVAALCERFQRSLPQAGLTIHLHNTRGMGLANALAAWQTGVTRFDAAAGGLGGCPFA 249

Query: 244 PGSSGNAATEDIVYMLEQMDIKTNVKLEKLL 274
           PG+SGN +TE++V+M + M + T V L +LL
Sbjct: 250 PGASGNVSTEELVHMFDAMGVDTGVDLARLL 280


Lambda     K      H
   0.315    0.132    0.381 

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: 215
Number of extensions: 8
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: 299
Length of database: 322
Length adjustment: 27
Effective length of query: 272
Effective length of database: 295
Effective search space:    80240
Effective search space used:    80240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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