GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Brucella inopinata BO1

Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_008511219.1 BIBO1_RS19100 SDR family oxidoreductase

Query= SwissProt::A3LZU7
         (258 letters)



>NCBI__GCF_000182725.1:WP_008511219.1
          Length = 249

 Score =  148 bits (374), Expect = 9e-41
 Identities = 88/248 (35%), Positives = 133/248 (53%), Gaps = 10/248 (4%)

Query: 5   LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64
           + GKV+A+TGG +G+G  +   +A +GA+V+         +       E +      VL 
Sbjct: 9   VRGKVIAVTGGSSGLGLRMVHMLAGHGARVI---------SISRTHAGESLCPSGGEVLE 59

Query: 65  IPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAF 124
           I  D++ PE   R  +    +FG I+   +NAGV      L+ T + L     +N+ GAF
Sbjct: 60  IMADVTRPEEIARAFDEGESRFGPISTLFNNAGVAHMARALDTTRDMLEHIFEVNVAGAF 119

Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYGI 184
           FA Q  A++M+ QG+GGSII ++SI           Y+ +KA +  + ++ A     + I
Sbjct: 120 FAAQEVARRMIAQGQGGSIINVTSILGERPQKGAAAYSMSKACVSQMTRALALEWAAHDI 179

Query: 185 RCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSNYVNG 244
           R NAI PG   T +NEE L+ P    Y++GR P+ R+GDP D+ G  + LASD S Y+ G
Sbjct: 180 RVNAISPGWFPTRINEEQLQGP-AAGYLKGRNPMRRLGDPNDLDGVVLLLASDASRYMTG 238

Query: 245 AQLLVDGG 252
           + L VDGG
Sbjct: 239 SILTVDGG 246


Lambda     K      H
   0.317    0.136    0.382 

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: 119
Number of extensions: 5
Number of successful extensions: 4
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: 258
Length of database: 249
Length adjustment: 24
Effective length of query: 234
Effective length of database: 225
Effective search space:    52650
Effective search space used:    52650
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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