GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Bacteroides clarus YIT 12056

Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_009122072.1 BUB52_RS10340 glucose 1-dehydrogenase

Query= SwissProt::A3LZU7
         (258 letters)



>NCBI__GCF_900129655.1:WP_009122072.1
          Length = 250

 Score =  126 bits (317), Expect = 4e-34
 Identities = 82/253 (32%), Positives = 139/253 (54%), Gaps = 10/253 (3%)

Query: 5   LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64
           L GKV  +TGG   +GRAI+I+ A+ GAKVVVN+  + E A  A+ LK   + G   ++ 
Sbjct: 3   LQGKVAIVTGGARDLGRAISIKFAQEGAKVVVNYFDNPEDA--AETLKLIQAAGSEGII- 59

Query: 65  IPGDISLPETGRRIVELAVEKFG-EINVFVSNAGVCGFREFLEITPETLFQ-TVNINLNG 122
           + GD++     + + + A+E FG  I+  V+  G    R+ +    ET +   +++N+  
Sbjct: 60  VQGDMTKATDVKNLFDKAIEAFGNHIDALVNVVGGIVGRKLVTEQDETWYDFLMDVNMRS 119

Query: 123 AFFAIQAAAQQMVKQGKGGSIIGISSISALVGGA-HQTHYTPTKAGILSLMQSTACALGK 181
            F   + A   M     G +I+  SS++A  GG    + Y   K  +++  ++ A  LG 
Sbjct: 120 VFLCTREAVPYM---SAGSTIVNFSSLAARDGGGPGASMYATAKGAVMTYTRAMAKELGP 176

Query: 182 YGIRCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSNY 241
            GIR NA+ PGTI+T+ ++     PE R+ ++    L R G+ K++A   I+L+S+ S+Y
Sbjct: 177 KGIRVNALAPGTIATSFHDR-FNTPENRERLKATYALRREGEAKEVADLVIYLSSEDSSY 235

Query: 242 VNGAQLLVDGGLF 254
           + GA + ++GG F
Sbjct: 236 ITGANIDINGGSF 248


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: 145
Number of extensions: 8
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: 258
Length of database: 250
Length adjustment: 24
Effective length of query: 234
Effective length of database: 226
Effective search space:    52884
Effective search space used:    52884
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.

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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