GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsB in Brucella inopinata BO1

Align LacI family transcriptional regulator; SubName: Full=Ribose transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_008507131.1 BIBO1_RS11580 sugar ABC transporter substrate-binding protein

Query= uniprot:A0A1N7UEH6
         (318 letters)



>NCBI__GCF_000182725.1:WP_008507131.1
          Length = 329

 Score = 95.5 bits (236), Expect = 2e-24
 Identities = 78/273 (28%), Positives = 126/273 (46%), Gaps = 15/273 (5%)

Query: 15  LAAASAALPLSSAFADDAAKPKVGLVMKSLANEFFVTMQDGAKTYQKEHAADFDMITNGI 74
           LAAASA +   S   D   K K+G     L  EF     +  K +      + ++     
Sbjct: 8   LAAASALIATPSLAQDK--KLKIGAAPYGLNAEFMQVWSEALKKHPAVKNGEVELTI--F 63

Query: 75  KNETDTSAQIDIVNQMILAKVNAIVIAPADSKALVTVLKKASDAGIKVVNIDNRLDPDVL 134
               D   Q +  N MI  K +AI+  P D +A  T ++ ASDAGI VV  + R++ D+L
Sbjct: 64  DGRYDALVQQEQFNTMITQKFDAIIFVPIDIEAGATAVQAASDAGIPVVGSNTRVNSDLL 123

Query: 135 KSKNLDIPFVGPDNRKGSKLVGDYLAKQLASGDKVGIIEGVPTTTNAQ-QRTAGYKDAM- 192
            +      +VG D+     +    +  ++     V I+EG P   +AQ  R  G K A+ 
Sbjct: 124 AA------YVGSDDTVSGYMEAKDVLDKIGCKGNVVILEG-PIGQSAQISRLEGNKKALA 176

Query: 193 DAAGMKIVSTQSGNWEIDQGQKVASAMLSEYP-DLKALLAGNDNMALGAVSAVRAAG-KA 250
           +   +K++  Q+ NW   + Q +    L+ +P  +  ++  ND MALGA+ A++AA  K 
Sbjct: 177 ECPNVKVLEDQTANWSRAEAQTLMENWLTAHPGQINGVIGQNDEMALGAIEAIKAANLKP 236

Query: 251 GKVLVVGYDNIEAIKPMLQDGRVLATADQAAAQ 283
           G   + G D I      +++G + +    A AQ
Sbjct: 237 GDFAIAGIDGITDALHAVKEGTMTSILQDANAQ 269


Lambda     K      H
   0.314    0.130    0.349 

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: 214
Number of extensions: 12
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: 318
Length of database: 329
Length adjustment: 28
Effective length of query: 290
Effective length of database: 301
Effective search space:    87290
Effective search space used:    87290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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