GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Rhizorhabdus wittichii RW1

Align BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= TCDB::Q93A35
         (328 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  196 bits (497), Expect = 7e-55
 Identities = 108/239 (45%), Positives = 150/239 (62%), Gaps = 3/239 (1%)

Query: 1   MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60
           MI FD+V K Y+      +++V+L I+ G F   +G SG GKTT LK INRL+ + TGTI
Sbjct: 1   MISFDHVGKHYAGRHV--LDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTI 58

Query: 61  YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120
            I  + ++   + ELR  IGYV Q I LFPHM++ EN+A+VP L+   +E+   R+ ELL
Sbjct: 59  AIEGRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELL 118

Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180
           D V L P  +  R+PA+LSGG+ QRVG  RALAA P I+LMDEPF ALDP++R  L    
Sbjct: 119 DLVAL-PADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAY 177

Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLA 239
            AL + +  T + VTHDM EAL L DR+ V+  G I+    P+ ++    +  ++  +A
Sbjct: 178 RALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEAMIA 236


Lambda     K      H
   0.318    0.136    0.386 

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: 173
Number of extensions: 8
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: 328
Length of database: 252
Length adjustment: 26
Effective length of query: 302
Effective length of database: 226
Effective search space:    68252
Effective search space used:    68252
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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