GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Alicycliphilus denitrificans K601

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_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= TCDB::Q93A35
         (328 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  179 bits (453), Expect = 1e-49
 Identities = 100/222 (45%), Positives = 140/222 (63%), Gaps = 4/222 (1%)

Query: 17  AAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKRISDYDIHELR 76
           +A+ ++ L ++ GE   F+GPSGCGKTT L++I  L   T+G+I  + + IS     E  
Sbjct: 33  SALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDISWLPASER- 91

Query: 77  WDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGLDPESYRHRKPA 136
            D G V Q  ALFP++TI EN+A      K  K +I  R+ ELL   GL     ++  P+
Sbjct: 92  -DYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGLPTAGGKY--PS 148

Query: 137 ELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIKKTIVFVTH 196
           +LSGG+QQRV + RALA +PG++L+DEP SALD   R RL+ +I  LQK++  T + VTH
Sbjct: 149 QLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQVGITTIMVTH 208

Query: 197 DMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238
           D +EAL++ DRI VM  G I QV TP EI + P + FV +F+
Sbjct: 209 DQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFV 250


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: 273
Number of extensions: 12
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: 328
Length of database: 377
Length adjustment: 29
Effective length of query: 299
Effective length of database: 348
Effective search space:   104052
Effective search space used:   104052
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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