GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Azospirillum brasilense Sp245

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 AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein

Query= TCDB::Q93A35
         (328 letters)



>FitnessBrowser__azobra:AZOBR_RS30410
          Length = 371

 Score =  187 bits (474), Expect = 5e-52
 Identities = 99/241 (41%), Positives = 147/241 (60%), Gaps = 6/241 (2%)

Query: 2   IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61
           +R D V   Y   +   + ++ LDIK GEFF F+GPSGCGKTT L++I        G + 
Sbjct: 19  VRIDGVDLSYGSHRV--LKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVT 76

Query: 62  INEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLD 121
           I  + IS    H+   D+G V Q  AL+PHMT+  N+A   E ++  + +I  R+   LD
Sbjct: 77  IGGRDISGLPAHKR--DVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALD 134

Query: 122 SVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDIS 181
            VGL  +    R+P++LSGG+QQRV + R +  +P ++L+DEP S LD   R +++Q++ 
Sbjct: 135 LVGL--KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELL 192

Query: 182 ALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLASG 241
           +LQ+K+  T +FVTHD +EA  + DRI VM+ G + QV TPQE+  +P N FV  FL + 
Sbjct: 193 SLQRKLGLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGTA 252

Query: 242 H 242
           +
Sbjct: 253 N 253


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: 283
Number of extensions: 14
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: 371
Length adjustment: 29
Effective length of query: 299
Effective length of database: 342
Effective search space:   102258
Effective search space used:   102258
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 Sep 17 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