GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Methylocystis bryophila S285

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_085772365.1 B1812_RS15290 ATP-binding cassette domain-containing protein

Query= TCDB::Q93A35
         (328 letters)



>NCBI__GCF_002117405.1:WP_085772365.1
          Length = 257

 Score =  162 bits (410), Expect = 8e-45
 Identities = 90/238 (37%), Positives = 139/238 (58%), Gaps = 3/238 (1%)

Query: 1   MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60
           MI+ D VSK Y  D    +++V+L +  G     +G SG GK+T L +I  L     G +
Sbjct: 1   MIKLDKVSKSY--DALRVLDDVSLTLAQGCTTAVMGLSGSGKSTLLALIVGLEAPDQGEV 58

Query: 61  YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120
            I + R++      LR  +GYV+Q   LFPH+T   NI ++     W   +   R+ EL 
Sbjct: 59  RIGDDRMAPASALNLRRRMGYVIQDGGLFPHLTARRNIELMSRELGWRAARRSKRLQELC 118

Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180
                  E+   R PAELSGG++QRV ++RAL  DP I+L+DEP  ALDP++R RLQ+D+
Sbjct: 119 TLTRFPAEALE-RYPAELSGGQRQRVSLMRALMLDPPILLLDEPLGALDPMTRARLQEDL 177

Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238
            ++ + +KKT+V VTHD+ EA  LGD I  +  G ++Q  + ++++  P + F+ +F+
Sbjct: 178 KSIFRTLKKTVVIVTHDVSEAAFLGDTIVFLHQGRVLQQGSFRDLIAAPADPFITEFI 235


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: 192
Number of extensions: 9
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: 257
Length adjustment: 26
Effective length of query: 302
Effective length of database: 231
Effective search space:    69762
Effective search space used:    69762
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: 48 (23.1 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