GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Pseudomonas stutzeri RCH2

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 GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= TCDB::Q93A35
         (328 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  179 bits (455), Expect = 7e-50
 Identities = 94/235 (40%), Positives = 144/235 (61%), Gaps = 6/235 (2%)

Query: 6   NVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEK 65
           ++ K Y  D T    ++ LDI+DGEF VF+GPSGCGK+T L++I  L  +T+G + I+ +
Sbjct: 8   DICKSY--DGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQ 65

Query: 66  RISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGL 125
           R++D    +    +G V Q  AL+PHMT+ EN+A   +L    K +I  R+  + + + L
Sbjct: 66  RVNDLPPKDR--SVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123

Query: 126 DPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQK 185
           D      RKP +LSGG++QRV + R +  +P + L DEP S LD   R +++ +I+ L +
Sbjct: 124 D--KLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQ 181

Query: 186 KIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240
           +I+ T+++VTHD  EA+ L D+I V+  GEI QV  P  +   P+N FV  FL S
Sbjct: 182 RIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGS 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: 276
Number of extensions: 15
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.

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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