GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Pseudomonas fluorescens FW300-N2E3

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 AO353_05440 AO353_05440 glycine/betaine ABC transporter ATP-binding protein

Query= TCDB::Q93A35
         (328 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05440
          Length = 385

 Score =  255 bits (652), Expect = 1e-72
 Identities = 122/240 (50%), Positives = 175/240 (72%), Gaps = 2/240 (0%)

Query: 1   MIRFDNVSKKYSDD--KTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTG 58
           MI   N+SK +  +     AV++V+L + +GE  VF+GPSGCGK+TTLKMINRLI  T+G
Sbjct: 1   MIELQNLSKTFQSNGKDVKAVDSVSLIVNEGEICVFLGPSGCGKSTTLKMINRLIKPTSG 60

Query: 59  TIYINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITE 118
            I IN +  +D D   LR +IGYV+QQI LFP+MTIEENI IVP L  W K++ HDR  E
Sbjct: 61  KILINGEDTTDLDAVTLRRNIGYVIQQIGLFPNMTIEENITIVPRLLGWDKQQCHDRARE 120

Query: 119 LLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQ 178
           L++ + L+P+ Y  R P ELSGG+QQR+GV+RALAAD  ++LMDEPF A+DPI+R+ +Q 
Sbjct: 121 LMNMIKLEPKQYLSRYPRELSGGQQQRIGVIRALAADAPLLLMDEPFGAVDPINREMIQN 180

Query: 179 DISALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238
           +   +Q+ + KT++ V+HD+ EA+ LGD+I + +GG+++QV  P  ++ +P +DFV +F+
Sbjct: 181 EFFEMQRALGKTVIMVSHDIDEAIKLGDKIAIFRGGKLIQVDHPDTLLAHPADDFVSNFV 240


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: 303
Number of extensions: 6
Number of successful extensions: 1
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: 385
Length adjustment: 29
Effective length of query: 299
Effective length of database: 356
Effective search space:   106444
Effective search space used:   106444
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