GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0030 in Pseudomonas fluorescens FW300-N2C3

Align TM0030, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate AO356_07705 AO356_07705 ABC transporter permease

Query= TCDB::Q9WXN7
         (338 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07705
          Length = 315

 Score =  168 bits (425), Expect = 2e-46
 Identities = 101/329 (30%), Positives = 178/329 (54%), Gaps = 21/329 (6%)

Query: 7   FKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLM 66
           ++++L R + LL      + I F+L R+IPG+P   +L      +++ PEA+      + 
Sbjct: 6   YRFILSRPLQLLPVLFGISMITFVLVRSIPGDPARALLG-----SRSTPEALIR----IR 56

Query: 67  EEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWI 126
            ++GL +P ++QYF F+   L+GDLG S+  Y    + LI   I  TL L+L + ++A +
Sbjct: 57  AQYGLDQPLWMQYFYFLKNLLKGDLGQSL-LYKVDALQLISTRIEPTLFLVLGSVLLALL 115

Query: 127 LGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQG 186
           +   L  +AA  ++ W D  +   +     +P +WLG++ I L  V+LG  PV G    G
Sbjct: 116 IAVPLATVAARNKSGWQDHLIRLFTTAGLGMPAFWLGIMLILLLSVQLGLFPVSGYGRTG 175

Query: 187 TIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDK 246
                 W    D L H ++P  +I ++        +R  ++ EL +D+A  +   G+ ++
Sbjct: 176 ------W----DKLHHMVLPCLTIALALSAVLVRNLRASMLMELQADHATAARARGLSER 225

Query: 247 RIFK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQG 305
            IF+ +V  NSL+P +  LA+++G ++ G ++ E +F  PG G LL R + T DY ++QG
Sbjct: 226 AIFRRHVLPNSLVPAVNLLAVNIGWLISGTVVIESLFAIPGIGQLLVRGIFTRDYMVVQG 285

Query: 306 IFVILIASIYLANFIVDFLYALIDPRIRL 334
           + ++L  +    NF+ D L  +IDPR+ +
Sbjct: 286 VAMVLALATVTVNFLADVLTVMIDPRVNM 314


Lambda     K      H
   0.329    0.146    0.449 

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: 293
Number of extensions: 19
Number of successful extensions: 5
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: 338
Length of database: 315
Length adjustment: 28
Effective length of query: 310
Effective length of database: 287
Effective search space:    88970
Effective search space used:    88970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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