GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Pseudomonas fluorescens FW300-N2E2

Align TreV, component of Trehalose porter (characterized)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889
          Length = 386

 Score =  235 bits (600), Expect = 1e-66
 Identities = 124/299 (41%), Positives = 184/299 (61%), Gaps = 6/299 (2%)

Query: 2   TVELIDIVKKYGKNI--VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKI 59
           T+EL ++ K YG  +   +  I   I+ GEF +++GPSG GKSTL+  +AG+E +  G I
Sbjct: 3   TLELRNVNKTYGVGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGGAI 62

Query: 60  IADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKL 119
           +    D++   P+ R++AMVFQ+YALYP MSVR+NI F LK+R M +  I E V + AKL
Sbjct: 63  MIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQAAIDEEVTRVAKL 122

Query: 120 LGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQ 179
           L I  +L++K  Q+SGGQQQRVA+ RA+ R P  +L DEPLSNLDA++R   R E+K + 
Sbjct: 123 LQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMH 182

Query: 180 KELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMN 239
           + LK T +YVTHDQ EA++L D++A++  G  +Q   PK +Y  P   +VA F+G  PMN
Sbjct: 183 QRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPPMN 242

Query: 240 FLPGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVEASGESRYLICNFKNNNITILSQE 298
           F+P  L ++  + +      ++ G+      +   +A  E R +I   +   I +   E
Sbjct: 243 FIPLRLQRKDGRLLAL----LDSGQARCELPMGMQDAGLEDREVILGMRPEQIMLAGSE 297


Lambda     K      H
   0.318    0.137    0.385 

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: 286
Number of extensions: 10
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: 324
Length of database: 386
Length adjustment: 29
Effective length of query: 295
Effective length of database: 357
Effective search space:   105315
Effective search space used:   105315
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