GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treV in Herbaspirillum seropedicae SmR1

Align TreV, component of Trehalose porter (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS18940 HSERO_RS18940
           sn-glycerol-3-phosphate ABC transporter ATP-binding
           protein
          Length = 364

 Score =  240 bits (612), Expect = 4e-68
 Identities = 127/289 (43%), Positives = 190/289 (65%), Gaps = 16/289 (5%)

Query: 3   VELIDIVKKYGKNI----VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGK 58
           + L  + K YG       VI+GI  +I  GEF V++GPSG GKSTLL+++AG+E++  G+
Sbjct: 4   IHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEISSGQ 63

Query: 59  IIADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAK 118
           I+     + D  P++R++AMVFQNYALYP+M+V  N+A+ LK++G+ K EI  RV++AA 
Sbjct: 64  IVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQRAAA 123

Query: 119 LLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRI 178
           +L +  +L++   Q+SGGQ+QRVA+ RAIVR P+ FL DEPLSNLDA++R   R E++++
Sbjct: 124 ILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIQKL 183

Query: 179 QKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPM 238
              L+ T +YVTHDQ EA++L  R+ ++++G  EQ+  P  +Y  P T +VA F+G  PM
Sbjct: 184 HASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGSPPM 243

Query: 239 NFLPGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVE----ASGESRYL 283
           N L G+L  + A          EV KGN S ++   +    A+G+ R L
Sbjct: 244 NLLQGKLSADGAS--------FEVSKGNASDILRLPQPLTGAAGQERIL 284


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: 273
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: 364
Length adjustment: 29
Effective length of query: 295
Effective length of database: 335
Effective search space:    98825
Effective search space used:    98825
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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