GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Herbaspirillum seropedicae SmR1

Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate HSERO_RS22745 HSERO_RS22745 sugar ABC transporter permease

Query= TCDB::Q88P36
         (281 letters)



>FitnessBrowser__HerbieS:HSERO_RS22745
          Length = 300

 Score =  129 bits (325), Expect = 6e-35
 Identities = 81/268 (30%), Positives = 134/268 (50%), Gaps = 6/268 (2%)

Query: 17  IHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNL-LSWPAVITGIGWVKAWGAVSG--Y 73
           +H VL +  ++ L P+ ++L+ S KT   I  G + L     +T  G+ K         Y
Sbjct: 35  VHTVLCLYAVIALFPIALILINSVKTRNAIFEGPMALPTAETLTFAGFQKVLAGTHFLLY 94

Query: 74  FWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133
           F NS+ +TV A+ +    GA+  + L+ +RF G++     +  G  +P +   +     +
Sbjct: 95  FGNSLAVTVAALFLIVLFGAMAAWALTEYRFFGNRALNFFIAIGIMIPIRLGTVSILQLV 154

Query: 134 GKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRRIILP 193
             L L +T   LVLV+   GL    +    F   IP  L  AAR DG G  +IF R+ILP
Sbjct: 155 VALDLINTRTALVLVYTAQGLPLAVMILSEFMRQIPGELKDAARCDGVGELSIFFRVILP 214

Query: 194 MSTPIIMVCLIWQFTQIWNDFLFGVVFSSG-DSQPITVALNNLVNTSTGAKEYNVDMAAA 252
           +  P I    ++     WND  F ++ + G D++ +T+ +   +     A ++N  +AA 
Sbjct: 215 LLRPAIATVAVFTMIPAWNDLWFPLILAPGEDTRTVTLGVQQFIGQY--ATDWNSVLAAL 272

Query: 253 MIAGLPTLLVYVVAGKYFVRGLTAGAVK 280
            +A +P LL+Y+   +  +RGLT+GAVK
Sbjct: 273 SMAVIPVLLLYMAFSRQLIRGLTSGAVK 300


Lambda     K      H
   0.329    0.142    0.443 

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: 186
Number of extensions: 8
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: 281
Length of database: 300
Length adjustment: 26
Effective length of query: 255
Effective length of database: 274
Effective search space:    69870
Effective search space used:    69870
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