GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuG in Synechococcus elongatus PCC 7942

Align ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter

Query= TCDB::G4FGN6
         (278 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0948 Synpcc7942_0948 permease
           protein of sugar ABC transporter
          Length = 275

 Score =  223 bits (567), Expect = 5e-63
 Identities = 112/267 (41%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 13  IAVVLILIWCVFPLYWAFISSIKPDRDLFEKNPSLFPKRITFENYVKVFKERP-FHINIK 71
           IA + + ++ + P+ W  ++SIK + D+       +P++ T E+Y  ++++ P F   + 
Sbjct: 9   IAALALSLFSLAPILWQLLTSIKVNADIAAIPTIYWPRQWTVEHYQALWQQTPAFGRYLL 68

Query: 72  NSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVSILGSLFLILRG 131
           NS +V+ I T+ AL++G+   YAIAR + R   +++  +L V++FP V +   L  ++R 
Sbjct: 69  NSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLFQGLLEVVRW 128

Query: 132 LKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRTLWSIVLPMS 191
           L+  N Y  L++PYTA+NLPL + +L+SFF +LP E+EE+A IDG S  + LW I++P++
Sbjct: 129 LQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLWLILVPLT 188

Query: 192 APGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEIPWGQLMAAAVI 251
           AP LV  G+L FI +WNE++ AL+F+ + +L TVP+AVA   G S +++P+G + AA V+
Sbjct: 189 APALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGDIAAATVV 248

Query: 252 VTLPLVILVLVFQNRIIAGLSAGAVKG 278
            TLPL+ LVLV Q RI+ GL+AGAVKG
Sbjct: 249 ATLPLIGLVLVAQRRILEGLTAGAVKG 275


Lambda     K      H
   0.329    0.142    0.424 

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: 228
Number of extensions: 10
Number of successful extensions: 2
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: 278
Length of database: 275
Length adjustment: 25
Effective length of query: 253
Effective length of database: 250
Effective search space:    63250
Effective search space used:    63250
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: 47 (22.7 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