GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Dinoroseobacter shibae DFL-12

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 3608247 Dshi_1651 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::G4FGN7
         (293 letters)



>FitnessBrowser__Dino:3608247
          Length = 334

 Score =  128 bits (321), Expect = 2e-34
 Identities = 91/291 (31%), Positives = 154/291 (52%), Gaps = 20/291 (6%)

Query: 11  WMIL-PTILVISVVAFFPLFKTFYDSFYSFGLRPGIERRFVGLQNYFRLFEDTRFIMALK 69
           W+ L P + V+ +   +P+ +T   S       PG   ++VGL NY ++  + +F  A++
Sbjct: 54  WIFLFPALFVLLLYLGYPVVETLRLSLLE--RVPGGGYQWVGLDNYAQMASEPKFWEAMR 111

Query: 70  NTVFFTVISVSLETVLGVLIAIVVHQRFALRGVVRAAMLVPWAIPTAISSQMWRWMF--- 126
           N +F+ ++  +L T  G+L A +   R     V ++ + +P AI    +S +W+ ++   
Sbjct: 112 NNMFWLIVVPALSTAFGLLAAQLT-DRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGR 170

Query: 127 ---HDQFGIMSRLWEKLGIIEPGTPI--LGTPGLAMWAIIFVDVWKTTPFMALLILAGLQ 181
               +Q GI++ +   LG    G P+  L  P    + ++ V VW  T F  +++ A L+
Sbjct: 171 PIEQEQIGILNAIIVGLG----GDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALR 226

Query: 182 VIPEDIYEAARIDGANTIQRFFRITLPLITPTIGVALIFRTLDALRVFDVVYIMTRGAVN 241
            IPE+  EAA IDGA+ +Q FF+I +P I PT+ V     TL  L+VFD+V+ MT G   
Sbjct: 227 GIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWE 286

Query: 242 TETLAVYNRHVLMDRAFTGAWFGYGSAISVFIFVLISVFAILYIKSLRLKL 292
           T+ LA Y    + D+ F    +G GSA ++ I +L++   I  I S R ++
Sbjct: 287 TQVLANY----MFDKLFRANDWGVGSASAMVIMLLVTPILIWNIHSARKEM 333


Lambda     K      H
   0.333    0.145    0.457 

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: 310
Number of extensions: 20
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: 293
Length of database: 334
Length adjustment: 27
Effective length of query: 266
Effective length of database: 307
Effective search space:    81662
Effective search space used:    81662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 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