GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pedobacter sp. GW460-11-11-14-LB5

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Pedo557:CA265_RS15880
          Length = 330

 Score =  137 bits (346), Expect = 3e-37
 Identities = 77/223 (34%), Positives = 132/223 (59%), Gaps = 8/223 (3%)

Query: 19  VKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVN----DVPPKD 74
           +K+ + E + G+ V  +G SG GK+T L+ I GL +  EG I+  D+ V      + P  
Sbjct: 23  IKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIFFEDKRVKGPDEQLIPGH 82

Query: 75  RDIAMVFQNYALYPHMNVYENMAFGL-RLRRYPKDEIDRRVKEAARILKIEHLLNRKPRE 133
           + + MV Q+++L  +  VY+N+A  L       K E   ++ E  RIL ++   N+K  E
Sbjct: 83  KQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEKTLQIMEHLRILPLQ---NKKIIE 139

Query: 134 LSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHD 193
           LSGG++QRVA+ +A+V + +V L+DEP S +DA L+ ++RA+I ++    GVT I V+HD
Sbjct: 140 LSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADIKRVASETGVTVILVSHD 199

Query: 194 QVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGS 236
             + + L  +++++K+GE+ Q   P  +Y  P + + A  +G+
Sbjct: 200 PADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGN 242


Lambda     K      H
   0.320    0.139    0.400 

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: 289
Number of extensions: 12
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: 376
Length of database: 330
Length adjustment: 29
Effective length of query: 347
Effective length of database: 301
Effective search space:   104447
Effective search space used:   104447
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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