GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Bacteroides thetaiotaomicron VPI-5482

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 350222 BT0694 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Btheta:350222
          Length = 224

 Score =  132 bits (331), Expect = 1e-35
 Identities = 79/219 (36%), Positives = 123/219 (56%), Gaps = 12/219 (5%)

Query: 4   VRLEHVWKRFG----KVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59
           +++E++ K F     + VA+   NLE ++GEFV  +GPSGCGK+T L ++  L+  +EG+
Sbjct: 2   IQIENISKVFRTTEVETVALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEGS 61

Query: 60  IYIGDRLVNDVPPKDRD------IAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRR 113
             +    V  +  K+R       +  VFQ++ L   +NV+EN+   L        E  R 
Sbjct: 62  YRLLGEEVAGLKEKERTGVRKGKLGFVFQSFNLIDELNVFENVELPLTYLGIKSSERRRM 121

Query: 114 VKEAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMR 173
           V++  + + I H     P++LSGGQ+QRVA+ RA+V  PK+ L DEP  NLD+K   E+ 
Sbjct: 122 VEDILKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGNLDSKNGAEVM 181

Query: 174 AEIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEI 212
             + +L +  G T I VTH Q +A +  HR V + DG +
Sbjct: 182 NLLTELNKE-GTTIIMVTHSQHDA-SFAHRTVHLFDGSV 218


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: 228
Number of extensions: 16
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: 376
Length of database: 224
Length adjustment: 26
Effective length of query: 350
Effective length of database: 198
Effective search space:    69300
Effective search space used:    69300
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: 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