GapMind for catabolism of small carbon sources

 

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

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 350222 BT0694 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__Btheta:350222
          Length = 224

 Score =  143 bits (361), Expect = 3e-39
 Identities = 83/218 (38%), Positives = 129/218 (59%), Gaps = 17/218 (7%)

Query: 8   LEIRNLHKRYGDLEV----LKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63
           ++I N+ K +   EV    L  ++L  ++G+ ++I+G SG GKST L  + LL+NP +G 
Sbjct: 2   IQIENISKVFRTTEVETVALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEGS 61

Query: 64  ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123
             + GEE+   K K         ++    + +LGFVFQ+FNL   +++ +NV E P   L
Sbjct: 62  YRLLGEEVAGLKEK---------ERTGVRKGKLGFVFQSFNLIDELNVFENV-ELPLTYL 111

Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183
           G   +E   + E +L ++ I+ +   +P QLSGGQQQR AIAR +   PK+IL DEPT  
Sbjct: 112 GIKSSERRRMVEDILKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGN 171

Query: 184 LDPEMVQEVLNVIRALAEEGRTMLLVT---HEMSFARQ 218
           LD +   EV+N++  L +EG T+++VT   H+ SFA +
Sbjct: 172 LDSKNGAEVMNLLTELNKEGTTIIMVTHSQHDASFAHR 209


Lambda     K      H
   0.317    0.133    0.367 

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: 137
Number of extensions: 7
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: 257
Length of database: 224
Length adjustment: 23
Effective length of query: 234
Effective length of database: 201
Effective search space:    47034
Effective search space used:    47034
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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