GapMind for catabolism of small carbon sources

 

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

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate 350388 BT0860 putative ABC transporter ATP-binding protein (NCBI ptt file)

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__Btheta:350388
          Length = 224

 Score =  140 bits (352), Expect = 4e-38
 Identities = 86/203 (42%), Positives = 119/203 (58%), Gaps = 13/203 (6%)

Query: 19  IKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIVNQLTPSRRG-- 76
           +  VS+E+K GEF+  +GPSGCGKSTLL ++  L+  T G    +G  V++ T S+R   
Sbjct: 21  LNNVSIEVKQGEFVAIMGPSGCGKSTLLNILGLLDNPTGGEYYLNGTEVSKYTESQRTSL 80

Query: 77  ----IAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPR 132
               I  VFQS+ L   + VYEN+   +   G    + +KRVE A E + +T   +  P+
Sbjct: 81  RKGVIGFVFQSFNLIDELNVYENIELPLLYMGISASERKKRVETAMERMAITHRSKHFPQ 140

Query: 133 QLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHK--TTMIY 190
           QLSGGQ+QRVAI RA+V +PK+ L DEP  NLD+        E+  L   ++K  TT++ 
Sbjct: 141 QLSGGQQQRVAIARAVVANPKLILADEPTGNLDS----KNGKEVMGLLSELNKEGTTIVM 196

Query: 191 VTHDQVEAMTLADRICVLRDGLV 213
           VTH Q +A   ADRI  L DG V
Sbjct: 197 VTHSQHDA-GYADRIINLFDGQV 218


Lambda     K      H
   0.321    0.138    0.396 

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: 173
Number of extensions: 9
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: 342
Length of database: 224
Length adjustment: 25
Effective length of query: 317
Effective length of database: 199
Effective search space:    63083
Effective search space used:    63083
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 (21.9 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:

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