GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Bacteroides clarus YIT 12056

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_009120430.1 BUB52_RS15225 polyamine ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_900129655.1:WP_009120430.1
          Length = 465

 Score =  245 bits (625), Expect = 2e-69
 Identities = 119/241 (49%), Positives = 169/241 (70%), Gaps = 2/241 (0%)

Query: 4   ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63
           I++ +V K FG+  V+  ++L +  GEFV  +GPSGCGK+TLLRLIAG +  S+G I I 
Sbjct: 8   ISVEHVSKFFGDKAVLNDVNLSVRKGEFVTILGPSGCGKTTLLRLIAGFQTASEGVITIA 67

Query: 64  GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123
           G+D T+ PP +R +  VFQ YAL+PH+ V  NIAF L++ K+    IE++V  A +++ +
Sbjct: 68  GKDITQTPPHRRPVNTVFQKYALFPHLNVFNNIAFGLKLKKLPAATIEKKVKQALRMVGM 127

Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183
           T+Y DR    LSGGQ+QRVAI RAIV EP   L DEPL+ LD  +R +M++E+ E+HQ L
Sbjct: 128 TDYEDRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHQKL 187

Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIE 243
             T +YVTHDQ EA+T++D IVV++ G+I+Q G+P+ +Y  P N FVA FIG  + N++ 
Sbjct: 188 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQTGTPIDIYNEPINSFVADFIG--ESNILN 245

Query: 244 G 244
           G
Sbjct: 246 G 246


Lambda     K      H
   0.320    0.137    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: 361
Number of extensions: 7
Number of successful extensions: 1
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: 332
Length of database: 465
Length adjustment: 31
Effective length of query: 301
Effective length of database: 434
Effective search space:   130634
Effective search space used:   130634
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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