GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Methanospirillum lacunae Ki8-1

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_109969948.1 DK846_RS15740 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>NCBI__GCF_003173355.1:WP_109969948.1
          Length = 250

 Score =  152 bits (385), Expect = 7e-42
 Identities = 90/238 (37%), Positives = 138/238 (57%), Gaps = 7/238 (2%)

Query: 4   LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63
           L++ DIRKSFG+ +V+KGVS  +K GE + F+GPSG GKSTLLR I  L    SG +  +
Sbjct: 8   LKVEDIRKSFGSSEVLKGVSFNVKKGETICFIGPSGTGKSTLLRCINQLTIPDSGKVLLN 67

Query: 64  GQIV----NQLTPSRRGIAMVFQSYALYPHMTVYENMAFG-MQLAGKDKQQCRKRVEAAA 118
           G+ V    +Q+   R+ I MVFQ++ L+ H+T   N+    +++ G + +  R +     
Sbjct: 68  GEEVTHSGSQINHFRQKIGMVFQNFFLFDHLTAVRNVEIALLKVKGMNAKDARAKAMKEL 127

Query: 119 EMLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAK 178
           + + +  + +  P +LSGGQ QRV+I RA+  DP V LFDEP S LD  L     LE+ K
Sbjct: 128 QQVGMAEWADHFPAELSGGQAQRVSIARALAMDPDVMLFDEPTSALDPEL-TREVLEVMK 186

Query: 179 LHRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIG 236
              ++   TM+ VTH+   A ++A++I  +  G++++ G+P  L   P       FIG
Sbjct: 187 -KLALDGMTMLVVTHEMGFACSVANQILFMEHGVIKEQGSPQVLLNDPKFERCKAFIG 243


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: 198
Number of extensions: 9
Number of successful extensions: 4
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: 250
Length adjustment: 26
Effective length of query: 316
Effective length of database: 224
Effective search space:    70784
Effective search space used:    70784
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: 48 (23.1 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