GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Sulfurivirga caldicuralii DSM 17737

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  114 bits (285), Expect = 2e-30
 Identities = 70/216 (32%), Positives = 112/216 (51%), Gaps = 11/216 (5%)

Query: 7   RNVQKRF----GEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMI 62
           RN+ K +     E  V+  + L +   E V  VG SG GKSTLL L+ GL+  +DG++++
Sbjct: 9   RNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLL 68

Query: 63  DGRDATEMPPAKRG------LAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSN 116
            G+  +++  A RG      +  V+Q + L P +T ++N+  PL + +        +   
Sbjct: 69  LGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDKALA 128

Query: 117 AAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEI 176
               + L+     +P +LSGG+RQRVA+ RA+V EP   L DEP  NLD+     +   +
Sbjct: 129 LLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLM 188

Query: 177 TELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRI 212
            +L+Q   T ++ VTHD V      D+ + L  G I
Sbjct: 189 DDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223


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: 180
Number of extensions: 4
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: 332
Length of database: 227
Length adjustment: 25
Effective length of query: 307
Effective length of database: 202
Effective search space:    62014
Effective search space used:    62014
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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