GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Sulfurivirga caldicuralii DSM 17737

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  119 bits (297), Expect = 1e-31
 Identities = 84/223 (37%), Positives = 121/223 (54%), Gaps = 19/223 (8%)

Query: 4   LEIRNIRKRY----GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59
           LE RN+ K Y     E   LKG+ + L   E + ++GSSG GKSTLL+++ GL  P+ G+
Sbjct: 6   LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65

Query: 60  ILIGER--SVLGVHPK----DRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKA 113
           +L+  +  S LG   +    +R +  V+Q + L P L+   N+   L +RR    E +  
Sbjct: 66  VLLLGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRR----ESEAT 121

Query: 114 VRDTA-RLLQIENLLDR---KPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLR 169
            RD A  LL    L  R   KPS+LSGG+RQRVA+ RALV  P   L DEP  NLD++  
Sbjct: 122 ARDKALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSA 181

Query: 170 MEMRTELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRI 212
            ++ + +  L+Q   T ++ VTHD +       R   +RDG I
Sbjct: 182 EQVLSLMDDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223


Lambda     K      H
   0.320    0.136    0.385 

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: 194
Number of extensions: 10
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: 360
Length of database: 227
Length adjustment: 26
Effective length of query: 334
Effective length of database: 201
Effective search space:    67134
Effective search space used:    67134
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