GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Sulfurivirga caldicuralii DSM 17737

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  117 bits (292), Expect = 4e-31
 Identities = 77/219 (35%), Positives = 115/219 (52%), Gaps = 11/219 (5%)

Query: 4   LQLTNVCKSF--GPVE--VLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGE 59
           L+  N+ K++  GP E  VLK ++L +   E V  VG SG GKSTLL ++ GL+  T GE
Sbjct: 6   LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65

Query: 60  ISIGGQTVTTTPPAKRG------IAMVFQSYALYPHLSVRENMALALKQERQPKEEIAAR 113
           + + GQ  +    A RG      +  V+Q + L P L+  EN+ + L   R+ +     +
Sbjct: 66  VLLLGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDK 125

Query: 114 VAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTR 173
                  + L      +PSELSGG+RQRVA+ RA+V EP   L DEP  NLD+       
Sbjct: 126 ALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVL 185

Query: 174 LEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRI 212
             +  L+++   +++ VTHD +      D+ + LRDG I
Sbjct: 186 SLMDDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223


Lambda     K      H
   0.320    0.137    0.391 

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: 186
Number of extensions: 12
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: 331
Length of database: 227
Length adjustment: 25
Effective length of query: 306
Effective length of database: 202
Effective search space:    61812
Effective search space used:    61812
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