GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Sulfurivirga caldicuralii DSM 17737

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= TCDB::Q88P35
         (384 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  122 bits (306), Expect = 1e-32
 Identities = 74/220 (33%), Positives = 122/220 (55%), Gaps = 9/220 (4%)

Query: 4   LELRNVNKTYGSGLPDT--LKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGA 61
           LE RN+ KTY  G  +T  LK + L +   E + +VG SG GKSTL++ + GL++ T G 
Sbjct: 6   LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65

Query: 62  ILIDEQDVSGMSP------KDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEE 115
           +L+  Q  S +        ++R +  V+Q + L P ++  EN+   L IR+  +A   ++
Sbjct: 66  VLLLGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDK 125

Query: 116 VARVAKLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMR 175
              +   + +    A KP++LSGG++QRVA+ RAL   P   L DEP  NLD++   ++ 
Sbjct: 126 ALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVL 185

Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQ 215
           + M  ++QR  T  + VTHD +      D+   ++DG+I+
Sbjct: 186 SLMDDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMIR 224


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: 209
Number of extensions: 9
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: 384
Length of database: 227
Length adjustment: 26
Effective length of query: 358
Effective length of database: 201
Effective search space:    71958
Effective search space used:    71958
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: 48 (23.1 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