GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Streptococcus massiliensis 4401825

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_026129775.1 BN415_RS00760 cell division ATP-binding protein FtsE

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000341525.1:WP_026129775.1
          Length = 230

 Score =  103 bits (257), Expect = 3e-27
 Identities = 66/227 (29%), Positives = 115/227 (50%), Gaps = 19/227 (8%)

Query: 24  LSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSIG 83
           + K   G  A+    + +  G    ++GP+GAGK+T   LL   I+ D+G +   G ++ 
Sbjct: 10  VKKYDNGTTALRGVTVTIHPGEFAYIVGPSGAGKSTFIRLLYREIKLDKGSLQVAGFNLA 69

Query: 84  QLAPHQIAL--RGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEER 141
           ++    I +  R     FQ  K+L + TV EN+  A +                V  E R
Sbjct: 70  KIKKRDIPMLRRNVGVVFQDYKLLPKKTVYENIAYAME----------------VIGERR 113

Query: 142 AN-REKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPT 200
           ++ +++ M +L+ VGL  K + +   LSGG+++ + +ARA+++NPK+++ DEP   ++P 
Sbjct: 114 SHIKKRVMEVLDLVGLKHKVRSFPNELSGGEQQRIAIARAIVNNPKVLIADEPTGNLDPD 173

Query: 201 LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLAD 247
              +I   +   N QG T L+  HN  ++ TL H V  +  GR + D
Sbjct: 174 NSWEIMNLLERINLQGTTVLMATHNSQIVNTLRHRVIAIENGRVVRD 220


Lambda     K      H
   0.319    0.136    0.389 

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: 145
Number of extensions: 6
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: 267
Length of database: 230
Length adjustment: 24
Effective length of query: 243
Effective length of database: 206
Effective search space:    50058
Effective search space used:    50058
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 (21.7 bits)
S2: 46 (22.3 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