GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Streptococcus massiliensis 4401825

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_018371978.1 BN415_RS05890 amino acid ABC transporter ATP-binding protein

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>NCBI__GCF_000341525.1:WP_018371978.1
          Length = 246

 Score =  130 bits (327), Expect = 4e-35
 Identities = 81/238 (34%), Positives = 131/238 (55%), Gaps = 13/238 (5%)

Query: 6   LRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGM 65
           +++++K++ +NEV++DI+L I +GE +  +G SG GKSTL+R I  LE  SGG++   G 
Sbjct: 8   IKHLKKSFGKNEVLKDISLTIHEGEVISIIGSSGSGKSTLLRSINLLEQPSGGEIHYKGT 67

Query: 66  RV----NDVAPAKRGIAMVFQSYALYPHMTLYDN--MAFGLKLAGTKKPEIDAAVRNAAK 119
            V     D+   +  + MVFQS+ L+ ++ + +N  +A    L   +      A  N  K
Sbjct: 68  NVLAEGYDLTHYREKLGMVFQSFNLFENLNVLENTIVAQTTVLKRDRSEAEKIAKENLEK 127

Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179
           +   +     KPKQLSGGQ+QRVAI RA++  P   LFDEP S LD     +M  E  ++
Sbjct: 128 VGMGERFWQAKPKQLSGGQKQRVAIARALSMNPDAILFDEPTSALDP----EMVGEVLKI 183

Query: 180 HDELK---TTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFI 234
             +L     TMI VTH+   A  ++D+++ +  G + + G+P  ++  P       F+
Sbjct: 184 MQDLAKEGLTMIVVTHEMEFARDVSDRVIFMDKGVIAEEGNPKDIFTNPKEERTKEFL 241


Lambda     K      H
   0.320    0.135    0.384 

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: 215
Number of extensions: 7
Number of successful extensions: 4
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: 369
Length of database: 246
Length adjustment: 27
Effective length of query: 342
Effective length of database: 219
Effective search space:    74898
Effective search space used:    74898
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 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