GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Pontibacillus litoralis JSM 072002

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_036833161.1 N784_RS05555 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_000775615.1:WP_036833161.1
          Length = 250

 Score =  155 bits (391), Expect = 1e-42
 Identities = 93/255 (36%), Positives = 142/255 (55%), Gaps = 10/255 (3%)

Query: 8   VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67
           V+++   ++  FGG  A+  V + I   +   +IGPNGAGKTTFFN+++G   P  G+  
Sbjct: 3   VIMETKDVTVSFGGHVAVDQVSVQILERKFTSIIGPNGAGKTTFFNLLSGQMKPTNGSIY 62

Query: 68  LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENV--MVGRHIRTGSGLFGAVFRTK 125
             G      +  E  + GI R+FQ   +F  +T  ENV   V    +    +F    + K
Sbjct: 63  FKGADVTKRSATERTRLGIGRSFQITNVFPNLTVFENVRLAVQSQAKVRYQMFAHFNQYK 122

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
            F+       ++  E+L  V +   A+  A  L++G++R+LEIA  LA + +L+ LDEP 
Sbjct: 123 QFQ-------EKTDEILALVFLQDKANSLAMNLAHGEKRKLEIAMLLALETELLLLDEPT 175

Query: 186 AGMNATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244
           AGM+  E   + ++I  I+   NRTI+LIEH + ++MG+ D V VL +G+ IA+G P E+
Sbjct: 176 AGMSLEEVPAIIDVIHEIKQQGNRTIVLIEHKMDMIMGMSDEVLVLYHGELIAKGTPNEI 235

Query: 245 QKNEKVIEAYLGTGG 259
             NE V  AYLG GG
Sbjct: 236 VHNEIVQSAYLGGGG 250


Lambda     K      H
   0.319    0.137    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: 149
Number of extensions: 7
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: 260
Length of database: 250
Length adjustment: 24
Effective length of query: 236
Effective length of database: 226
Effective search space:    53336
Effective search space used:    53336
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: 47 (22.7 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