GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Pantoea rwandensis LMG 26275

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084934314.1 HA51_RS09630 LPS export ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_002095475.1:WP_084934314.1
          Length = 241

 Score =  144 bits (364), Expect = 1e-39
 Identities = 78/242 (32%), Positives = 133/242 (54%), Gaps = 14/242 (5%)

Query: 15  ISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYE 74
           ++K + G + + DV + +K G++ GL+GPNGAGKTT F ++ G+   DAG   +  +   
Sbjct: 9   LAKAYKGRRVVEDVSLQVKSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGRIVIDDEDIS 68

Query: 75  PTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAI 134
              +H  A+ GI    Q   +F  ++  +N+M             AV + +    EE   
Sbjct: 69  ILPLHARARRGIGYLPQEASIFRRLSVFDNLM-------------AVLQIRDDLTEEQR- 114

Query: 135 AKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKV 194
             RA EL++   I    D   + LS G++RR+EIARALA +P+ I LDEP AG++    +
Sbjct: 115 QDRANELMEEFHIEHLRDSMGQALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVI 174

Query: 195 QLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEKVIEAY 254
            ++++I+ +R+    +L+ +H+V+  + +C+R  ++  G  IA G P E+  +E+V   Y
Sbjct: 175 DIKKIIEHLRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPDEILADEQVKRVY 234

Query: 255 LG 256
           LG
Sbjct: 235 LG 236


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: 157
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: 260
Length of database: 241
Length adjustment: 24
Effective length of query: 236
Effective length of database: 217
Effective search space:    51212
Effective search space used:    51212
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