GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Pontibacter ramchanderi LP43

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_101444435.1 BD749_RS11320 LPS export ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_002846395.1:WP_101444435.1
          Length = 243

 Score =  132 bits (332), Expect = 7e-36
 Identities = 75/249 (30%), Positives = 133/249 (53%), Gaps = 15/249 (6%)

Query: 8   VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67
           ++L+   + K++     ++DV + + +G++ GL+GPNGAGKTT F +I GL  P+ G   
Sbjct: 1   MILRAEHLYKKYKSRLVVNDVSVEVNQGEIVGLLGPNGAGKTTSFYMIVGLVKPNEGRIY 60

Query: 68  LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127
           L  +      +++ AK G+    Q   +F ++T  EN++    +            T   
Sbjct: 61  LDKEDITDLPMYQRAKRGVGYLAQEASVFRQLTVEENILAPLEM------------TNRP 108

Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187
           K E+    ++ +ELL+   +      K   LS G++RR EIARALA DP+ + LDEP AG
Sbjct: 109 KKEQL---EKVEELLEEFSLTHVRKNKGIVLSGGERRRTEIARALAVDPKFVLLDEPFAG 165

Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247
           ++     +++ ++ ++++ N  IL+ +H+V   + + DR  +L  GK +  G   E+  +
Sbjct: 166 VDPIAVEEIQSIVAKLKSKNIGILITDHNVNETLSITDRAYLLFEGKILKSGTAEELAAD 225

Query: 248 EKVIEAYLG 256
           E+V   YLG
Sbjct: 226 EQVRRVYLG 234


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: 151
Number of extensions: 8
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: 243
Length adjustment: 24
Effective length of query: 236
Effective length of database: 219
Effective search space:    51684
Effective search space used:    51684
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