GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Methylocystis bryophila S285

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085771912.1 B1812_RS12645 LPS export ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_002117405.1:WP_085771912.1
          Length = 288

 Score =  140 bits (352), Expect = 4e-38
 Identities = 85/251 (33%), Positives = 135/251 (53%), Gaps = 15/251 (5%)

Query: 2   SQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGT 61
           S+ +L I +++K +   + +  V + + RG+  GL+GPNGAGKTT F +ITGL +PD+G 
Sbjct: 48  SEGVLAIHNLAKSYKTRRVVEDVSLHVRRGEAVGLLGPNGAGKTTVFYMITGLVKPDSGR 107

Query: 62  FELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHK 121
             LDG   +P   +  A+ GI    Q + +F  +TV EN++          V   V   K
Sbjct: 108 ITLDGYDVTPLPMYRRARLGIGYLPQEMSVFRGLTVEENILA---------VLEIVEPDK 158

Query: 122 AAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPA 181
             R E+         LL+   +    K  A  +S G++RR EIARA+A  P  + LDEP 
Sbjct: 159 KKRAEQL------DGLLEEFRLAHLRKTPAIAVSGGERRRCEIARAIAGRPSFMLLDEPF 212

Query: 182 AGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241
           AG++     G+++L+  ++  G  +L+ +H V+  +GL +R  ++  G  + EG PA++ 
Sbjct: 213 AGIDPIAIGGIQDLVRHLKQRGIGVLITDHSVRETLGLTDRAYIIYNGHVLTEGAPAEIV 272

Query: 242 KNPAVIEAYLG 252
            NP V   YLG
Sbjct: 273 ANPDVRRIYLG 283


Lambda     K      H
   0.320    0.138    0.394 

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: 194
Number of extensions: 13
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: 255
Length of database: 288
Length adjustment: 25
Effective length of query: 230
Effective length of database: 263
Effective search space:    60490
Effective search space used:    60490
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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