GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Mesorhizobium ciceri biovar biserrulae WSM1271

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_013525179.1 MESCI_RS31065 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000185905.1:WP_013525179.1
          Length = 254

 Score =  256 bits (653), Expect = 4e-73
 Identities = 132/249 (53%), Positives = 172/249 (69%), Gaps = 1/249 (0%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           LL++RD+   FGGL+ L+ +  ++E+G I  LIGPNGAGKT+ FN +TG Y+P  G+  L
Sbjct: 3   LLEVRDLRLSFGGLKVLHDISFSVEKGAINSLIGPNGAGKTSLFNCLTGFYKPKGGSISL 62

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
            G+P +   PH +   G+ARTFQNIRLF EM+VLEN M G H R++  +  A+    A R
Sbjct: 63  SGRPITGLPPHRITALGLARTFQNIRLFKEMSVLENAMSGQHCRSRHGIVSAILHLPAQR 122

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
            EE AIR    + L FVGI Q A R A  LSYGDQRRLE+ARALA+ P+L+ LDEPAAG+
Sbjct: 123 REEEAIRAIGMRWLGFVGIEQHAHRRAGGLSYGDQRRLELARALASAPELILLDEPAAGL 182

Query: 185 NATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243
           N  EKL L  L+ +I+ E G T+LLIEHD+ L+M +  +I V DYG+ IA+G P  V+ +
Sbjct: 183 NEREKLDLIHLIRRIRDETGVTVLLIEHDMGLVMQVSEKIVVFDYGQKIADGAPEAVRAD 242

Query: 244 PAVIEAYLG 252
           P VIEAYLG
Sbjct: 243 PRVIEAYLG 251


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: 199
Number of extensions: 7
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: 254
Length adjustment: 24
Effective length of query: 231
Effective length of database: 230
Effective search space:    53130
Effective search space used:    53130
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