GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Hydrogenovibrio kuenenii DSM 12350

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000526715.1:WP_024852149.1
          Length = 263

 Score =  138 bits (347), Expect = 2e-37
 Identities = 89/220 (40%), Positives = 127/220 (57%), Gaps = 6/220 (2%)

Query: 17  PPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGG-TVVNDLPARE 75
           PPVL  ++L+I  G+   ++G SGCGKST+L+MIAGL   S G +RI G TVV   P+ +
Sbjct: 22  PPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGKTVVK--PSAK 79

Query: 76  RNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAM 135
            N  M+FQ  +LYP MSV +N A GL        + DR V E+  ++ L    ++  + +
Sbjct: 80  WN--MMFQKPSLYPWMSVRENAALGLVFAGTYKQKQDR-VEELLDMVGLSEHKDKNVQEL 136

Query: 136 SGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQ 195
           SGGQQQR A+AR++   P + L DEP S LDA  R  L+ ++ ++      T + VTHD 
Sbjct: 137 SGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGITMIMVTHDI 196

Query: 196 LEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235
            EA+ +AD+V++M        G       YPR+  AA FI
Sbjct: 197 EEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236


Lambda     K      H
   0.321    0.137    0.403 

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: 193
Number of extensions: 12
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: 406
Length of database: 263
Length adjustment: 28
Effective length of query: 378
Effective length of database: 235
Effective search space:    88830
Effective search space used:    88830
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: 48 (23.1 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