GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Thiothrix lacustris DSM 21227

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  217 bits (553), Expect = 4e-61
 Identities = 121/287 (42%), Positives = 179/287 (62%), Gaps = 13/287 (4%)

Query: 9   LAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVV 68
           ++K +A    VL   +L I DGEF  +LGPSGCGK+T+LR+IAG E  + G + + G  +
Sbjct: 12  ISKRFAS-QEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGDDI 70

Query: 69  NDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALL 128
             +PA +R    VFQ+YAL+PH++V+DN+AFGL+       +I  RV +  A++ L    
Sbjct: 71  ARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSEFA 130

Query: 129 ERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTT 188
            RKP  +SGGQ+QR AIARA++  P + L DE LS LD KLR Q++ ++K+L ++L  T 
Sbjct: 131 TRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGITF 190

Query: 189 VYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQ 248
           VYVTHDQ EA++++DR+++M +G+  Q G+P E+Y  PRNLF A FIG   +N   G + 
Sbjct: 191 VYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG--EINVFDGEIV 248

Query: 249 RQDGQLFIETAHQRWALTG-ERFSRLRHAMA----VKLAVRPDHVRI 290
           +  G+   E      ++ G  R  R  H  A    V + +RP+ +RI
Sbjct: 249 QALGEYQYEA-----SINGVVREIRCDHRFAVGDKVHVMLRPEDLRI 290


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: 329
Number of extensions: 13
Number of successful extensions: 1
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: 369
Length adjustment: 30
Effective length of query: 376
Effective length of database: 339
Effective search space:   127464
Effective search space used:   127464
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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