GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Shewanella amazonensis SB2B

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  197 bits (501), Expect = 4e-55
 Identities = 111/258 (43%), Positives = 162/258 (62%), Gaps = 11/258 (4%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           M+ +  Q L   Y G   VL  L+L +  GE   LLGPSGCGK+T+LR IAGL+DIS G+
Sbjct: 1   MSTLSIQGLHSDYRG-EQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGS 59

Query: 61  LRIGGTVVND----LPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVR 116
           + I G  V+     +   +R++ M+FQ+YAL+PH++V DNI FG+R+L + +  +  R+ 
Sbjct: 60  IAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSV--RLE 117

Query: 117 EVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGD 176
           E+ +L+ LE L +R P  +SGGQQQR +IARA+   P + L DEP SN+DA++R  L  +
Sbjct: 118 EMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLE 177

Query: 177 IKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG 236
           I+ + +    + V+VTH + EA   AD + L + GRIVQ G P  LY+ P   + A F+G
Sbjct: 178 IRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLG 237

Query: 237 TPAMNFLSGTVQRQDGQL 254
             A N+L   V+ + GQL
Sbjct: 238 --ASNYLD--VRLEAGQL 251


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: 292
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: 341
Length adjustment: 30
Effective length of query: 376
Effective length of database: 311
Effective search space:   116936
Effective search space used:   116936
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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