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.
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:
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