Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 306 bits (785), Expect = 5e-88 Identities = 168/370 (45%), Positives = 233/370 (62%), Gaps = 8/370 (2%) Query: 1 MADIHCQALAKHYAGGP-PVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 MA + + + K Y L + L I GEF++L+GPSGCGKST++ IAGLE+I+GG Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 60 TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119 + + G ++ ++R++AMVFQ+YALYP MSV DNIAFGL+ K PAA+I+ V VA Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179 LL +E LLERKP +SGGQQQR A+ RA+ + P ++LFDEPLSNLDAKLR ++R +IK Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239 +HQRL+TTTVYVTHDQ+EAMTL D+V +M+DG I Q G+P E+Y P NLF A FIG+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 240 MNFLSGTVQRQDGQ----LFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGERE 295 MNF+ ++++DG+ L E L LR + L +RP+ + +A Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELI-LGIRPEQIGLA--PA 297 Query: 296 PAASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVF 355 +A + V +E+VE G D L+ + D+ P+ G TL L D +F Sbjct: 298 GSADFSLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFDPRRALLF 357 Query: 356 DVESGENLSL 365 D ++GE L + Sbjct: 358 DAQTGERLGV 367 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: 387 Number of extensions: 11 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: 406 Length of database: 390 Length adjustment: 31 Effective length of query: 375 Effective length of database: 359 Effective search space: 134625 Effective search space used: 134625 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 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