Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 319 bits (818), Expect = 8e-92 Identities = 176/381 (46%), Positives = 245/381 (64%), Gaps = 7/381 (1%) Query: 1 MADIHCQALAKHYAGG-PPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 MA + + + K Y G P L ++L I +GEF++L+GPSGCGKST++ IAGLE I+GG Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 60 TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119 + IG V+ + ++R++AMVFQ+YALYP MSV +NI FGL+ K P A+ID V VA Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179 LL +E LL RKP +SGGQQQR A+ RA+ + P ++LFDEPLSNLDAKLR ++R ++K Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239 +HQRL+TTTVYVTHDQ+EAMTL D+V +M+DG I Q G+P E+Y P N F A FIG+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 240 MNFLSGTVQRQDGQL--FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRI-AGEREP 296 MNF+ +QR+DG+L +++ R L V L +RP+ + + AGE + Sbjct: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 Query: 297 AASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356 A+S+ V++ E G D L+ + D + + D PQ G TLTL D ++ +FD Sbjct: 301 ASSIR--AEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358 Query: 357 VESGENLSLPDAALTAPGSDD 377 +GE L ++L A G D Sbjct: 359 ANTGERLGTA-SSLPAQGHAD 378 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: 379 Number of extensions: 13 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: 386 Length adjustment: 31 Effective length of query: 375 Effective length of database: 355 Effective search space: 133125 Effective search space used: 133125 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