Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 291 bits (745), Expect = 2e-83 Identities = 155/370 (41%), Positives = 233/370 (62%), Gaps = 6/370 (1%) Query: 1 MADIHCQALAKHYAG-GPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 M+ + +++ K Y G L +D+ I GEF++L+GPSGCGKST++ IAGLE I+ G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 60 TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119 ++ + G ++ + ++R++AMVFQ+YALYP MSV +NIAFGL+ P EID+ V VA Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179 LL + L+ +KP +SGGQQQR A+ RA+ + P ++LFDEPLSNLDAKLR ++R +IK+ Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239 LHQRL+TT VYVTHDQ+EAMTLADR+ +++DG + Q G+P E+Y P NLF AGF+G+PA Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 240 MNFLSGTVQRQDGQLFIETA---HQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREP 296 M+F+ TV++ +G L E + L F R V L +RP+H+ +++ Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300 Query: 297 AASLTC--PVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHV 354 +L ++E+ E G D + + D + + + G T L D ++ Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVVF 360 Query: 355 FDVESGENLS 364 FD E+ + ++ Sbjct: 361 FDPETEKRIA 370 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: 407 Number of extensions: 15 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: 372 Length adjustment: 30 Effective length of query: 376 Effective length of database: 342 Effective search space: 128592 Effective search space used: 128592 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