Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 293 bits (750), Expect = 6e-84 Identities = 173/374 (46%), Positives = 229/374 (61%), Gaps = 11/374 (2%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + K + G VL + L I GEF++L+GPSGCGKST++ IAGLE ++ G Sbjct: 1 MAALEINNVCKDF-GSEQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSGE 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 +RI G V ER++AMVFQ+YALYP M+V NI+FGL K P AE + V VA Sbjct: 60 IRIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVAD 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 LL + LLERKP +SGGQ+QR A+ RA+ + P V+LFDEPLSNLDAKLR +R +IK+L Sbjct: 120 LLQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKKL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 HQRL TT VYVTHDQ+EAMTLAD + +M+DGRI+Q GSP E+Y P +LF AGF+G+P+M Sbjct: 180 HQRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPSM 239 Query: 241 NFLSGTVQRQDG--QLFIETAHQRWALTGERFSRLRHAMAVK------LAVRPDHVRIAG 292 NF+S T+ G +L +ET + R A+ K L +RP+H Sbjct: 240 NFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVILGLRPEHFTEDD 299 Query: 293 ER--EPAASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQH 350 R E A + + +VE GAD LL + GD TA V + G LTL +D Sbjct: 300 ARLGEYAEGVALTPRITVVEPTGADILLQLKLGDGEATARVGPKCRVKAGERLTLRIDMG 359 Query: 351 ELHVFDVESGENLS 364 +FD E+ + L+ Sbjct: 360 RAVMFDRETEKRLA 373 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: 399 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: 373 Length adjustment: 30 Effective length of query: 376 Effective length of database: 343 Effective search space: 128968 Effective search space used: 128968 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 24 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