Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate H281DRAFT_01223 H281DRAFT_01223 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Burk376:H281DRAFT_01223 Length = 509 Score = 388 bits (997), Expect = e-112 Identities = 240/534 (44%), Positives = 324/534 (60%), Gaps = 37/534 (6%) Query: 8 STKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADP 67 ++ P L LR+ K+F VRAL +L+ + GEVHAL+GENGAGKSTL+KIL+G + D Sbjct: 5 TSAVPRLELRHASKSFGRVRALSDGDLSLWPGEVHALLGENGAGKSTLVKILAGVHQPD- 63 Query: 68 GGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLVARGD 126 GE +DG + P ARD G+AVIYQE +L +LS+AENI++GR + R G + Sbjct: 64 SGELLVDGVARRFATPAQARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRFGRIQYDA 123 Query: 127 MVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186 M R LA LG D V LSIA +Q++EIA+A+ A +L+MDEPT LS E Sbjct: 124 MRREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLTEV 183 Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246 +RLFA++R+LR +AIL+I+HR+ E+ L RVT++RDG V A L+ A+V M Sbjct: 184 ERLFAIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGMTADLNTDAIVSKM 243 Query: 247 VGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306 VGRDL FY K + E LSVR + K SFD+RAGE++ LAGLVGAGR+E+ Sbjct: 244 VGRDLETFYPK--AERPPGEARLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEV 301 Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366 AR +FG D G+++I G L G P A+ AG+A + EDR+ QGL L+ S+ Sbjct: 302 ARAIFGIDPLDAGQIQI-------GGKPLADGSPAAAVRAGLALVPEDRRQQGLALELSI 354 Query: 367 HENINLIVAARDALGLGRLNR--TAARRRTTEAIDTLGIRV----AHAQVNVGALSGGNQ 420 N ++ V LGRL R R T+ + G R+ VG LSGGNQ Sbjct: 355 ARNASMTV-------LGRLVRHGLITTRSETQLANQWGTRLRLKAGDPNAPVGMLSGGNQ 407 Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480 QKV+L + L P+VLI+DEPTRG+D+GAK+E+Y + L + G+A+LMISSELPEV+G+ Sbjct: 408 QKVVLGKWLATNPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGM 467 Query: 481 CDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAPAWVDVPLPGAGNA 534 DRVLVM EG ++ ++ A +ERI+A A G P+P GNA Sbjct: 468 ADRVLVMHEGRISADI---ARAEADEERIMAAALGQ----------PIPPLGNA 508 Lambda K H 0.320 0.136 0.382 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: 726 Number of extensions: 44 Number of successful extensions: 10 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: 540 Length of database: 509 Length adjustment: 35 Effective length of query: 505 Effective length of database: 474 Effective search space: 239370 Effective search space used: 239370 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: 52 (24.6 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