Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate SM_b20855 SM_b20855 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Smeli:SM_b20855 Length = 504 Score = 380 bits (976), Expect = e-110 Identities = 215/508 (42%), Positives = 315/508 (62%), Gaps = 15/508 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 L L++I K+F G+ ALR V GEVHAL+GENGAGKSTLM++L G G E Sbjct: 5 LANLKSISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQG-EVV 63 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132 I+G+R ++ P+ AR LG+ VI+QEL+LAP+LSVAENI+LG + L++R + R Sbjct: 64 INGKRTELRDPRDARALGIVVIHQELALAPDLSVAENIFLG---ELPTLISRFSLRRRAK 120 Query: 133 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 192 + RLG D P V +LS+A +Q+VEIA+A+ + +I+V DEPT L + +L + Sbjct: 121 QLIDRLGFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQI 180 Query: 193 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252 IR LR G+ I+YISHR+ E+ ++ADR+TV++DG VGT+ + +++MMVGR ++ Sbjct: 181 IRGLRDRGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRPIA 240 Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312 + + + + E +L+V+ + GR V+ SF +RAGE++GL GL+G+GRTE+AR +FG Sbjct: 241 NMFPERSQRTIGAE-LLNVKKLNAGRMVRDVSFSVRAGEIVGLGGLIGSGRTEVARAIFG 299 Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372 AD G + + A L PR A+ AGI + EDRK G+ +D+ + N + Sbjct: 300 ADPLDSGTISLKGKA-------LKLKSPRDAVKAGIGLVPEDRKEHGVVIDKPIRVNATM 352 Query: 373 IVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQ 432 + LG L R T +L ++ + V +LSGGNQQKV+L++ Sbjct: 353 ARMSSVVNALGFLKPALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKVVLAKWFHAG 412 Query: 433 PRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 492 V+ILDEPTRGVD+GAK+EIY LIN LA+ G A+L+ISSE E+ GLCDRVL M +G + Sbjct: 413 GDVIILDEPTRGVDVGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDRVLAMGQGQI 472 Query: 493 AGEVRPAGSAAETQERIIALATGAAAAA 520 GE+ P+ ++E ++ L+ A A Sbjct: 473 RGELTPSN---YSEENLLGLSMMGGARA 497 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: 630 Number of extensions: 41 Number of successful extensions: 9 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: 504 Length adjustment: 35 Effective length of query: 505 Effective length of database: 469 Effective search space: 236845 Effective search space used: 236845 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