Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 340 bits (871), Expect = 1e-97 Identities = 204/492 (41%), Positives = 300/492 (60%), Gaps = 19/492 (3%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 +L ++NI K F GV+AL V L AG V A++GENGAGKSTLMKILSG Y D G + Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYP-DYKGTIY 59 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQR-RGLVARGDMVRAC 131 +G V+ + A++ G+ +I+QEL+L P LS+ ENI+LGR + GL+ M + Sbjct: 60 YNGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEA 119 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 A L RL + P V+ L + Q+QLVEIA+A+ E+++++MDEPT+ +S E + LF Sbjct: 120 AQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 +IR LR EG AI YISH++ E+ +ADR VLRDG + + + +++ AL++ MVGR++ Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239 Query: 252 SGFYTKTHGQAVEREVMLSVR-------DVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304 G+ + E +LSV+ +AD ++ +F+L GEVLG+ GL+GAGRT Sbjct: 240 V-IERSCSGRQFD-ETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRT 297 Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364 EL +FG E+ +A P++A+DAG+A + EDRK GL L Sbjct: 298 ELMEALFGVLPHQGAEITLAGKVHE-------FQKPQEAMDAGLALVPEDRKQDGLVLCM 350 Query: 365 SVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVM 424 + N +L V L G L+ + + + L I+ + + V LSGGNQQKV+ Sbjct: 351 DLCTNSSLTV-VDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVV 409 Query: 425 LSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRV 484 L++ L +P+VL+LDEPTRG+DI AK+EIY+LI LA G+ ++++SSELPE++ + DRV Sbjct: 410 LAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRV 469 Query: 485 LVMREGTLAGEV 496 LVM EG L + Sbjct: 470 LVMAEGRLTANI 481 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: 552 Number of extensions: 30 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: 502 Length adjustment: 35 Effective length of query: 505 Effective length of database: 467 Effective search space: 235835 Effective search space used: 235835 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