Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 339 bits (870), Expect = 1e-97 Identities = 200/483 (41%), Positives = 296/483 (61%), Gaps = 32/483 (6%) Query: 44 LMGENGAGKSTLMKILSGAYTADPG-GECHIDGQRV-QIDGPQSARDLGVAVIYQELSLA 101 L+GENGAGKST++KIL+GA AD G G +G + + D P +++G+ IYQE +L Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 102 PNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEI 161 ++SVAEN+YLGR R G V M L LG +P V LS+A++Q+VEI Sbjct: 61 ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVEI 120 Query: 162 ARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVT 221 A+A+ A++++MDEPT LS E D+L +I L+ +G++I+Y+SH++ E+ DR T Sbjct: 121 AKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRYT 180 Query: 222 VLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDV----ADG 277 + RDG ++ + D +S +V++MVGRD+ + + EVML V+ V A G Sbjct: 181 IFRDGAYITSGDVCDVSVDDIVRLMVGRDVE--FVRKPLTGAPGEVMLKVQSVSRTAAGG 238 Query: 278 RR------VKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGG 331 R + S D+RAGE++G AGLVGAGRTELAR++FGAD G + + G Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYV------NG 292 Query: 332 LVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAAR 391 P PR+ I AG+A + EDRK Q FL S+ N++L GL R Sbjct: 293 RQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLG----GLQRWGMFIDD 348 Query: 392 RRTTEAID----TLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDI 447 R T+ I L I++++ V +G LSGGNQQKV+L+R + ++P+VLI+DEPTRG+D+ Sbjct: 349 RAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDV 408 Query: 448 GAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQE 507 GAK+E+++L+ +A++GVA+++ISSELPEV+ + DR++ REG + G V SA E E Sbjct: 409 GAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIV----SADEATE 464 Query: 508 RII 510 ++ Sbjct: 465 ELL 467 Score = 62.8 bits (151), Expect = 3e-14 Identities = 61/262 (23%), Positives = 121/262 (46%), Gaps = 27/262 (10%) Query: 13 LLALRNICKTFPG------VRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTAD 66 +L ++++ +T G L + + AGE+ G GAG++ L +++ GA D Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCD 284 Query: 67 PGGECHIDGQRVQ-IDGPQSARDLGVAVIYQEL---------SLAPNLSVAENIYLGRAL 116 G +++G++V P+ GVA++ ++ S+ N+S+ LG L Sbjct: 285 EG-MIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPS---LG-GL 339 Query: 117 QRRGLV----ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARIL 172 QR G+ A +++ L ++ S A + +LS +Q V +AR + + ++L Sbjct: 340 QRWGMFIDDRAETQLIQDYQKRLRIKMSNDSVA--IGTLSGGNQQKVILARCMALKPKVL 397 Query: 173 VMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL 232 ++DEPT + + L+ + G+A++ IS + E+ ++DR+ R+G G + Sbjct: 398 IVDEPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIV 457 Query: 233 DRAHLSQAALVKMMVGRDLSGF 254 ++ L+ M S F Sbjct: 458 SADEATEELLMARMAQGVSSSF 479 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: 629 Number of extensions: 35 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 540 Length of database: 485 Length adjustment: 35 Effective length of query: 505 Effective length of database: 450 Effective search space: 227250 Effective search space used: 227250 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