Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_012385982.1 BIND_RS15565 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_000019845.1:WP_012385982.1 Length = 511 Score = 336 bits (862), Expect = 1e-96 Identities = 204/510 (40%), Positives = 306/510 (60%), Gaps = 25/510 (4%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71 +L +R I K+F GV+AL V LT AGE+HAL+GENGAGKSTLMK+LSG Y G Sbjct: 4 ILEMRGISKSFTGVKALNDVNLTVKAGEIHALVGENGAGKSTLMKVLSGVYPHGSYEGAI 63 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 DG+ LG+ +I+QEL+L P +S+AENI++ R G++ R + Sbjct: 64 FYDGEERHFHDINDTEALGIIIIHQELALIPLMSIAENIFIANPPSRFGVIDRDTVYTRA 123 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 LA++G + +P + ++ + ++QLVEIA+A+ + R+L++DEPT L+ ++++ L Sbjct: 124 KELLAKVGLNEAPDTLITNIGVGKQQLVEIAKALSKKVRLLILDEPTASLNENDSEALLD 183 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD--RAHLSQAALVKMMVGR 249 L+ + R +G+ + ISH++ E+ +AD++TVLRDG V T+D + + +++ MV R Sbjct: 184 LLIEFRAQGITSILISHKLNEVSRVADQITVLRDGRTVDTMDCHAEAIEEDRIIRKMVDR 243 Query: 250 DLSGFYTKTH---GQAVEREVMLSV--RDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304 DL Y K G A+ SV D + +K +F ++ GE++G+AGL+GAGRT Sbjct: 244 DLEHRYPKREPKIGAAIFSIENWSVYHPQHPDRQLIKNVNFHVKRGEIVGIAGLMGAGRT 303 Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364 E A VFG R+ G+ +G V L +AI+AG+AY+TEDRK GL L Sbjct: 304 EFAMSVFG---RSWGQKITGRAVLNGREVDLST--VSRAINAGLAYVTEDRKELGLLLSD 358 Query: 365 SVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420 + +N+ L VA + + + + A+ R+ I + G+ VG LSGGNQ Sbjct: 359 DIRKNVTLANLEGVANQRVIDDMKEFKVASDYRSRMRIRSSGV-----YQEVGKLSGGNQ 413 Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480 QKV+LS+ L P +LILDEPTRG+DIGAK EIY +IN LA +G +++ISSE+PE++G+ Sbjct: 414 QKVVLSKWLFAGPEILILDEPTRGIDIGAKYEIYCIINDLANAGKGVVVISSEMPELLGI 473 Query: 481 CDRVLVMREGTLAGEVRPAGSAAETQERII 510 DR+ VM EG GE +A TQE+I+ Sbjct: 474 SDRIYVMNEGAFVGEF---PTAEATQEKIM 500 Score = 63.2 bits (152), Expect = 2e-14 Identities = 49/231 (21%), Positives = 104/231 (45%), Gaps = 7/231 (3%) Query: 24 PGVRALRKVELTAYAGEVHALMGENGAGKSTL-MKILSGAYTADPGGECHIDGQRVQIDG 82 P + ++ V GE+ + G GAG++ M + ++ G ++G+ V + Sbjct: 274 PDRQLIKNVNFHVKRGEIVGIAGLMGAGRTEFAMSVFGRSWGQKITGRAVLNGREVDLST 333 Query: 83 PQSARDLGVAVIYQ---ELSLAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLAR 137 A + G+A + + EL L + + +N+ L + + ++ + + +R Sbjct: 334 VSRAINAGLAYVTEDRKELGLLLSDDIRKNVTLANLEGVANQRVIDDMKEFKVASDYRSR 393 Query: 138 LGADFSPA-ANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196 + S V LS +Q V +++ + IL++DEPT + ++ +I L Sbjct: 394 MRIRSSGVYQEVGKLSGGNQQKVVLSKWLFAGPEILILDEPTRGIDIGAKYEIYCIINDL 453 Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 G ++ IS M E+ ++DR+ V+ +G FVG A +Q +++ ++ Sbjct: 454 ANAGKGVVVISSEMPELLGISDRIYVMNEGAFVGEFPTAEATQEKIMRSIM 504 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: 577 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 540 Length of database: 511 Length adjustment: 35 Effective length of query: 505 Effective length of database: 476 Effective search space: 240380 Effective search space used: 240380 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 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