Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Dino:3609459 Length = 548 Score = 290 bits (742), Expect = 1e-82 Identities = 204/540 (37%), Positives = 292/540 (54%), Gaps = 33/540 (6%) Query: 1 MSDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILS 60 + MSDT +AP + LR I K F V+A + + + G +H ++GENGAGKSTLM IL Sbjct: 15 VGSMSDT--QAPAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILY 72 Query: 61 GAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRG 120 G Y AD GE I GQ+ +I Q+A G+ +++Q L N +V EN+ LG G Sbjct: 73 GFYKAD-AGEIFIKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGA---EEG 128 Query: 121 LVARGDMVRACAPTLARLGADF----SPAANVASLSIAQRQLVEIARAVHFEARILVMDE 176 + R + +A L L ++ +P A + LS+ +Q VEI +A++ +A IL++DE Sbjct: 129 ALLRPSLAKA-RKLLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDE 187 Query: 177 PTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAH 236 PT L+ E D LF ++ L+ EG I+ I+H++ EI E D V+V+R G T+ A Sbjct: 188 PTGVLTPAEADHLFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTAD 247 Query: 237 LSQAALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGR---RVKGCSFDLRAGEVL 293 S L ++MVGR + KT Q + + V D + RVKG S +RAGEVL Sbjct: 248 TSPEQLAELMVGRKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVL 307 Query: 294 GLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPA----GGPRQAIDAGIA 349 G+AG+ G G++EL ++ G T G V + SG + L G R+A GIA Sbjct: 308 GIAGVAGNGQSELLEVLGGMRPAT-GRVTV-----SGQQIDLTGKHSNGKTRRA--QGIA 359 Query: 350 YLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEA-IDTLGIRVAHA 408 ++ EDR+ +GL +D EN+ A G L A R E I +R A Sbjct: 360 HVPEDRQAEGLIMDYHAWENVAFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADC 419 Query: 409 QVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAIL 468 + SGGNQQK++L+R +E P +L++ +PTRGVDIGA I++ I AL +G AIL Sbjct: 420 WLAAKNFSGGNQQKIVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAIL 479 Query: 469 MISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAPAWVDVPL 528 ++S EL E++ L DRV VM +G + GE RP AAET E+ + L P D PL Sbjct: 480 LVSVELEEILSLSDRVAVMFDGRIMGE-RP---AAETNEKELGLLMAGITEPP--TDKPL 533 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: 656 Number of extensions: 39 Number of successful extensions: 8 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: 548 Length adjustment: 35 Effective length of query: 505 Effective length of database: 513 Effective search space: 259065 Effective search space used: 259065 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