Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 402 bits (1033), Expect = e-116 Identities = 231/512 (45%), Positives = 323/512 (63%), Gaps = 18/512 (3%) Query: 9 TKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG 68 T P L +RNI +TFPGV+AL +V L AGEV AL GENGAGKSTLMKIL+G Y DPG Sbjct: 5 TGVPFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPG 64 Query: 69 GECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDM 127 G ++GQ V + AR LGV +IYQEL++ NL+V ENI+L R + R GL+ R M Sbjct: 65 GTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRM 124 Query: 128 VRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187 R LA + D PA V+ LS+ Q+Q++EIA+A+ ++ ++MDEPT LS HET Sbjct: 125 YREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETS 184 Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 L ++++LR +A++YISHR+ EI ELADRVTVLRDG VGT A +++ LV++MV Sbjct: 185 VLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMV 244 Query: 248 GRDLSGFYTKTHGQAVEREVM----LSVRDVADGR-RVKGCSFDLRAGEVLGLAGLVGAG 302 R+LS Y + A V+ LS++ V R++ SF L GEVLG+AGLVG+G Sbjct: 245 ARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSG 304 Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362 RTE+ ++FG A T G V+I S P AI +GI ++TEDRK QGL L Sbjct: 305 RTEIMEMIFGMRACT-GSVKIEGKPVS-------IRNPHDAIRSGIGFVTEDRKAQGLIL 356 Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422 +V EN +L R + + R + LGI+ + V LSGGNQQK Sbjct: 357 GMTVRENFSLTHLERYS-PFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQK 415 Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482 +++++ + P+VLI+DEPTRG+D+GAK+E++ LI LA G+ +++ISS+L EV+ + D Sbjct: 416 IVIAKWVARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSD 475 Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALAT 514 R+L +REG ++GE+ A +QE+++ALAT Sbjct: 476 RILTVREGRISGEL---SRAQASQEKVMALAT 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: 643 Number of extensions: 32 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: 505 Length adjustment: 35 Effective length of query: 505 Effective length of database: 470 Effective search space: 237350 Effective search space used: 237350 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