Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 410 bits (1054), Expect = e-119 Identities = 248/513 (48%), Positives = 330/513 (64%), Gaps = 17/513 (3%) Query: 4 MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63 M+D S+ PLL L I K + AL V +AGEVHALMGENGAGKSTLMKILSG Sbjct: 1 MADISSP-PLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNE 59 Query: 64 TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLV 122 D G IDGQ + I P+ AR G+A+I+QEL+ P+++VAEN++LG+ G++ Sbjct: 60 QRD-SGVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGIL 118 Query: 123 ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 182 R M R L R+ AD P A + SLSI ++Q+VEIARAV A++LV+DEPT LS Sbjct: 119 DRKRMHREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALS 178 Query: 183 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 242 ET +L+ LI Q+R +G+ ++YISHRM E+ +LA+RVTV RDG ++GT + ++S + Sbjct: 179 RAETLQLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDI 238 Query: 243 VKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAG 302 V+MMVGR + Y H +V+L VRD+A G SF++ AGEV+ ++GLVG+G Sbjct: 239 VRMMVGRQIVDLY--QHEPRTPGDVLLEVRDLA-GSATGPVSFEVSAGEVVSMSGLVGSG 295 Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362 RTE+ARL+FGAD R++G VR+A G + P+ P AI GI +TEDRK QGLFL Sbjct: 296 RTEVARLLFGADPRSQGSVRLA------GRESQPS-DPTAAIADGIGMVTEDRKTQGLFL 348 Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422 SV NI++ G G + R R E + L +R ++ V ALSGGNQQK Sbjct: 349 GHSVEHNIDISSLDNFVAG-GVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQK 407 Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482 L+R L R+LILDEPTRGVDIGAK EIY LI+ LA++G AIL+ISS+LPE +G+ D Sbjct: 408 AALARWLLRDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISD 467 Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATG 515 RVLVMR G + V S + T+E ++ ATG Sbjct: 468 RVLVMRGGRI---VHQLPSCSATEEEVMLHATG 497 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: 660 Number of extensions: 36 Number of successful extensions: 9 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: 510 Length adjustment: 35 Effective length of query: 505 Effective length of database: 475 Effective search space: 239875 Effective search space used: 239875 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