Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate HSERO_RS05195 HSERO_RS05195 xylose ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__HerbieS:HSERO_RS05195 Length = 518 Score = 347 bits (889), Expect = e-100 Identities = 213/512 (41%), Positives = 306/512 (59%), Gaps = 26/512 (5%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71 +L +R I K+FPGV+AL V L GE+HA++GENGAGKSTLMK+LSG Y G+ Sbjct: 4 ILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGDI 63 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 G+ + + LG+ +I+QEL+L P LSV EN++LG R G++ Sbjct: 64 VYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNEQARGGVIDWEQSYVRA 123 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 LA++G SP V L + ++QL+EIA+A+ E ++L++DEPT L+ ++D L Sbjct: 124 KELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDALLE 183 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD-RAH-LSQAALVKMMVGR 249 L+ +L+ +G+A + ISH++ EI ++AD +TVLRDG V T D RA +S+ +++ MVGR Sbjct: 184 LLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHMVGR 243 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDV-------ADGRRVKGCSFDLRAGEVLGLAGLVGAG 302 +++ Y + Q EV+ VRD D +K + +RAGE++G+AGL+GAG Sbjct: 244 EMADRYPQRDPQI--GEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGAG 301 Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362 RTELA+ +FG R G+ G V L +AI GIAY+TEDRK GL L Sbjct: 302 RTELAKSIFG---RAYGKKITGQAFLHGKEVDLST--IEKAIAKGIAYVTEDRKGDGLVL 356 Query: 363 DQSVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGG 418 ++ + +NI+L V+ R + R + AA + + IR + V LSGG Sbjct: 357 EEDIKKNISLANLGGVSERTVIDEAREYKIAADFK-----QQMRIRCSSVLQKVVNLSGG 411 Query: 419 NQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVV 478 NQQKV+LS+ L QP VLILDEPTRG+D+GAK EIY +I+ LA G I+MISSE+PE++ Sbjct: 412 NQQKVVLSKWLFSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELL 471 Query: 479 GLCDRVLVMREGTLAGEVRPAGSAAETQERII 510 G+CDR+ VM EG G + A + E R I Sbjct: 472 GMCDRIYVMNEGQFVGHLPKAEATQENIMRAI 503 Score = 81.3 bits (199), Expect = 8e-20 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 13/230 (5%) Query: 28 ALRKVELTAYAGEVHALMGENGAGKSTLMKILSG-AYTADPGGECHIDGQRVQIDGPQSA 86 A++ V ++ AGE+ + G GAG++ L K + G AY G+ + G+ V + + A Sbjct: 278 AIKDVNMSVRAGEIVGIAGLMGAGRTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKA 337 Query: 87 RDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADF---- 142 G+A + ++ L + E+I +L G V+ ++ ++ ADF Sbjct: 338 IAKGIAYVTEDRK-GDGLVLEEDIKKNISLANLGGVSERTVIDEAREY--KIAADFKQQM 394 Query: 143 -----SPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLR 197 S V +LS +Q V +++ + + +L++DEPT + ++ +I +L Sbjct: 395 RIRCSSVLQKVVNLSGGNQQKVVLSKWLFSQPEVLILDEPTRGIDVGAKFEIYNIISKLA 454 Query: 198 GEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 EG I+ IS M E+ + DR+ V+ +G FVG L +A +Q +++ ++ Sbjct: 455 AEGKCIIMISSEMPELLGMCDRIYVMNEGQFVGHLPKAEATQENIMRAIM 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: 604 Number of extensions: 24 Number of successful extensions: 9 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: 518 Length adjustment: 35 Effective length of query: 505 Effective length of database: 483 Effective search space: 243915 Effective search space used: 243915 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