Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 376 bits (966), Expect = e-109 Identities = 226/504 (44%), Positives = 306/504 (60%), Gaps = 16/504 (3%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P+LA+R + + F V+ L V+ GEVHAL+GENGAGKST MKIL+G Y A GE Sbjct: 4 PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAG-YLAPSAGEV 62 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 +DG+ V + A GV +I+QE +LA L+V ENI+LGR L+R + M Sbjct: 63 LLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAES 122 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 L RL P A V++LS+ RQ+VEIA+A+ +AR+L+MDEPT L+ ETD L Sbjct: 123 RRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLE 182 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 + +LR G AILY SH++ E+ +ADRVTVLRDG V T LS+ + + MVGR+L Sbjct: 183 QVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGREL 242 Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311 SG + A E +L V + V+ SF LR GEVLG AGLVG+GRTEL + Sbjct: 243 SGLFPPKSSPA--PEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIV 300 Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371 G T GEVR+ LP A AG+ YLTEDRK +GL L + + EN+ Sbjct: 301 GLRPAT-GEVRMEGS-------PLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLT 352 Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 L+ A D G +++ A R T+AI IRV ++ G+LSGGNQQK++L++ + Sbjct: 353 LL--ALDRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLA 410 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 +PRV+I+DEPTRG+D+G K +IY I LA G +++++SSELPEV+GL +RV+VM G Sbjct: 411 EPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGR 470 Query: 492 LAGEVRPAGSAAETQERIIALATG 515 +AGEV A T+E I+ LA G Sbjct: 471 IAGEVE---GEAITEENIVRLAMG 491 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: 33 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: 499 Length adjustment: 35 Effective length of query: 505 Effective length of database: 464 Effective search space: 234320 Effective search space used: 234320 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