Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_012385783.1 BIND_RS14440 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_000019845.1:WP_012385783.1 Length = 518 Score = 553 bits (1424), Expect = e-162 Identities = 299/508 (58%), Positives = 369/508 (72%), Gaps = 8/508 (1%) Query: 8 STKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADP 67 + + +L +RN+ KTF V+ALR V L GE+HALMGENGAGKSTLMKILSGAY DP Sbjct: 6 NARTTILEMRNVSKTFGSVKALRDVSLEIREGEIHALMGENGAGKSTLMKILSGAYIPDP 65 Query: 68 GGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDM 127 G +D + V I GP +AR+LG+++IYQEL+LAPNL+VAENIYLGR ++R GLV R M Sbjct: 66 GSTILLDNKPVSITGPLAARELGISIIYQELALAPNLTVAENIYLGREIRRGGLVDRAAM 125 Query: 128 VRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187 + A L RLGA F V SLSIA+RQLVEIARAVH +RILVMDEPTT L+ ETD Sbjct: 126 IAGSAKVLQRLGATFQAKDLVQSLSIAERQLVEIARAVHAHSRILVMDEPTTTLTERETD 185 Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 RLF +R LR +G++I+YISHRM EI L+DRV++LRDG ++GTLD ++ A+VKMMV Sbjct: 186 RLFETVRALREDGLSIIYISHRMNEIYALSDRVSILRDGTYIGTLDHDEITPDAVVKMMV 245 Query: 248 GRDLSGFYTKTHGQAVER-EVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306 GRDL+ FY K H R ++LSV+++ D +R+ CSFDL GEVLG+AGLVG+GRTEL Sbjct: 246 GRDLTSFYKKEHDAHDGRGNIILSVKNIGDSKRIFDCSFDLHEGEVLGIAGLVGSGRTEL 305 Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366 ARL++G D R G + + + V+ +AI+AG+ YLTEDRK GLFLD SV Sbjct: 306 ARLIYGVDRRRSGIIMLNGESKKIASVS-------EAIEAGLLYLTEDRKQLGLFLDMSV 358 Query: 367 HENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426 ENINL VA+RDA L AR R AI L I+V + VGALSGGNQQKV+LS Sbjct: 359 GENINLGVASRDAYKGCFLKLGKARERADAAIGDLSIKVKSPKTPVGALSGGNQQKVLLS 418 Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486 RLLE++PRVLILDEPTRG+DIGAKSEIYRLIN L +SG+ +++ISSELPE+VG+CDRVLV Sbjct: 419 RLLELKPRVLILDEPTRGIDIGAKSEIYRLINDLVKSGIGVIVISSELPEIVGVCDRVLV 478 Query: 487 MREGTLAGEVRPAGSAAETQERIIALAT 514 M EG +AG V + TQE IIAL T Sbjct: 479 MSEGRIAGTVGGPDAPPITQENIIALTT 506 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: 707 Number of extensions: 35 Number of successful extensions: 6 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: 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 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