Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_012385743.1 BIND_RS14235 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_000019845.1:WP_012385743.1 Length = 511 Score = 380 bits (977), Expect = e-110 Identities = 218/503 (43%), Positives = 313/503 (62%), Gaps = 14/503 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 LL NI K FPGV AL VEL VHALMGENGAGKSTLMKI++G Y D G Sbjct: 21 LLTAENIRKEFPGVLALDGVELKLRRSSVHALMGENGAGKSTLMKIIAGIYKPD-AGRIR 79 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLVARGDMVRAC 131 + G + P A + G+++I+QEL+L ++VAENI++ R L R G V +M R Sbjct: 80 LKGNEISFQSPLDALESGISMIHQELNLMDYMTVAENIWIRREPLNRFGFVDHDEMRRMT 139 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 RL D P A V LS+A RQ+VEIA+AV + + +L+MDEPT+ L+ E D LF Sbjct: 140 QALFRRLRIDLDPDAEVRDLSVANRQIVEIAKAVSYGSDVLIMDEPTSALTEREVDHLFE 199 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 +IR LR +G+ I+YI+H+M E+ E+AD ++ RDG ++ T ++ +++MMVGR+L Sbjct: 200 IIRDLRAQGIGIVYITHKMNELFEIADEFSIFRDGRYISTHAACDVTCDDIIRMMVGREL 259 Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311 + + K + +V LSV++V +G +FDLRAGE+LG+AGL+G+GR+ LA +F Sbjct: 260 TQMFPKE--EVPIGDVALSVKNVGLDGVFQGVNFDLRAGEILGIAGLIGSGRSSLAATLF 317 Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371 G T G + I AG+ ++ PA R +A+LTEDRK+ G L S+ EN+ Sbjct: 318 GVTPATSGSIAI---AGNDVVIDSPATAMRHQ----MAFLTEDRKVSGCLLSLSILENLQ 370 Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 L V + G ++ E L ++ + Q +G LSGGNQQKV++ R L Sbjct: 371 LAVLQDKYVTNGFVHEKELFSACDEMARKLRVKTPNLQEIIGNLSGGNQQKVLIGRWLLN 430 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 +PR+LILDEPTRG+D+GAK+EI+RL+ LA+ GVAI++ISSE+PEV+G+ DR++VM EG Sbjct: 431 KPRILILDEPTRGIDVGAKAEIHRLVTELAREGVAIILISSEMPEVLGMSDRIMVMHEGR 490 Query: 492 LAGEVRPAGSAAETQERIIALAT 514 + G + + TQ +I+ LA+ Sbjct: 491 MTGIL---DRSEATQVKIMELAS 510 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: 613 Number of extensions: 37 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: 511 Length adjustment: 35 Effective length of query: 505 Effective length of database: 476 Effective search space: 240380 Effective search space used: 240380 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