Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_055444834.1 AMD28_RS14385 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_001418105.1:WP_055444834.1 Length = 506 Score = 351 bits (901), Expect = e-101 Identities = 196/483 (40%), Positives = 296/483 (61%), Gaps = 8/483 (1%) Query: 14 LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73 L + I K+F V L+ V L +GE+HAL+GENGAGKSTL+KILSG + D G + Sbjct: 10 LEMTGISKSFGVVSVLKNVNLKVKSGEIHALLGENGAGKSTLIKILSGVHQKDTGTVV-L 68 Query: 74 DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133 DGQ + + LG+ V+YQELSL +LSVAENIYL + + + +++ Sbjct: 69 DGQEITPKNTHEGQVLGINVVYQELSLVNDLSVAENIYLHKLGANKTWMNWKGLIKDAQE 128 Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193 L L + +A V LSI Q+Q+VEIA+A+ + +IL++DEPTT + +LF ++ Sbjct: 129 LLDSLDFKINASAKVKDLSIVQKQVVEIAKAISEDTKILILDEPTTVFDPKDVKKLFNIL 188 Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSG 253 +L+ +G +I+YISH + EI ++AD VTVLRDG G+L A + ++ +M+GR+L Sbjct: 189 FKLKEKGTSIIYISHHLDEIFKIADSVTVLRDGVDTGSLAIADTDKDGVIHLMIGRELKD 248 Query: 254 FYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGA 313 Y K + E + A V SF ++ GEVLG+AGL G+GRTE A+L+FGA Sbjct: 249 LYPKRDVKIGEVPIFEVKNLTAKDTMVHDVSFHVKPGEVLGIAGLGGSGRTETAKLIFGA 308 Query: 314 DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLI 373 D + G + + + P A I +++EDRK +G+FL S+ NI++ Sbjct: 309 DKKKSGTLILEGK-------EIVTNSPVDAARYQIGFVSEDRKEEGVFLPLSIRRNISVT 361 Query: 374 VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQP 433 + LG +N + ++ I+ L I+ ++++NV LSGGNQQKV L++ L I+ Sbjct: 362 SFDSISSKLGFINVESEYKKVLGLIEKLNIKTPNSEINVKNLSGGNQQKVALAKWLSIES 421 Query: 434 RVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLA 493 +V+ +DEPTRGVD+GAK EIY+LIN +A+ GV +++ISS++PE++G+ DR+LVM EGT Sbjct: 422 KVIFIDEPTRGVDVGAKIEIYKLINEVAKKGVGVVVISSDMPEIMGISDRILVMHEGTFY 481 Query: 494 GEV 496 GE+ Sbjct: 482 GEL 484 Score = 70.5 bits (171), Expect = 1e-16 Identities = 51/223 (22%), Positives = 104/223 (46%), Gaps = 14/223 (6%) Query: 39 GEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQE- 97 GEV + G G+G++ K++ GA G ++G+ + + P A + + ++ Sbjct: 285 GEVLGIAGLGGSGRTETAKLIFGA-DKKKSGTLILEGKEIVTNSPVDAARYQIGFVSEDR 343 Query: 98 --------LSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADF-SPAANV 148 LS+ N+SV + L G + + + +L + NV Sbjct: 344 KEEGVFLPLSIRRNISVTSFDSISSKL---GFINVESEYKKVLGLIEKLNIKTPNSEINV 400 Query: 149 ASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISH 208 +LS +Q V +A+ + E++++ +DEPT + ++ LI ++ +G+ ++ IS Sbjct: 401 KNLSGGNQQKVALAKWLSIESKVIFIDEPTRGVDVGAKIEIYKLINEVAKKGVGVVVISS 460 Query: 209 RMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 M EI ++DR+ V+ +G F G L + S+ +++ +G L Sbjct: 461 DMPEIMGISDRILVMHEGTFYGELPKEKFSEENILRYSIGEPL 503 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: 550 Number of extensions: 24 Number of successful extensions: 6 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: 506 Length adjustment: 35 Effective length of query: 505 Effective length of database: 471 Effective search space: 237855 Effective search space used: 237855 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