Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 369 bits (946), Expect = e-106 Identities = 218/529 (41%), Positives = 314/529 (59%), Gaps = 28/529 (5%) Query: 1 MSDMSDTSTKAP-LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKIL 59 MSD S P LL +R + K+F ++AL+ V+ T GE+HAL+GENGAGKSTL+K++ Sbjct: 1 MSDSSAPPAARPSLLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVV 60 Query: 60 SGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR 119 +G + D G + G + + A + G+A +YQE++L PNLSVA+N+YLGR R Sbjct: 61 TGVFARD-AGTVRLAGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRF 119 Query: 120 GLVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTT 179 G+V + +M R L G D A +AS S+A + + IARAV AR+L++DEPT Sbjct: 120 GVVRQAEMRRRAHALLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTA 179 Query: 180 PLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239 L HE + LF ++R+L +G+ I+++SH + ++ E+ DRVTVLR+G +GT D L + Sbjct: 180 SLDRHEVEILFRVMRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPR 239 Query: 240 AALVKMMVGRDLSGFYTKTHGQAVE-----REVMLSVRDVADGRRVKGCSFDLRAGEVLG 294 L++MM+GR+L+ TH +A REV +S + V +LR GEV+G Sbjct: 240 LDLIRMMLGRELA---ETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVG 296 Query: 295 LAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTED 354 LAGL+G+GRTE ARLVFGA+ GE +A A + PR A G Y E+ Sbjct: 297 LAGLLGSGRTETARLVFGAERADSGEASVAGKA-------VRLNSPRDAAGLGFGYCPEE 349 Query: 355 RKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEA----IDTLGIRVAHAQV 410 RK +G+ D +V ENI L + AR L+R +RR E I L IR + Sbjct: 350 RKTEGIVADLTVRENIVLALQARRG-----LHRPLSRREQDEIAMRYIRMLDIRPPDPER 404 Query: 411 NVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMI 470 +G LSGGNQQK +L+R L P++L+LDEPTRG+D+GA +EI RL+ L + G+A+L+I Sbjct: 405 PIGLLSGGNQQKALLARWLATSPKLLVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVI 464 Query: 471 SSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAA 519 SSEL E+V +RV+V+R+ E++ G A E + A+A A A Sbjct: 465 SSELDEIVTYSNRVVVLRDRAHVEELK--GDAVEVSSILAAIAADAPTA 511 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: 667 Number of extensions: 33 Number of successful extensions: 8 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: 516 Length adjustment: 35 Effective length of query: 505 Effective length of database: 481 Effective search space: 242905 Effective search space used: 242905 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 Apr 09 2024. 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