Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 350 bits (897), Expect = e-101 Identities = 226/508 (44%), Positives = 303/508 (59%), Gaps = 20/508 (3%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 +L R + K F AL V+L AGEVHALMG+NGAGKSTL+K+L+G D G Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGS-VE 70 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL-VARGDMVRAC 131 +DG+ + P A+ G+ +YQE++L PNLSVAEN+Y GR +RR L + VR Sbjct: 71 LDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDG 130 Query: 132 APTLAR-LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 A +L R L + A + S +A RQ+V IARA+ AR+L++DEPT+ L E LF Sbjct: 131 ARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 +I QLR GMAIL+++H + ++ ++DR+TVLRDGC VG A L AALV MVGRD Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250 Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDL--RAGEVLGLAGLVGAGRTELAR 308 L +A + ++ G R K DL R GE+LGL GL+G+GRTELAR Sbjct: 251 LPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELAR 310 Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368 L+FG D RGE+RI G V L P A+ G+A E+RK G+ + SV E Sbjct: 311 LLFGLDRAERGELRIG-----GERVELKH--PADAVVRGLALCPEERKTDGIVAELSVRE 363 Query: 369 NINLIVAARDAL-GLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427 NI L + AR G+ R + R+ +A LGI+ A + VG LSGGNQQKVML+R Sbjct: 364 NIVLALQARQGWRGMSRARQDELARQLVQA---LGIKAADIETPVGLLSGGNQQKVMLAR 420 Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487 L +PR+LILDEPTRG+D+ AK E+ + A +G+A+L IS+E E+ CDR+ VM Sbjct: 421 WLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVM 480 Query: 488 REGTLAGEVRPAGSAAETQERIIALATG 515 RE AGE+ P GS T+ R++A+ G Sbjct: 481 RERRKAGEL-PGGS---TEARVLAMIAG 504 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: 736 Number of extensions: 35 Number of successful extensions: 10 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: 505 Length adjustment: 35 Effective length of query: 505 Effective length of database: 470 Effective search space: 237350 Effective search space used: 237350 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