Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Smeli:SMc02337 Length = 501 Score = 389 bits (999), Expect = e-112 Identities = 227/506 (44%), Positives = 320/506 (63%), Gaps = 16/506 (3%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 L++L I K F GV+AL+ V+ AGEVHAL+GENGAGKSTLM++L+G G Sbjct: 4 LVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPT-SGTVS 62 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132 I G+ +Q GP+ A G++VI+QEL+LAP+L+VAENI+LGR + +V + +A + Sbjct: 63 IHGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPR---IVNHRRLRKAAS 119 Query: 133 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 192 L RLG D PA + L++A +Q+VEIA+A+ ARI+V DEPT L+ + +RL A+ Sbjct: 120 EILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLLAI 179 Query: 193 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252 IR+LR G +YISHR+ E+ +L+DR+TV++DG V TL+ + A++ MVGR +S Sbjct: 180 IRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGRQMS 239 Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312 + G+ V EV++ VR+V+ GR+V+ SF +RAGEV+GL GLVG+GRTE+ARLVFG Sbjct: 240 ALFPSKAGR-VPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLVFG 298 Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372 AD G V + L PR+A+ A I + EDRK QG+ LD + N L Sbjct: 299 ADKMDSGTVELNGK-------PLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTL 351 Query: 373 IVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQ 432 R LG L+ R+ + ++ + V +LSGGNQQKV L++ Sbjct: 352 -AKIRSISRLGFLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHAD 410 Query: 433 PRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 492 +LILDEPTRGVD+GAK EIY LIN LA++G AIL+ISSE E+ G+CDRVLVM EG + Sbjct: 411 CDLLILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAI 470 Query: 493 AGEVRPAGSAAETQERIIALATGAAA 518 GE+ + T+++++ LA +A Sbjct: 471 VGELT---ESKFTEQQLLTLAMTRSA 493 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: 646 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: 501 Length adjustment: 35 Effective length of query: 505 Effective length of database: 466 Effective search space: 235330 Effective search space used: 235330 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 17 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