Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 263 bits (672), Expect = 1e-74 Identities = 179/520 (34%), Positives = 271/520 (52%), Gaps = 53/520 (10%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P+L L I K F + A + L GEV AL+GENGAGKSTL+ IL G Y AD G Sbjct: 4 PILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVAD-AGTV 62 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA----LQRRGLVARGDM 127 +DGQ + P++A G+ +++Q +LA NLSV +NI LG + G ARG + Sbjct: 63 EVDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKV 122 Query: 128 VRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187 + R G P A V LS+ +RQ VEI +A++ AR+L++DEPT L+ HE + Sbjct: 123 LALAE----RFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAE 178 Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 LF+ + QL EG+++++ISH++ E+ ++DR+ VLR G V A ++A L ++MV Sbjct: 179 TLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMV 238 Query: 248 GRDLSGFYTKTHGQAVEREVMLSVRDVADGRR--------------------VKGCSFDL 287 GR ++ ER S D A+G ++ S + Sbjct: 239 GRVVA---------MPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQV 289 Query: 288 RAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAG 347 RAGE++G+AG+ G G+ LA L G + G + +A S PR I AG Sbjct: 290 RAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMS--------AKPRAWIGAG 341 Query: 348 IAYLTEDRKLQGLFLDQSVHEN-INLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVA 406 +A + EDR G+ D +V EN ++ ++ G + R AA+R + + +R A Sbjct: 342 VARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTA 401 Query: 407 HAQVNVGALSGGNQQKVMLSRLLEIQ-----PRVLILDEPTRGVDIGAKSEIYRLINALA 461 V +SGGN QK++L R L ++ PR+++ +PT G+DIGA + + + A Sbjct: 402 GIDVPARTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAA 461 Query: 462 QSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGS 501 + G A+L+IS +L E+ L DR+ VM G L E RP + Sbjct: 462 REGAAVLLISEDLDELHALADRIAVMHAGHLT-EARPTAA 500 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: 720 Number of extensions: 38 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: 530 Length adjustment: 35 Effective length of query: 505 Effective length of database: 495 Effective search space: 249975 Effective search space used: 249975 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