Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 264 bits (675), Expect = 5e-75 Identities = 177/503 (35%), Positives = 263/503 (52%), Gaps = 21/503 (4%) Query: 5 MSELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64 MS+ ++ P++ + K F AL V + GE HAL+G NGAGKSTL+ IL+G Sbjct: 1 MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 60 Query: 65 KPDTG-EVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVID 123 D G E G + A VA +YQ ++ +LSVAEN+++ R R G++ Sbjct: 61 TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVA 120 Query: 124 WQAMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDG 183 M R L D A LS+ RQLVEIARA+ + AR +++DEPT L Sbjct: 121 RGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLST 180 Query: 184 DEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243 E RLF I +L+ EG+ L+ISH + E+ E+ VTVLRD + + + L + L+ Sbjct: 181 HETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALV 240 Query: 244 EAMTGERGGLAVADAAARGALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATS 302 + M G L+ G + V L ++++ G +G SF ++ GEV+GL G Sbjct: 241 KMMVGR--DLSGFYTKTHGQ-AVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVG 297 Query: 303 SGRTSVAEAIAGLRAAKRGTISVDG-------AILPPGDVPASLAHGIGCVPKDRHHEGL 355 +GRT +A + G A RG + + LP G ++ GI + +DR +GL Sbjct: 298 AGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGL 357 Query: 356 VLTQSVAENASMTIAR----VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSG 411 L QSV EN ++ +A LG+ A ++ + ID LGI + V LSG Sbjct: 358 FLDQSVHENINLIVAARDALGLGRLNRTAARRRTT---EAIDTLGIRVAHAQVNVGALSG 414 Query: 412 GNQQKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD- 470 GNQQKV+++R L P VL+L +PT GVD+ +K + +++ + + G A+L++S EL + Sbjct: 415 GNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEV 474 Query: 471 LRTCDRVLVMFRGRVAAEF-PAG 492 + CDRVLVM G +A E PAG Sbjct: 475 VGLCDRVLVMREGTLAGEVRPAG 497 Lambda K H 0.318 0.134 0.377 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: 651 Number of extensions: 36 Number of successful extensions: 9 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: 510 Length of database: 537 Length adjustment: 35 Effective length of query: 475 Effective length of database: 502 Effective search space: 238450 Effective search space used: 238450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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