Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Ga0059261_2412 Ga0059261_2412 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__Korea:Ga0059261_2412 Length = 602 Score = 110 bits (276), Expect = 7e-29 Identities = 77/230 (33%), Positives = 122/230 (53%), Gaps = 13/230 (5%) Query: 3 ELQLRDIRKSFGAF-DVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLA 61 E++ +R + A D++KG+ + I PG+ + VGPSG GKSTL R++ ++T G + Sbjct: 357 EVRFEGVRFGYEANRDILKGIDLVIAPGQTVAVVGPSGAGKSTLARILYRFYDLTGGRVT 416 Query: 62 FDGQIVNQLTPS--RRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAE 119 DGQ + Q+T R I +V Q L+ + TV N+A+G + A D+ R A A Sbjct: 417 IDGQDIAQVTQGSLRAAIGIVPQDTVLF-NDTVGYNIAYGREGATADQVAAAARGAAIAG 475 Query: 120 MLQLTP--YLERLPR---QLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRL 174 ++ P Y R+ +LSGG++QRVAI R +++DP + + DE S LD+ T Sbjct: 476 FIESMPDGYDTRVGERGLKLSGGEKQRVAIARTLLKDPPILILDEATSALDS----RTEA 531 Query: 175 EIAKLHRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYE 224 EI ++ + V ++ + ADRI VL G + + GT +L E Sbjct: 532 EILDTLEAIERGRTTIVIAHRLSTVVNADRIVVLEAGRIAEQGTHAQLLE 581 Lambda K H 0.321 0.138 0.396 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: 390 Number of extensions: 11 Number of successful extensions: 2 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: 342 Length of database: 602 Length adjustment: 33 Effective length of query: 309 Effective length of database: 569 Effective search space: 175821 Effective search space used: 175821 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 (21.9 bits) S2: 51 (24.3 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