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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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