Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 213 bits (543), Expect = 4e-60 Identities = 126/332 (37%), Positives = 191/332 (57%), Gaps = 16/332 (4%) Query: 4 LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63 +++ I K FG F + +++ I+ GE + +GPSGCGK++LLR+IAGLE SG++ F Sbjct: 3 IEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVFH 62 Query: 64 GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCR----KRVEAAAE 119 G+ V+ R + VFQ YAL+ HMTV+EN+AFG+++ K ++ ++V Sbjct: 63 GEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELLG 122 Query: 120 MLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKL 179 ++QL +R P QLSGGQRQR+A+ RA+ +PKV L DEP LDA +R R +A+L Sbjct: 123 LVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLARL 182 Query: 180 HRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPK 239 H +H T+ ++VTHDQ EAM +ADRI V+ G++EQIGTP E+Y P S FV F+G Sbjct: 183 HEDVHLTS-VFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGDAN 241 Query: 240 MNFLSGAFAEPYKADTIGIR----AEHL--EIDEQGGEWSGTVIHSEMLGSDSYIYLDIG 293 L + ++ + + AEHL E+ + + T + ++ G I ++G Sbjct: 242 RLQLDDQRSVLFRPHEVALSREAVAEHLAGEVRDIRPLGALTRVTLKVAGQAEPIEAEVG 301 Query: 294 TGEPVIV---RESGIAKHQPGQTIRISPAAGQ 322 +V R + + GQ +R PAA Q Sbjct: 302 NDHASLVGVQRGATLYFQPKGQAVR--PAAAQ 331 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: 298 Number of extensions: 11 Number of successful extensions: 3 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: 334 Length adjustment: 28 Effective length of query: 314 Effective length of database: 306 Effective search space: 96084 Effective search space used: 96084 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: 49 (23.5 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