Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 212 bits (540), Expect = 1e-59 Identities = 120/285 (42%), Positives = 168/285 (58%), Gaps = 18/285 (6%) Query: 4 LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63 + +R + K FG + + V +EI GE + +GPSG GK+TLLR IAGLE +G + FD Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 64 GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQL-AGKD---KQQCRKRVEAAAE 119 GQ V + + R + VFQ YAL+ HMTV +N+AFG+ + GKD K + +RVE + Sbjct: 63 GQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLK 122 Query: 120 MLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKL 179 +++L R P QLSGGQRQRVA+ RA+ P V L DEP LDA +R + R E+ ++ Sbjct: 123 LVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRV 182 Query: 180 HRSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPK 239 H + TT I+VTHDQ EA+ LADR+ +L +G +EQIGTP ++++ P + FV GF+G Sbjct: 183 HDATGVTT-IFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGEAN 241 Query: 240 M--------NFLSGAFAEPYK-----ADTIGIRAEHLEIDEQGGE 271 F +GA P A T +R +DE G E Sbjct: 242 RFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGFE 286 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: 327 Number of extensions: 15 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: 339 Length adjustment: 28 Effective length of query: 314 Effective length of database: 311 Effective search space: 97654 Effective search space used: 97654 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