Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__WCS417:GFF1168 Length = 344 Score = 213 bits (541), Expect = 7e-60 Identities = 127/324 (39%), Positives = 183/324 (56%), Gaps = 16/324 (4%) Query: 4 LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63 +Q + + FG + VS++I+ GEF +GPSG GK+T LRLIAG E+ ++G++ Sbjct: 5 VQFTHVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIH 64 Query: 64 GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQL 123 G+ L P +R + VFQ YAL+PHM V +N+A+G+++ G K + R E A M+ L Sbjct: 65 GEEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVAL 124 Query: 124 TPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSM 183 Y +R P QLSGGQRQRVA+ RA+V P+V L DEPL LD LR + E+ KL R + Sbjct: 125 GGYGDRKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQL 184 Query: 184 HKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFL 243 T I+VTHDQ EA++++DR+ V G +EQ+ TP LY P + FVA F+G+ N + Sbjct: 185 -GITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGT--SNVI 241 Query: 244 SGAFAEPY--KADTIGIRAEHLEIDE-----QGGEWSGTVIHSEMLGSDSYIYLDIGTGE 296 G A+ A IR EH+ E E SG + + GS + L + G+ Sbjct: 242 RGELAQRLGGTAQPFSIRPEHVRFAEGPLGTGEVEISGLLHDIQYQGSATRYELKLENGQ 301 Query: 297 PVIVRESG------IAKHQPGQTI 314 + + + A HQ GQT+ Sbjct: 302 ALNISRANNQWLDTTAGHQVGQTL 325 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: 307 Number of extensions: 12 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: 344 Length adjustment: 29 Effective length of query: 313 Effective length of database: 315 Effective search space: 98595 Effective search space used: 98595 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