Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate AO353_04275 AO353_04275 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04275 Length = 345 Score = 217 bits (553), Expect = 3e-61 Identities = 128/324 (39%), Positives = 183/324 (56%), Gaps = 16/324 (4%) Query: 4 LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63 +Q ++ + FG + VS+EI+ GEF +GPSG GK+T LRLIAG E+ ++G++ Sbjct: 5 VQFTNVSRQFGEVKAVDRVSIEIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIH 64 Query: 64 GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQL 123 G L P +R + VFQ YAL+PHM V +N+A+G+++ G K + KR E A +M+ L Sbjct: 65 GAEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKAERLKRAEEALDMVAL 124 Query: 124 TPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSM 183 Y ER P QLSGGQRQRVA+ RA+V P+V L DEPL LD LR + E+ KL R + Sbjct: 125 GGYGERKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQRQL 184 Query: 184 HKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFL 243 T I+VTHDQ EA++++DR+ V G +EQ+ TP LY PN+ FVA F+G+ N + Sbjct: 185 -GITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPNTTFVAEFVGT--SNVI 241 Query: 244 SGAFAEPYKA--DTIGIRAEHLEIDE-----QGGEWSGTVIHSEMLGSDSYIYLDIGTGE 296 G A IR EH+ E E SG + + GS + + + G+ Sbjct: 242 RGELARQLSGHPQPFSIRPEHVRFAEGPKASHEIEVSGLLHDIQYQGSATRYEMKLENGQ 301 Query: 297 PVIVRESG------IAKHQPGQTI 314 + + + +HQ GQ I Sbjct: 302 TLSISHANNQWLDVSVQHQTGQRI 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: 301 Number of extensions: 16 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: 345 Length adjustment: 29 Effective length of query: 313 Effective length of database: 316 Effective search space: 98908 Effective search space used: 98908 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