Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate PfGW456L13_4204 ABC transporter, ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4204 Length = 329 Score = 218 bits (555), Expect = 2e-61 Identities = 128/322 (39%), Positives = 188/322 (58%), Gaps = 8/322 (2%) Query: 1 MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 M+ + ++ ++KSF V ++ EI+ GEF+ +GPSGCGKSTLLR IAGL + G + Sbjct: 1 MSYVSVQHLQKSFAGTTVFSDINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGGKI 60 Query: 61 AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120 DG + ++P +RGI MVFQSYAL+P+MTV +N+AFG+++ + RKRV ++ Sbjct: 61 LLDGADIVPVSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSRKRVAEVLKL 120 Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180 ++L + R P QLSGGQ QRVA+ R++V P++ L DEPLS LDA +R R +I ++ Sbjct: 121 VELNDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQ 180 Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240 R + TT I+VTHDQ EA+T++DRI ++ G + Q G LY P VF AGFIG+ + Sbjct: 181 RELGLTT-IFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAAGFIGNYNL 239 Query: 241 ---NFLSGAFAEPYKADTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEP 297 + S P I IR E +E+ GE V +LG+ ++ E Sbjct: 240 LDADSASKLLQRPIN-KRIAIRPEAIEL-SLDGELDAQVRSHSLLGNVIRYRVEARGVEL 297 Query: 298 V--IVRESGIAKHQPGQTIRIS 317 V ++ S H GQ + +S Sbjct: 298 VVDVLNRSAADLHPDGQRLALS 319 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: 251 Number of extensions: 10 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: 329 Length adjustment: 28 Effective length of query: 314 Effective length of database: 301 Effective search space: 94514 Effective search space used: 94514 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