Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_101443649.1 BD749_RS06040 ABC transporter ATP-binding protein
Query= TCDB::Q9R9Q4 (342 letters) >NCBI__GCF_002846395.1:WP_101443649.1 Length = 317 Score = 125 bits (313), Expect = 2e-33 Identities = 92/302 (30%), Positives = 149/302 (49%), Gaps = 26/302 (8%) Query: 18 VIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIV----NQLTPS 73 V+ G+S E + G +G GKSTLL+ IAGL + ++G + F+G+ V ++L P Sbjct: 8 VLHGISFRQGEYEKLAIAGETGSGKSTLLQAIAGLVQPSAGQITFEGKRVIGPHDKLVPG 67 Query: 74 RRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPRQ 133 GIA + Q Y L + V + + + L G + E E+ +++ +R Q Sbjct: 68 HEGIAYLSQHYDLPQFLRVEQVLRYANILQGDE-------AETLYEVCRISHLKQRKTHQ 120 Query: 134 LSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHKTTMIYVTH 193 LSGG+RQR+A+ R + P + L DEP SNLD + + I + + T I ++H Sbjct: 121 LSGGERQRIALARLLSTWPSLLLLDEPYSNLDKGHKELLKEVIHDITERL-AITCILISH 179 Query: 194 DQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFLSGAFAEPYKA 253 D + ++ ADRI +++ G + Q GTP ++Y P + AG G+ N + A P+ A Sbjct: 180 DPHDTLSWADRILIIKGGRMVQQGTPEQVYRHPVDAYTAGLFGN--YNLIPAHVALPF-A 236 Query: 254 DTIGI---------RAEHLE-IDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVIVRES 303 + +GI R EH + ++ G +GTV G + + + TG V VR Sbjct: 237 EKLGIAVTARDLLVRPEHFRFVAKEAGSLNGTVQKVTFFGGYYDVQVQV-TGFSVTVRTQ 295 Query: 304 GI 305 I Sbjct: 296 AI 297 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: 257 Number of extensions: 18 Number of successful extensions: 4 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: 317 Length adjustment: 28 Effective length of query: 314 Effective length of database: 289 Effective search space: 90746 Effective search space used: 90746 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 24 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