Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= TCDB::P54933 (332 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 224 bits (572), Expect = 2e-63 Identities = 135/341 (39%), Positives = 194/341 (56%), Gaps = 18/341 (5%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 I +RN+ KRFG V + + L I GE V +GPSGCGK+TLLR+IAG+E +GQ+M + Sbjct: 3 IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQ----EIERRVSNAAK 119 G +AT + +R + VFQ YAL+ HM V +N+AF LR+ + + EI +RV + Sbjct: 63 GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122 Query: 120 ILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITEL 179 ++ L DR P QLSGGQRQR+A+ RA+ EP L DEP LD +R +R + L Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182 Query: 180 HQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKM 239 H + + ++VTHDQ EA+ +AD++VV+N GRIEQVGSP +Y NPA+ FV F+G+ + Sbjct: 183 HDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGNVNV 242 Query: 240 --NLIEG--PEAAKH----GATTIG-IRPEHIDLSREA--GAWEGEVGVSEHLGSDTFLH 288 + + G E A+ G + IRP ID+ A + E +V + +G + Sbjct: 243 FHSRVHGAWAEVARDDVPAGQEAVAFIRPHDIDIDTVATPESLEAKVSYVQTIGPLVRVE 302 Query: 289 VHVAG---MPTLTVRTGGEFGVHHGDRVWLTPQADKIHRFG 326 V G LT G+ G +VWL P+ K+ G Sbjct: 303 VIHQGELVEVELTRERQQVLGLTAGQQVWLKPRQVKVFANG 343 Lambda K H 0.320 0.137 0.400 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: 319 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: 332 Length of database: 360 Length adjustment: 29 Effective length of query: 303 Effective length of database: 331 Effective search space: 100293 Effective search space used: 100293 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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