Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SM_b21423 SM_b21423 sugar uptake ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Smeli:SM_b21423 Length = 331 Score = 207 bits (526), Expect = 4e-58 Identities = 119/306 (38%), Positives = 184/306 (60%), Gaps = 14/306 (4%) Query: 35 LPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDL 94 L +V ++F+ L+ + F + N +N+ ++I VLAAG T +++ DL Sbjct: 33 LLAFLVAEIIFFSLS-------SPYFLTWGNWVNVFTALSITGVLAAGGTMLLIAGQFDL 85 Query: 95 SVGSVLA-VSAVLGMQV-SLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGT 152 SVGS +A V+ VL + + SLG P + M + G+ +G++NG +V + +NA + TLGT Sbjct: 86 SVGSGVAFVALVLALTIDSLGVLPASVLAMLV--GVGIGLINGFLVTRIGVNALITTLGT 143 Query: 153 MTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLG 212 + FRG + G + I +F+W FL++P V + V ++ ++L+++V G Sbjct: 144 LAIFRGLTQSIGGGRNI---PIANFDWAIWRPFLNIPLSALVFLLVAIMVGIVLKRSVFG 200 Query: 213 MHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELD 272 IYAIG N AARL GIR V+ + +SG F GL G +SAS+L +G G G EL Sbjct: 201 RSIYAIGANENAARLVGIRTKGVVFAGFLLSGAFIGLGGLISASQLGSTSGTTGLGLELA 260 Query: 273 AIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVIL 332 + AV+LGGTSL GG G++ GTV+G LI+GV+NNGLT++ ++S WQ A G +++LAV Sbjct: 261 VVTAVILGGTSLKGGTGTMLGTVIGLLIVGVLNNGLTLMNVNSSWQQAATGLLLILAVSF 320 Query: 333 DKWRQK 338 D+ RQ+ Sbjct: 321 DQLRQR 326 Lambda K H 0.324 0.138 0.417 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: 351 Number of extensions: 20 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: 344 Length of database: 331 Length adjustment: 28 Effective length of query: 316 Effective length of database: 303 Effective search space: 95748 Effective search space used: 95748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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