Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SMc01627 SMc01627 ABC transporter permease
Query= uniprot:D8IPH8 (292 letters) >FitnessBrowser__Smeli:SMc01627 Length = 307 Score = 139 bits (349), Expect = 1e-37 Identities = 90/289 (31%), Positives = 148/289 (51%), Gaps = 6/289 (2%) Query: 2 FNRGKTSLPYLFLGPSLLVMLVLGLVPTVAAINLALKNRVLRYPDS-DYVWLRNLERLMS 60 F K +LPY+ P+LLV + + L+P A+ + + L P + + W N + Sbjct: 14 FRISKRALPYVLSLPALLVCIGI-LIPFFTAVIYSFQRYRLSQPWARQFNWGENYLNFFT 72 Query: 61 DRRFLNAIEVSAVWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSA 120 D F N +++S ++ VTV +++G+ IA+ L + ++L+ P++ A Sbjct: 73 DPGFWNTLKISLLYAGVTVTLELLLGLGIALLLQRR--STVNNFISIMLLLPLMTAPALA 130 Query: 121 AFIWKFMYSPLTGILGWLLGLVGIHDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLL 180 A +WK M +P GIL +L LVG+ + + S P AL V LVDIW + F +++L L Sbjct: 131 ALMWKLMTNPGFGILSYLASLVGLENFRWASSPDTALLTVVLVDIWVYTPFIMILLLAGL 190 Query: 181 ETLPPEPLEAARLDYARTWQVYAYIALPMLKGPLISLVFIKMVESLRSFDLIYVMTKGGP 240 +LP +P EAA LD V+ I LPML +++ ++++S++ FD+IY MT+GGP Sbjct: 191 RSLPTQPFEAAALDGVPRSFVFFRITLPMLTPYILTATLFRLLDSIQQFDIIYAMTQGGP 250 Query: 241 GVATETLDMYAYAQGIGLSGKVSYASTMAVLMMIATTL--IFTLIWKRV 287 G + AY + A+ + +L I L IF W R+ Sbjct: 251 GDTLTVFQVEAYLNFFQSTNVGRSAALLIILWAITYALSNIFIKNWLRL 299 Lambda K H 0.328 0.141 0.439 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: 245 Number of extensions: 9 Number of successful extensions: 3 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: 292 Length of database: 307 Length adjustment: 27 Effective length of query: 265 Effective length of database: 280 Effective search space: 74200 Effective search space used: 74200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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