Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SM_b20327 SM_b20327 trehalosemaltose transporter permease
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__Smeli:SM_b20327 Length = 276 Score = 134 bits (337), Expect = 2e-36 Identities = 84/266 (31%), Positives = 139/266 (52%), Gaps = 9/266 (3%) Query: 7 RCAVWGVGIVLVLVAVFPLLWALLNSVKTLLDIVTPTPRFLFTPT---LENYRQVIGSPE 63 R A + + V++LVAVFP +A+L S+K+ T R + PT L NY + Sbjct: 8 RTAFYALVAVIILVAVFPFYYAILTSLKS----GTALFRIDYWPTDISLANYAGIFSHGT 63 Query: 64 VLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAVAIPL 123 + L NS ++ V + + V AAY +AR G+ + +LS+ P +AV L Sbjct: 64 FVRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGL 123 Query: 124 IAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYAVFWK 183 + +G+++T ++I +Y++ TL W+ + +P EIEEAA +DG P+ V + Sbjct: 124 FELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITR 183 Query: 184 IALPNCATTLLGGIIFSFVLVWNELMIALALTSSNSATLPVVASAFTSMGQ--EVPWGVI 241 + +P L+ + +F+ WNE + AL TSSN+ VA A S G E+PWG I Sbjct: 184 VFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNI 243 Query: 242 NASTVLLALPPLIFVGVLSRLLNSML 267 A++V++ +P ++ V + R + S L Sbjct: 244 MAASVIVTVPLVVLVLIFQRRIISGL 269 Lambda K H 0.327 0.142 0.434 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: 226 Number of extensions: 13 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: 270 Length of database: 276 Length adjustment: 25 Effective length of query: 245 Effective length of database: 251 Effective search space: 61495 Effective search space used: 61495 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: 47 (22.7 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