Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b20326 SM_b20326 trehalosemaltose transporter permease
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__Smeli:SM_b20326 Length = 328 Score = 152 bits (384), Expect = 1e-41 Identities = 91/295 (30%), Positives = 155/295 (52%), Gaps = 18/295 (6%) Query: 31 AYAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAPFIGLKNYYE-ILFDEKS 89 A+ L PTF+ + + P+++ IY S + + +T A F+G NY I Sbjct: 31 AWLFLAPTFLVLALVAGWPLIRTIYFSFTNAS---LTNLSGAEFVGFANYLSWITLKSGR 87 Query: 90 LIRRG------FWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWV 143 I RG +W A+ NT +TV+ ALG+I+A+++N +F GRG+VR A+L+PW Sbjct: 88 TIYRGLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQFPGRGLVRAAILIPWA 147 Query: 144 VPSYVVGMTWGFLWRQDSGLINIILCDILHILPEKPYWLVGSNQIW-AIIIPTIWRGLPL 202 +P+ V W ++ G++N +L L ++ EK W + A +I +W+ P Sbjct: 148 IPTIVSAKMWAWMLNDQFGILNDMLIG-LGLIGEKIAWTASPDTAMIAELIVDVWKTTPF 206 Query: 203 SMILMLAGLQSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNI 262 +L+LAGLQ + D YEAA IDG + + FW +TLPL++P L + V+F ++ + F++ Sbjct: 207 MALLILAGLQMVPGDIYEAAKIDGVHPVRVFWRVTLPLIRPALMVAVIFRMLDALRIFDL 266 Query: 263 VSMMFGNGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVALWY 317 + ++ N A + + N F +F GAAA ++F ++ + + Y Sbjct: 267 IYVLTPNNAQT-----KTMSVMARENLFDFDKFAYGAAA-STMLFLIIATITILY 315 Lambda K H 0.330 0.145 0.468 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: 339 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 327 Length of database: 328 Length adjustment: 28 Effective length of query: 299 Effective length of database: 300 Effective search space: 89700 Effective search space used: 89700 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 (21.8 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