Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b20326 SM_b20326 trehalosemaltose transporter permease
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Smeli:SM_b20326 Length = 328 Score = 136 bits (343), Expect = 6e-37 Identities = 94/305 (30%), Positives = 157/305 (51%), Gaps = 37/305 (12%) Query: 24 AYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQFVGLKNYEE---LLNPHDPL 80 A+ +L+P + + +++ P+ TIY SFTN + + +FVG NY L + Sbjct: 31 AWLFLAPTFLVLALVAGWPLIRTIYFSFTNASLTNLSGAEFVGFANYLSWITLKSGRTIY 90 Query: 81 SNLFLPTFIW-----TLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVP 135 L W TL + + + ++ +GL +A++LN + R L R +++PWA+P Sbjct: 91 RGLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQ-FPGRGLVRAAILIPWAIP 149 Query: 136 NLISMLAWQGLLNDQYGQINALLHGVFGL--PRIPWLTSALWARIAVIMVNVWAGFPYMM 193 ++S W +LNDQ+G +N +L G+ GL +I W S A IA ++V+VW P+M Sbjct: 150 TIVSAKMWAWMLNDQFGILNDMLIGL-GLIGEKIAWTASPDTAMIAELIVDVWKTTPFMA 208 Query: 194 TVCLGALQSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSY--------N 245 + L LQ +P D YEAA+IDG + +VF WR++LPL+ P+ Sbjct: 209 LLILAGLQMVPGDIYEAAKIDGVHPVRVF--------WRVTLPLIRPALMVAVIFRMLDA 260 Query: 246 FNNFNASYLLTGGGPPNSNNPFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILVALI 305 F+ Y+LT PN+ QT ++ A + F+++ GA S +LF+++A I Sbjct: 261 LRIFDLIYVLT----PNN-----AQTKTMSVMARENLFDFDKFAYGAAASTMLFLIIATI 311 Query: 306 SWVQM 310 + + M Sbjct: 312 TILYM 316 Lambda K H 0.327 0.140 0.451 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: 344 Number of extensions: 19 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: 321 Length of database: 328 Length adjustment: 28 Effective length of query: 293 Effective length of database: 300 Effective search space: 87900 Effective search space used: 87900 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