Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 174 bits (441), Expect = 3e-48 Identities = 109/303 (35%), Positives = 171/303 (56%), Gaps = 14/303 (4%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+++++ + ++ T+L L+L + GE LLG SGCGK+TLL IAGL +S G+I Sbjct: 1 MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60 Query: 61 FIKDRNVTWEEP----KDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKR 116 I R ++ E + R +GM+FQ YAL+P +TV +N+ FG+K + A + R+ Sbjct: 61 SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARLGE 118 Query: 117 ASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEI 176 +++++ L R P ELSGGQ+QRV+I RAL + ++ L DEP SN+DAK+R E+ VEI Sbjct: 119 MLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEI 178 Query: 177 KRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGS 236 + + + + ++VTH + EA AD++A+ K G I Q ++Y P + +VA F+G Sbjct: 179 REILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLG- 237 Query: 237 PSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296 +N+ EV KD G + P G + L LRPE +++ G Sbjct: 238 -QVNYLSCEV--KDRARLQTLLGEVQSSSDLPK----AAGYRGELLLRPEQLQMAGDEQG 290 Query: 297 EPT 299 E T Sbjct: 291 EGT 293 Lambda K H 0.320 0.137 0.392 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: 285 Number of extensions: 20 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: 361 Length of database: 342 Length adjustment: 29 Effective length of query: 332 Effective length of database: 313 Effective search space: 103916 Effective search space used: 103916 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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