Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 182 bits (462), Expect = 1e-50 Identities = 108/301 (35%), Positives = 172/301 (57%), Gaps = 18/301 (5%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+++S++ L ++ VL LNL + GE LLG SGCGK+TLL IAGL D+S G I Sbjct: 1 MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60 Query: 61 FIKDRNVTWE----EPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKR 116 I + V+ + P+ R IGM+FQ YAL+P +TV N+ FG++ ++ R++ Sbjct: 61 AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVR--QLDKQSRSVRLEE 118 Query: 117 ASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEI 176 +++++ L KR P ELSGGQ+QRV+I RAL + D+ L DEP SN+DA++R L +EI Sbjct: 119 MLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEI 178 Query: 177 KRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGS 236 + + ++ + ++VTH + EA AD +A+ ++G I Q P T+Y +P +VA F+G+ Sbjct: 179 RAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGA 238 Query: 237 PSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLG-LRPEHVKVDEARD 295 + R + AG + + A+P + + LRPE + ++ D Sbjct: 239 SNYLDVR-----------LEAGQLISTLGAFPLPQDFKAASETGRWLLRPEQLLIEARAD 287 Query: 296 G 296 G Sbjct: 288 G 288 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: 274 Number of extensions: 15 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: 341 Length adjustment: 29 Effective length of query: 332 Effective length of database: 312 Effective search space: 103584 Effective search space used: 103584 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