Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate SM_b21377 SM_b21377 sugar uptake ABC transporter substrate-binding protein precursor
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__Smeli:SM_b21377 Length = 296 Score = 136 bits (342), Expect = 7e-37 Identities = 87/286 (30%), Positives = 148/286 (51%), Gaps = 7/286 (2%) Query: 14 LLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDL 73 L+A A +A+ +G ++ +PF++ +A+ ++ A + N +V + + DL Sbjct: 10 LVAGTALTLLASGAFADGIGASLLTQQHPFYIELAEAMKAEAKEKNVALEVAIANQ--DL 67 Query: 74 NTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAGADVT--VMS 131 N Q+ +E+FI VD+IV++ DS+GV A+ KA+KAGI V+ VDV A GA VT + + Sbjct: 68 NKQLADVEDFIVKGVDVIVISPVDSQGVRAAIAKAEKAGIKVITVDVPANGATVTSHIGT 127 Query: 132 DNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQNA 191 DN G ++ + +AE L KG V I++ P V +V++RV G K K P ++I++ Sbjct: 128 DNFTGGVKAGELMAEVLGNKGKVAIIDYPTVQSVVNRVNGFKEAIAKHPEMEIVA--TQT 185 Query: 192 GGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPDAE 251 G +R + N+L A P I +F D A+ A +A++ A + G DG +A Sbjct: 186 GITRAEALAAAQNMLQANPDITGIFGFGDDAALAAAVAVKAAGLESQVKVIGFDGMKEAR 245 Query: 252 RALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLP 297 A+ D + Q P M +++ V+ G + ++P Sbjct: 246 DAV-DGNPVMVGVIQQFPDQMGKQAIDTAVKVVAGETVPAEQPIVP 290 Lambda K H 0.314 0.129 0.360 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: 192 Number of extensions: 9 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: 316 Length of database: 296 Length adjustment: 27 Effective length of query: 289 Effective length of database: 269 Effective search space: 77741 Effective search space used: 77741 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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