Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 201 bits (512), Expect = 2e-56 Identities = 125/327 (38%), Positives = 175/327 (53%), Gaps = 31/327 (9%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + V +S FG+ + ++L ++ G + LLG SG GKSTLL IAGL G+IF+ Sbjct: 3 IQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLT 62 Query: 64 DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123 R+ T E +DR IG VFQ YAL+ +TV KN++FGL++ K ++ RV+ E++Q+ Sbjct: 63 GRDATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQL 122 Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183 L R PS+LSGGQRQRVA+ RAL V L DEP LDAK+R +LR +++LH + Sbjct: 123 TGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEV 182 Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIG------SP 237 T ++VTHDQ EA+ +AD+I VM G ++Q+ P IY+ P FV FIG + Sbjct: 183 HVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIGPVNVLPNS 242 Query: 238 SMNFFRGEVEPKDGRSFVRAGGIAFDVTAYP------------------AHTRLQPGQKV 279 S F G ++ F+R I + P A RL+ GQ + Sbjct: 243 SHIFQAGGLDTPHPEVFLRPHDIEIAIDPIPETVPARIDRIVHLGWEVQAEVRLEDGQVL 302 Query: 280 VLGLRPEHVKVDEARD--GEPTHQAVV 304 V H+ D RD EP Q V Sbjct: 303 V-----AHLPRDRYRDLQLEPEQQVFV 324 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: 325 Number of extensions: 14 Number of successful extensions: 1 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: 338 Length adjustment: 29 Effective length of query: 332 Effective length of database: 309 Effective search space: 102588 Effective search space used: 102588 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