Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 154 bits (389), Expect = 2e-42 Identities = 87/250 (34%), Positives = 150/250 (60%), Gaps = 23/250 (9%) Query: 8 LEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILVA 67 +++ + K++G + +K V LT G ++++LG SGSGKST LR I LE P+ G+I + Sbjct: 3 IQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLT 62 Query: 68 GEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNI---IEAPRRVLG 124 G + ++ ++ +IGFVFQ++ L+ H++V NI +E + Sbjct: 63 GRDATNESVRD---------------RQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKE 107 Query: 125 QSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184 + +A E+ E L+ G+ D+ YP++LSGGQ+QR A+AR LA+QP+V+L DEP AL Sbjct: 108 KVRARVEELLE-LVQLTGLGDR---YPSQLSGGQRQRVALARALAVQPQVLLLDEPFGAL 163 Query: 185 DPEMVQEVLSVIRALAEEGR-TMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFEN 243 D ++ +++ S +R L +E T + VTH+ A +V+ ++V ++ G VE+ GSP ++++N Sbjct: 164 DAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDN 223 Query: 244 PLSARCKQFM 253 P + F+ Sbjct: 224 PATPFVMSFI 233 Lambda K H 0.317 0.132 0.363 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: 177 Number of extensions: 9 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: 257 Length of database: 338 Length adjustment: 26 Effective length of query: 231 Effective length of database: 312 Effective search space: 72072 Effective search space used: 72072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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