Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_1894 Synpcc7942_1894 integral membrane protein of the ABC-type Nat permease for neutral amino acids
Query= TCDB::P74455 (372 letters) >FitnessBrowser__SynE:Synpcc7942_1894 Length = 359 Score = 340 bits (873), Expect = 3e-98 Identities = 179/370 (48%), Positives = 247/370 (66%), Gaps = 14/370 (3%) Query: 4 GYLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLRGLPIPLAVL 63 GY+I L+ + A + +F +GLNL WG+ GL+NFGHVAF+ +GAY+ +LL+ +G P+ LA + Sbjct: 3 GYIILLVCTIALFALFCVGLNLHWGYTGLLNFGHVAFLLIGAYSVSLLAQQGWPLWLAAI 62 Query: 64 VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSFPWPM 123 G+ LA LGL++G ++LRL +DYL IVT+G++E++R+ NE LTQG+FGVQ++P + Sbjct: 63 AGVTLAALLGLVMGVASLRLSQDYLGIVTVGLAEVLRIFVQNETGLTQGSFGVQAYPIIL 122 Query: 124 D-FNPTLLSRIVFVIWLTVLTIYAESILIKSLLKQWKEGKKIQGKSYQPRKPLALLIWGI 182 + P + + V+ L + + L QW +GK + LA++ G Sbjct: 123 QGWEPPIWQTHLLVVGLLAIAAWGYW-----QLWQWWRSSASRGKHW-----LAIVALG- 171 Query: 183 ITTALILTAYVPGVVSLYNYSGKAGLMLLALTLLALTYAGLEFWVHSPWGRILKAIREDE 242 ++ ++L G+ Y ++G MLL L L LT A ++ V SPWGR+LKAIREDE Sbjct: 172 -SSLIVLPPAALGLADYERYP-RSGQMLLLLGALWLTVAAVDRLVRSPWGRVLKAIREDE 229 Query: 243 EIPRALGKNVFWYKLQAFMGGGAIAGLAGALFAWQLTSIYPSNFDTLLTFNAWIIVVLGG 302 + ALGKNV YKLQ+ GGAIAGLAG +AWQLT+IYP NF LTF+ W ++VLGG Sbjct: 230 TVAIALGKNVLSYKLQSLALGGAIAGLAGVFYAWQLTAIYPDNFRPQLTFDVWTMLVLGG 289 Query: 303 AGSNAGTVLGTIIFWAYDSLTRFLLPQIAFLDQSQAGALRVMVIGLILMVLMVWRPQGIL 362 G VLG +FW YDSLTRFLLP I LD SQ GALR+ ++GL+LM LM+WRPQGIL Sbjct: 290 TAHRFGPVLGAAVFWLYDSLTRFLLPAILPLDGSQIGALRIALVGLLLMALMIWRPQGIL 349 Query: 363 GKKEELTLGR 372 G++EEL+LGR Sbjct: 350 GRREELSLGR 359 Lambda K H 0.327 0.143 0.442 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: 462 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 372 Length of database: 359 Length adjustment: 30 Effective length of query: 342 Effective length of database: 329 Effective search space: 112518 Effective search space used: 112518 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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