Align ABC transporter permease (characterized, see rationale)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__SynE:Synpcc7942_2495 Length = 313 Score = 173 bits (438), Expect = 5e-48 Identities = 111/310 (35%), Positives = 173/310 (55%), Gaps = 23/310 (7%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIG---MMQGAM 61 LQ +INGL +G +YAL ALGYT+V+ I+ +INFAHG V +GA +++ +G G + Sbjct: 4 LQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFNGLL 63 Query: 62 PGA--PGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILLQT 117 A P + LA ++ ++A + +IE+VA+RPLR + L LI+++G+++ + Sbjct: 64 ANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAVFIVN 123 Query: 118 LAMIIWKPNYKPYPTMLPSS-PFEIG-GAFITPTQI----LILGVTAVALASLV-YLVNH 170 L I+ +P+ + P I G+ P QI +IL V A+A+ SL+ +L+N Sbjct: 124 LIQILVGAEIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTWLING 183 Query: 171 TNLGRAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFL 230 T +G A++A AE+ ASL+G+ PD I TF + VL +AG + ++ G Sbjct: 184 TRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYFGIA 243 Query: 231 PGLKAFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLI 290 GLK + V GG+GN+ G + GG+LLGL EA ++ G Y D AF +L Sbjct: 244 YGLKGLSVMVLGGLGNIPGTIAGGLLLGLAEA----WVPPQWSG-----YRDAVAFALLF 294 Query: 291 IILTLRPSGL 300 +L +RP GL Sbjct: 295 AMLLIRPQGL 304 Lambda K H 0.327 0.142 0.419 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: 245 Number of extensions: 11 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: 309 Length of database: 313 Length adjustment: 27 Effective length of query: 282 Effective length of database: 286 Effective search space: 80652 Effective search space used: 80652 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: 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