Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__SynE:Synpcc7942_2495 Length = 313 Score = 202 bits (515), Expect = 6e-57 Identities = 118/313 (37%), Positives = 182/313 (58%), Gaps = 14/313 (4%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMG-- 65 +LQ + NG+ +G YAL A+GYT+V+ I+G+INFAHG V+ +G+Y+++ ++ Sbjct: 3 WLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFNGL 62 Query: 66 IDTGWLLVAAGFVGAIVIAS--AYGWS--IERVAYRPVRNSKR--LIALISAIGMSIFLQ 119 + L + F A+++ S A G S IE+VA+RP+R + L+ LIS++G+++F+ Sbjct: 63 LANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAVFIV 122 Query: 120 NYVSLTEGSRDVALPSLFNGQWV----VGHSENFSASITTMQAVIWIVTFLAMLALTIFI 175 N + + G+ PS G +G S+ I T+Q ++++V LT I Sbjct: 123 NLIQILVGAEIYTFPSNIYGDLPSAINLGSSDR-PIQIRTVQIILFVVAIAMFSLLTWLI 181 Query: 176 RYSRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIG 235 +R+G A +A AED ASLLGI+ DR I LTF + + +AG L+G + PY G Sbjct: 182 NGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYFG 241 Query: 236 FMAGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVM 295 G+K + VLGG+G+IPG + GGL+LG+AEA S Y+D V+FALL +LL+ Sbjct: 242 IAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLAEAWVPPQWS-GYRDAVAFALLFAMLLIR 300 Query: 296 PTGILGRPEVEKV 308 P G+ R EKV Sbjct: 301 PQGLFSRARTEKV 313 Lambda K H 0.328 0.141 0.410 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: 274 Number of extensions: 13 Number of successful extensions: 5 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: 308 Length of database: 313 Length adjustment: 27 Effective length of query: 281 Effective length of database: 286 Effective search space: 80366 Effective search space used: 80366 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 (21.8 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