Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= TCDB::P21627 (307 letters) >FitnessBrowser__SynE:Synpcc7942_2495 Length = 313 Score = 198 bits (504), Expect = 1e-55 Identities = 118/313 (37%), Positives = 178/313 (56%), Gaps = 14/313 (4%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAIT-------L 59 +LQ L+NGL +G YAL A+GYT+V+ I+G+INFAHG V+ +G+Y+ + + L Sbjct: 3 WLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFNGL 62 Query: 60 LAMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRG--GNRLIPLISAIGMSIFL 117 LA L LA S++ A IE+VA+RPLR + L+ LIS++G+++F+ Sbjct: 63 LANAALPFSLPFALALLLGSLLAGGA-SLLIEQVAFRPLRRRQADPLLTLISSLGVAVFI 121 Query: 118 QNAVMLSQDSKEKAIPTLLPGNFVFG---ESSMNGVVISYMQILIFVVTFLVMFGLTLFI 174 N + + ++ P+ + G+ SS + I +QI++FVV + LT I Sbjct: 122 VNLIQILVGAEIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTWLI 181 Query: 175 SRSRLGRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIG 234 + +R+G A +A AED +LLGI+ + I LTF + L +A L+G + P G Sbjct: 182 NGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYFG 241 Query: 235 FLAGIKAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFR 294 G+K + VLGG+G+IPG + GGLLLG+AEA+ + Y+D VAF LL +LL R Sbjct: 242 IAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLAEAWVPPQWSG-YRDAVAFALLFAMLLIR 300 Query: 295 PTGILGRPEVEKV 307 P G+ R EKV Sbjct: 301 PQGLFSRARTEKV 313 Lambda K H 0.328 0.145 0.413 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: 289 Number of extensions: 15 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: 307 Length of database: 313 Length adjustment: 27 Effective length of query: 280 Effective length of database: 286 Effective search space: 80080 Effective search space used: 80080 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