Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate GFF3088 HP15_3031 extracellular solute-binding protein, family 3
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Marino:GFF3088 Length = 250 Score = 157 bits (398), Expect = 2e-43 Identities = 92/257 (35%), Positives = 147/257 (57%), Gaps = 12/257 (4%) Query: 1 MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 MKK++ + AL++++ A E+ L+I + Y PF K +G + GF+ ++ A+CEE Sbjct: 1 MKKMIFAASCALALIAGGAQAQERDLRIAFDVPYEPFEYKDENGELTGFEVELAEAMCEE 60 Query: 61 MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLV--MKA 118 M C +V Q +DG+IP L RK D I+SSMSIT +R + V F+ YYNTP Sbjct: 61 MNANCEFVIQAWDGMIPGLLARKFDLIMSSMSITPERAERVLFSEPYYNTPGGWFGPESF 120 Query: 119 GTAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGT 178 T V++ ++ ++GK +GVQRG+ + + E + + IK Y + +++ LD+ RLD Sbjct: 121 NTDVTD-MSAMEGKTVGVQRGTTMDTYVTENMGGI-VTIKRYTTADDMVLDLEGQRLDVV 178 Query: 179 VADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAAIR 237 D + + L + GF VG A G+GVG+A+R+ D L +++N A+ ++ Sbjct: 179 FVDYPVGEQTVLTKE---GFKEVGEAVK----LGEGVGVAMRQRDTDLAEEVNAALRTLK 231 Query: 238 ENGKYKQIQDKYFAFDI 254 E+G Y I KYFA+DI Sbjct: 232 EDGTYDTIMQKYFAYDI 248 Lambda K H 0.318 0.138 0.394 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: 178 Number of extensions: 13 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: 250 Length adjustment: 24 Effective length of query: 233 Effective length of database: 226 Effective search space: 52658 Effective search space used: 52658 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: 47 (22.7 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