Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate AO353_28165 AO353_28165 ABC transporter substrate-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28165 Length = 259 Score = 236 bits (603), Expect = 3e-67 Identities = 112/249 (44%), Positives = 163/249 (65%), Gaps = 1/249 (0%) Query: 10 LALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVE 69 + ++ P ++ +K G++ +YPPF K PDGS+ GFD D+GNALC E+ VKC+WVE Sbjct: 11 MLFGLIITPLSQAQQVIKFGVDPSYPPFEQKQPDGSLSGFDIDLGNALCAELSVKCIWVE 70 Query: 70 QEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTAVSENLAEL 129 Q FDG++PALK +K DAILS+ S TE R++ VDF++K Y P+ LV + + A L Sbjct: 71 QNFDGMVPALKAKKFDAILSAFSATEARRQQVDFSHKIYTAPSSLVARKNAGLLPTAASL 130 Query: 130 KGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGF 189 KGK++GV +GS+ E FA+ G EI Y +Q++++ D+ GRL+ + D G Sbjct: 131 KGKSVGVVQGSLQESFAKSEWGSQGVEILSYQTQDQVFSDLINGRLEAAFQASVQADIGL 190 Query: 190 LKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAAIRENGKYKQIQDK 248 L+ G+GFAF G TD + GDGV I VRK + L++++NTAIA IR++G+Y +I + Sbjct: 191 LQKPQGQGFAFAGDPITDKRIIGDGVAIGVRKNEPDLREQLNTAIAGIRQSGQYDRIAKQ 250 Query: 249 YFAFDIYGK 257 YF FDIYG+ Sbjct: 251 YFNFDIYGE 259 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: 206 Number of extensions: 10 Number of successful extensions: 2 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: 259 Length adjustment: 24 Effective length of query: 233 Effective length of database: 235 Effective search space: 54755 Effective search space used: 54755 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