Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate GFF138 Psest_0138 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__psRCH2:GFF138 Length = 251 Score = 200 bits (509), Expect = 2e-56 Identities = 115/255 (45%), Positives = 157/255 (61%), Gaps = 9/255 (3%) Query: 3 KLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMK 62 K +LL A A ++ FA EK L+IG E AYPPF G +VGFD DI +ALC +MK Sbjct: 5 KKILLTAAASLIIGTQAFAAEK-LRIGTEGAYPPFNLIDASGKVVGFDLDISHALCAKMK 63 Query: 63 VKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQV 122 V+C V ++DG+IPAL K D + +SMS+T++RK +VDFT+ YY + V + Sbjct: 64 VECEVVTSDWDGIIPALNAGKFDFLAASMSVTEERKNAVDFTDHYYTNKLQFVAPKNVEF 123 Query: 123 SDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADA 182 + LKGK IG QR +I + E+ L + +IK Y +Q YLD+A+GR+DG +AD Sbjct: 124 QTDEGYLKGKVIGAQRATIAGTWLEDNLDRV-VDIKLYDTQENAYLDLASGRVDGILAD- 181 Query: 183 TLLDDGFLKTDSGKGFAFVG-PAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANG 241 T + +LK+D+GK F F G P F D+K I IAVRKG+ +++N A+ I A+G Sbjct: 182 TFVQWEWLKSDAGKNFEFKGEPVFDDDK-----IAIAVRKGNDELRERLNKALAEIIADG 236 Query: 242 KYKQIQDKYFNFDIY 256 YKQI DKYF F IY Sbjct: 237 TYKQINDKYFPFSIY 251 Lambda K H 0.318 0.138 0.395 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: 234 Number of extensions: 14 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: 258 Length of database: 251 Length adjustment: 24 Effective length of query: 234 Effective length of database: 227 Effective search space: 53118 Effective search space used: 53118 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 Apr 09 2024. 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