Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate GFF137 Psest_0137 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__psRCH2:GFF137 Length = 231 Score = 217 bits (552), Expect = 2e-61 Identities = 105/227 (46%), Positives = 161/227 (70%), Gaps = 2/227 (0%) Query: 2 LKGYGAVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPD 61 L G+G ++ G W+T+QLAL+S+ L +VLGL+G + SP L WLG YST++RG+P+ Sbjct: 5 LHGFGPALIAGTWMTIQLALASLALGLVLGLLGALAKTSPYSALRWLGGTYSTIVRGVPE 64 Query: 62 LVLILLIFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIP 121 L+ +LLI++G ++ + +FG ++ + L+P AAG LG FGAY +E FRGA +AIP Sbjct: 65 LLWVLLIYFGTISMIRGIGELFGIEN-LALSPFAAGTIALGLCFGAYATEVFRGALLAIP 123 Query: 122 KGQAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181 KG EAG+A G+ ++F R+++PQM RLA+PG N +++L K TAL+SV+GL+++M ++ Sbjct: 124 KGHREAGLALGLGKRRIFTRLILPQMWRLALPGLGNLFMILMKDTALVSVIGLEEIMRRS 183 Query: 182 KQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVG-VRAA 227 + A A++EPFTFFL A +YL +T V+++ + LEKR G VR+A Sbjct: 184 QIAVTASKEPFTFFLVAAFIYLCLTIVAMVGMHFLEKRAGRGFVRSA 230 Lambda K H 0.329 0.144 0.428 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: 212 Number of extensions: 9 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: 229 Length of database: 231 Length adjustment: 23 Effective length of query: 206 Effective length of database: 208 Effective search space: 42848 Effective search space used: 42848 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: 46 (22.3 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