Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate RR42_RS29655 RR42_RS29655 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__Cup4G11:RR42_RS29655 Length = 237 Score = 221 bits (564), Expect = 7e-63 Identities = 120/237 (50%), Positives = 153/237 (64%), Gaps = 5/237 (2%) Query: 1 MIFDYNVIWEALPLY----FGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAW 56 MI N W A + F GL TL LL SL G + A+PL + R+SK ++++ W Sbjct: 1 MIDILNQFWRAFLYWDGQGFSGLAVTLWLLDASLFIGFILAVPLAVARISKNKFLSVAVW 60 Query: 57 LYTYVIRGTPMLVQLFLIYYGLAQFEAVRES-FLWPWLSSATFCACLAFAINTSAYTAEI 115 YTYV RGTP+ VQL LIY GL FE VR + L S +C+ +AFA+NT AYT EI Sbjct: 61 CYTYVFRGTPLYVQLLLIYTGLYGFEFVRSTEVLSAVFRSGYYCSIIAFALNTCAYTTEI 120 Query: 116 IAGSLRATPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIV 175 AG++R T +GEIEAA+A GMS F MY+RI++PSALRR+LPQY NEVI+ML TS+A Sbjct: 121 FAGAMRTTNHGEIEAARAYGMSWFTMYRRIVIPSALRRSLPQYGNEVILMLHATSVAFTA 180 Query: 176 TLIDITGAARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPRKH 232 T+ DI AR NA Y F+++ A + YL ++F LV LF+ AE RWL YLA R H Sbjct: 181 TVPDILKVARDANAATYQSFQSFGIAALLYLAVSFALVALFRQAEQRWLAYLAVRPH 237 Lambda K H 0.329 0.139 0.427 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: 164 Number of extensions: 7 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: 232 Length of database: 237 Length adjustment: 23 Effective length of query: 209 Effective length of database: 214 Effective search space: 44726 Effective search space used: 44726 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 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