Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_008812664.1 M988_RS14705 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_001655005.1:WP_008812664.1 Length = 254 Score = 119 bits (297), Expect = 7e-32 Identities = 79/244 (32%), Positives = 122/244 (50%), Gaps = 24/244 (9%) Query: 3 FDYNVIWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQP----------IVN 52 F + +I E PL+ G T+K + ++ G L L LGL R++K V Sbjct: 4 FRWEIIQEYAPLFAEGAWMTIKCTIICVILGTLWGLTLGLGRMAKAENGPWRIVLRYFVQ 63 Query: 53 MSAWLYTYVIRGTPMLVQLFLIYYGLAQFEA-VRESFL-WPWLSSATFCACL-------- 102 +Y RGTP+ VQ+ ++++ L R+ L L SA F L Sbjct: 64 WPVRVYVSAFRGTPLFVQIMVVHFALVPLLINPRDGVLVTSGLMSADFARMLRSDYGAFL 123 Query: 103 ----AFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQY 158 A +N AY +EI +++ +G++EA++A+GMS K ++++LP A RR LP Sbjct: 124 SCIVAITLNAGAYVSEIFRAGIQSIDHGQMEASRALGMSWGKTMRKVILPQAFRRILPPL 183 Query: 159 SNEVIMMLQTTSLASIVTLIDITGAARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKM 218 N I +++ +SLAS + L D+ AARTV+ Y +E Y+T V Y +TFIL L + Sbjct: 184 GNNAIAIVKDSSLASAIGLADLAYAARTVSGAYATYWEPYLTISVIYWMLTFILSLLVQH 243 Query: 219 AEHR 222 E R Sbjct: 244 MEKR 247 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: 130 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: 254 Length adjustment: 23 Effective length of query: 209 Effective length of database: 231 Effective search space: 48279 Effective search space used: 48279 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 24 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