Align L-Arginine ABC transporter, permease component 1 (characterized)
to candidate 209325 DVU0389 amino acid ABC tranporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo5_N2C3_1:AO356_18710 (232 letters) >MicrobesOnline__882:209325 Length = 224 Score = 126 bits (316), Expect = 4e-34 Identities = 73/208 (35%), Positives = 119/208 (57%), Gaps = 10/208 (4%) Query: 2 IFDYNVIY-EALPLYFSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTY 60 +FD + ++ E LP GL+T++ L+ S GLL + +G RV V +YT Sbjct: 1 MFDPDFVFGEMLPALNRGLITSMMLIVPSATLGLLFGIIVGTGRVFGPAWVRKAGDIYTA 60 Query: 61 VIRGTPMLVQLFLIYYGLAQFAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSL 120 RG P++VQL +IY+GL I E F A L F + ++AY +E + G+L Sbjct: 61 TFRGVPLVVQLMIIYFGLPNIGIYLEPFP---------AAVLGFVLCSAAYNSEYVRGAL 111 Query: 121 RATPNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDI 180 + G+++AA+A+G S+ K I++P A+RRALP NE+I +++ +SLA ++T I++ Sbjct: 112 LSIRQGQLKAAQALGFSKLKTVLFIVVPQAVRRALPGCGNEIIYLIKYSSLAYVITCIEL 171 Query: 181 TGAARTVNAQYYLPFEAYITAGAFYLCL 208 TG + V A+ + E ++ GA+YL L Sbjct: 172 TGEGKVVAARSFRFTEVFLFVGAYYLFL 199 Lambda K H 0.330 0.140 0.425 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: 120 Number of extensions: 3 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: 224 Length adjustment: 23 Effective length of query: 209 Effective length of database: 201 Effective search space: 42009 Effective search space used: 42009 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 (21.9 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