Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate 209323 DVU0387 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >MicrobesOnline__882:209323 Length = 225 Score = 115 bits (287), Expect = 9e-31 Identities = 68/211 (32%), Positives = 112/211 (53%), Gaps = 11/211 (5%) Query: 9 ILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILLI 68 IL+G+ +T+ L S+AL +G+ ++ R + L LY RG+P LVL+ L Sbjct: 15 ILEGSAVTIATVLGSLALGFCMGVPMAVAQVYGGRPVRYLVGLYVWFFRGMPILVLLFLF 74 Query: 69 FYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAG 128 ++G L+ ++L+ A LG AY S+ FRG+ +A+P+GQ +A Sbjct: 75 YFGLFQALD-----------LNLSAFTASCLVLGMASAAYQSQIFRGSILALPQGQLKAA 123 Query: 129 AAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADAT 188 A GMS +++PQ +RL+IP ++N + +L K +AL V+G ++M + A T Sbjct: 124 RALGMSDGAAIRSIVLPQALRLSIPAWSNEYSILLKDSALAFVLGTPEIMARTHFVASRT 183 Query: 189 REPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 E ++ A+Y +IT L LRHLE++ Sbjct: 184 YEHLPLYMTAGALYFIITLAGLKVLRHLERK 214 Lambda K H 0.329 0.144 0.421 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: 168 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: 225 Length adjustment: 22 Effective length of query: 207 Effective length of database: 203 Effective search space: 42021 Effective search space used: 42021 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