Align L-Arginine ABC transporter, permease component 1 (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= reanno::pseudo5_N2C3_1:AO356_18710 (232 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 100 bits (250), Expect = 3e-26 Identities = 68/210 (32%), Positives = 108/210 (51%), Gaps = 9/210 (4%) Query: 16 FSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTYVIRGTPMLVQLFLIY 75 +SGLL TL +S+ L + L L R S P + + Y + RG P++ LF Sbjct: 188 WSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILF--- 244 Query: 76 YGLAQFAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMG 135 +G ++ +S W A + I SAY AE + G L+A P G+ EAA A+G Sbjct: 245 FGQVMVPLMLDS---EWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALG 301 Query: 136 MSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTV--NAQYYL 193 ++ ++ YR I+LP ALR ++P + +LQ T+L SIV L+++ G +R++ N Y Sbjct: 302 LNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLG 361 Query: 194 PF-EAYITAGAFYLCLTFILVRLFKLAERR 222 + E Y+ G Y + L +L + E+R Sbjct: 362 RYAEVYLFLGVLYWLCCYGLAQLSRRLEQR 391 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: 237 Number of extensions: 8 Number of successful extensions: 1 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: 396 Length adjustment: 27 Effective length of query: 205 Effective length of database: 369 Effective search space: 75645 Effective search space used: 75645 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: 48 (23.1 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