Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Smeli:SMc03865 Length = 273 Score = 113 bits (283), Expect = 5e-30 Identities = 84/261 (32%), Positives = 140/261 (53%), Gaps = 30/261 (11%) Query: 144 LLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRS 203 + LLV L+A++ F T V T + GL VT+ ++ VG ++ LG+ +AL S Sbjct: 20 IALLVIAAALAAVIAANDIF--TQVFTVVLKGLGVTVFVTLVGFVLATVLGLGVALMALS 77 Query: 204 NMPVIKMLCTVFIEVIRGVPLITVLFMAS-------------VMLPL----FLPQGVTFD 246 V++ + + EVIRGVP++ +LF + V PL ++ V D Sbjct: 78 EHVVLRQIARFYTEVIRGVPILVLLFYIAFVGAPALVTVANFVAAPLISAGWIEPFVVRD 137 Query: 247 KFL--RALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKL 304 L RA++ + + SA++AEV R G+Q++ KGQ E A +LGLS +Q+ +V PQA+++ Sbjct: 138 VSLMWRAIMALMIGYSAFIAEVFRAGIQSVDKGQVEAAKALGLSRYQRFRLVVFPQAIRV 197 Query: 305 VIPGIVNTFIGLFKDTSLVSIIGMFDL--LGIVRLNFSDTNWATAVTPLTGLIFAGFVFW 362 ++P + N F+ + KD+SLVS++G+ D+ +G V + S + T +V+ Sbjct: 198 ILPPLGNDFVAMVKDSSLVSVLGVADITQMGKVYASGSFRFFET-------YSIVAYVYL 250 Query: 363 LFCFGMSRYSGFMERLLDRSQ 383 + G+S +ER L RSQ Sbjct: 251 VLTIGLSLALRAVERRLRRSQ 271 Lambda K H 0.329 0.144 0.454 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: 245 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: 384 Length of database: 273 Length adjustment: 28 Effective length of query: 356 Effective length of database: 245 Effective search space: 87220 Effective search space used: 87220 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: 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