Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 206139 DVU0714 branched-chain amino acid ABC transporter, permease protein
Query= uniprot:G8ALI9 (505 letters) >MicrobesOnline__882:206139 Length = 317 Score = 219 bits (559), Expect = 8e-62 Identities = 127/315 (40%), Positives = 184/315 (58%), Gaps = 28/315 (8%) Query: 154 IAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYS 213 +AV++A+ F D D+ + + Y +L LN+++G AGL +G+ AFYAVGAY+ Sbjct: 11 LAVLIAVLPLFL---DPYWTDVCVSIGLYAVLALSLNLILGQAGLFHMGHAAFYAVGAYT 67 Query: 214 YALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILI-N 272 A+L + +P+AG LAA+ +++ P++ LRGDY IVT+G EI+RI LI N Sbjct: 68 AAILNTVYHVPVLWTMPVAGLLAALFALVVARPIIHLRGDYLLIVTIGIVEIVRIALINN 127 Query: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVL 332 + TGG NGI GI RP FG + + I YYLI Sbjct: 128 VFGITGGANGIFGISRPMLFGY-----------------------KISKPIQFYYLIWTW 164 Query: 333 ALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFA 392 + L R+ GRA ++EDD+A G++ KLAAF + A++ G G+F+A Sbjct: 165 VAISILLFRRLECSRFGRALNYIKEDDVAAEGSGVDTAYYKLAAFVLGALWAGMTGTFYA 224 Query: 393 TRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFG 452 + ISPESF+F ES ++ AIV+LGG GS GV++ AFL+IGLPE FR+ A RML FG Sbjct: 225 AKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPELFRDFASARMLIFG 283 Query: 453 MGMVLIMLWRPRGLL 467 + MV++M++RP+G+L Sbjct: 284 LAMVVMMIFRPQGML 298 Score = 24.3 bits (51), Expect = 0.007 Identities = 27/118 (22%), Positives = 46/118 (38%), Gaps = 26/118 (22%) Query: 17 ILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGL---------VFLGR 67 I ++A+ L+ +PL L+ W +V ++GL + LG+ Sbjct: 2 ISRKASYAGLAVLIAVLPLF------------LDPYWTDVCVSIGLYAVLALSLNLILGQ 49 Query: 68 LGLCLIREGHAVTVLVLAAAATAAGFFIAMP---TEALRVILIAGGAVIAIRAVLAIR 122 G L GHA V A A +P T + +L A A++ R ++ +R Sbjct: 50 AG--LFHMGHAAFYAVGAYTAAILNTVYHVPVLWTMPVAGLLAALFALVVARPIIHLR 105 Lambda K H 0.329 0.144 0.438 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: 397 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 505 Length of database: 317 Length adjustment: 31 Effective length of query: 474 Effective length of database: 286 Effective search space: 135564 Effective search space used: 135564 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: 50 (23.9 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