Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate AO353_17115 AO353_17115 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17115 Length = 418 Score = 415 bits (1066), Expect = e-120 Identities = 220/399 (55%), Positives = 280/399 (70%), Gaps = 7/399 (1%) Query: 78 AVTVLVLAAAATAAGFFIAMPTEALRVILI-AGGAVIAIRAVLAIRTGRSKLSQAERDKR 136 AV VL + AG + + +LI A +V+ VL R + + + K Sbjct: 17 AVAYPVLGLKLSIAGINLEVQGATTSTLLIIAACSVLMFLRVLFDREYTAAMRSVPKGKL 76 Query: 137 MDHIAAQ---VQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVV 193 + A+ + RW+ +V+AL +PF R +DI L+L Y++LG GLNIVV Sbjct: 77 IPASASNFLTLPSTQRWVIMGLIVIALVWPF--FGSRGAVDIATLILIYVLLGLGLNIVV 134 Query: 194 GLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGD 253 GLAGLLDLGYV FYAVGAYSYALL+HY+G SFW+CLP+AG +AA G LLGFPVLRLRGD Sbjct: 135 GLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGLMAATFGFLLGFPVLRLRGD 194 Query: 254 YFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFG 313 Y AIVTLGFGEIIR+ L N TGGPNGIS IP+PS FG++ F RT AEG FHE FG Sbjct: 195 YLAIVTLGFGEIIRLFLRNLTGLTGGPNGISNIPKPSLFGLS-FERTAAEGMQTFHEFFG 253 Query: 314 LEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMK 373 L ++P+ +++FLY + L+LAL R+ ++P+GRAWEALRED+IAC +LG+N T +K Sbjct: 254 LTYNPVSKVVFLYLVALLLALFALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIK 313 Query: 374 LAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLV 433 L+AF + A F GFAGSFFA RQG ++PESFTFIESA ILAIVVLGGMGSQ+GVV+AA ++ Sbjct: 314 LSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESATILAIVVLGGMGSQLGVVLAAVVM 373 Query: 434 IGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDP 472 I LPE R+ ++YRML FG MVL+M+WRP+GLL + P Sbjct: 374 ILLPELMRDFSEYRMLMFGALMVLMMIWRPQGLLPMQRP 412 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: 608 Number of extensions: 34 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: 505 Length of database: 418 Length adjustment: 33 Effective length of query: 472 Effective length of database: 385 Effective search space: 181720 Effective search space used: 181720 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: 51 (24.3 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