Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Keio:1936976 Length = 393 Score = 270 bits (691), Expect = 4e-77 Identities = 165/405 (40%), Positives = 231/405 (57%), Gaps = 33/405 (8%) Query: 24 RSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDT 83 R+ QI+ ++ + + WL +N NL +G F+FL AG+ + Q LI Y DT Sbjct: 20 RAWLFQILAVVAVVGIVGWLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGDT 79 Query: 84 HFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLW 143 + R I GLLNTLLVS L + A++LG IG+ RLS NWL+ ++ T+Y+E FRNIP LL Sbjct: 80 YGRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLLQ 139 Query: 144 ILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLG 203 I + P P+ +A+ A FD ++NRG +P+P Sbjct: 140 IFFWYFAVLRNLPGPR-----QAVSA-----------FDLAFLSNRGLYIPSP------- 176 Query: 204 VVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTW-WPSLLILFAP 262 LG + A+ + V+S + + K Q TG TW ++LI+ P Sbjct: 177 --QLGDGFIAFILAVVMAIVLSVGLFRFN------KTYQIKTGQLRRTWPIAAVLIIGLP 228 Query: 263 ISAL-LYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAIS 321 + A L+G H D P + F+F GG ++ AL +AL++YT+AFIAEI+RAGIQA+ Sbjct: 229 LLAQWLFGAALHWDVPALRGFNFRGGMVLIPELAALTLALSVYTSAFIAEIIRAGIQAVP 288 Query: 322 RGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTL 381 GQ EAA +LGL T+ VI+PQALRVI+PPL SQ+LN+ KNSSLA A+ Y D+ Sbjct: 289 YGQHEAARSLGLPNPVTLRQVIIPQALRVIIPPLTSQYLNIVKNSSLAAAIGYPDMVSLF 348 Query: 382 GGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 G LNQTG+ +E + + M +YL ISLTIS LMN+YN+ I + ER Sbjct: 349 AGTVLNQTGQAIETIAMTMSVYLIISLTISLLMNIYNRRIAIVER 393 Lambda K H 0.326 0.139 0.419 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: 391 Number of extensions: 10 Number of successful extensions: 3 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: 426 Length of database: 393 Length adjustment: 31 Effective length of query: 395 Effective length of database: 362 Effective search space: 142990 Effective search space used: 142990 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 (21.7 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