Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__psRCH2:GFF3103 Length = 394 Score = 294 bits (752), Expect = 4e-84 Identities = 173/409 (42%), Positives = 244/409 (59%), Gaps = 33/409 (8%) Query: 20 DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79 D R R+ Q++ +L +A +L +N NL +G F FL AG+ ++Q LI YS Sbjct: 17 DPRIRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQHLIDYS 76 Query: 80 NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139 DT+ R GLLNTLLVSV+G LAT++G I+GV RLS NWL+ ++ T+Y+E FRNIP Sbjct: 77 ESDTYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIP 136 Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199 LL I + A P+P P+ S+ +D V V NRG +PAP+ Sbjct: 137 PLLLIFFV--YFAVISPLPG--------------PRNSLSLWDVVFVNNRGVQMPAPSAG 180 Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWW--PSLL 257 W ++L +A++AV+ + W A+A + ATG +W P L Sbjct: 181 DGF------WAFWLAL-LVALVAVVVLNRW--------ARARRHATGRMFPVFWTSPGLF 225 Query: 258 ILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317 + + + G F + P++ +F+ GG+ ++ ++++AL++YTAAFI E VR+GI Sbjct: 226 LAIPWLMTFIAGAPFTWEVPELQRFNIRGGWVVIPELVSIVVALSVYTAAFIGETVRSGI 285 Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377 Q++S GQTEAA +LGLRPG+ + LVI+PQALRVIVPPL SQ+LNL KNSSLA A+ Y D+ Sbjct: 286 QSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVIVPPLTSQYLNLAKNSSLAAAIGYPDM 345 Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426 G LNQTG+ +E M + M +YL IS++IS LMN YNK I L ER Sbjct: 346 VSLFAGTVLNQTGQAIETMAITMSVYLAISISISLLMNWYNKRIALIER 394 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: 406 Number of extensions: 20 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: 394 Length adjustment: 31 Effective length of query: 395 Effective length of database: 363 Effective search space: 143385 Effective search space used: 143385 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