Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__azobra:AZOBR_RS08660 Length = 399 Score = 271 bits (693), Expect = 3e-77 Identities = 176/422 (41%), Positives = 251/422 (59%), Gaps = 36/422 (8%) Query: 8 PKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRA 67 P A +S + D R++ Q++V+ + +A +L++N NL + F FL A Sbjct: 11 PSAPGGVSFSLSDPTVRAVFYQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREA 70 Query: 68 GYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARI 127 + + ++LI Y D++ RA + G+LNTL VS++G +LAT+LGT+IGV RLS NWL+A++ Sbjct: 71 SFGIGESLIDYHPRDSYGRAFLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKL 130 Query: 128 MTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVT 187 + YVE RNIP LL + +++E+ P + +A P V ++ Sbjct: 131 ASTYVEIVRNIPPLLQLFFWYALVSESMPPVR--------QALNPIP--------GVFLS 174 Query: 188 NRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGT 247 RG +P P+ D G +G+ L A+A++ V+ W AKA QE TG Sbjct: 175 QRGLFVPVPSADPVWGT--MGFAL-----AIAVIGVIFLRRW--------AKARQERTG- 218 Query: 248 RPT---TWWPSLLILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLY 304 +P T SLLI I+ + G LD P++ F+F GG + F A+L+ L +Y Sbjct: 219 QPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPKLQGFNFVGGVVLTPEFFAILVGLVVY 278 Query: 305 TAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTK 364 TAAFIAE+VR+GI A++ GQTEAA ALG+ G+T+ LV+LPQALRVIVPPL SQ+LNLTK Sbjct: 279 TAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLPQALRVIVPPLTSQYLNLTK 338 Query: 365 NSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLK 424 NSSLA+A+ Y DL ++ TLNQTG+ +E + ++M YL ISL IS MN YNK I L Sbjct: 339 NSSLALAIGYPDL-VSIANTTLNQTGQAIEGVAMIMGTYLVISLGISIFMNWYNKRIALV 397 Query: 425 ER 426 ER Sbjct: 398 ER 399 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: 407 Number of extensions: 14 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: 399 Length adjustment: 31 Effective length of query: 395 Effective length of database: 368 Effective search space: 145360 Effective search space used: 145360 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