Align N-acetylglucosamine porter, NagP (characterized)
to candidate 353115 BT3589 glucose/galactose transporter (NCBI ptt file)
Query= TCDB::Q8EBL0 (435 letters) >FitnessBrowser__Btheta:353115 Length = 438 Score = 318 bits (815), Expect = 2e-91 Identities = 172/444 (38%), Positives = 273/444 (61%), Gaps = 31/444 (6%) Query: 6 SQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTA 65 +++K+ ++ +AI+A +FFI GF +W+N L+PY + +L F++ + F+FYIA A Sbjct: 8 ARKKTYYISLAILAGMFFIFGFVSWVNSILIPYFRISCELTHFESYFVAFAFYIAYFVMA 67 Query: 66 LPSAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAV 125 +PS +++KVG+K G+ G + + +F+PAA + F +FL +G G +LQTA Sbjct: 68 IPSGILLKKVGFKKGIMYGFMLTALGAFIFVPAALARQFEIFLIGLFSIGTGLAILQTAA 127 Query: 126 NPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDE-- 183 NPYV +GP +SAA R+S+MGI NK AG+I+PL+F+ALIL + + + +DE Sbjct: 128 NPYVTIIGPIDSAARRISIMGICNKVAGIISPLIFAALILKANDSELFALIESGALDEAT 187 Query: 184 ---MANGL----VLPYLGMAVFIGILALAVKKSPLPELSNEDEVA------DHTDKSQIK 230 M N L ++PY+ + + + + + ++ S LPE++ +++ A HTDK K Sbjct: 188 KNAMLNELIQRVIIPYIILGIILLLTGIGIRYSVLPEINTDEQNATDEQDNKHTDK---K 244 Query: 231 AALSHPNLALGVLALFVYVAVEVIAGDTIGTFALSLGID--HYGVMTSYTMVCMVLGYIL 288 + L P L LG LA+F +V +VIA DTI +A S+G+D V SYT+ C ++GYIL Sbjct: 245 SILDFPYLILGALAIFFHVGTQVIAIDTIINYANSMGMDLLEAKVFPSYTLGCTMIGYIL 304 Query: 289 GILLIPRVISQPTALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIA 348 GI+LIP+ ISQ AL+ +LGL L+ G+++ D + + FG A L A Sbjct: 305 GIILIPKYISQKNALIGCTLLGLALSFGVVWADFD--------MTLFGHQANASIFFLNA 356 Query: 349 FLGLANAIVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGG 408 LG NA+++ +WPL++ G+GK T TGS+LLIMG+ G A P+ +G A + G Sbjct: 357 -LGFPNALIYAGIWPLSIHGLGKFTKTGSSLLIMGLCGNAILPLVYG--HFADQYSLRIG 413 Query: 409 YMVMLPCYLFILFYAVKGHKMRSW 432 Y V++PC+++++F+A+KGHK+ SW Sbjct: 414 YWVLIPCFIYLVFFAIKGHKINSW 437 Lambda K H 0.326 0.141 0.414 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: 634 Number of extensions: 35 Number of successful extensions: 6 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: 435 Length of database: 438 Length adjustment: 32 Effective length of query: 403 Effective length of database: 406 Effective search space: 163618 Effective search space used: 163618 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 (21.6 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