Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17535 Length = 571 Score = 479 bits (1232), Expect = e-139 Identities = 251/491 (51%), Positives = 331/491 (67%), Gaps = 18/491 (3%) Query: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67 QRLGRAL LPIA+LP+A LLLR G DLL++A I AG AIF NLA+IFAIG+A +++D Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLGDTDLLDIAIIHDAGQAIFANLAMIFAIGIAVGFARD 69 Query: 68 SAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFF 127 + G A LAGA+GY V+ + ++ INMG+LAGII+GL+ GA YNR+ DIKLP++L+FF Sbjct: 70 NNGTAGLAGAIGYLVMIATLKVLDASINMGMLAGIISGLLAGALYNRFKDIKLPEYLAFF 129 Query: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPT 187 GG+RFVPI TGF + L +FG +WPP+Q I+ G ++ +G+ G+ +FG NRLLI T Sbjct: 130 GGRRFVPIVTGFSAVGLGVVFGLIWPPIQQGINGFGALLMESGSFGAFVFGVFNRLLIVT 189 Query: 188 GLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAAL 246 GLH +LN +AWF G FT+ A G V GD++R++AGD G FM+G FP+M+FGLP A L Sbjct: 190 GLHHILNNMAWFIFGSFTDPATGAVVTGDLSRYFAGDPKGGQFMTGMFPVMLFGLPAACL 249 Query: 247 AMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVA 306 AMY A +RR ++GG+LLS+A+T+FLTGVTEP+EF FMFLAPLL+L+HALLTG+S+ V Sbjct: 250 AMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLFLVHALLTGVSMAVT 309 Query: 307 TLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKT 366 LLGIH GF+FS G ID L + S N W+++ +G+ + AIY++VF IR F+LKT Sbjct: 310 NLLGIHLGFTFSGGFIDMVLGW---GKSTNGWLVVPVGLAYAAIYYLVFDFCIRRFDLKT 366 Query: 367 PGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARV 426 PGRE+ A Q A YI A+GG DNL I AC TRLRL + D + Sbjct: 367 PGREE-------VPAGDKPAIAENQRAAAYIQALGGADNLITIGACTTRLRLDMVDRNKA 419 Query: 427 NDTMCKRLGASGVVKL-NKQTIQVIVGAKAESIGDAMKKVV------ARGPVAAASAEAT 479 +D K LGA VV+ N ++QV+VG A+SI D ++ V PV A A T Sbjct: 420 SDAQLKALGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAVPSSLRPVTAPVPNAPAPTT 479 Query: 480 PATAAPVAKPQ 490 PA + Q Sbjct: 480 PAALSSTEAQQ 490 Score = 39.7 bits (91), Expect = 4e-07 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 7/86 (8%) Query: 378 TEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACIT-RLRLTVADSARVNDTMCKRLGA 436 T A S+TE A ++ A+GG DN+ ++ T RLR+ +AD ++++ K LG Sbjct: 479 TPAALSSTE------AQQWLDALGGQDNVLQLECVATSRLRVRLADDKGLSESRLKGLGC 532 Query: 437 SGVVKLNKQTIQVIVGAKAESIGDAM 462 G+ L +++G KA + A+ Sbjct: 533 QGMSSLEDGVWHLLLGEKAPRLWQAL 558 Lambda K H 0.324 0.139 0.408 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: 932 Number of extensions: 49 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 648 Length of database: 571 Length adjustment: 37 Effective length of query: 611 Effective length of database: 534 Effective search space: 326274 Effective search space used: 326274 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 53 (25.0 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