Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter
Query= BRENDA::P45604 (651 letters) >FitnessBrowser__WCS417:GFF4494 Length = 568 Score = 484 bits (1245), Expect = e-141 Identities = 264/514 (51%), Positives = 347/514 (67%), Gaps = 23/514 (4%) Query: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQAGGAIFDNLALIFAIGVASSWSKD 67 QRLGRAL LPIA+LP+A LLLR G DLLN+ + AG AIF NLALIFAIG+A +++D Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLGDTDLLNIAVMHDAGQAIFANLALIFAIGIAVGFARD 69 Query: 68 NAGSAALAGAVGYFVMTKAMVTINPEINMGVLAGIITGLVAGAVYNRWAGIKLPDFLSFF 127 N G+A LAGA+GY VM + ++ INMG+LAGI +GL+AG +YNR+ IKLP++L+FF Sbjct: 70 NNGTAGLAGAIGYLVMVSTLKVMDTSINMGMLAGIASGLMAGGLYNRFKDIKLPEYLAFF 129 Query: 128 GGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGEWIVSAGALGSGIFGFINRLLIPT 187 GG+RFVPI TGF + L IFG +WPP+QH I+S G ++ +G+LG+ +FG NRLLI T Sbjct: 130 GGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGINSFGVLLMESGSLGAFVFGVFNRLLIVT 189 Query: 188 GLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAAL 246 GLH +LN +AWF G FT+ G V GD+ R++AGD G FM+G FP+M+FGLP A L Sbjct: 190 GLHHILNNMAWFVFGSFTDPVTGAVVTGDLTRYFAGDPKGGQFMTGMFPVMLFGLPAACL 249 Query: 247 AMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTGISLFIA 306 AMY A RR ++GG+ LS+A+T+FLTGVTEP+EF F+FLAP LYL+HAVLTG+S+ + Sbjct: 250 AMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAVLTGLSMAVT 309 Query: 307 TALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVFFFVYFLLFSAVIRMFNLKT 366 L IH GF+FS G ID VL + S N W++ +G+ + +Y+ +F+ IR FNLKT Sbjct: 310 NMLNIHLGFTFSGGFIDMVLGW---GKSTNGWLVFPVGLAYALIYYSVFNYCIRHFNLKT 366 Query: 367 PGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLKAIDACITRLRLTVGDSAKV 426 PGRED VV EA S+ Q AT+YI A+GG NL ++ AC TRLRL + D K Sbjct: 367 PGRED--TQVVQAEAMSD-----NQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKA 419 Query: 427 NDAACKRLGASGVVKL-NKQTIQVIVGAKAESIGDEMKKVVTRGPVAAAAAAPAGNVATA 485 DA K LGA VV+ N ++QV+VG A+SI DE+ ++ G VAAA Sbjct: 420 VDAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEI-RLAMPGFVAAAP-------VVV 471 Query: 486 APAAKPQAVANAKTVESLVSPI--TGDVVALEQV 517 AP KP AV N + E ++ + G+V LE V Sbjct: 472 APVEKPVAV-NVQEAEKWLNALGGRGNVRQLEAV 504 Score = 51.6 bits (122), Expect = 1e-10 Identities = 26/86 (30%), Positives = 52/86 (60%), Gaps = 1/86 (1%) Query: 391 QLATSYIAAVGGTDNLKAIDA-CITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQV 449 Q A ++ A+GG N++ ++A +TRLR+ +GD + +++A LG GV +L + Sbjct: 483 QEAEKWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLESGVWHL 542 Query: 450 IVGAKAESIGDEMKKVVTRGPVAAAA 475 ++G KA +G+ ++++V + A+A Sbjct: 543 LIGDKATGLGEALERLVGAQQIGASA 568 Lambda K H 0.323 0.138 0.406 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: 948 Number of extensions: 58 Number of successful extensions: 6 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: 651 Length of database: 568 Length adjustment: 37 Effective length of query: 614 Effective length of database: 531 Effective search space: 326034 Effective search space used: 326034 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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