Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= BRENDA::P45604 (651 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 441 bits (1135), Expect = e-128 Identities = 254/564 (45%), Positives = 340/564 (60%), Gaps = 46/564 (8%) Query: 3 ILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQAGGAIFDNLALIFAIGVAS 62 IL Q LGRAL LPIAVLPVA LLLR GQPDLL++ F++ AG AIF NL ++FAIGVA Sbjct: 4 ILETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIGVAV 63 Query: 63 SWSKDNAGSAALAGAVGYFVMTKAMVTI---NPEINMG---------------------- 97 +++D G+AALAG Y V T T PE+ G Sbjct: 64 GFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQAWATGQIDRLE 123 Query: 98 VLAGIITGLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQH 157 V GII+GL+ G YNR+A I LP++L+FFGG+RFVPIA G L+LA + GY + + Sbjct: 124 VPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGYGYAHISS 183 Query: 158 AIHSGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDIN 217 A+ + +V +G G ++G +NRLL+ TGLH +LN +AWF +G+F A G D+ Sbjct: 184 ALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDFGGATG-----DLG 238 Query: 218 RFYAGDGTAGMFMSGFFPIMMFGLPGAALAMYLAAPKARRPMVGGMLLSVAITAFLTGVT 277 RF+AGD AG FMSGFFP+MMFGLP A LAMY A RR VGGML S+A T+FLTGVT Sbjct: 239 RFFAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVT 298 Query: 278 EPLEFLFLFLAPLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNV 337 EP+EF F+FLAP+LY +HAVLTG+++ + LGI GF FSAG DYVL + L S Sbjct: 299 EPIEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFKL---STRP 355 Query: 338 WMLLVMGVVFFFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYI 397 WMLL +G + +Y+ LF IR +L TPGRE A E + E G +++ Sbjct: 356 WMLLPVGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERG-----AAFV 410 Query: 398 AAVGGTDNLKAIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAES 457 A+GG NL ++DAC TRLRL V D + V+DAA LGA G+++ + QV++G A+ Sbjct: 411 KALGGAANLTSVDACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIADL 470 Query: 458 IGDEMKKVVTRGPVAAAAAAPAGNVATAA---PAAKPQAV---ANAKTVESLVSPITGDV 511 + +E++ + G AA +AAPA +A A PAA A+ AN + +++L +V Sbjct: 471 VAEEIRGAI-GGGAAAVSAAPAQALADEAVTLPAAILAALGGEANIRALQALHGRFRVEV 529 Query: 512 VALEQVPDEAFASKAVGDGIAVKP 535 V + DEA A ++ +P Sbjct: 530 VDAART-DEASLLAAANGAVSPQP 552 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: 922 Number of extensions: 53 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: 651 Length of database: 560 Length adjustment: 37 Effective length of query: 614 Effective length of database: 523 Effective search space: 321122 Effective search space used: 321122 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