Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter
Query= BRENDA::P45604 (651 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04465 Length = 571 Score = 486 bits (1250), Expect = e-141 Identities = 259/525 (49%), Positives = 351/525 (66%), Gaps = 13/525 (2%) Query: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQAGGAIFDNLALIFAIGVASSWSKD 67 QRLGRAL LPIA+LP+A LLLR G DLLN+ I AG IF NLALIFAIG+A +++D Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAIGIAVGFARD 69 Query: 68 NAGSAALAGAVGYFVMTKAMVTINPEINMGVLAGIITGLVAGAVYNRWAGIKLPDFLSFF 127 N G+A LAGA+GY VM + ++ INMG+LAGII+GL+AGA+YNR+ IKLP++L+FF Sbjct: 70 NNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDIKLPEYLAFF 129 Query: 128 GGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGEWIVSAGALGSGIFGFINRLLIPT 187 GG+RFVPIATGF + L IFG +WPP+QH I+S G+ ++ +G++G+ +FG NRLLI T Sbjct: 130 GGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFGVFNRLLIVT 189 Query: 188 GLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAAL 246 GLH +LN +AWF G FT+ G + GD+ R++AGD G FM+G FP+M+FGLP A L Sbjct: 190 GLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMMIFGLPAACL 249 Query: 247 AMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTGISLFIA 306 AMY A RR ++GG+ LS+A+T+FLTGVTEP+EF F+FLAPLLYLLH +LTG+++ I Sbjct: 250 AMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVLLTGMAMAIT 309 Query: 307 TALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVFFFVYFLLFSAVIRMFNLKT 366 AL IH GF+FS GAID L + S N W++ +G+ + +Y+++F IR FNLKT Sbjct: 310 NALNIHLGFTFSGGAIDMALGW---GKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFNLKT 366 Query: 367 PGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLKAIDACITRLRLTVGDSAKV 426 PGRE VV E +E Q A +YI A+GG +NL + AC TRLRL + D K Sbjct: 367 PGRE----GVVVGEKVVLSE---NQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKA 419 Query: 427 NDAACKRLGASGVVKLNK-QTIQVIVGAKAESIGDEMKKVV-TRGPVAAAAAAPAGNVAT 484 +D+ K LGA VV+ K ++QV+VG A+SI DE+++ + T G AA Sbjct: 420 SDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPK 479 Query: 485 AAPAAKPQAVANAKTVESLVSPITGDVVALEQVPDEAFASKAVGD 529 AAP P+A V + + D VA+ ++ + KA+ + Sbjct: 480 AAPVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSE 524 Score = 56.6 bits (135), Expect = 3e-12 Identities = 38/111 (34%), Positives = 60/111 (54%), Gaps = 2/111 (1%) Query: 364 LKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLKAIDA-CITRLRLTVGD 422 + T G AA VVTEEA T A ++ AVGG+DN+ +D +TR+RL + D Sbjct: 460 MPTAGSALVAAVVVTEEAPKAAPVE-TPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLAD 518 Query: 423 SAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMKKVVTRGPVAA 473 +++ K LG GV L+ +++G KA S+ + ++ +V R V+A Sbjct: 519 GKALSECQLKDLGCQGVSALDGGVWHLLIGDKALSLSEALEGLVNRSEVSA 569 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: 936 Number of extensions: 54 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: 651 Length of database: 571 Length adjustment: 37 Effective length of query: 614 Effective length of database: 534 Effective search space: 327876 Effective search space used: 327876 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