Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 477 bits (1228), Expect = e-139 Identities = 254/527 (48%), Positives = 352/527 (66%), Gaps = 19/527 (3%) Query: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67 QRLGRAL LPIA+LP+A LLLR G DLLN+A I AG IF NLA+IFAIG+A +++D Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLAMIFAIGIAVGFARD 69 Query: 68 SAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFF 127 + G A LAG +GY V+ + ++P INMG+LAGI++GL+ GA YNR+ DIKLP++L+FF Sbjct: 70 NNGTAGLAGVIGYLVMISTLKALDPSINMGMLAGIVSGLMAGALYNRFKDIKLPEYLAFF 129 Query: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPT 187 GG+RFVPI TGF + L +FGY+WPP+QH I++ G ++ +G+ G+ +FG NRLLI T Sbjct: 130 GGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINSFGTLMMESGSFGAFVFGLFNRLLIVT 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 GLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYFAGDPKGGQFMTGMFPMMIFGLPAACL 249 Query: 247 AMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVA 306 AMY A RR ++GG+ LS+A+TAFLTGVTEP+EF FMFLAPLL++LHALLTG+S+ + Sbjct: 250 AMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHALLTGLSMAIT 309 Query: 307 TLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKT 366 L IH GF+FS G ID L + S N W++ +G+ + IY+VVF IR F+LKT Sbjct: 310 NALNIHLGFTFSGGFIDMILGW---GKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFDLKT 366 Query: 367 PGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARV 426 PGRE D V + A ++ E A YI A+GG +NL + AC TRLRL + D + Sbjct: 367 PGRETSAD--VEQVAVADNER-----AGAYIKALGGAENLITVGACTTRLRLDMVDRNKA 419 Query: 427 NDTMCKRLGASGVVKLNK-QTIQVIVGAKAESIGDAMK---KVVARGPVAAASAEATPAT 482 +DT K LGA VV+ K ++QV+VG A++I D ++ + R V++ +AE Sbjct: 420 SDTDLKALGAMAVVRPGKGGSLQVVVGPMADAIADEIRLAMPALGRAMVSSPAAEIDAPP 479 Query: 483 AAPVAKPQAVP--NAVSIAELVSPITGDVVALDQVPDEAFASKAVGD 527 A +A P+A NA+ + V + D VA+ ++ + KA+ + Sbjct: 480 PAAMATPEAQQWLNALGGGDNVLQL--DCVAMTRIRLQLADGKALSE 524 Score = 52.0 bits (123), Expect = 7e-11 Identities = 29/85 (34%), Positives = 51/85 (60%), Gaps = 1/85 (1%) Query: 390 TQLATNYIAAVGGTDNLKAIDA-CITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQ 448 T A ++ A+GG DN+ +D +TR+RL +AD +++ K LG GV +L+ Sbjct: 485 TPEAQQWLNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDGGIWH 544 Query: 449 VIVGAKAESIGDAMKKVVARGPVAA 473 +++G KA ++ DA++ +V R V+A Sbjct: 545 LLIGDKAPTLSDALEVLVNRSEVSA 569 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: 966 Number of extensions: 56 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: 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