Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17535 Length = 571 Score = 461 bits (1186), Expect = e-134 Identities = 231/454 (50%), Positives = 313/454 (68%), Gaps = 9/454 (1%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64 LQ+LG++ MLPIA+LP G++L LG D+ +I ++ AG A+F +L +IFAIGIA+G ++ Sbjct: 9 LQRLGRALMLPIAILPIAGLLLRLGDTDLLDIAIIHDAGQAIFANLAMIFAIGIAVGFAR 68 Query: 65 DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124 D+NG AGL+GAI YL++ A K +D + NM + GII+GL+AG YNRFKD KLPEYL F Sbjct: 69 DNNGTAGLAGAIGYLVMIATLKVLDASINMGMLAGIISGLLAGALYNRFKDIKLPEYLAF 128 Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184 F GRR VPI+T + L +FG++WPPIQ IN FG ++ G GA +FG+FNRLLI Sbjct: 129 FGGRRFVPIVTGFSAVGLGVVFGLIWPPIQQGINGFGALLMESGSFGAFVFGVFNRLLIV 188 Query: 185 LGLHHVLNNIFWFQFGEYNG------VTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAAC 238 GLHH+LNN+ WF FG + VTGDL+R+FA DP G +MTG FP+M+FGLPAAC Sbjct: 189 TGLHHILNNMAWFIFGSFTDPATGAVVTGDLSRYFAGDPKGGQFMTGMFPVMLFGLPAAC 248 Query: 239 LAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFI 298 LAM A P +RK G+++ ALT+F+TG+TEPIEFAFMFL+PLL+ VHA+LTG+S+ + Sbjct: 249 LAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLFLVHALLTGVSMAV 308 Query: 299 VNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPG 358 N LGI GF+FS G ID VL +G + L++ VG+ YAA+Y++VF I+ +LKTPG Sbjct: 309 TNLLGIHLGFTFSGGFIDMVLGWGKSTNGWLVVPVGLAYAAIYYLVFDFCIRRFDLKTPG 368 Query: 359 REDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKK 418 RE+ + ++ ++ LGG +NL TI C TRLRL + D +A LK Sbjct: 369 REEVPAGD--KPAIAENQRAAAYIQALGGADNLITIGACTTRLRLDMVDRNKASDAQLKA 426 Query: 419 AGAKGVVKSG-GQSVQVIIGPNVEFAAEELRAAV 451 GA VV+ G G S+QV++GP + A+E+R AV Sbjct: 427 LGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAV 460 Lambda K H 0.326 0.144 0.429 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: 698 Number of extensions: 35 Number of successful extensions: 4 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: 452 Length of database: 571 Length adjustment: 34 Effective length of query: 418 Effective length of database: 537 Effective search space: 224466 Effective search space used: 224466 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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