Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__WCS417:GFF4494 Length = 568 Score = 459 bits (1181), Expect = e-133 Identities = 234/454 (51%), Positives = 308/454 (67%), Gaps = 9/454 (1%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64 LQ+LG++ MLPIA+LP G++L LG D+ NI ++ AG A+F +L LIFAIGIA+G ++ Sbjct: 9 LQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAVMHDAGQAIFANLALIFAIGIAVGFAR 68 Query: 65 DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124 D+NG AGL+GAI YL++ + K +D + NM + GI +GL+AG YNRFKD KLPEYL F Sbjct: 69 DNNGTAGLAGAIGYLVMVSTLKVMDTSINMGMLAGIASGLMAGGLYNRFKDIKLPEYLAF 128 Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184 F GRR VPI+T + L IFG++WPPIQ INSFG ++ G +GA +FG+FNRLLI Sbjct: 129 FGGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGINSFGVLLMESGSLGAFVFGVFNRLLIV 188 Query: 185 LGLHHVLNNIFWFQFGEYNG------VTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAAC 238 GLHH+LNN+ WF FG + VTGDL R+FA DP G +MTG FP+M+FGLPAAC Sbjct: 189 TGLHHILNNMAWFVFGSFTDPVTGAVVTGDLTRYFAGDPKGGQFMTGMFPVMLFGLPAAC 248 Query: 239 LAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFI 298 LAM A P +RK G+ + ALT+F+TG+TEPIEFAFMFL+P LY +HAVLTGLS+ + Sbjct: 249 LAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAVLTGLSMAV 308 Query: 299 VNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPG 358 N L I GF+FS G ID VL +G + L+ VG+ YA +Y+ VF I+ NLKTPG Sbjct: 309 TNMLNIHLGFTFSGGFIDMVLGWGKSTNGWLVFPVGLAYALIYYSVFNYCIRHFNLKTPG 368 Query: 359 REDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKK 418 RED V V E + ++ LGG +NL ++ C TRLRL + D +A LK Sbjct: 369 REDTQV--VQAEAMSDNQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKAVDAELKA 426 Query: 419 AGAKGVVKSG-GQSVQVIIGPNVEFAAEELRAAV 451 GA VV+ G G S+QV++GP + A+E+R A+ Sbjct: 427 LGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAM 460 Score = 31.2 bits (69), Expect = 9e-05 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 1/71 (1%) Query: 382 LKGLGGKENLQTIDHCA-TRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNV 440 L LGG+ N++ ++ A TRLR+ + D + + EA L G +GV + ++IG Sbjct: 489 LNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLESGVWHLLIGDKA 548 Query: 441 EFAAEELRAAV 451 E L V Sbjct: 549 TGLGEALERLV 559 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: 37 Number of successful extensions: 5 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: 452 Length of database: 568 Length adjustment: 34 Effective length of query: 418 Effective length of database: 534 Effective search space: 223212 Effective search space used: 223212 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