Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04465 Length = 571 Score = 463 bits (1191), Expect = e-135 Identities = 238/456 (52%), Positives = 311/456 (68%), Gaps = 13/456 (2%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64 LQ+LG++ MLPIA+LP G++L LG D+ NI ++ AG +F +L LIFAIGIA+G ++ Sbjct: 9 LQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAIGIAVGFAR 68 Query: 65 DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124 D+NG AGL+GAI YL++ + K +D + NM + GII+GL+AG YNRFKD KLPEYL F Sbjct: 69 DNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDIKLPEYLAF 128 Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184 F GRR VPI T + L IFG++WPPIQ INSFG+ +L G IGA +FG+FNRLLI Sbjct: 129 FGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFGVFNRLLIV 188 Query: 185 LGLHHVLNNIFWFQFGEYNG------VTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAAC 238 GLHH+LNN+ WF FG + VTGDLAR+FA DP G +MTG FP+M+FGLPAAC Sbjct: 189 TGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMMIFGLPAAC 248 Query: 239 LAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFI 298 LAM A P +RK G+ + ALT+F+TG+TEPIEFAFMFL+PLLY +H +LTG+++ I Sbjct: 249 LAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVLLTGMAMAI 308 Query: 299 VNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPG 358 N L I GF+FS GAID L +G + L+ VG+ YA +Y++VF I+ NLKTPG Sbjct: 309 TNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFNLKTPG 368 Query: 359 REDDDVDE--VLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALL 416 RE V E VL EN ++ LGG ENL T+ C TRLRL + D ++ L Sbjct: 369 REGVVVGEKVVLSENQ----RAGAYIQALGGAENLITVGACTTRLRLEMVDRNKASDSEL 424 Query: 417 KKAGAKGVVKSG-GQSVQVIIGPNVEFAAEELRAAV 451 K GA VV+ G G S+QV++GP + A+E+R A+ Sbjct: 425 KALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAM 460 Score = 35.4 bits (80), Expect = 5e-06 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 1/71 (1%) Query: 382 LKGLGGKENLQTIDHCA-TRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNV 440 L +GG +N+ +D A TR+RL + D + E LK G +GV G ++IG Sbjct: 492 LNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDGGVWHLLIGDKA 551 Query: 441 EFAAEELRAAV 451 +E L V Sbjct: 552 LSLSEALEGLV 562 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: 701 Number of extensions: 36 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: 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