Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (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= SwissProt::O34521 (452 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 459 bits (1182), Expect = e-134 Identities = 232/455 (50%), Positives = 309/455 (67%), Gaps = 11/455 (2%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64 LQ+LG++ MLPIA+LP G++L LG D+ NI ++ AG +F +L +IFAIGIA+G ++ Sbjct: 9 LQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLAMIFAIGIAVGFAR 68 Query: 65 DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124 D+NG AGL+G I YL++ + K +D + NM + GI++GL+AG YNRFKD KLPEYL F Sbjct: 69 DNNGTAGLAGVIGYLVMISTLKALDPSINMGMLAGIVSGLMAGALYNRFKDIKLPEYLAF 128 Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184 F GRR VPI+T + L +FG +WPPIQ INSFG M+ G GA +FGLFNRLLI Sbjct: 129 FGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINSFGTLMMESGSFGAFVFGLFNRLLIV 188 Query: 185 LGLHHVLNNIFWFQFGEYNG------VTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAAC 238 GLHH+LNN+ WF FG + VTGDL+R+FA DP G +MTG FP+M+FGLPAAC Sbjct: 189 TGLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYFAGDPKGGQFMTGMFPMMIFGLPAAC 248 Query: 239 LAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFI 298 LAM A P++RK G+ + ALTAF+TG+TEPIEFAFMFL+PLL+ +HA+LTGLS+ I Sbjct: 249 LAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHALLTGLSMAI 308 Query: 299 VNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPG 358 N L I GF+FS G ID +L +G + L+ VG+ YA +Y++VF I+ +LKTPG Sbjct: 309 TNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFDLKTPG 368 Query: 359 REDD-DVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLK 417 RE DV++V + +K LGG ENL T+ C TRLRL + D + LK Sbjct: 369 RETSADVEQVA---VADNERAGAYIKALGGAENLITVGACTTRLRLDMVDRNKASDTDLK 425 Query: 418 KAGAKGVVKSG-GQSVQVIIGPNVEFAAEELRAAV 451 GA VV+ G G S+QV++GP + A+E+R A+ Sbjct: 426 ALGAMAVVRPGKGGSLQVVVGPMADAIADEIRLAM 460 Score = 34.7 bits (78), Expect = 8e-06 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%) Query: 382 LKGLGGKENLQTIDHCA-TRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNV 440 L LGG +N+ +D A TR+RL + D + E LK G +GV + G ++IG Sbjct: 492 LNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDGGIWHLLIGDKA 551 Query: 441 EFAAEELRAAV 451 ++ L V Sbjct: 552 PTLSDALEVLV 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: 709 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