Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 254 bits (648), Expect = 6e-72 Identities = 161/513 (31%), Positives = 263/513 (51%), Gaps = 74/513 (14%) Query: 4 FLQKLGKSFMLPIAVLPAVGIILALGRE----DVFNI-------------PFVYQAGTAV 46 F Q+LGK+FMLP+A+L GI+L +G DV + ++ + G+ Sbjct: 14 FFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFA 73 Query: 47 FDHLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATK--------------TIDKTN 92 F LP++F I I +G+++++ G A +G I Y +++ A + K N Sbjct: 74 FSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKAN 133 Query: 93 NM-----------AVFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITII 141 N+ + G +IAG+I + RF + +LP+ L FF G R VPI+++++ + Sbjct: 134 NIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGL 193 Query: 142 LAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGE 201 + + +VWP I+ G + G G +FG RLL+P GLHH+L + +F + Sbjct: 194 VGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHIL--VALIRFTD 251 Query: 202 YNG--------VTGDLARFFAKDPTAGTY----------MTGFFPIMMFGLPAACLAMVV 243 G V+G L F A+ T+ G P + GLP A LAM Sbjct: 252 AGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYH 311 Query: 244 TAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLG 303 A+P R G++I + + G TEP+EF F+F++P+LY +HA+LTGL +++ LG Sbjct: 312 CARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLG 371 Query: 304 IRSGFSFSAGAIDYV---LSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGRE 360 + G + ID+V + +G++ K ++ +V + VY+++F I NLKTPGR+ Sbjct: 372 VTIG-NTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRD 430 Query: 361 DDDVDEVLDENTV------QDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEA 414 + + E V N +L+ LGG +N+ ++D+C TRLRL+VKD +LV+ Sbjct: 431 SEVASSI--EKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQ 488 Query: 415 LLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEEL 447 LK A GVV+ ++QV+IGP V+ +E+ Sbjct: 489 ALKDNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521 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: 662 Number of extensions: 47 Number of successful extensions: 8 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: 530 Length adjustment: 34 Effective length of query: 418 Effective length of database: 496 Effective search space: 207328 Effective search space used: 207328 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