Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Caulo:CCNA_00572 Length = 582 Score = 424 bits (1089), Expect = e-123 Identities = 219/490 (44%), Positives = 313/490 (63%), Gaps = 41/490 (8%) Query: 2 LSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQA---------------GTAV 46 L LQ LG++ MLPIAVLP ++L +G+ D+ P + A G A+ Sbjct: 5 LEILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAI 64 Query: 47 FDHLPLIFAIGIAIGISKDSNGAAGLSGAISYLML------------DAATKTIDKTNNM 94 F L LIFAIG+A+G++++++GAAGL+G + Y++ + A K ++ ++ Sbjct: 65 FASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAKDL 124 Query: 95 AVFG-------------GIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITII 141 A+ GI++G+I+G YNR+ +LPEYL FF GRR VPI+ + ++ Sbjct: 125 AIAAWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIVAGLAGVV 184 Query: 142 LAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGE 201 LA +FG W +++ ++ + G +G ++GL NRLLI GLHH+LNN+ WF G+ Sbjct: 185 LALLFGAFWSTLEAGVDGLSGLVTASGDLGLVVYGLLNRLLIVTGLHHILNNVVWFILGD 244 Query: 202 YNGVTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFA 261 +NGVTGDL RF A D TAG +M+GFFP+MMFGLPAACLAM+ TA+P +RKA AGM+ A Sbjct: 245 FNGVTGDLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGMLGSLA 304 Query: 262 LTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSY 321 LT+F+TG+TEPIEF FMFL+P+L+A+HA+LTGLS+ ++N L ++ GF FSAG DYVL++ Sbjct: 305 LTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGFGFSAGLFDYVLNF 364 Query: 322 GIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIM 381 A +PLLL+ VG+ Y A+Y+ VF I +LKTPGRED+ T + M Sbjct: 365 NKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGREDEAPPSAQAVTTGGGRGAD-M 423 Query: 382 LKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441 L LGG NL ++D C TRLRL V D LV+E LK GA+GVV+ +++QV++GP + Sbjct: 424 LAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKALGARGVVRPSDKALQVVLGPIAD 483 Query: 442 FAAEELRAAV 451 A E+R A+ Sbjct: 484 TVAGEIRHAI 493 Score = 52.8 bits (125), Expect = 3e-11 Identities = 28/68 (41%), Positives = 40/68 (58%) Query: 381 MLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNV 440 +L LGG +NL+ + A+RLR+ + D VD+A L AG +G +V +IIGP+ Sbjct: 514 LLAALGGADNLRDLSVHASRLRVVLNDPERVDQAALHTAGVRGFAAVAPGAVHIIIGPHA 573 Query: 441 EFAAEELR 448 E AE LR Sbjct: 574 ERIAEVLR 581 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: 727 Number of extensions: 33 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: 582 Length adjustment: 35 Effective length of query: 417 Effective length of database: 547 Effective search space: 228099 Effective search space used: 228099 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 Apr 09 2024. 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