Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Keio:14809 Length = 648 Score = 474 bits (1219), Expect = e-138 Identities = 234/465 (50%), Positives = 316/465 (67%), Gaps = 15/465 (3%) Query: 1 MLSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAI 60 +L F Q+LG++ LPIAVLP ++L G+ D+ N+ F+ QAG A+FD+L LIFAIG+A Sbjct: 3 ILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVAS 62 Query: 61 GISKDSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPE 120 SKDS GAA L+GA+ Y +L A TI+ NM V GII GL+ G YNR+ D KLP+ Sbjct: 63 SWSKDSAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPD 122 Query: 121 YLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNR 180 +L FF G+R VPI T ++LA IFG VWPP+Q I++ GEW++ G +G+GIFG NR Sbjct: 123 FLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINR 182 Query: 181 LLIPLGLHHVLNNIFWFQFGEYNGVT-----GDLARFFAKDPTAGTYMTGFFPIMMFGLP 235 LLIP GLH VLN I WFQ GE+ GD+ RF+A D TAG +M+GFFPIMMFGLP Sbjct: 183 LLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLP 242 Query: 236 AACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLS 295 A LAM A +R GM++ A+TAF+TG+TEP+EF FMFL+PLLY +HA+LTG+S Sbjct: 243 GAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGIS 302 Query: 296 LFIVNWLGIRSGFSFSAGAIDYVLSYGI---AEKPLLLLLVGICYAAVYFIVFYVLIKAL 352 LF+ LGI +GFSFSAGAIDY L Y + ++ +LL++G+ + A+YF+VF ++I+ Sbjct: 303 LFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMF 362 Query: 353 NLKTPGREDDDVDEVLDENTVQDVNENI------MLKGLGGKENLQTIDHCATRLRLTVK 406 NLKTPGRED + DE++ E + E + + +GG +NL+ ID C TRLRLTV Sbjct: 363 NLKTPGREDKE-DEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVA 421 Query: 407 DTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAV 451 D+A V++ + K+ GA GVVK Q++QVI+G E + ++ V Sbjct: 422 DSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVV 466 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: 762 Number of extensions: 41 Number of successful extensions: 4 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: 648 Length adjustment: 35 Effective length of query: 417 Effective length of database: 613 Effective search space: 255621 Effective search space used: 255621 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