Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 269 bits (687), Expect = 2e-76 Identities = 163/461 (35%), Positives = 246/461 (53%), Gaps = 34/461 (7%) Query: 4 FLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFV-----YQAGTAVFDHLPLIFAIGI 58 F Q+L ++ ++PIA+LPA G+++ + + IP V G +FD +P++FAI + Sbjct: 22 FAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAIAV 81 Query: 59 AIGISKDSNGAAGLSGAISYLMLDAATKTIDK-------------TNNMAVFGGIIAGLI 105 AIG +D G A S A Y +L + K T + + GG++ G I Sbjct: 82 AIGFCRDQ-GIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGGI 140 Query: 106 AGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWML 165 + +LP FF GRR P++ + ++LA + +WPP+ I +W + Sbjct: 141 TCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWAV 200 Query: 166 GLG-GIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNG----VTGDLARFFAKDPTAG 220 I G +G+ RLL+PLGLHH+ N F+ + G+Y V G++AR+FA DP+AG Sbjct: 201 YQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHDGEIVRGEMARYFAGDPSAG 260 Query: 221 TYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFL 280 G+ I M+GLPAA LA+ A ++R AG+M+ A +++TG+TEPIEFAF+F+ Sbjct: 261 NLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFLFV 319 Query: 281 SPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAV 340 +PLLY HA+LTGL+ I L + FS G +D+VL + + + +G + Sbjct: 320 APLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTFVI 379 Query: 341 YFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATR 400 Y+I+F I A NLKTPGR + D T Q N ++ LGG N+ + C TR Sbjct: 380 YYILFRASILAFNLKTPGRFEAD--------TGQKRNLIAIVSALGGGGNIADLSACLTR 431 Query: 401 LRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441 LR++V D + VD L GAKGV+ G VQ++ G E Sbjct: 432 LRISVADPSQVDRQRLMSLGAKGVIVV-GSGVQLVFGTKAE 471 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: 531 Number of extensions: 25 Number of successful extensions: 7 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: 485 Length adjustment: 33 Effective length of query: 419 Effective length of database: 452 Effective search space: 189388 Effective search space used: 189388 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: 51 (24.3 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