Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 273 bits (698), Expect = 9e-78 Identities = 167/464 (35%), Positives = 250/464 (53%), Gaps = 40/464 (8%) Query: 4 FLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFV--------YQAGTAVFDHLPLIFA 55 F Q+L ++ +LPIA+LPA G+++ L IPF+ + G VF +P++FA Sbjct: 26 FAQRLSQALLLPIAILPAAGVMIGLATNP---IPFISADLATLMWTVGNLVFSMMPMLFA 82 Query: 56 IGIAIGISKDSNGAAGLSGAISYLMLDAATKTIDK-------------TNNMAVFGGIIA 102 + IAIG +D G A S Y + ++ + K T + + GG++ Sbjct: 83 VTIAIGFCRDQ-GIAAFSAVFGYGVFFSSLSALAKIYHLPTEMILGQATIDTGIAGGMMV 141 Query: 103 GLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGE 162 G + +LP FF GRR P+L + I+LA +F ++WP + + I Sbjct: 142 GAFTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISN 201 Query: 163 WMLGLGGIGA-GIFGLFNRLLIPLGLHHVLNNIFWFQFGEY-NG---VTGDLARFFAKDP 217 W + A ++G+ RLLIPLGLHH+ N F+ + G+Y NG V G++AR+ A DP Sbjct: 202 WAVYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGDEWVRGEVARYLAGDP 261 Query: 218 TAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAF 277 AG G+ I M+GLPAA LA+ A +R AG+M+ A ++TG+TEPIEFAF Sbjct: 262 QAGNLAGGYL-IKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAF 320 Query: 278 MFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICY 337 MF++PLL+ +HA++TG++ + L I FS G +D+ L G + L++G Sbjct: 321 MFVAPLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSLLLGQSRNVEWFLILGPLT 380 Query: 338 AAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHC 397 A +Y++VF I A NLKTPGR ++ + Q M+ LGG++N+ + C Sbjct: 381 AVIYYLVFRGAILAFNLKTPGR--------MEAGSGQRAGLISMITALGGQDNINELTAC 432 Query: 398 ATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441 TRLR++VK LVD+A L K GAKGVV G VQ++ G E Sbjct: 433 LTRLRISVKHAELVDKAQLNKLGAKGVVLV-GNGVQLVYGTKAE 475 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: 553 Number of extensions: 34 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: 490 Length adjustment: 33 Effective length of query: 419 Effective length of database: 457 Effective search space: 191483 Effective search space used: 191483 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