Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 312 bits (799), Expect = 3e-89 Identities = 184/503 (36%), Positives = 289/503 (57%), Gaps = 39/503 (7%) Query: 2 WKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMME 61 W KF QR+ +AL++P+AILPAAG++L L S +PF+ + + +M Sbjct: 24 WFKF---AQRLSQALLIPIAILPAAGVMLGL--------TVSPIPFMP----EVLNVLML 68 Query: 62 GAGGIIFDNLAIIFALGVAIGLASGDGVAAIAAFVGFIVLNKTMGMFLGV--TPEKAADA 119 G +IF + I+FA+ VAIG G+AA A G+ V+ T+ + P + Sbjct: 69 AVGKLIFAIMPILFAVAVAIGFCRDQGIAAFTAVFGYGVMTATLAALADLYQLPTQL--- 125 Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179 VLG+ TL TG+ GG++IG + + I LP+ FF G+R +++ + Sbjct: 126 ------VLGMETLDTGIAGGMLIGGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLA 179 Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239 L + +A IWPS+ + S+ + +A ++G ++RLLIP GLHHI++APF+ E Sbjct: 180 MGLGYVLAHIWPSLSLLIERVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLE 239 Query: 240 FGSYKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKE 299 G Y+ +++ G+ ++ AG + G + + M+GLPAAALAI++ A Sbjct: 240 VGQYQLQDAEVVRGEVARYLAGDPQ-----AGN-LAGGYLIKMWGLPAAALAIWRCADNS 293 Query: 300 NKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGY 359 + VAG+MLS A S+LTG+TEP+EF+F+FVAPLLF IH +L GL++ + +LD+H Sbjct: 294 ERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPLLFLIHVMLSGLAYFVCIMLDIHHSI 353 Query: 360 TFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEVKS 419 FS G +DF LL L T W+ V+ G + A IYYI+FR I+ FN KTPGR ++S Sbjct: 354 VFSHGLVDFTLLFSLSRNTGWFAVL--GPLTAVIYYILFRGSILAFNLKTPGR----LQS 407 Query: 420 SNVAASELPFK-VLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLEVG 478 S+ + ++ A+GG+ NI L+AC+TRLR+ V+ V+ L LGA GV+ +G Sbjct: 408 DGTKGSKESLRAIIAALGGRDNIVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMG 467 Query: 479 NNMQAIFGPKSDQIKHDMQQIMD 501 +Q ++G K++ ++ +Q+ +D Sbjct: 468 KGVQIVYGTKAETLRKVLQRYLD 490 Lambda K H 0.324 0.143 0.421 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: 805 Number of extensions: 43 Number of successful extensions: 5 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: 675 Length of database: 499 Length adjustment: 36 Effective length of query: 639 Effective length of database: 463 Effective search space: 295857 Effective search space used: 295857 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 53 (25.0 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