Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 321 bits (822), Expect = 6e-92 Identities = 189/504 (37%), Positives = 290/504 (57%), Gaps = 43/504 (8%) Query: 3 KKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAK-MME 61 + +F QR+ + L++P+AILPAAG+++ + + +PFI +VA +M Sbjct: 17 RHWFRFAQRLSQTLLIPIAILPAAGVMIGIAT--------NPLPFIP-----DVANVLML 63 Query: 62 GAGGIIFDNLAIIFALGVAIGLASGDGVAAIAAFVGFIVLNKTMGMFLGV--TPEKAADA 119 G +IFD + ++FA+ VAIG G+AA +A G+ VL T+ V P Sbjct: 64 SVGKLIFDIMPMLFAIAVAIGFCRDQGIAAFSAAFGYGVLLSTLAAAAKVYHLPSHI--- 120 Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179 V G PT+ TG+ GG+++G + + LP+ FF G+R P++M Sbjct: 121 ------VWGTPTIDTGIAGGMLVGGITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLV 174 Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239 +LA +A IWP + + S+ + +A +G ++RLL+P GLHHI++APF+ E Sbjct: 175 MLLAVMLAFIWPPLALSIERLSDWAVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLE 234 Query: 240 FGSYKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKE 299 G Y + G+I+ G+ + +AG + G + + M+GLPAAALAI++ A + Sbjct: 235 VGQYAHD-GEIVRGEMARYFAG-----DPSAGN-LAGGYLIKMWGLPAAALAIWRCADRN 287 Query: 300 NKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGY 359 + VAG+MLS A S+LTG+TEP+EF+FLFVAPLL+ HA+L GL++ I LLD+H Sbjct: 288 QRNRVAGVMLSAATASWLTGVTEPIEFAFLFVAPLLYLCHALLTGLAYSIAILLDMHHSV 347 Query: 360 TFSGGFIDFFLLGILPNKTQW-WLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEV- 417 FS G +DF LL + T W W + P+ V IYYI+FR I+ FN KTPGR + + Sbjct: 348 VFSHGLVDFVLLFPQSSNTHWIWFLGPLTFV---IYYILFRASILAFNLKTPGRFEADTG 404 Query: 418 KSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLEV 477 + N+ A ++ A+GG NI L AC+TRLR+ V D ++VD Q L LGA GV+ V Sbjct: 405 QKRNLIA------IVSALGGGGNIADLSACLTRLRISVADPSQVDRQRLMSLGAKGVIVV 458 Query: 478 GNNMQAIFGPKSDQIKHDMQQIMD 501 G+ +Q +FG K++ ++ +Q+ +D Sbjct: 459 GSGVQLVFGTKAETLRKLLQRYLD 482 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: 774 Number of extensions: 35 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: 485 Length adjustment: 36 Effective length of query: 639 Effective length of database: 449 Effective search space: 286911 Effective search space used: 286911 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