Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 365 bits (936), Expect = e-105 Identities = 216/506 (42%), Positives = 304/506 (60%), Gaps = 52/506 (10%) Query: 1 MWKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMM 60 M++ F LQR+G+ALMLP+AILP AGLLL LG+ D L N+A ++ Sbjct: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDT---DLL-------------NIA-II 43 Query: 61 EGAGGIIFDNLAIIFALGVAIGLA-SGDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADA 119 AG +IF NLA+IFA+G+A+G A +G A +A +G++V+ T+ KA D Sbjct: 44 HDAGQVIFANLAMIFAIGIAVGFARDNNGTAGLAGVIGYLVMISTL---------KALD- 93 Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179 P++ G+ GI+ G +A YN+F +I LP YL FF G+RFVPI+ + Sbjct: 94 ----------PSINMGMLAGIVSGLMAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFAA 143 Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239 L IWP IQ G+N+F ++ S + F+FG RLLI GLHHI + WF Sbjct: 144 VGLGVVFGYIWPPIQHGINSFGTLMMESGS-FGAFVFGLFNRLLIVTGLHHILNNMAWFV 202 Query: 240 FGSYKN-AAGQIIHGD-QRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAK 297 FG++ + G ++ GD R F + G+FM G FP+M+FGLPAA LA+Y+ A Sbjct: 203 FGNFTDPTTGALVTGDLSRYFAGDPK------GGQFMTGMFPMMIFGLPAACLAMYRNAL 256 Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357 +KV+ G+ LS ALT+FLTG+TEP+EF+F+F+APLLF +HA+L GLS I L++HL Sbjct: 257 PARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHALLTGLSMAITNALNIHL 316 Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGRE-DKE 416 G+TFSGGFID +LG T WLV PVGL YA IYY++F F I +F+ KTPGRE + Sbjct: 317 GFTFSGGFID-MILG-WGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFDLKTPGRETSAD 374 Query: 417 VKSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476 V+ VA +E + A+GG N+ + AC TRLR+++ D+ K +LK LGA V+ Sbjct: 375 VEQVAVADNERAGAYIKALGGAENLITVGACTTRLRLDMVDRNKASDTDLKALGAMAVVR 434 Query: 477 --VGNNMQAIFGPKSDQIKHDMQQIM 500 G ++Q + GP +D I +++ M Sbjct: 435 PGKGGSLQVVVGPMADAIADEIRLAM 460 Score = 34.3 bits (77), Expect = 2e-05 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 2/72 (2%) Query: 432 LDAMGGKANIKHLDA-CITRLRVEVNDKAKVDVQELKDLGASGVLEV-GNNMQAIFGPKS 489 L+A+GG N+ LD +TR+R+++ D + +LK LG GV ++ G + G K+ Sbjct: 492 LNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDGGIWHLLIGDKA 551 Query: 490 DQIKHDMQQIMD 501 + ++ +++ Sbjct: 552 PTLSDALEVLVN 563 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: 997 Number of extensions: 57 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 675 Length of database: 571 Length adjustment: 37 Effective length of query: 638 Effective length of database: 534 Effective search space: 340692 Effective search space used: 340692 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