Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17535 Length = 571 Score = 370 bits (949), Expect = e-106 Identities = 224/543 (41%), Positives = 312/543 (57%), Gaps = 60/543 (11%) Query: 1 MWKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMM 60 M++ F LQR+G+ALMLP+AILP AGLLL LG+ D L ++ Sbjct: 1 MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDT---DLLD--------------IAII 43 Query: 61 EGAGGIIFDNLAIIFALGVAIGLA-SGDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADA 119 AG IF NLA+IFA+G+A+G A +G A +A +G++V+ T+ K DA Sbjct: 44 HDAGQAIFANLAMIFAIGIAVGFARDNNGTAGLAGAIGYLVMIATL---------KVLDA 94 Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179 + + G+ GII G LA YN+F +I LP YL FF G+RFVPI+ + Sbjct: 95 S-----------INMGMLAGIISGLLAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFSA 143 Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239 L +IWP IQ G+N F LL + F+FG RLLI GLHHI + WF Sbjct: 144 VGLGVVFGLIWPPIQQGINGFG-ALLMESGSFGAFVFGVFNRLLIVTGLHHILNNMAWFI 202 Query: 240 FGSYKN-AAGQIIHGD-QRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAK 297 FGS+ + A G ++ GD R F + G+FM G FPVM+FGLPAA LA+Y+ A Sbjct: 203 FGSFTDPATGAVVTGDLSRYFAGDPK------GGQFMTGMFPVMLFGLPAACLAMYRNAL 256 Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357 + +KV+ G++LS ALTSFLTG+TEP+EF+F+F+APLLF +HA+L G+S + LL +HL Sbjct: 257 PQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLFLVHALLTGVSMAVTNLLGIHL 316 Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEV 417 G+TFSGGFID +LG T WLV+PVGL YAAIYY++F F I +F+ KTPGRE+ Sbjct: 317 GFTFSGGFID-MVLG-WGKSTNGWLVVPVGLAYAAIYYLVFDFCIRRFDLKTPGREEVPA 374 Query: 418 -KSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476 +A ++ + A+GG N+ + AC TRLR+++ D+ K +LK LGA V+ Sbjct: 375 GDKPAIAENQRAAAYIQALGGADNLITIGACTTRLRLDMVDRNKASDAQLKALGAMAVVR 434 Query: 477 VGN--NMQAIFGPKSDQIKHDMQQIMDGKI--------TSPEETTVTEEGDKETAEIAAA 526 GN ++Q + GP +D I +++ + + +P TT E + A Sbjct: 435 PGNGGSLQVVVGPMADSIADEIRLAVPSSLRPVTAPVPNAPAPTTPAALSSTEAQQWLDA 494 Query: 527 GGG 529 GG Sbjct: 495 LGG 497 Score = 34.7 bits (78), Expect = 1e-05 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 2/74 (2%) Query: 432 LDAMGGKANIKHLDACIT-RLRVEVNDKAKVDVQELKDLGASGVLEVGNNM-QAIFGPKS 489 LDA+GG+ N+ L+ T RLRV + D + LK LG G+ + + + + G K+ Sbjct: 492 LDALGGQDNVLQLECVATSRLRVRLADDKGLSESRLKGLGCQGMSSLEDGVWHLLLGEKA 551 Query: 490 DQIKHDMQQIMDGK 503 ++ + + G+ Sbjct: 552 PRLWQALDGLAHGR 565 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: 1009 Number of extensions: 51 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