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) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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