Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate BWI76_RS10675 BWI76_RS10675 phosphoenolpyruvate--protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Koxy:BWI76_RS10675 Length = 833 Score = 333 bits (853), Expect = 3e-95 Identities = 231/658 (35%), Positives = 336/658 (51%), Gaps = 37/658 (5%) Query: 185 GLHARPAALLRKTAQGFSSQAE---LHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGED 241 G+HARPA+L+ FSS E + G+ + S + I+G + D E+I GED Sbjct: 14 GVHARPASLVETLCNTFSSSVEWLNIRTEGR-GNAKSALAIIGTNTLKGDRCELIVSGED 72 Query: 242 SEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLAG--------VCASPGLA 293 E A AL A + DAP A +P + + VCA G A Sbjct: 73 EEQAFAALSAFIRDEFPHC--DAPLPTAEQMDVQPVPESLSRLNPTLFHALPVCA--GSA 128 Query: 294 SGPLARLGAISLP---ADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGDENEAAI 350 G L L ++ L A E++ ALD+ L + +++ L L D +AI Sbjct: 129 GGRLTHLKSLDLRDLGALPAAGAIEQEQAALDKGLTLLVKNIEFRL----LDNDGTASAI 184 Query: 351 FSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDL 410 AH +L D L + G+ A A + + C A GN L ER D+RD+ Sbjct: 185 LEAHRSLATDASLRQHLLDGLLSGLSCAEAVVASGEHFCAQFSASGNSYLQERVLDVRDV 244 Query: 411 EKRVLRVLLGDT---APLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAI 467 ++L+ + G+ AP ++ AI A E+TPS L GL + GG TSH I Sbjct: 245 CFQLLQHIYGEARFPAPGKLTEEAICLADELTPSQFLELDKTLLKGLLLRSGGTTSHTVI 304 Query: 468 LARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPD---ARRLEQVALQVAQREEQ 524 LARS +P LV + L R+V +D G + ++P+ AR +Q A AQ Sbjct: 305 LARSFNIPTLVGVDMEALLPWVDRRVQIDGNAGLVVVNPNQAVARYYQQEAWVQAQI--- 361 Query: 525 RRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPD 584 RR+QQA +E T DG R+E+ AN+A EA AF NGA VGL RTE L+++R +AP Sbjct: 362 RRQQQAWLDKEGRTEDGIRLEVAANIAHSVEATAAFNNGAQSVGLFRTEMLYMDRPSAPS 421 Query: 585 EEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPEL 644 E E N + + L+ R +IIRT+D+GGDK + YL +P E NP LG R + + L Sbjct: 422 ENELYNIFCQALEPANGRGIIIRTMDIGGDKPVAYLNIPAENNPFLGYRAVRIYAEYQAL 481 Query: 645 LDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLP-----ELGVM 699 QLRA+LR +I++PM+S ++E+ ++ +L + L E +P LG+M Sbjct: 482 FRTQLRAILRASAHGALKIMIPMISSMEEILWVKEQLADAKQSLRSEHIPFDEKIPLGIM 541 Query: 700 IEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTC 759 +EVPS + DQ E DF SIG+NDL+QY LA+DR +A + ++L+PA LR + Sbjct: 542 LEVPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAV 601 Query: 760 AGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRR 817 R G+W+G+CG L + P+LVGLG++ELS+ + K R+ QLD+ CR+ Sbjct: 602 QAVHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPATKARLAQLDSRACRQ 659 Lambda K H 0.319 0.136 0.390 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: 1415 Number of extensions: 52 Number of successful extensions: 4 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: 842 Length of database: 833 Length adjustment: 42 Effective length of query: 800 Effective length of database: 791 Effective search space: 632800 Effective search space used: 632800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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