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 Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833 Length = 844 Score = 654 bits (1688), Expect = 0.0 Identities = 388/848 (45%), Positives = 522/848 (61%), Gaps = 34/848 (4%) Query: 4 KNLALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHAL 63 + L L APLSG +MPL++VPD VFSS +G+G+ IDP + L AP G++S++ + HA+ Sbjct: 5 QQLQLLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVSGHAV 64 Query: 64 SLRADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITV 123 S+ DNG ++L+H+GLDTV L G+GF LVEEG RVI GQ L+ FD D +A +RSL+T+ Sbjct: 65 SITDDNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARSLLTL 124 Query: 124 MILTNGDGFQVRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHH 183 M++ +G+ F T VE G PLL L+P + GE + V + + Sbjct: 125 MLVVSGEPFTWLAPETGVVESGQPLLSLNPSEGAADEGIAQEGEALFSKPVT----LPNT 180 Query: 184 GGLHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSE 243 GLHARPAA+ + A+GF++ LH A+ SLV IM L A D ++V G D+E Sbjct: 181 NGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTAHGDVLQVSAAGADAE 240 Query: 244 AALGALLAALASATAGAPKDAPRAIAPGEP-ARPAAVAGTLAGVCASPGLASGPLARLGA 302 A+ L LA+ +A +A E A + L GVCASPG A G + ++ Sbjct: 241 VAIKTLAELLAAGCG----EAVTLMAEVETVAAQVSSLTVLRGVCASPGAAFGQVVQIAE 296 Query: 303 ISLPADDGRHRP--EEQHL--ALDQA---LQRVRDDVQGSLQQARLGGDENEAAIFSAHL 355 +L + P E +HL AL +A LQ++RD G Q A IF AH Sbjct: 297 QTLEVSESGVSPQVEREHLSRALAKAVLALQQLRDKATGDAQ----------ADIFKAHQ 346 Query: 356 ALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVL 415 LLEDPGLLD A LID G A AW A ++ + + LGN LLAERA DL D+ +RVL Sbjct: 347 ELLEDPGLLDQALALIDAGKSAGFAWRAATESTATLFKKLGNALLAERAADLADVGQRVL 406 Query: 416 RVLLG-DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGL 474 +++LG + + +P GAI+ A ++TPS A L G GGATSHVAILAR+ GL Sbjct: 407 KLILGVEDRAMELPDGAILIAEQLTPSQTAGLDTRKVLGFATVGGGATSHVAILARASGL 466 Query: 475 PCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQ---AD 531 P + L +L L G +V+LDA +G L+L P+ +EQ+ A R+ Q++RQQ A+ Sbjct: 467 PAICGLPVQVLTLINGTRVLLDADKGELQLDPELAAIEQLQ---ANRQLQKQRQQYELAN 523 Query: 532 AQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNA 591 A A TRDG +EI AN+AS EA +A A G DGVGLLR+EFL+L+R AP +EQ + Sbjct: 524 AGLAARTRDGHHVEITANIASLAEAEQAMALGGDGVGLLRSEFLYLDRNHAPSHDEQAST 583 Query: 592 YQEVLDAMGQ-RKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLR 650 Y + A+G R +++RT+DVGGDK L Y+P+ E NP LG+RGI L RP+LL Q + Sbjct: 584 YGAIARALGPARNLVVRTLDVGGDKPLAYVPMDRETNPFLGMRGIRLCLERPQLLRDQFK 643 Query: 651 ALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLAD 710 A+L L R I+LPMV+++ ELR R+ L E A LG+ LP+LG+MIEVP+AAL+AD Sbjct: 644 AILSSAGLARLHIMLPMVTQLSELRLARQLLEEEALALGLTELPKLGIMIEVPAAALMAD 703 Query: 711 QLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVG 770 A DF SIGTNDL+QY LAMDR H LA + D+ HP++LRLIA T A HG+WVG Sbjct: 704 LFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIATTVKAAHAHGKWVG 763 Query: 771 VCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARA 830 VCGALAS+ LA P+L+GLGV+ELSV L+ IK VR++D +C+ AQ +L L SA Sbjct: 764 VCGALASEKLAVPLLLGLGVDELSVSVPLIPAIKAAVREVDLLDCQAIAQQVLGLESAEQ 823 Query: 831 VRDACLQH 838 VR+A +H Sbjct: 824 VREALRRH 831 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: 1640 Number of extensions: 71 Number of successful extensions: 7 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: 844 Length adjustment: 42 Effective length of query: 800 Effective length of database: 802 Effective search space: 641600 Effective search space used: 641600 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 Apr 09 2024. 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