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 Ga0059261_1646 Ga0059261_1646 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Korea:Ga0059261_1646 Length = 830 Score = 647 bits (1668), Expect = 0.0 Identities = 377/831 (45%), Positives = 506/831 (60%), Gaps = 18/831 (2%) Query: 6 LALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALSL 65 L + +PL G PL+ VPDPVF+ +G+G+AI PL D + AP G V L HA+SL Sbjct: 3 LIITSPLRGWAAPLDSVPDPVFAQRMMGDGVAIQPLADTVCAPFDGEVVTLHEAGHAVSL 62 Query: 66 RADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVMI 125 R+D GAE+L+H+GLDTV L+G GF LV GA V G PL+RFD+D VA G+ SLIT +I Sbjct: 63 RSDEGAEVLIHIGLDTVGLKGRGFTPLVAPGATVARGDPLIRFDMDAVALGATSLITPVI 122 Query: 126 LTNGDGFQVRPLTTNPVEVGA--PLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHH 183 +TN + F + T +GA L+ L+P + + R + +G+ + R + Sbjct: 123 VTNAEAFTITRRTMGRA-IGAHEELMALAPARTQPRRWSD---DGTV---IEERVTLILP 175 Query: 184 GGLHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSE 243 G+HARPAA L + A+ F ++ L + S VG++ LG DE+ V RG D+E Sbjct: 176 HGIHARPAARLGECARQFEAEIHLLHGDKRGDARSTVGLLALGTRLGDELVVQARGSDAE 235 Query: 244 AALGALLAALASATA-GAPKDAPRAIAPGEPARPAAVAGTLAGVCASPGLASGPLARLGA 302 AAL A++A L S GAP AP A PA P G + GV ASPGLA GP ARL Sbjct: 236 AALAAIVALLGSDMGEGAPAHAP---AIAVPAAPVLQPGQIGGVIASPGLAMGPAARLRQ 292 Query: 303 ISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALLEDPG 362 ++ + + + ALD A VR + A GG + AA+ AHLALL+DP Sbjct: 293 TAIAVEREGKGVDAERTALDAARTEVRVRIGARADAA--GG--SVAAVMRAHLALLDDPE 348 Query: 363 LLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLRVLLGDT 422 L A+ I G A +AW A+ Q L+A GN L ER +DL D+E++VL VL G Sbjct: 349 LAAGAETRIAAGNSAGYAWRGAVHDQIAALKATGNAHLIERTDDLVDIERQVLGVLTGIP 408 Query: 423 APL-RVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALG 481 A + AGAI+ A ++ PS L + + AG+C+ GG TSHVAIL GLP LVA+G Sbjct: 409 AEADAIAAGAILVADDLLPSQLVSIAASKPAGICLVRGGPTSHVAILCAGMGLPALVAMG 468 Query: 482 AGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQADAQREALTRDG 541 + +E+G ++LDA G + P + A ++A+RE +R +A A T DG Sbjct: 469 DAIEAIEDGTALLLDAEAGHVTPDPSQADADAFAARLAKREARRDAARAAAGNACQTADG 528 Query: 542 RRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQ 601 RIE+ AN+ + +A A A GA+G GL+R+EFLFL+R AP E+EQ AYQ + DA+ Sbjct: 529 VRIELFANLGTVEDAKAAAAQGAEGSGLVRSEFLFLDREDAPSEDEQHAAYQGIADALPG 588 Query: 602 RKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALLRVEPLERC 661 + VI+R +DVGGDK Y+P EENPALGLRGI +G A +LL+ Q+RA+LRV+P+ +C Sbjct: 589 KPVIVRLLDVGGDKPAAYIPFDAEENPALGLRGIRVGLAHRDLLETQIRAILRVQPVGQC 648 Query: 662 RILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLAEHADFLSI 721 RI+LPMV+ V E+RA+R + L ++GIE E+GVM+E P+AA+ AD LA ADFLSI Sbjct: 649 RIMLPMVASVSEIRAVREVVERLRGEMGIETPIEVGVMVETPAAAITADLLAAEADFLSI 708 Query: 722 GTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALASDPLA 781 GTNDL+QY LAMDR + +A +DA+HPA+LR+IA+TC A GRWVGVCG LASDP A Sbjct: 709 GTNDLTQYVLAMDRGNPAVASGVDAMHPAVLRMIAETCRRATAKGRWVGVCGGLASDPAA 768 Query: 782 TPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVR 832 P+L+GLG ELS P V E K VR + A+ R HA+ L SA VR Sbjct: 769 VPILIGLGATELSTVPGFVPEAKAIVRSVTLADARDHAERALHCSSAAEVR 819 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: 1874 Number of extensions: 95 Number of successful extensions: 5 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: 830 Length adjustment: 42 Effective length of query: 800 Effective length of database: 788 Effective search space: 630400 Effective search space used: 630400 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