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 AO353_15995 AO353_15995 PTS mannose transporter subunit IIC
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15995 Length = 844 Score = 639 bits (1647), Expect = 0.0 Identities = 381/841 (45%), Positives = 516/841 (61%), Gaps = 32/841 (3%) Query: 6 LALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALSL 65 L L APLSG +MPL+ VPDPVF+S +G+G+ IDP + L AP AG+VS+L + HA+S+ Sbjct: 7 LQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHSGHAISI 66 Query: 66 RADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVMI 125 D+G ++LLH+GLDTV L+G+GF ALVE+G RV GQPL+ FD D VA +RSL+T+M+ Sbjct: 67 TDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARSLLTLML 126 Query: 126 LTNGDGFQVRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHHGG 185 + +G+ F + + V P+L+LS A GE + V + + G Sbjct: 127 VVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEE-GEALFSKPVH----LPNPNG 181 Query: 186 LHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEAA 245 LHARPAA+ + A+GF++ LH A+ SLV IM L D ++V GED+E A Sbjct: 182 LHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELA 241 Query: 246 LGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLAGVCASPGLASGPLARLGAISL 305 + L LA G +AP A+ + L GVCAS G A G + ++ +L Sbjct: 242 ISTLAQLLADG-CGEAVTPVAVVAPVVEAQEVSTK-LLRGVCASAGSAFGYVVQVAERTL 299 Query: 306 P----ADDGRHRPEEQHLAL---DQALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALL 358 A D + E AL QALQR+RD+ G E +A IF AH LL Sbjct: 300 EMPEFAADQQLERESLERALMHATQALQRLRDNAAG----------EAQADIFKAHQELL 349 Query: 359 EDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL 418 EDP LL+ A LI +G AA AW+ A +A + ++LG+ LLAERA DL D+ +RVL+++ Sbjct: 350 EDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLI 409 Query: 419 LG-DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCL 477 LG +P AI+ A ++TPS A L G GGATSHVAILAR+ GLP + Sbjct: 410 LGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAV 469 Query: 478 VALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQAD---AQR 534 L +L L G +V+LDA +G L L P +EQ+ A+R++QR+R Q + A R Sbjct: 470 CGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLH---AKRQQQRQRHQHELENAAR 526 Query: 535 EALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQE 594 A+TRDG E+ ANVAS E +A + GA+G+GLLR+EFL+ +R AP +EQ Y Sbjct: 527 AAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSA 586 Query: 595 VLDAMG-QRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALL 653 + A+G QR +++RT+DVGGDK L Y+P+ E NP LG+RGI L RP+LL +Q RA+L Sbjct: 587 IARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAIL 646 Query: 654 RVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLA 713 L R I+LPMVS++ ELR R L E A LG+ LP+LG+MIEVP+AAL+AD A Sbjct: 647 SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFA 706 Query: 714 EHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCG 773 DF SIGTNDL+QY LAMDR H LA + D+ HP++LRLIA T A HG+WVGVCG Sbjct: 707 PEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCG 766 Query: 774 ALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVRD 833 ALAS+ LA P+L+GLGV+ELSV L+ IK +R+++ ++C+ A +L L SA VR+ Sbjct: 767 ALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVRE 826 Query: 834 A 834 A Sbjct: 827 A 827 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: 1662 Number of extensions: 77 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 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