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 GFF4500 PS417_23035 PTS mannose transporter subunit IIC
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__WCS417:GFF4500 Length = 838 Score = 661 bits (1706), Expect = 0.0 Identities = 391/844 (46%), Positives = 520/844 (61%), Gaps = 36/844 (4%) Query: 6 LALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALSL 65 L L APLSG ++ L++VPDPVFSS +G+G+ IDP + L AP AG++S++ + HA+S+ Sbjct: 7 LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66 Query: 66 RADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVMI 125 DNG ++L+H+GLDTV L G+GF LV+EG RV GQPL+ FD D VA +RSL+T+M+ Sbjct: 67 TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126 Query: 126 LTNGDGFQVRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHHGG 185 + +G+ F + L VE G PLLQLSP A + A E + + G Sbjct: 127 VVSGEPFSL--LADGLVETGQPLLQLSPSGAVE-----AVDEEEGDALFSKPLTLPNANG 179 Query: 186 LHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEAA 245 LHARPAA+ + A+GF++ LH Q A+ SLV IM L + D ++V GED+EAA Sbjct: 180 LHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAA 239 Query: 246 LGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLAGVCASPGLASGPLARLGAISL 305 + AL+A LA A + EP + A L GVCASPG A G + ++ L Sbjct: 240 IKALVALLAEGCGEA------VVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPEL 293 Query: 306 P-ADDGRHRPEEQH------LALDQALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALL 358 + G E+ LA ++ALQ ++D GS Q A IF AH LL Sbjct: 294 VITEQGTGGATERAALTRGLLAANEALQVLQDKAAGSAQ----------AEIFRAHQELL 343 Query: 359 EDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL 418 EDP LL+ A L+ +G AA AW+ A A + Q LGN L+AERA DL D+ +RVL+++ Sbjct: 344 EDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLI 403 Query: 419 LG-DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCL 477 LG + +P AI+ A ++TPS A L G GGATSHVAILAR+ GLP + Sbjct: 404 LGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAI 463 Query: 478 VALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQ--ADAQRE 535 + A +L L G+QV+LDA +G L L P+ +EQ L+ A++ + R Q+ A A Sbjct: 464 CGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQ--LEAARKHQVLRHQRDVAQASLP 521 Query: 536 ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEV 595 A TRDG +E+ ANVAS +E A G +GVGLLR+EFL+L+R AP EEQ Y + Sbjct: 522 ATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAI 581 Query: 596 LDAMG-QRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALLR 654 A+G +R +++RT+DVGGDK L Y+P+ E NP LGLRGI L RP+LL +Q RA+L Sbjct: 582 ARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILA 641 Query: 655 VEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLAE 714 R I+LPMVS + EL R+ L E A LG+ LP+LG+MIEVPSAAL+AD A Sbjct: 642 SAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAP 701 Query: 715 HADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGA 774 H DF SIGTNDL+QY LAMDR H LA++ D+ HPA+LRLIA T A HG+WVGVCGA Sbjct: 702 HVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGA 761 Query: 775 LASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVRDA 834 LAS+ LA PVL+GLGV+ELSV L+ IK VR+LD A+C+ A+ +L L A VR+A Sbjct: 762 LASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREA 821 Query: 835 CLQH 838 Q+ Sbjct: 822 LRQY 825 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: 1626 Number of extensions: 72 Number of successful extensions: 8 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: 838 Length adjustment: 42 Effective length of query: 800 Effective length of database: 796 Effective search space: 636800 Effective search space used: 636800 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