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 CCNA_00571 CCNA_00571 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Caulo:CCNA_00571 Length = 878 Score = 683 bits (1762), Expect = 0.0 Identities = 399/841 (47%), Positives = 518/841 (61%), Gaps = 24/841 (2%) Query: 6 LALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALSL 65 L L APL G V L PD VF+ LG+G+AIDPL LHAPC G V + R RHA++L Sbjct: 32 LVLTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRARHAVTL 91 Query: 66 RADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVMI 125 RA NGAE+L+HVGL+TV L GEGFE VEEG V G L+ DLD +A+ +RSLIT ++ Sbjct: 92 RATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPVV 151 Query: 126 LTNGDGFQ-VRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHHG 184 +TNG+ FQ VR + VG L++LSP R A A Q+ + V Sbjct: 152 ITNGEAFQIVRRDQDRQIGVGQFLMELSPIAGASRAA-----ASGAADQITRQIIVPLAH 206 Query: 185 GLHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEA 244 G+HARPAA + + A+ F+S L + A+ S VG+M L + D ++++ G D++A Sbjct: 207 GIHARPAARIAQMAKTFASDLTLATGPRRANARSPVGLMSLAIRHGDTIQLLASGPDAQA 266 Query: 245 ALGALL---------AALASATAGAPKDAPRAIAPGEPARPAAVA--GTLAGVCASPGLA 293 A+ AL A +A + K AP P EP PA + G L GV A+PGLA Sbjct: 267 AVTALAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGVLKGVPAAPGLA 326 Query: 294 SGPLARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGDENEAAIFSA 353 G RL + + + AL AL+ VR + +A GD+ AI +A Sbjct: 327 IGKAVRLSTAEIVVREAGEGVAHEEAALAVALETVR----ARIGKAAETGDKARKAILAA 382 Query: 354 HLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKR 413 H A L+DP L A LI +G A AW RA+ + LQALG+ +AER +DL DLE++ Sbjct: 383 HQAFLDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVDDLIDLERQ 442 Query: 414 VLRVLLGD--TAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARS 471 VLR L G+ T P G+I+ A E+ PS L A AG A GG TSHVAILA + Sbjct: 443 VLRALSGEEETGAALAP-GSILLADELLPSQLMGADPAALAGFATARGGPTSHVAILAAA 501 Query: 472 KGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQAD 531 G+P LVA+G L ++++G ++LDA G L ++PDA+ LE +AQR++++ +A Sbjct: 502 MGVPALVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQRKAAAKAA 561 Query: 532 AQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNA 591 A A+TRDG RIE+ AN S +A A ANGA+G GLLRTEFLFL+R PDE+EQ Sbjct: 562 AHEPAVTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPDEDEQARQ 621 Query: 592 YQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRA 651 YQ + +A+ R +IIRT+DVGGDK YLP+P EENPALGLRG+ + RP LL QLRA Sbjct: 622 YQAIAEALDGRPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHLLKAQLRA 681 Query: 652 LLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQ 711 +LRVEP +C+I++PMV+ +DELRA+R L E +LGI +LGVMIE P+AA+ AD Sbjct: 682 ILRVEPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPAAAVTADL 741 Query: 712 LAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGV 771 LA ADFLSIGTNDL+QY LAMDR + LA IDALHPA+LR+I QTC GAARH RWVGV Sbjct: 742 LAAEADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAARHHRWVGV 801 Query: 772 CGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAV 831 CG LASD ATP+L+GLGV ELS ++ ++K RVR L CR A L+ S +AV Sbjct: 802 CGGLASDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALEQTSPQAV 861 Query: 832 R 832 R Sbjct: 862 R 862 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: 1842 Number of extensions: 92 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: 878 Length adjustment: 42 Effective length of query: 800 Effective length of database: 836 Effective search space: 668800 Effective search space used: 668800 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