Query 022261
Match_columns 300
No_of_seqs 127 out of 160
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:16:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022261.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022261hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3074 Transcriptional regula 100.0 9.7E-74 2.1E-78 521.5 18.1 217 13-285 6-244 (263)
2 PF04845 PurA: PurA ssDNA and 100.0 1.6E-70 3.6E-75 495.8 10.3 199 30-280 1-218 (218)
3 PF04845 PurA: PurA ssDNA and 100.0 9.2E-43 2E-47 315.4 6.6 125 30-160 80-217 (218)
4 KOG3074 Transcriptional regula 100.0 9.4E-39 2E-43 292.1 13.3 148 91-285 20-173 (263)
5 smart00712 PUR DNA/RNA-binding 99.9 1.4E-22 3.1E-27 153.1 7.6 60 222-281 3-63 (63)
6 smart00712 PUR DNA/RNA-binding 99.8 3.5E-21 7.6E-26 145.5 7.3 61 95-160 1-61 (63)
7 PF11680 DUF3276: Protein of u 97.2 0.00085 1.8E-08 57.4 6.0 64 220-283 11-84 (124)
8 PF11680 DUF3276: Protein of u 97.0 0.0022 4.8E-08 54.9 6.4 60 29-88 8-77 (124)
9 PF14201 DUF4318: Domain of un 65.5 28 0.00061 27.5 6.4 65 42-126 1-74 (74)
10 PTZ00146 fibrillarin; Provisio 61.6 19 0.00042 35.0 5.9 18 108-125 135-152 (293)
11 PTZ00146 fibrillarin; Provisio 52.8 21 0.00046 34.7 4.5 10 44-53 67-76 (293)
12 PLN03138 Protein TOC75; Provis 44.9 17 0.00036 40.0 2.7 11 227-237 339-349 (796)
13 PLN03138 Protein TOC75; Provis 40.0 23 0.0005 39.0 2.9 6 58-63 148-153 (796)
14 PF13691 Lactamase_B_4: tRNase 35.9 25 0.00055 26.8 1.7 19 223-241 14-33 (63)
15 cd04863 MtLigD_Pol_like MtLigD 35.6 60 0.0013 30.7 4.5 74 65-139 144-226 (231)
16 PLN02596 hexokinase-like 35.5 1.1E+02 0.0023 32.0 6.7 45 230-278 95-153 (490)
17 KOG3915 Transcription regulato 33.6 36 0.00077 35.8 2.9 27 122-155 186-212 (641)
18 TIGR02778 ligD_pol DNA polymer 32.0 95 0.0021 29.7 5.3 74 65-139 156-238 (245)
19 cd04861 LigD_Pol_like LigD_Pol 29.0 89 0.0019 29.5 4.5 74 65-139 140-222 (227)
20 KOG3973 Uncharacterized conser 27.4 56 0.0012 33.2 3.0 14 15-28 369-382 (465)
21 PLN00066 PsbP domain-containin 25.4 1.5E+02 0.0032 28.7 5.3 52 223-278 200-254 (262)
22 cd04864 LigD_Pol_like_1 LigD_P 25.2 1.1E+02 0.0024 28.9 4.5 74 65-139 141-223 (228)
23 cd04862 PaeLigD_Pol_like PaeLi 24.7 1.2E+02 0.0026 28.7 4.5 74 65-139 140-222 (227)
24 cd04865 LigD_Pol_like_2 LigD_P 24.2 1.2E+02 0.0026 28.6 4.5 74 65-139 141-223 (228)
25 PF15026 FAM74: FAM74 protein 22.0 63 0.0014 27.5 1.9 29 255-283 61-89 (127)
26 cd04866 LigD_Pol_like_3 LigD_P 21.4 1.5E+02 0.0032 28.0 4.4 75 64-139 134-218 (223)
27 TIGR02776 NHEJ_ligase_prk DNA 20.2 2.2E+02 0.0049 30.0 5.9 81 65-152 433-523 (552)
No 1
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=100.00 E-value=9.7e-74 Score=521.46 Aligned_cols=217 Identities=49% Similarity=0.839 Sum_probs=189.5
Q ss_pred CCCCCCCCCCCCCCCCCccceeeeeeeeeceeEEEeccCCCCcceEEEEEecCCcceEEEeecccHHHHHHHHhhhhc--
Q 022261 13 GGSGGVTGGGAGGGGGNDVELVCKTLQVEHKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVN-- 90 (300)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~eL~Sk~l~ie~KrFYlDlKeN~RGRFLKIaE~~~g~rs~I~lp~~g~~efrd~L~~y~~-- 90 (300)
+++..++|| |||+.++++|||||+|+||+||||||||||+|||||||||++.+.+|+|+||+++++||+|+|.+|++
T Consensus 6 ~~g~~~~gG-gGG~~~~~~eLask~l~iq~KrfYlDvkqN~rGRflKIaE~g~~~~Sri~ls~s~aaef~d~l~~f~~~y 84 (263)
T KOG3074|consen 6 GGGGAVTGG-GGGGGGEDQELASKRLQIQHKRFYLDVKQNPRGRFLKIAEVGAGGRSRIILSLSVAAEFRDILNDFIEHY 84 (263)
T ss_pred CCCCCCcCC-CCCccchhHHHhhhhhhhhhheEEEEeccCCCcceEEEEEeccCCcceEEEehhhHHHHHHHHHHHHHHH
Confidence 334445555 44678889999999999999999999999999999999999999999999999999999999966653
Q ss_pred -------------CCCccccccceecccceEEEecCCCCccceeEEeeeccCC--CCce---EeecCCCCchhHHHHHHH
Q 022261 91 -------------SDDHELFSKELQLDSKVFYFDIGENRRGRFLKVSEASVSR--NRST---IIVPAGSSRDEGWAAFRN 152 (300)
Q Consensus 91 -------------~e~~~~~s~~l~vdnKrFYfDvkeN~RGrFLRISEv~~~~--~Rst---I~IPa~~~~~qGw~~FRd 152 (300)
.+++.++|+.|.+|||+||||||||+|||||||+|...++ .|++ |++|+ |||++|||
T Consensus 85 a~lg~~~~~~~~~~ee~~lkSe~L~~d~RkfY~DLKEN~RGRFLRI~qt~~rg~~~~~Q~~tIalPa-----qG~aEfrd 159 (263)
T KOG3074|consen 85 AQLGPPPPELAAPSEEHELKSEELQRDNRKFYLDLKENQRGRFLRISQTPMRGRQTRTQVQTIALPA-----QGIAEFRD 159 (263)
T ss_pred HhcCCCCcccccchhhhhHHHHHHhhcCceEEEEcccccccceEEeeecccCCCCccccccceeccc-----hhHHHHHH
Confidence 2445688999999999999999999999999999877543 3556 99999 99999999
Q ss_pred HHHHHHHHhhhhccCCCCCCccchhccccccccCCccccCCCCCCCCCCccccccCCCCCcccccCCcccceeEeeccce
Q 022261 153 ILAEINEASRLLILPNQQGSEQSEHLVGLSDDVGAGFISGHGSQPAPASELNVDRSVDLPAQDEIGNMGVSKVIRADQKR 232 (300)
Q Consensus 153 ~L~ei~e~~~~~~~p~~~~~~~~e~l~~l~d~~G~g~~~~~~~q~~~~~~~~~~~~~~lP~~~~~~~~~~s~~irvdnKr 232 (300)
+|++|. ++||++-. .| +||+ .++|+||||+
T Consensus 160 aLaell------------------------e~~G~~~~----gq-------------elpe---------g~~~tvDnk~ 189 (263)
T KOG3074|consen 160 ALAELL------------------------EDFGEGDE----GQ-------------ELPE---------GTSITVDNKR 189 (263)
T ss_pred HHHHHH------------------------HHhCCccc----cC-------------CCCC---------CCeEEEecce
Confidence 999975 45665432 12 6787 4889999999
Q ss_pred EEEEcCCCCceeEEEEeeecC--CCCceeEechhhHHHHHHHHHHHHHHHHhhhc
Q 022261 233 FFFDLGSNNRGHFLRISEVTG--SDRSSIILPLSGLKQFHEIVGHFVEITKDRIE 285 (300)
Q Consensus 233 FyFDlg~N~RG~FLRISEv~g--~~RssI~IP~~~~~~F~d~l~~~~d~m~~~~~ 285 (300)
||||+|+|+||.|||||||++ .+|++||||.++|.+|+++|++|+++|++..+
T Consensus 190 F~Fd~G~N~~G~f~riSEVk~n~~yRnsITvP~k~w~~F~~~f~~y~e~mk~~~e 244 (263)
T KOG3074|consen 190 FLFDVGKNKRGVFVRISEVKSNGSYRNSITVPFKAWKRFGEVFGKYSEEMKKISE 244 (263)
T ss_pred eEEecCCCCccceEEEEEecCCCCcccceeeehhHhhhhhhHHHHHHHHHHHhhh
Confidence 999999999999999999997 89999999999999999999999999998755
No 2
>PF04845 PurA: PurA ssDNA and RNA-binding protein; InterPro: IPR006628 The Pur protein family consists of four known members in humans and is strongly conserved throughout evolution. Pur-alpha is a highly conserved, sequence-specific DNA- and RNA-binding protein involved in diverse cellular and viral functions including transcription, replication, and cell growth. Pur-alpha has a modular structure with alternating three basic aromatic class I and two acidic leucine-rich class II repeats in the central region of the protein []. In addition to its involved in basic cellular function, Pur-alpha, has been implicated in the development of blood cells and cells of the central nervous system; it has also been implicated in the inhibition of oncogenic transformation and along with Pur-beta in myelodysplastic syndrome progressing to acute myelogenous leukemia. Pur-alpha can influence viral interaction through functional associations, for example with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JC virus. JC virus causes opportunistic infections in the brains of certain HIV-1-infected individuals [].; PDB: 3K44_A.
Probab=100.00 E-value=1.6e-70 Score=495.80 Aligned_cols=199 Identities=39% Similarity=0.700 Sum_probs=109.0
Q ss_pred ccceeeeeeeeeceeEEEeccCCCCcceEEEEEecCC-cceEEEeecccHHHHHHHHhhhh----c---------CCC--
Q 022261 30 DVELVCKTLQVEHKLFYFDLKENPRGRYLKISEKTSA-TRSTIIVPSSGISWFLDLFNYYV----N---------SDD-- 93 (300)
Q Consensus 30 ~~eL~Sk~l~ie~KrFYlDlKeN~RGRFLKIaE~~~g-~rs~I~lp~~g~~efrd~L~~y~----~---------~e~-- 93 (300)
++|||||+|+||+||||||||||.|||||||||++.+ +||+|+|+|+++++|+|+|.+|+ . .++
T Consensus 1 e~eLask~l~iq~KrfYlDVkqN~RGrfiKiaE~~~~g~ksri~lsm~~A~efrd~L~~f~~~ya~l~p~n~~~~~~~~~ 80 (218)
T PF04845_consen 1 EQELASKMLQIQNKRFYLDVKQNRRGRFIKIAEVGAGGRKSRITLSMSAAAEFRDHLGDFIEFYAQLGPSNPENLPDEGR 80 (218)
T ss_dssp -EEEEEEEEEETTEEEEEEEEEETTEEEEEEEEE-TT--EEEEEEEHHHHHHHHHHHHHHHHHHHCS-S--SS---TT--
T ss_pred CchhhhhheEecceEEEEEecccCcceeEEEeeccCCCCcceEEEechhHHHHHHHHHHHHHHHhccCCCCccccccccc
Confidence 4799999999999999999999999999999999974 89999999999999999996554 2 122
Q ss_pred ccccccceecccceEEEecCCCCccceeEEeeecc-C--CCCceEeecCCCCchhHHHHHHHHHHHHHHHhhhhccCCCC
Q 022261 94 HELFSKELQLDSKVFYFDIGENRRGRFLKVSEASV-S--RNRSTIIVPAGSSRDEGWAAFRNILAEINEASRLLILPNQQ 170 (300)
Q Consensus 94 ~~~~s~~l~vdnKrFYfDvkeN~RGrFLRISEv~~-~--~~RstI~IPa~~~~~qGw~~FRd~L~ei~e~~~~~~~p~~~ 170 (300)
..++|+.|.+|+|+||||||||+|||||||||... + ..|++|+||+ +|+.+|+++|++|.+
T Consensus 81 ~~lkSe~i~~e~r~yylDLKEN~RGrfLRisq~~~~~~~~~R~qIaiPa-----~G~~ef~~al~~lid----------- 144 (218)
T PF04845_consen 81 SELKSEKINVENRRYYLDLKENSRGRFLRISQTVSRGPRGRRSQIAIPA-----QGMIEFRDALTDLID----------- 144 (218)
T ss_dssp -ECEEEEEEETTEEEEEEEEEETTEEEEEEEEEETTT----EEEEEEEG-----GGHHHHHHHHHHHHH-----------
T ss_pred ceeeehheeeccceEEEEcccccCcceEEEEEeeccCCCCCccEEEEeh-----HHHHHHHHHHHHHHH-----------
Confidence 25789999999999999999999999999999875 1 4799999999 999999999999754
Q ss_pred CCccchhccccccccCCccccCCCCCCCCCCccccccCCCCCcccccCCcccceeEeeccceEEEEcCCCCceeEEEEee
Q 022261 171 GSEQSEHLVGLSDDVGAGFISGHGSQPAPASELNVDRSVDLPAQDEIGNMGVSKVIRADQKRFFFDLGSNNRGHFLRISE 250 (300)
Q Consensus 171 ~~~~~e~l~~l~d~~G~g~~~~~~~q~~~~~~~~~~~~~~lP~~~~~~~~~~s~~irvdnKrFyFDlg~N~RG~FLRISE 250 (300)
+||++... +.+.+||+ |++|++|||+||||||+|+||+||||||
T Consensus 145 -------------~~g~~~~~--------------~~~~~Lpe---------s~~lrvdnK~FyFD~g~N~rG~fLrISE 188 (218)
T PF04845_consen 145 -------------EFGEDDEE--------------DEQGELPE---------SKSLRVDNKRFYFDVGSNRRGVFLRISE 188 (218)
T ss_dssp -------------HH-----------------------------------------------------------------
T ss_pred -------------HhcCcccc--------------cccccCCC---------CcEEEECCeEEEEECCCCCCeeEEEecc
Confidence 44433210 12346887 7999999999999999999999999999
Q ss_pred ecCCCCceeEechhhHHHHHHHHHHHHHHH
Q 022261 251 VTGSDRSSIILPLSGLKQFHEIVGHFVEIT 280 (300)
Q Consensus 251 v~g~~RssI~IP~~~~~~F~d~l~~~~d~m 280 (300)
|++.+||+||||+++|.+|+|+|++|+++|
T Consensus 189 v~~~~Rs~ItIP~~~w~~Fr~~~~~~~e~M 218 (218)
T PF04845_consen 189 VKSNFRSAITIPESAWSRFRDIFNEYAEEM 218 (218)
T ss_dssp ------------------------------
T ss_pred cCCCCCceeeCCHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999998
No 3
>PF04845 PurA: PurA ssDNA and RNA-binding protein; InterPro: IPR006628 The Pur protein family consists of four known members in humans and is strongly conserved throughout evolution. Pur-alpha is a highly conserved, sequence-specific DNA- and RNA-binding protein involved in diverse cellular and viral functions including transcription, replication, and cell growth. Pur-alpha has a modular structure with alternating three basic aromatic class I and two acidic leucine-rich class II repeats in the central region of the protein []. In addition to its involved in basic cellular function, Pur-alpha, has been implicated in the development of blood cells and cells of the central nervous system; it has also been implicated in the inhibition of oncogenic transformation and along with Pur-beta in myelodysplastic syndrome progressing to acute myelogenous leukemia. Pur-alpha can influence viral interaction through functional associations, for example with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JC virus. JC virus causes opportunistic infections in the brains of certain HIV-1-infected individuals [].; PDB: 3K44_A.
Probab=100.00 E-value=9.2e-43 Score=315.44 Aligned_cols=125 Identities=43% Similarity=0.758 Sum_probs=52.7
Q ss_pred ccceeeeeeeeeceeEEEeccCCCCcceEEEEEecC----CcceEEEeecccHHHHHHHH----hhhhcCC-----Cccc
Q 022261 30 DVELVCKTLQVEHKLFYFDLKENPRGRYLKISEKTS----ATRSTIIVPSSGISWFLDLF----NYYVNSD-----DHEL 96 (300)
Q Consensus 30 ~~eL~Sk~l~ie~KrFYlDlKeN~RGRFLKIaE~~~----g~rs~I~lp~~g~~efrd~L----~~y~~~e-----~~~~ 96 (300)
+.+|||++|++|+|+||||||||+|||||||+|+.. ++|+||+||+|||.||+|+| ++|+.++ .+.+
T Consensus 80 ~~~lkSe~i~~e~r~yylDLKEN~RGrfLRisq~~~~~~~~~R~qIaiPa~G~~ef~~al~~lid~~g~~~~~~~~~~Lp 159 (218)
T PF04845_consen 80 RSELKSEKINVENRRYYLDLKENSRGRFLRISQTVSRGPRGRRSQIAIPAQGMIEFRDALTDLIDEFGEDDEEDEQGELP 159 (218)
T ss_dssp --ECEEEEEEETTEEEEEEEEEETTEEEEEEEEEETTT----EEEEEEEGGGHHHHHHHHHHHHHHH-------------
T ss_pred cceeeehheeeccceEEEEcccccCcceEEEEEeeccCCCCCccEEEEehHHHHHHHHHHHHHHHHhcCcccccccccCC
Confidence 569999999999999999999999999999999976 78999999999999999888 5665533 1235
Q ss_pred cccceecccceEEEecCCCCccceeEEeeeccCCCCceEeecCCCCchhHHHHHHHHHHHHHHH
Q 022261 97 FSKELQLDSKVFYFDIGENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEINEA 160 (300)
Q Consensus 97 ~s~~l~vdnKrFYfDvkeN~RGrFLRISEv~~~~~RstI~IPa~~~~~qGw~~FRd~L~ei~e~ 160 (300)
.+++|+++||+|||||++|+||+|||||||+ +..|++|+||+ ++|.+||++|++|+|+
T Consensus 160 es~~lrvdnK~FyFD~g~N~rG~fLrISEv~-~~~Rs~ItIP~-----~~w~~Fr~~~~~~~e~ 217 (218)
T PF04845_consen 160 ESKSLRVDNKRFYFDVGSNRRGVFLRISEVK-SNFRSAITIPE-----SAWSRFRDIFNEYAEE 217 (218)
T ss_dssp ----------------------------------------------------------------
T ss_pred CCcEEEECCeEEEEECCCCCCeeEEEecccC-CCCCceeeCCH-----HHHHHHHHHHHHHHhc
Confidence 6899999999999999999999999999999 56899999998 8999999999999753
No 4
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=100.00 E-value=9.4e-39 Score=292.14 Aligned_cols=148 Identities=37% Similarity=0.603 Sum_probs=126.3
Q ss_pred CCCccccccceecccceEEEecCCCCccceeEEeeeccCCCCceEeecCCCCchhHHHHHHHHHHHHHHHhhhhccCCCC
Q 022261 91 SDDHELFSKELQLDSKVFYFDIGENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEINEASRLLILPNQQ 170 (300)
Q Consensus 91 ~e~~~~~s~~l~vdnKrFYfDvkeN~RGrFLRISEv~~~~~RstI~IPa~~~~~qGw~~FRd~L~ei~e~~~~~~~p~~~ 170 (300)
.++++++|+.|+|++||||||||+|+|||||||+|+++. .||+|++|. .+.++|||.|+++.++|+++.||..+
T Consensus 20 ~~~~eLask~l~iq~KrfYlDvkqN~rGRflKIaE~g~~-~~Sri~ls~-----s~aaef~d~l~~f~~~ya~lg~~~~~ 93 (263)
T KOG3074|consen 20 GEDQELASKRLQIQHKRFYLDVKQNPRGRFLKIAEVGAG-GRSRIILSL-----SVAAEFRDILNDFIEHYAQLGPPPPE 93 (263)
T ss_pred chhHHHhhhhhhhhhheEEEEeccCCCcceEEEEEeccC-CcceEEEeh-----hhHHHHHHHHHHHHHHHHhcCCCCcc
Confidence 456789999999999999999999999999999999975 679999999 56789999999999999999877531
Q ss_pred CCccchhccccccccCCccccCCCCCCCCCCccccccCCCCCcccccCCcccceeEeeccceEEEEcCCCCceeEEEEee
Q 022261 171 GSEQSEHLVGLSDDVGAGFISGHGSQPAPASELNVDRSVDLPAQDEIGNMGVSKVIRADQKRFFFDLGSNNRGHFLRISE 250 (300)
Q Consensus 171 ~~~~~e~l~~l~d~~G~g~~~~~~~q~~~~~~~~~~~~~~lP~~~~~~~~~~s~~irvdnKrFyFDlg~N~RG~FLRISE 250 (300)
. ..|.. + ..++|+.|..|||+|||||++|+|||||||+|
T Consensus 94 ~--------------------------------------~~~~e-e--~~lkSe~L~~d~RkfY~DLKEN~RGRFLRI~q 132 (263)
T KOG3074|consen 94 L--------------------------------------AAPSE-E--HELKSEELQRDNRKFYLDLKENQRGRFLRISQ 132 (263)
T ss_pred c--------------------------------------ccchh-h--hhHHHHHHhhcCceEEEEcccccccceEEeee
Confidence 0 00111 1 46789999999999999999999999999998
Q ss_pred ec--CC-CCce---eEechhhHHHHHHHHHHHHHHHHhhhc
Q 022261 251 VT--GS-DRSS---IILPLSGLKQFHEIVGHFVEITKDRIE 285 (300)
Q Consensus 251 v~--g~-~Rss---I~IP~~~~~~F~d~l~~~~d~m~~~~~ 285 (300)
.. ++ .|++ |++|+++|++|||+|.+|+++--+-.+
T Consensus 133 t~~rg~~~~~Q~~tIalPaqG~aEfrdaLaelle~~G~~~~ 173 (263)
T KOG3074|consen 133 TPMRGRQTRTQVQTIALPAQGIAEFRDALAELLEDFGEGDE 173 (263)
T ss_pred cccCCCCccccccceeccchhHHHHHHHHHHHHHHhCCccc
Confidence 54 54 6666 999999999999999999998765544
No 5
>smart00712 PUR DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
Probab=99.87 E-value=1.4e-22 Score=153.07 Aligned_cols=60 Identities=42% Similarity=0.727 Sum_probs=57.4
Q ss_pred cceeEeeccceEEEEcCCCCceeEEEEeeecCCC-CceeEechhhHHHHHHHHHHHHHHHH
Q 022261 222 VSKVIRADQKRFFFDLGSNNRGHFLRISEVTGSD-RSSIILPLSGLKQFHEIVGHFVEITK 281 (300)
Q Consensus 222 ~s~~irvdnKrFyFDlg~N~RG~FLRISEv~g~~-RssI~IP~~~~~~F~d~l~~~~d~m~ 281 (300)
.|++|++++|+|||||++|+||+||||||++... |++|+||+++|.+|+|+|++++|.|.
T Consensus 3 ~Sk~l~~~~k~fyfDvk~N~rG~fLrIsE~~~~~~r~~I~lp~~~~~~F~~~l~~~~~~~~ 63 (63)
T smart00712 3 ASKKLTVENKRFYFDVKENRRGRFLRISEVKNNGGRSSITVPEQGAAEFRDALNKLIEKYG 63 (63)
T ss_pred cccEEEeCCcEEEEEecccCCccEEEEEEecCCCCceEEEEEHHHHHHHHHHHHHHHHhhC
Confidence 4899999999999999999999999999999887 99999999999999999999999873
No 6
>smart00712 PUR DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
Probab=99.84 E-value=3.5e-21 Score=145.48 Aligned_cols=61 Identities=51% Similarity=0.825 Sum_probs=56.5
Q ss_pred cccccceecccceEEEecCCCCccceeEEeeeccCCCCceEeecCCCCchhHHHHHHHHHHHHHHH
Q 022261 95 ELFSKELQLDSKVFYFDIGENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEINEA 160 (300)
Q Consensus 95 ~~~s~~l~vdnKrFYfDvkeN~RGrFLRISEv~~~~~RstI~IPa~~~~~qGw~~FRd~L~ei~e~ 160 (300)
++.|+.|+++||+||||||+|+||+||||||++.+..|++|+||+ ++|.+|+++|++++|.
T Consensus 1 el~Sk~l~~~~k~fyfDvk~N~rG~fLrIsE~~~~~~r~~I~lp~-----~~~~~F~~~l~~~~~~ 61 (63)
T smart00712 1 ELASKKLTVENKRFYFDVKENRRGRFLRISEVKNNGGRSSITVPE-----QGAAEFRDALNKLIEK 61 (63)
T ss_pred CCcccEEEeCCcEEEEEecccCCccEEEEEEecCCCCceEEEEEH-----HHHHHHHHHHHHHHHh
Confidence 367999999999999999999999999999999765599999998 8999999999999765
No 7
>PF11680 DUF3276: Protein of unknown function (DUF3276); InterPro: IPR021694 This bacterial family of proteins has no known function. ; PDB: 3NM7_C 3N8B_A.
Probab=97.18 E-value=0.00085 Score=57.43 Aligned_cols=64 Identities=28% Similarity=0.539 Sum_probs=53.4
Q ss_pred cccceeEeeccceEEEEcCCCCce-eEEEEeeec----CC-----CCceeEechhhHHHHHHHHHHHHHHHHhh
Q 022261 220 MGVSKVIRADQKRFFFDLGSNNRG-HFLRISEVT----GS-----DRSSIILPLSGLKQFHEIVGHFVEITKDR 283 (300)
Q Consensus 220 ~~~s~~irvdnKrFyFDlg~N~RG-~FLRISEv~----g~-----~RssI~IP~~~~~~F~d~l~~~~d~m~~~ 283 (300)
.+-|+.|+++.++|||||++|..| .||-|+|-+ +. .|..|.|=..-+.+|.++|.+.++-++..
T Consensus 11 eifSk~v~agkRtYFFDVK~~r~gD~yLtItESKk~~~~~g~~~f~khkI~LYkEDf~~F~~~L~e~i~~i~~~ 84 (124)
T PF11680_consen 11 EIFSKVVKAGKRTYFFDVKENRKGDYYLTITESKKFTDGDGSFSFEKHKIFLYKEDFEKFLEGLDEAIDFIKKE 84 (124)
T ss_dssp EEEEEE--SSSEEEEEEEEE-TTS-EEEEEEEEEE-TTS-----EEEEEEEEEGGGHHHHHHHHHHHHHHHHHH
T ss_pred eeeeeeeecCCeeEEEEeecccCCCEEEEEEeecccCCCCcceeeeeeEEEEeHHHHHHHHHHHHHHHHHHHHh
Confidence 346899999999999999999997 689999966 22 68999999999999999999999988755
No 8
>PF11680 DUF3276: Protein of unknown function (DUF3276); InterPro: IPR021694 This bacterial family of proteins has no known function. ; PDB: 3NM7_C 3N8B_A.
Probab=96.95 E-value=0.0022 Score=54.91 Aligned_cols=60 Identities=25% Similarity=0.511 Sum_probs=47.5
Q ss_pred CccceeeeeeeeeceeEEEeccCCCCcc-eEEEEEec-----CC----cceEEEeecccHHHHHHHHhhh
Q 022261 29 NDVELVCKTLQVEHKLFYFDLKENPRGR-YLKISEKT-----SA----TRSTIIVPSSGISWFLDLFNYY 88 (300)
Q Consensus 29 ~~~eL~Sk~l~ie~KrFYlDlKeN~RGR-FLKIaE~~-----~g----~rs~I~lp~~g~~efrd~L~~y 88 (300)
...+|.|+.|...+|.||+|||+|..|. ||-|+|.. .| .|.+|.|=.+-+..|.+.|++.
T Consensus 8 ~r~eifSk~v~agkRtYFFDVK~~r~gD~yLtItESKk~~~~~g~~~f~khkI~LYkEDf~~F~~~L~e~ 77 (124)
T PF11680_consen 8 DREEIFSKVVKAGKRTYFFDVKENRKGDYYLTITESKKFTDGDGSFSFEKHKIFLYKEDFEKFLEGLDEA 77 (124)
T ss_dssp -TTEEEEEE--SSSEEEEEEEEE-TTS-EEEEEEEEEE-TTS-----EEEEEEEEEGGGHHHHHHHHHHH
T ss_pred ccceeeeeeeecCCeeEEEEeecccCCCEEEEEEeecccCCCCcceeeeeeEEEEeHHHHHHHHHHHHHH
Confidence 4578999999999999999999999997 89999973 22 5889999999999998888653
No 9
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=65.52 E-value=28 Score=27.47 Aligned_cols=65 Identities=20% Similarity=0.437 Sum_probs=42.9
Q ss_pred ceeEEEeccCCCCcceEEEEEecCCcceEEEeecccHHHHHHHHhhhhcCCCccc------cccceecccceEEEecCCC
Q 022261 42 HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVNSDDHEL------FSKELQLDSKVFYFDIGEN 115 (300)
Q Consensus 42 ~KrFYlDlKeN~RGRFLKIaE~~~g~rs~I~lp~~g~~efrd~L~~y~~~e~~~~------~s~~l~vdnKrFYfDvkeN 115 (300)
+|.|++||++.+- -+...+|.+++++|...+...+ .+-.+.+|++.|=.++.+-
T Consensus 1 kK~f~IeLdd~~~--------------------yPs~e~i~~aIE~YC~~~~~~l~Fisr~~Pi~~~idg~lYev~i~~~ 60 (74)
T PF14201_consen 1 KKSFFIELDDSPK--------------------YPSKEEICEAIEKYCIKNGESLEFISRDKPITFKIDGVLYEVEIDEE 60 (74)
T ss_pred CceEEEEcccCCC--------------------CCCHHHHHHHHHHHHHHcCCceEEEecCCcEEEEECCeEEEEEEEee
Confidence 4678888887542 2467889999999975433222 2334678999998888433
Q ss_pred ---CccceeEEeee
Q 022261 116 ---RRGRFLKVSEA 126 (300)
Q Consensus 116 ---~RGrFLRISEv 126 (300)
.-|.+|..+|+
T Consensus 61 ~~~rggy~i~c~E~ 74 (74)
T PF14201_consen 61 YMARGGYYIKCKEV 74 (74)
T ss_pred ecccCcEEEEEEeC
Confidence 33667776663
No 10
>PTZ00146 fibrillarin; Provisional
Probab=61.59 E-value=19 Score=34.97 Aligned_cols=18 Identities=17% Similarity=0.156 Sum_probs=9.8
Q ss_pred EEEecCCCCccceeEEee
Q 022261 108 FYFDIGENRRGRFLKVSE 125 (300)
Q Consensus 108 FYfDvkeN~RGrFLRISE 125 (300)
--|||++-+=.--+-+++
T Consensus 135 ~VLDLGaG~G~~t~~lAd 152 (293)
T PTZ00146 135 KVLYLGAASGTTVSHVSD 152 (293)
T ss_pred EEEEeCCcCCHHHHHHHH
Confidence 347777766554444444
No 11
>PTZ00146 fibrillarin; Provisional
Probab=52.83 E-value=21 Score=34.72 Aligned_cols=10 Identities=20% Similarity=0.262 Sum_probs=5.2
Q ss_pred eEEEeccCCC
Q 022261 44 LFYFDLKENP 53 (300)
Q Consensus 44 rFYlDlKeN~ 53 (300)
-|.+..|++.
T Consensus 67 v~~~~~~~~~ 76 (293)
T PTZ00146 67 VFIAKGKSDA 76 (293)
T ss_pred EEEeecCCce
Confidence 3555556643
No 12
>PLN03138 Protein TOC75; Provisional
Probab=44.88 E-value=17 Score=39.98 Aligned_cols=11 Identities=0% Similarity=-0.227 Sum_probs=5.6
Q ss_pred eeccceEEEEc
Q 022261 227 RADQKRFFFDL 237 (300)
Q Consensus 227 rvdnKrFyFDl 237 (300)
.++.+..|..+
T Consensus 339 V~EG~i~~I~V 349 (796)
T PLN03138 339 VVEGDITKVVI 349 (796)
T ss_pred EecccEEEEEE
Confidence 44555555554
No 13
>PLN03138 Protein TOC75; Provisional
Probab=40.01 E-value=23 Score=38.95 Aligned_cols=6 Identities=50% Similarity=0.556 Sum_probs=3.0
Q ss_pred EEEEEe
Q 022261 58 LKISEK 63 (300)
Q Consensus 58 LKIaE~ 63 (300)
.||+|+
T Consensus 148 ~~vs~v 153 (796)
T PLN03138 148 YKVSEI 153 (796)
T ss_pred EEEEEE
Confidence 345555
No 14
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=35.88 E-value=25 Score=26.77 Aligned_cols=19 Identities=26% Similarity=0.597 Sum_probs=16.3
Q ss_pred ceeEeeccceEEE-EcCCCC
Q 022261 223 SKVIRADQKRFFF-DLGSNN 241 (300)
Q Consensus 223 s~~irvdnKrFyF-Dlg~N~ 241 (300)
+=.|..|++||+| +++++-
T Consensus 14 ~l~l~~d~~rYlFGn~gEGt 33 (63)
T PF13691_consen 14 SLLLFFDSRRYLFGNCGEGT 33 (63)
T ss_pred EEEEEeCCceEEeccCCcHH
Confidence 4678999999999 999873
No 15
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=35.56 E-value=60 Score=30.70 Aligned_cols=74 Identities=15% Similarity=0.263 Sum_probs=46.1
Q ss_pred CCcceEEEeecccH------HHHHHHHhhhhcCCCccccccceecc--cceEEEecCCCCccceeEEeeecc-CCCCceE
Q 022261 65 SATRSTIIVPSSGI------SWFLDLFNYYVNSDDHELFSKELQLD--SKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~------~efrd~L~~y~~~e~~~~~s~~l~vd--nKrFYfDvkeN~RGrFLRISEv~~-~~~RstI 135 (300)
.+..-+|.+|...- ..|...|..+.....++..+..+..+ ..+-|+|--+|.||.=+ |+=-++ .+..-.+
T Consensus 144 G~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~~~~P~~~t~~~~k~~R~grvfiDylqN~~g~T~-vapYS~RarpgA~V 222 (231)
T cd04863 144 GSKGLHLYVPLDGPVSSDQTKEFAKALARELEREHPDLVVSRMTKSLRAGKVFVDWSQNDAAKTT-IAPYSLRAREVPTV 222 (231)
T ss_pred CCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHhhCCCcEEEECccCCCCCeE-EeccccCCCCCCce
Confidence 45788999999753 34555555554444444444444332 34689999999999866 332222 2356688
Q ss_pred eecC
Q 022261 136 IVPA 139 (300)
Q Consensus 136 ~IPa 139 (300)
..|-
T Consensus 223 S~Pl 226 (231)
T cd04863 223 ATPV 226 (231)
T ss_pred ecCC
Confidence 8886
No 16
>PLN02596 hexokinase-like
Probab=35.54 E-value=1.1e+02 Score=31.96 Aligned_cols=45 Identities=16% Similarity=0.385 Sum_probs=26.7
Q ss_pred cceEE-EEcCCCCceeEEEEeeec--CCC-------CceeEechhhHH----HHHHHHHHHHH
Q 022261 230 QKRFF-FDLGSNNRGHFLRISEVT--GSD-------RSSIILPLSGLK----QFHEIVGHFVE 278 (300)
Q Consensus 230 nKrFy-FDlg~N~RG~FLRISEv~--g~~-------RssI~IP~~~~~----~F~d~l~~~~d 278 (300)
.-+|| .|+| |.-+||--|. +.. .....||..-+. +|-|.+.+.+.
T Consensus 95 ~G~yLAlDlG----GTNfRV~~V~L~g~~~~~~~~~~~~~~Ip~~l~~~t~~eLFd~IA~~i~ 153 (490)
T PLN02596 95 KGLYYGLNLR----GSNFLLLRARLGGKNEPISDLYREEISIPSNVLNGTSQELFDYIALELA 153 (490)
T ss_pred ceEEEEEeeC----CceEEEEEEEEcCCCCceEEEEEEEecCChHhhcCCHHHHHHHHHHHHH
Confidence 44666 8998 6677888666 321 134577877542 55555555333
No 17
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=33.62 E-value=36 Score=35.76 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=17.9
Q ss_pred EEeeeccCCCCceEeecCCCCchhHHHHHHHHHH
Q 022261 122 KVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILA 155 (300)
Q Consensus 122 RISEv~~~~~RstI~IPa~~~~~qGw~~FRd~L~ 155 (300)
||.-+... +..-|.+| |.+.-|.+.|-
T Consensus 186 kVAsF~i~-g~emiCLP------QafdlFLKhlV 212 (641)
T KOG3915|consen 186 KVASFTIE-GCELICLP------QAFDLFLKHLV 212 (641)
T ss_pred eeeEEEec-CceEEecH------HHHHHHHHHHh
Confidence 45544443 56778888 78888877663
No 18
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=32.04 E-value=95 Score=29.65 Aligned_cols=74 Identities=19% Similarity=0.251 Sum_probs=45.7
Q ss_pred CCcceEEEeecccH------HHHHHHHhhhhcCCCccccccceecc--cceEEEecCCCCccceeEEeeecc-CCCCceE
Q 022261 65 SATRSTIIVPSSGI------SWFLDLFNYYVNSDDHELFSKELQLD--SKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~------~efrd~L~~y~~~e~~~~~s~~l~vd--nKrFYfDvkeN~RGrFLRISEv~~-~~~RstI 135 (300)
++..-+|.+|...- ..|...|......+.++..+.....+ ..+-|+|--+|.||.=+ |+=-++ .+..-.+
T Consensus 156 G~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~Pd~~t~~~~k~~R~gkvfiDylqN~~g~T~-vapYS~Rar~ga~V 234 (245)
T TIGR02778 156 GGKGLHVYVPLRPTLSWDEVKDFAKALAQALAQQMPDRFTAEMSKKNRVGKIFVDYLRNARGKTT-VAPYSLRAREGATV 234 (245)
T ss_pred CCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHHhCCCCEEEECccCCCCCeE-EeccccCCCCCCce
Confidence 45788999999753 33445555444444444444333222 35689999999999866 332222 2356788
Q ss_pred eecC
Q 022261 136 IVPA 139 (300)
Q Consensus 136 ~IPa 139 (300)
..|-
T Consensus 235 S~Pl 238 (245)
T TIGR02778 235 STPL 238 (245)
T ss_pred eccC
Confidence 8886
No 19
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=29.03 E-value=89 Score=29.53 Aligned_cols=74 Identities=20% Similarity=0.263 Sum_probs=45.2
Q ss_pred CCcceEEEeecccH------HHHHHHHhhhhcCCCccccccceecc--cceEEEecCCCCccceeEEeeecc-CCCCceE
Q 022261 65 SATRSTIIVPSSGI------SWFLDLFNYYVNSDDHELFSKELQLD--SKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~------~efrd~L~~y~~~e~~~~~s~~l~vd--nKrFYfDvkeN~RGrFLRISEv~~-~~~RstI 135 (300)
++..-+|.+|...- ..|...|..+.....++..+.....+ ..|-|+|--+|.||.=+ |+=-++ .+..-++
T Consensus 140 G~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k~~R~grvfiDy~qN~~g~T~-vapYS~Rar~ga~V 218 (227)
T cd04861 140 GGKGLHVYVPLAPRYTWDEVRAFAKALARELARRLPDLFTAEMAKAKRGGKIFVDYLQNARGKTT-VAPYSVRARPGAPV 218 (227)
T ss_pred CCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHHhCCCCEEEECccCCCCCeE-EeccccCCCCCCce
Confidence 45678999999753 34555555554444444444333332 45688999999999866 322221 2345688
Q ss_pred eecC
Q 022261 136 IVPA 139 (300)
Q Consensus 136 ~IPa 139 (300)
..|-
T Consensus 219 S~Pl 222 (227)
T cd04861 219 STPL 222 (227)
T ss_pred ecCC
Confidence 8886
No 20
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=27.38 E-value=56 Score=33.25 Aligned_cols=14 Identities=64% Similarity=1.313 Sum_probs=5.8
Q ss_pred CCCCCCCCCCCCCC
Q 022261 15 SGGVTGGGAGGGGG 28 (300)
Q Consensus 15 ~~~~~~~~~~~~~~ 28 (300)
-+|+-||||+|+.+
T Consensus 369 rGgGRGggG~GGGg 382 (465)
T KOG3973|consen 369 RGGGRGGGGRGGGG 382 (465)
T ss_pred CCCCCCCCCCCCCC
Confidence 34444444433333
No 21
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=25.38 E-value=1.5e+02 Score=28.73 Aligned_cols=52 Identities=15% Similarity=0.192 Sum_probs=36.3
Q ss_pred ceeEeeccceEE-EEcCCCCceeEEEEeeecCC--CCceeEechhhHHHHHHHHHHHHH
Q 022261 223 SKVIRADQKRFF-FDLGSNNRGHFLRISEVTGS--DRSSIILPLSGLKQFHEIVGHFVE 278 (300)
Q Consensus 223 s~~irvdnKrFy-FDlg~N~RG~FLRISEv~g~--~RssI~IP~~~~~~F~d~l~~~~d 278 (300)
+..-.++.|.|| |++ . -|.|-.-=|.++ |=-.+..|++-|.+-.+.|..+++
T Consensus 200 a~~re~dGktYY~~E~---~-rH~LasaTV~~GrLYt~~asape~rW~k~~~~lr~v~d 254 (262)
T PLN00066 200 MEVAEHSGRTYYQFEL---P-PHTLVTATAAGNRVYIFSVTANGLQWKRHYKDLKRIAK 254 (262)
T ss_pred eeeeecCCcEEEEEEE---e-CceEEEEEEECCEEEEEEeecchHhhHHHHHHHHHHhh
Confidence 444566888988 899 2 355544334432 667788999999999888877665
No 22
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=25.23 E-value=1.1e+02 Score=28.87 Aligned_cols=74 Identities=22% Similarity=0.332 Sum_probs=45.5
Q ss_pred CCcceEEEeecccH------HHHHHHHhhhhcCCCccccccceecc--cceEEEecCCCCccceeEEeeecc-CCCCceE
Q 022261 65 SATRSTIIVPSSGI------SWFLDLFNYYVNSDDHELFSKELQLD--SKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~------~efrd~L~~y~~~e~~~~~s~~l~vd--nKrFYfDvkeN~RGrFLRISEv~~-~~~RstI 135 (300)
.+..-+|.+|...- ..|...|..+.....++..+...... ..+-|+|--+|.||.=+ |+=-++ .+..-.+
T Consensus 141 G~kGlHv~vPl~~~~~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k~~R~grvfiDylqN~~g~T~-vapYS~Rar~ga~V 219 (228)
T cd04864 141 GSRGFHVVVPLDGRGDFDDVRAFAAEAADALAKRDPDLLTTEARKAKRGDRVFLDIGRNAYGQTA-VAPYAVRARPGAPV 219 (228)
T ss_pred CCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhHHhCCCcEEEECccCCCCCeE-EeccccCCCCCCce
Confidence 45678999999753 34555565554444445544333222 35689999999999866 332222 2345678
Q ss_pred eecC
Q 022261 136 IVPA 139 (300)
Q Consensus 136 ~IPa 139 (300)
..|-
T Consensus 220 S~Pl 223 (228)
T cd04864 220 AAPI 223 (228)
T ss_pred ecCC
Confidence 8886
No 23
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=24.71 E-value=1.2e+02 Score=28.67 Aligned_cols=74 Identities=19% Similarity=0.251 Sum_probs=45.3
Q ss_pred CCcceEEEeecccH------HHHHHHHhhhhcCCCccccccceecc--cceEEEecCCCCccceeEEeeecc-CCCCceE
Q 022261 65 SATRSTIIVPSSGI------SWFLDLFNYYVNSDDHELFSKELQLD--SKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~------~efrd~L~~y~~~e~~~~~s~~l~vd--nKrFYfDvkeN~RGrFLRISEv~~-~~~RstI 135 (300)
.+..-+|.+|...- ..|...|..+...+.++..+..+..+ ..+-|+|--+|.||.=+ |+=-++ .+..-.+
T Consensus 140 G~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k~~R~gkvfiDylqN~~g~T~-vapYS~Rar~ga~V 218 (227)
T cd04862 140 GGKGLHVVVPLAPRAGWDEVKAFAKALAQHLARTNPDRFVATMGKAKRVGKIFIDYLRNGRGATA-VAPYSVRARPGAPV 218 (227)
T ss_pred CCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhHHhCCCcEEEECccCCCCCeE-EeccccCCCCCCce
Confidence 45678999999753 33555555554444444444333222 35689999999999866 332222 2345678
Q ss_pred eecC
Q 022261 136 IVPA 139 (300)
Q Consensus 136 ~IPa 139 (300)
..|-
T Consensus 219 S~Pl 222 (227)
T cd04862 219 SVPV 222 (227)
T ss_pred ecCC
Confidence 8886
No 24
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=24.23 E-value=1.2e+02 Score=28.64 Aligned_cols=74 Identities=24% Similarity=0.247 Sum_probs=44.5
Q ss_pred CCcceEEEeecccH------HHHHHHHhhhhcCCCccccccceec--ccceEEEecCCCCccceeEEeeecc-CCCCceE
Q 022261 65 SATRSTIIVPSSGI------SWFLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~------~efrd~L~~y~~~e~~~~~s~~l~v--dnKrFYfDvkeN~RGrFLRISEv~~-~~~RstI 135 (300)
.+..-+|.+|...- ..|...|........++..+..... -..+-|+|--+|.||.=+ |+=-++ .+..-++
T Consensus 141 G~kGlHv~vPl~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k~~R~grvfiDylqN~~g~T~-vapYS~Rar~ga~V 219 (228)
T cd04865 141 GARGLHIYVPIAPRYTFEEVRRFAELLAREVERRLPDLATTERWKKERGGRVYLDYLQNARGKTL-AAPYSVRPLPGAPV 219 (228)
T ss_pred CCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHHhCCCCEEEECccCCCCCeE-EeccccCCCCCCce
Confidence 45678999999754 3344455444433334444333322 235789999999999866 332221 2346688
Q ss_pred eecC
Q 022261 136 IVPA 139 (300)
Q Consensus 136 ~IPa 139 (300)
..|-
T Consensus 220 StPl 223 (228)
T cd04865 220 STPL 223 (228)
T ss_pred ecCC
Confidence 8886
No 25
>PF15026 FAM74: FAM74 protein
Probab=22.03 E-value=63 Score=27.46 Aligned_cols=29 Identities=24% Similarity=0.143 Sum_probs=23.4
Q ss_pred CCceeEechhhHHHHHHHHHHHHHHHHhh
Q 022261 255 DRSSIILPLSGLKQFHEIVGHFVEITKDR 283 (300)
Q Consensus 255 ~RssI~IP~~~~~~F~d~l~~~~d~m~~~ 283 (300)
-|++-+||++.|.+.|.-+.+=++..+.+
T Consensus 61 lr~setvpektwkqlrgc~qedvervqrl 89 (127)
T PF15026_consen 61 LRNSETVPEKTWKQLRGCLQEDVERVQRL 89 (127)
T ss_pred hhccccCcHHHHHHHhCccHHHHHHHHHH
Confidence 46777899999999998888777766644
No 26
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=21.44 E-value=1.5e+02 Score=28.03 Aligned_cols=75 Identities=17% Similarity=0.318 Sum_probs=44.3
Q ss_pred cCCcceEEEeecc-cH------HHHHHHHhhhhcCCCccccccceec--ccceEEEecCCCCccceeEEeeecc-CCCCc
Q 022261 64 TSATRSTIIVPSS-GI------SWFLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRS 133 (300)
Q Consensus 64 ~~g~rs~I~lp~~-g~------~efrd~L~~y~~~e~~~~~s~~l~v--dnKrFYfDvkeN~RGrFLRISEv~~-~~~Rs 133 (300)
+.+..-+|.+|.. .- ..|...|......+.++..+..... -..+-|+|--+|.||.=+ |+=-++ .+..-
T Consensus 134 SG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k~~R~gkVfiDylqN~~g~T~-vapYS~Rar~gA 212 (223)
T cd04866 134 SGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLCQQFPELFTTERLKKNRHNRLYLDYVQHAEGKTI-IAPYSARGNELG 212 (223)
T ss_pred cCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhHHhCCCCEEEECccCCCCCeE-EeccccCCCCCC
Confidence 3457889999998 43 2344445444433334444333222 235689999999999866 332221 23456
Q ss_pred eEeecC
Q 022261 134 TIIVPA 139 (300)
Q Consensus 134 tI~IPa 139 (300)
++..|-
T Consensus 213 ~VStPl 218 (223)
T cd04866 213 TVAAPL 218 (223)
T ss_pred ceecCC
Confidence 788886
No 27
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=20.20 E-value=2.2e+02 Score=30.02 Aligned_cols=81 Identities=20% Similarity=0.326 Sum_probs=51.3
Q ss_pred CCcceEEEeeccc-H------HHHHHHHhhhhcCCCccccccceecc--cceEEEecCCCCccceeEEeeecc-CCCCce
Q 022261 65 SATRSTIIVPSSG-I------SWFLDLFNYYVNSDDHELFSKELQLD--SKVFYFDIGENRRGRFLKVSEASV-SRNRST 134 (300)
Q Consensus 65 ~g~rs~I~lp~~g-~------~efrd~L~~y~~~e~~~~~s~~l~vd--nKrFYfDvkeN~RGrFLRISEv~~-~~~Rst 134 (300)
.+..-+|.+|... - ..|...|..+.....++..+...... ..+-|+|--+|.||.=+ |+=-++ .+..-.
T Consensus 433 G~kGlhv~vPl~~~~~~~~~~~~fa~~~a~~~~~~~P~~~t~~~~k~~R~grv~iDy~qn~~~~T~-~apYS~Rar~~a~ 511 (552)
T TIGR02776 433 GGKGLHVVVPLRPNTFTWDETKLFAKAIAEYLARQFPERFTTEMGKKNRVGRIFIDYLRNARGKTT-VAPYSPRAREGGP 511 (552)
T ss_pred CCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHCcceehhhhhHhhCCCCEEEEcccCCCCCeE-EeccccCCCCCCc
Confidence 4578899999987 2 33555565554444445544333322 45689999999999866 332222 235678
Q ss_pred EeecCCCCchhHHHHHHH
Q 022261 135 IIVPAGSSRDEGWAAFRN 152 (300)
Q Consensus 135 I~IPa~~~~~qGw~~FRd 152 (300)
+..|- -|.|..+
T Consensus 512 Vs~Pl------~W~El~~ 523 (552)
T TIGR02776 512 VSTPL------TWDELAS 523 (552)
T ss_pred eeccC------CHHHhcc
Confidence 99997 5766543
Done!