Query 022247
Match_columns 300
No_of_seqs 128 out of 154
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:09:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022247hhsearch_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 3.3E-74 7.3E-79 524.6 18.6 216 14-285 7-244 (263)
2 PF04845 PurA: PurA ssDNA and 100.0 2E-70 4.3E-75 495.3 9.4 199 30-280 1-218 (218)
3 PF04845 PurA: PurA ssDNA and 100.0 2.9E-42 6.3E-47 312.2 6.4 124 30-159 80-216 (218)
4 KOG3074 Transcriptional regula 100.0 2.7E-38 5.8E-43 289.2 13.3 148 91-285 20-173 (263)
5 smart00712 PUR DNA/RNA-binding 99.9 1.7E-22 3.6E-27 152.7 7.7 60 222-281 3-63 (63)
6 smart00712 PUR DNA/RNA-binding 99.8 6.2E-21 1.3E-25 144.2 6.8 61 95-160 1-61 (63)
7 PF11680 DUF3276: Protein of u 97.0 0.0013 2.8E-08 56.3 5.5 64 220-283 11-84 (124)
8 PF11680 DUF3276: Protein of u 96.8 0.003 6.6E-08 54.1 6.1 59 29-87 8-76 (124)
9 PF14201 DUF4318: Domain of un 71.5 17 0.00037 28.7 6.3 65 42-126 1-74 (74)
10 PTZ00146 fibrillarin; Provisio 59.6 22 0.00047 34.6 5.8 18 108-125 135-152 (293)
11 PTZ00146 fibrillarin; Provisio 50.9 24 0.00053 34.3 4.6 10 44-53 67-76 (293)
12 PLN03138 Protein TOC75; Provis 43.8 20 0.00043 39.5 3.0 11 227-237 339-349 (796)
13 PLN03138 Protein TOC75; Provis 39.7 23 0.00049 39.0 2.7 6 58-63 148-153 (796)
14 PF13691 Lactamase_B_4: tRNase 37.0 24 0.00052 26.9 1.8 18 223-240 14-32 (63)
15 cd04863 MtLigD_Pol_like MtLigD 31.7 82 0.0018 29.8 4.8 74 65-139 144-226 (231)
16 KOG3915 Transcription regulato 30.8 42 0.00092 35.2 2.9 27 122-155 186-212 (641)
17 TIGR02778 ligD_pol DNA polymer 28.8 1.3E+02 0.0027 28.8 5.5 74 65-139 156-238 (245)
18 cd04861 LigD_Pol_like LigD_Pol 25.7 1.2E+02 0.0026 28.7 4.7 74 65-139 140-222 (227)
19 PLN00066 PsbP domain-containin 23.9 1.5E+02 0.0033 28.6 5.1 53 224-280 201-256 (262)
20 cd04864 LigD_Pol_like_1 LigD_P 22.1 1.5E+02 0.0033 28.0 4.7 74 65-139 141-223 (228)
21 cd04865 LigD_Pol_like_2 LigD_P 21.8 1.6E+02 0.0034 27.9 4.7 74 65-139 141-223 (228)
22 cd04862 PaeLigD_Pol_like PaeLi 21.3 1.7E+02 0.0036 27.7 4.7 74 65-139 140-222 (227)
No 1
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=100.00 E-value=3.3e-74 Score=524.57 Aligned_cols=216 Identities=50% Similarity=0.834 Sum_probs=188.2
Q ss_pred CCCCCCCCCCCCCCCCcccceeeeeeeeceeEEEeccCCCCcceEEEEEecCCcceEEEeecccHHHHHHHhhh----hh
Q 022247 14 GSGGVTGGGAGGGGGNDVELVCKTLQVEHKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNY----YV 89 (300)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~eL~S~~l~ie~KrFYlDlKeN~RGRFLKIaE~~~g~rs~I~lp~~g~~efrd~L~~----y~ 89 (300)
++..++|| |||+.++++|||||+|+||+||||||||||+|||||||||++.+.+|+|+||+++++||+|+|.+ ||
T Consensus 7 ~g~~~~gG-gGG~~~~~~eLask~l~iq~KrfYlDvkqN~rGRflKIaE~g~~~~Sri~ls~s~aaef~d~l~~f~~~ya 85 (263)
T KOG3074|consen 7 GGGAVTGG-GGGGGGEDQELASKRLQIQHKRFYLDVKQNPRGRFLKIAEVGAGGRSRIILSLSVAAEFRDILNDFIEHYA 85 (263)
T ss_pred CCCCCcCC-CCCccchhHHHhhhhhhhhhheEEEEeccCCCcceEEEEEeccCCcceEEEehhhHHHHHHHHHHHHHHHH
Confidence 33444555 44678889999999999999999999999999999999999999999999999999999998854 44
Q ss_pred c-----------CCCCcccccccccccceEEEeccCCCccceeEEeecccCC--CCce---EeecCCCCchhHHHHHHHH
Q 022247 90 N-----------SDDHELFSKELQLDSKVFYFDIGENRRGRFLKVSEASVSR--NRST---IIVPAGSSRDEGWAAFRNI 153 (300)
Q Consensus 90 ~-----------~~~~~~~s~~l~vdnKrFYfDlkeN~RGRFLRISE~~~~~--~Rst---I~IPag~~~~~Gw~~FRd~ 153 (300)
. .+++.++|+.|.+|||+||||||||+|||||||+|..+++ .|++ |++|+ +||++|||+
T Consensus 86 ~lg~~~~~~~~~~ee~~lkSe~L~~d~RkfY~DLKEN~RGRFLRI~qt~~rg~~~~~Q~~tIalPa-----qG~aEfrda 160 (263)
T KOG3074|consen 86 QLGPPPPELAAPSEEHELKSEELQRDNRKFYLDLKENQRGRFLRISQTPMRGRQTRTQVQTIALPA-----QGIAEFRDA 160 (263)
T ss_pred hcCCCCcccccchhhhhHHHHHHhhcCceEEEEcccccccceEEeeecccCCCCccccccceeccc-----hhHHHHHHH
Confidence 3 2445678999999999999999999999999999877643 3566 99999 999999999
Q ss_pred HHHHHHHHhhhccCCCCCCccchhccccccccCCCcccCCCCCCCCCCcccccCCCCCCcccccCCcccceeEeeccceE
Q 022247 154 LAEINEASRLLILPNQQGSEQSEHLVGLSDDVGAGFISGHGSQPAPASELNVDRSVDLPAQDEIGNMGVSKVIRADQKRF 233 (300)
Q Consensus 154 L~ei~e~~~~l~~p~~~~~~~~e~l~~l~d~~G~~~~~~~~~q~~s~~~~~~~~~~~LP~~~~~~~~~~s~~ir~dnK~F 233 (300)
|++|. ++||.+.. + -+||+ .++|+||||+|
T Consensus 161 Laell------------------------e~~G~~~~-g----------------qelpe---------g~~~tvDnk~F 190 (263)
T KOG3074|consen 161 LAELL------------------------EDFGEGDE-G----------------QELPE---------GTSITVDNKRF 190 (263)
T ss_pred HHHHH------------------------HHhCCccc-c----------------CCCCC---------CCeEEEeccee
Confidence 99975 55665532 1 16777 37899999999
Q ss_pred EEecCCCCceeeEEEeeecC--CCCceeeechhhHHHHHHHHHHHHHHHHhhhc
Q 022247 234 FFDLGSNNRGHFLRISEVAG--SDRSSIILPLSGLKQFHEIVGHFVEITKDRIE 285 (300)
Q Consensus 234 yFDlg~N~RG~FLRISEv~~--~~Rs~I~iP~~~~~~Fre~l~~~~d~~~~~~~ 285 (300)
|||+|+|+||.|||||||++ .+|++||||.++|++|++.|++|+++||+..+
T Consensus 191 ~Fd~G~N~~G~f~riSEVk~n~~yRnsITvP~k~w~~F~~~f~~y~e~mk~~~e 244 (263)
T KOG3074|consen 191 LFDVGKNKRGVFVRISEVKSNGSYRNSITVPFKAWKRFGEVFGKYSEEMKKISE 244 (263)
T ss_pred EEecCCCCccceEEEEEecCCCCcccceeeehhHhhhhhhHHHHHHHHHHHhhh
Confidence 99999999999999999997 89999999999999999999999999998855
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=2e-70 Score=495.32 Aligned_cols=199 Identities=40% Similarity=0.709 Sum_probs=109.2
Q ss_pred cccceeeeeeeeceeEEEeccCCCCcceEEEEEecCC-cceEEEeecccHHHHHHHh----hhhhcC---------CC--
Q 022247 30 DVELVCKTLQVEHKLFYFDLKENPRGRYLKISEKTSA-TRSTIIVPSSGISWFLDLF----NYYVNS---------DD-- 93 (300)
Q Consensus 30 ~~eL~S~~l~ie~KrFYlDlKeN~RGRFLKIaE~~~g-~rs~I~lp~~g~~efrd~L----~~y~~~---------~~-- 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 4799999999999999999999999999999999975 8999999999999999987 456542 12
Q ss_pred CcccccccccccceEEEeccCCCccceeEEeeccc-C--CCCceEeecCCCCchhHHHHHHHHHHHHHHHHhhhccCCCC
Q 022247 94 HELFSKELQLDSKVFYFDIGENRRGRFLKVSEASV-S--RNRSTIIVPAGSSRDEGWAAFRNILAEINEASRLLILPNQQ 170 (300)
Q Consensus 94 ~~~~s~~l~vdnKrFYfDlkeN~RGRFLRISE~~~-~--~~RstI~IPag~~~~~Gw~~FRd~L~ei~e~~~~l~~p~~~ 170 (300)
..++|+.|.+|+|+||||||||+|||||||||... + ..|+||+||+ +|+.+|+++|.++.
T Consensus 81 ~~lkSe~i~~e~r~yylDLKEN~RGrfLRisq~~~~~~~~~R~qIaiPa-----~G~~ef~~al~~li------------ 143 (218)
T PF04845_consen 81 SELKSEKINVENRRYYLDLKENSRGRFLRISQTVSRGPRGRRSQIAIPA-----QGMIEFRDALTDLI------------ 143 (218)
T ss_dssp -ECEEEEEEETTEEEEEEEEEETTEEEEEEEEEETTT----EEEEEEEG-----GGHHHHHHHHHHHH------------
T ss_pred ceeeehheeeccceEEEEcccccCcceEEEEEeeccCCCCCccEEEEeh-----HHHHHHHHHHHHHH------------
Confidence 25789999999999999999999999999999875 2 5799999999 99999999999975
Q ss_pred CCccchhccccccccCCCcccCCCCCCCCCCcccccCCCCCCcccccCCcccceeEeeccceEEEecCCCCceeeEEEee
Q 022247 171 GSEQSEHLVGLSDDVGAGFISGHGSQPAPASELNVDRSVDLPAQDEIGNMGVSKVIRADQKRFFFDLGSNNRGHFLRISE 250 (300)
Q Consensus 171 ~~~~~e~l~~l~d~~G~~~~~~~~~q~~s~~~~~~~~~~~LP~~~~~~~~~~s~~ir~dnK~FyFDlg~N~RG~FLRISE 250 (300)
|+||++.. .+.+.+||+ |++|++|||+||||||+|+||+||||||
T Consensus 144 ------------d~~g~~~~--------------~~~~~~Lpe---------s~~lrvdnK~FyFD~g~N~rG~fLrISE 188 (218)
T PF04845_consen 144 ------------DEFGEDDE--------------EDEQGELPE---------SKSLRVDNKRFYFDVGSNRRGVFLRISE 188 (218)
T ss_dssp ------------HHH-----------------------------------------------------------------
T ss_pred ------------HHhcCccc--------------ccccccCCC---------CcEEEECCeEEEEECCCCCCeeEEEecc
Confidence 44554321 112346887 6999999999999999999999999999
Q ss_pred ecCCCCceeeechhhHHHHHHHHHHHHHHH
Q 022247 251 VAGSDRSSIILPLSGLKQFHEIVGHFVEIT 280 (300)
Q Consensus 251 v~~~~Rs~I~iP~~~~~~Fre~l~~~~d~~ 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=2.9e-42 Score=312.19 Aligned_cols=124 Identities=44% Similarity=0.764 Sum_probs=52.8
Q ss_pred cccceeeeeeeeceeEEEeccCCCCcceEEEEEecC----CcceEEEeecccHHHHHHHh----hhhhcCC-----CCcc
Q 022247 30 DVELVCKTLQVEHKLFYFDLKENPRGRYLKISEKTS----ATRSTIIVPSSGISWFLDLF----NYYVNSD-----DHEL 96 (300)
Q Consensus 30 ~~eL~S~~l~ie~KrFYlDlKeN~RGRFLKIaE~~~----g~rs~I~lp~~g~~efrd~L----~~y~~~~-----~~~~ 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 469999999999999999999999999999999987 78999999999999999876 7887644 2245
Q ss_pred cccccccccceEEEeccCCCccceeEEeecccCCCCceEeecCCCCchhHHHHHHHHHHHHHH
Q 022247 97 FSKELQLDSKVFYFDIGENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEINE 159 (300)
Q Consensus 97 ~s~~l~vdnKrFYfDlkeN~RGRFLRISE~~~~~~RstI~IPag~~~~~Gw~~FRd~L~ei~e 159 (300)
.+++|+++||+|||||++|+||+|||||||+ +..|++|+||+ ++|.+||++|++|++
T Consensus 160 es~~lrvdnK~FyFD~g~N~rG~fLrISEv~-~~~Rs~ItIP~-----~~w~~Fr~~~~~~~e 216 (218)
T PF04845_consen 160 ESKSLRVDNKRFYFDVGSNRRGVFLRISEVK-SNFRSAITIPE-----SAWSRFRDIFNEYAE 216 (218)
T ss_dssp ---------------------------------------------------------------
T ss_pred CCcEEEECCeEEEEECCCCCCeeEEEecccC-CCCCceeeCCH-----HHHHHHHHHHHHHHh
Confidence 7899999999999999999999999999999 56899999998 899999999999975
No 4
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=100.00 E-value=2.7e-38 Score=289.19 Aligned_cols=148 Identities=36% Similarity=0.580 Sum_probs=126.8
Q ss_pred CCCCcccccccccccceEEEeccCCCccceeEEeecccCCCCceEeecCCCCchhHHHHHHHHHHHHHHHHhhhccCCCC
Q 022247 91 SDDHELFSKELQLDSKVFYFDIGENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEINEASRLLILPNQQ 170 (300)
Q Consensus 91 ~~~~~~~s~~l~vdnKrFYfDlkeN~RGRFLRISE~~~~~~RstI~IPag~~~~~Gw~~FRd~L~ei~e~~~~l~~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 456789999999999999999999999999999999974 679999998 67789999999999999999887631
Q ss_pred CCccchhccccccccCCCcccCCCCCCCCCCcccccCCCCCCcccccCCcccceeEeeccceEEEecCCCCceeeEEEee
Q 022247 171 GSEQSEHLVGLSDDVGAGFISGHGSQPAPASELNVDRSVDLPAQDEIGNMGVSKVIRADQKRFFFDLGSNNRGHFLRISE 250 (300)
Q Consensus 171 ~~~~~e~l~~l~d~~G~~~~~~~~~q~~s~~~~~~~~~~~LP~~~~~~~~~~s~~ir~dnK~FyFDlg~N~RG~FLRISE 250 (300)
... .++ + ..++|+.|..|||+|||||++|+|||||||+|
T Consensus 94 ~~~-------------------------------------~~e--e--~~lkSe~L~~d~RkfY~DLKEN~RGRFLRI~q 132 (263)
T KOG3074|consen 94 LAA-------------------------------------PSE--E--HELKSEELQRDNRKFYLDLKENQRGRFLRISQ 132 (263)
T ss_pred ccc-------------------------------------chh--h--hhHHHHHHhhcCceEEEEcccccccceEEeee
Confidence 100 111 1 35678999999999999999999999999998
Q ss_pred e--cCC-CCce---eeechhhHHHHHHHHHHHHHHHHhhhc
Q 022247 251 V--AGS-DRSS---IILPLSGLKQFHEIVGHFVEITKDRIE 285 (300)
Q Consensus 251 v--~~~-~Rs~---I~iP~~~~~~Fre~l~~~~d~~~~~~~ 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 5 455 6677 999999999999999999999876655
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=1.7e-22 Score=152.70 Aligned_cols=60 Identities=42% Similarity=0.724 Sum_probs=57.4
Q ss_pred cceeEeeccceEEEecCCCCceeeEEEeeecCCC-CceeeechhhHHHHHHHHHHHHHHHH
Q 022247 222 VSKVIRADQKRFFFDLGSNNRGHFLRISEVAGSD-RSSIILPLSGLKQFHEIVGHFVEITK 281 (300)
Q Consensus 222 ~s~~ir~dnK~FyFDlg~N~RG~FLRISEv~~~~-Rs~I~iP~~~~~~Fre~l~~~~d~~~ 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 4799999999999999999999999999999887 99999999999999999999999874
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=99.83 E-value=6.2e-21 Score=144.16 Aligned_cols=61 Identities=51% Similarity=0.825 Sum_probs=56.5
Q ss_pred cccccccccccceEEEeccCCCccceeEEeecccCCCCceEeecCCCCchhHHHHHHHHHHHHHHH
Q 022247 95 ELFSKELQLDSKVFYFDIGENRRGRFLKVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILAEINEA 160 (300)
Q Consensus 95 ~~~s~~l~vdnKrFYfDlkeN~RGRFLRISE~~~~~~RstI~IPag~~~~~Gw~~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 9999999999999764
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=97.02 E-value=0.0013 Score=56.32 Aligned_cols=64 Identities=28% Similarity=0.537 Sum_probs=53.3
Q ss_pred cccceeEeeccceEEEecCCCCce-eeEEEeeec----CC-----CCceeeechhhHHHHHHHHHHHHHHHHhh
Q 022247 220 MGVSKVIRADQKRFFFDLGSNNRG-HFLRISEVA----GS-----DRSSIILPLSGLKQFHEIVGHFVEITKDR 283 (300)
Q Consensus 220 ~~~s~~ir~dnK~FyFDlg~N~RG-~FLRISEv~----~~-----~Rs~I~iP~~~~~~Fre~l~~~~d~~~~~ 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 356899999999999999999997 689999975 22 68999999999999999999999988765
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=96.81 E-value=0.003 Score=54.09 Aligned_cols=59 Identities=25% Similarity=0.532 Sum_probs=46.3
Q ss_pred CcccceeeeeeeeceeEEEeccCCCCcc-eEEEEEec-----CC----cceEEEeecccHHHHHHHhhh
Q 022247 29 NDVELVCKTLQVEHKLFYFDLKENPRGR-YLKISEKT-----SA----TRSTIIVPSSGISWFLDLFNY 87 (300)
Q Consensus 29 ~~~eL~S~~l~ie~KrFYlDlKeN~RGR-FLKIaE~~-----~g----~rs~I~lp~~g~~efrd~L~~ 87 (300)
...+|.|+.|.-.+|.||+|||+|..|. ||-|+|-. .| .|.+|.|=.+-+..|.+.|++
T Consensus 8 ~r~eifSk~v~agkRtYFFDVK~~r~gD~yLtItESKk~~~~~g~~~f~khkI~LYkEDf~~F~~~L~e 76 (124)
T PF11680_consen 8 DREEIFSKVVKAGKRTYFFDVKENRKGDYYLTITESKKFTDGDGSFSFEKHKIFLYKEDFEKFLEGLDE 76 (124)
T ss_dssp -TTEEEEEE--SSSEEEEEEEEE-TTS-EEEEEEEEEE-TTS-----EEEEEEEEEGGGHHHHHHHHHH
T ss_pred ccceeeeeeeecCCeeEEEEeecccCCCEEEEEEeecccCCCCcceeeeeeEEEEeHHHHHHHHHHHHH
Confidence 4578999999999999999999999997 89999973 22 588999999999999877653
No 9
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=71.53 E-value=17 Score=28.71 Aligned_cols=65 Identities=20% Similarity=0.437 Sum_probs=44.2
Q ss_pred ceeEEEeccCCCCcceEEEEEecCCcceEEEeecccHHHHHHHhhhhhcCCCCcc------cccccccccceEEEeccCC
Q 022247 42 HKLFYFDLKENPRGRYLKISEKTSATRSTIIVPSSGISWFLDLFNYYVNSDDHEL------FSKELQLDSKVFYFDIGEN 115 (300)
Q Consensus 42 ~KrFYlDlKeN~RGRFLKIaE~~~g~rs~I~lp~~g~~efrd~L~~y~~~~~~~~------~s~~l~vdnKrFYfDlkeN 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 4778888887642 2467789999999976544322 2344778999998998433
Q ss_pred ---CccceeEEeec
Q 022247 116 ---RRGRFLKVSEA 126 (300)
Q Consensus 116 ---~RGRFLRISE~ 126 (300)
.-|.+|..+|+
T Consensus 61 ~~~rggy~i~c~E~ 74 (74)
T PF14201_consen 61 YMARGGYYIKCKEV 74 (74)
T ss_pred ecccCcEEEEEEeC
Confidence 34677777663
No 10
>PTZ00146 fibrillarin; Provisional
Probab=59.57 E-value=22 Score=34.64 Aligned_cols=18 Identities=17% Similarity=0.156 Sum_probs=9.9
Q ss_pred EEEeccCCCccceeEEee
Q 022247 108 FYFDIGENRRGRFLKVSE 125 (300)
Q Consensus 108 FYfDlkeN~RGRFLRISE 125 (300)
--|||++-+=.--+-+++
T Consensus 135 ~VLDLGaG~G~~t~~lAd 152 (293)
T PTZ00146 135 KVLYLGAASGTTVSHVSD 152 (293)
T ss_pred EEEEeCCcCCHHHHHHHH
Confidence 346777666554444444
No 11
>PTZ00146 fibrillarin; Provisional
Probab=50.86 E-value=24 Score=34.29 Aligned_cols=10 Identities=20% Similarity=0.262 Sum_probs=5.1
Q ss_pred eEEEeccCCC
Q 022247 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 3455556643
No 12
>PLN03138 Protein TOC75; Provisional
Probab=43.84 E-value=20 Score=39.48 Aligned_cols=11 Identities=0% Similarity=-0.227 Sum_probs=5.5
Q ss_pred eeccceEEEec
Q 022247 227 RADQKRFFFDL 237 (300)
Q Consensus 227 r~dnK~FyFDl 237 (300)
.++.+..|..+
T Consensus 339 V~EG~i~~I~V 349 (796)
T PLN03138 339 VVEGDITKVVI 349 (796)
T ss_pred EecccEEEEEE
Confidence 34455555554
No 13
>PLN03138 Protein TOC75; Provisional
Probab=39.73 E-value=23 Score=39.03 Aligned_cols=6 Identities=50% Similarity=0.556 Sum_probs=3.0
Q ss_pred EEEEEe
Q 022247 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 345554
No 14
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=37.04 E-value=24 Score=26.91 Aligned_cols=18 Identities=28% Similarity=0.621 Sum_probs=15.7
Q ss_pred ceeEeeccceEEE-ecCCC
Q 022247 223 SKVIRADQKRFFF-DLGSN 240 (300)
Q Consensus 223 s~~ir~dnK~FyF-Dlg~N 240 (300)
+=.|..|++||+| +++++
T Consensus 14 ~l~l~~d~~rYlFGn~gEG 32 (63)
T PF13691_consen 14 SLLLFFDSRRYLFGNCGEG 32 (63)
T ss_pred EEEEEeCCceEEeccCCcH
Confidence 3578999999999 99987
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=31.70 E-value=82 Score=29.84 Aligned_cols=74 Identities=15% Similarity=0.255 Sum_probs=45.3
Q ss_pred CCcceEEEeecccHH------HHHHHhhhhhcCCCCccccccccc--ccceEEEeccCCCccceeEEeeccc-CCCCceE
Q 022247 65 SATRSTIIVPSSGIS------WFLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~~------efrd~L~~y~~~~~~~~~s~~l~v--dnKrFYfDlkeN~RGRFLRISE~~~-~~~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 456789999998533 344445444333333444433333 234689999999999876 443332 3456788
Q ss_pred eecC
Q 022247 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
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=30.82 E-value=42 Score=35.25 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=17.0
Q ss_pred EEeecccCCCCceEeecCCCCchhHHHHHHHHHH
Q 022247 122 KVSEASVSRNRSTIIVPAGSSRDEGWAAFRNILA 155 (300)
Q Consensus 122 RISE~~~~~~RstI~IPag~~~~~Gw~~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 45444443 56677777 67777777664
No 17
>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=28.76 E-value=1.3e+02 Score=28.85 Aligned_cols=74 Identities=19% Similarity=0.246 Sum_probs=45.1
Q ss_pred CCcceEEEeecccHHH------HHHHhhhhhcCCCCccccccccc--ccceEEEeccCCCccceeEEeeccc-CCCCceE
Q 022247 65 SATRSTIIVPSSGISW------FLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~~e------frd~L~~y~~~~~~~~~s~~l~v--dnKrFYfDlkeN~RGRFLRISE~~~-~~~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 4567899999986432 44445444333333444333222 245689999999999876 443332 2456788
Q ss_pred eecC
Q 022247 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 18
>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=25.71 E-value=1.2e+02 Score=28.68 Aligned_cols=74 Identities=20% Similarity=0.255 Sum_probs=44.6
Q ss_pred CCcceEEEeecccHH------HHHHHhhhhhcCCCCccccccccc--ccceEEEeccCCCccceeEEeeccc-CCCCceE
Q 022247 65 SATRSTIIVPSSGIS------WFLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~~------efrd~L~~y~~~~~~~~~s~~l~v--dnKrFYfDlkeN~RGRFLRISE~~~-~~~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 456779999998543 344445444333333444333322 245689999999999876 332232 2345688
Q ss_pred eecC
Q 022247 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 19
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=23.92 E-value=1.5e+02 Score=28.65 Aligned_cols=53 Identities=15% Similarity=0.142 Sum_probs=36.7
Q ss_pred eeEeeccceEE-EecCCCCceeeEEEeeec-CC-CCceeeechhhHHHHHHHHHHHHHHH
Q 022247 224 KVIRADQKRFF-FDLGSNNRGHFLRISEVA-GS-DRSSIILPLSGLKQFHEIVGHFVEIT 280 (300)
Q Consensus 224 ~~ir~dnK~Fy-FDlg~N~RG~FLRISEv~-~~-~Rs~I~iP~~~~~~Fre~l~~~~d~~ 280 (300)
..-.++.|.|| |++ .| |.|-.-=|. +. |=-.+..|++-|.+-.+.|..+++-.
T Consensus 201 ~~re~dGktYY~~E~---~r-H~LasaTV~~GrLYt~~asape~rW~k~~~~lr~v~dSF 256 (262)
T PLN00066 201 EVAEHSGRTYYQFEL---PP-HTLVTATAAGNRVYIFSVTANGLQWKRHYKDLKRIAKSF 256 (262)
T ss_pred eeeecCCcEEEEEEE---eC-ceEEEEEEECCEEEEEEeecchHhhHHHHHHHHHHhhce
Confidence 44456788888 898 23 555433343 33 77788899999999888887776643
No 20
>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=22.08 E-value=1.5e+02 Score=27.99 Aligned_cols=74 Identities=22% Similarity=0.335 Sum_probs=44.6
Q ss_pred CCcceEEEeecccHH------HHHHHhhhhhcCCCCccccccccc--ccceEEEeccCCCccceeEEeeccc-CCCCceE
Q 022247 65 SATRSTIIVPSSGIS------WFLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~~------efrd~L~~y~~~~~~~~~s~~l~v--dnKrFYfDlkeN~RGRFLRISE~~~-~~~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 356779999998533 344455544443334444333222 245789999999999876 433332 2345678
Q ss_pred eecC
Q 022247 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 8885
No 21
>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=21.76 E-value=1.6e+02 Score=27.91 Aligned_cols=74 Identities=24% Similarity=0.228 Sum_probs=44.1
Q ss_pred CCcceEEEeecccHHH------HHHHhhhhhcCCCCcccccccc--cccceEEEeccCCCccceeEEeeccc-CCCCceE
Q 022247 65 SATRSTIIVPSSGISW------FLDLFNYYVNSDDHELFSKELQ--LDSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~~e------frd~L~~y~~~~~~~~~s~~l~--vdnKrFYfDlkeN~RGRFLRISE~~~-~~~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 4567799999986433 4444444433333333333222 2245789999999999876 333332 2456688
Q ss_pred eecC
Q 022247 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 22
>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=21.32 E-value=1.7e+02 Score=27.75 Aligned_cols=74 Identities=19% Similarity=0.255 Sum_probs=44.5
Q ss_pred CCcceEEEeecccHH------HHHHHhhhhhcCCCCccccccccc--ccceEEEeccCCCccceeEEeeccc-CCCCceE
Q 022247 65 SATRSTIIVPSSGIS------WFLDLFNYYVNSDDHELFSKELQL--DSKVFYFDIGENRRGRFLKVSEASV-SRNRSTI 135 (300)
Q Consensus 65 ~g~rs~I~lp~~g~~------efrd~L~~y~~~~~~~~~s~~l~v--dnKrFYfDlkeN~RGRFLRISE~~~-~~~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 456779999998643 344445444433333444332222 245789999999999866 443332 2346678
Q ss_pred eecC
Q 022247 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
Done!