Query psy12967
Match_columns 222
No_of_seqs 224 out of 1037
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 15:42:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12967hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2518|consensus 100.0 6.1E-37 1.3E-41 283.1 8.8 157 56-222 1-181 (556)
2 PTZ00217 flap endonuclease-1; 100.0 2.5E-36 5.4E-41 277.4 8.9 156 56-221 1-190 (393)
3 TIGR03674 fen_arch flap struct 100.0 1.2E-34 2.5E-39 262.0 10.6 153 56-221 1-182 (338)
4 cd00128 XPG Xeroderma pigmento 100.0 1.9E-34 4.2E-39 258.1 9.5 156 56-221 1-180 (316)
5 KOG2519|consensus 100.0 2.4E-34 5.2E-39 262.9 9.8 156 56-221 1-184 (449)
6 PF00752 XPG_N: XPG N-terminal 100.0 3.9E-29 8.4E-34 188.9 6.8 95 56-150 1-101 (101)
7 smart00485 XPGN Xeroderma pigm 100.0 2.6E-29 5.6E-34 189.5 5.7 95 56-150 1-99 (99)
8 TIGR00600 rad2 DNA excision re 99.9 1.3E-26 2.9E-31 231.3 6.0 101 56-156 1-104 (1034)
9 PRK03980 flap endonuclease-1; 99.9 6.9E-25 1.5E-29 194.8 8.9 114 98-221 2-135 (292)
10 COG0258 Exo 5'-3' exonuclease 99.4 1.3E-12 2.8E-17 117.0 10.2 135 72-222 4-154 (310)
11 smart00485 XPGN Xeroderma pigm 99.3 1.1E-13 2.5E-18 104.0 -0.5 43 1-43 1-43 (99)
12 PF00752 XPG_N: XPG N-terminal 99.3 2.4E-13 5.2E-18 102.5 0.1 43 1-43 1-45 (101)
13 TIGR00600 rad2 DNA excision re 99.2 1.1E-12 2.5E-17 132.0 -0.4 54 1-54 1-62 (1034)
14 cd00008 53EXOc 5'-3' exonuclea 99.1 3.6E-10 7.8E-15 98.0 8.0 127 80-219 2-140 (240)
15 PF00867 XPG_I: XPG I-region; 99.1 8.1E-11 1.8E-15 88.0 2.7 40 172-221 1-43 (94)
16 smart00484 XPGI Xeroderma pigm 99.0 1.9E-10 4.1E-15 82.4 2.8 40 173-222 2-44 (73)
17 smart00475 53EXOc 5'-3' exonuc 99.0 2.6E-09 5.6E-14 93.8 9.8 127 81-220 3-140 (259)
18 PRK14976 5'-3' exonuclease; Pr 98.9 6.9E-09 1.5E-13 92.1 10.6 128 80-220 4-146 (281)
19 KOG2519|consensus 98.8 1.5E-09 3.3E-14 100.4 1.0 54 1-54 1-67 (449)
20 cd00128 XPG Xeroderma pigmento 98.7 1.6E-09 3.5E-14 97.1 -0.6 43 1-43 1-43 (316)
21 KOG2520|consensus 98.7 1.5E-08 3.3E-13 99.9 5.3 44 169-222 473-519 (815)
22 PRK05755 DNA polymerase I; Pro 98.7 7.9E-08 1.7E-12 97.1 8.9 127 80-220 3-142 (880)
23 PTZ00217 flap endonuclease-1; 98.7 4E-09 8.7E-14 97.6 -0.4 43 1-43 1-47 (393)
24 TIGR00593 pola DNA polymerase 98.6 2.6E-07 5.6E-12 93.3 9.7 125 82-220 2-140 (887)
25 TIGR03674 fen_arch flap struct 98.4 5.2E-08 1.1E-12 88.6 -0.4 39 1-42 1-39 (338)
26 KOG2518|consensus 98.0 1.7E-06 3.7E-11 81.6 0.7 54 1-54 1-58 (556)
27 PRK09482 flap endonuclease-lik 97.4 0.0019 4.1E-08 56.8 11.3 124 80-216 4-136 (256)
28 PF02739 5_3_exonuc_N: 5'-3' e 97.4 0.0042 9.2E-08 51.2 12.0 115 81-216 3-138 (169)
29 PRK03980 flap endonuclease-1; 96.6 0.0026 5.6E-08 56.9 4.6 47 156-202 6-52 (292)
30 PHA00439 exonuclease 96.4 0.054 1.2E-06 48.4 11.3 122 80-216 7-150 (286)
31 PF03159 XRN_N: XRN 5'-3' exon 95.9 0.0077 1.7E-07 52.4 3.4 93 56-148 1-104 (237)
32 PHA02567 rnh RnaseH; Provision 95.6 0.088 1.9E-06 47.4 9.0 128 80-216 15-159 (304)
33 PF05991 NYN_YacP: YacP-like N 92.2 0.71 1.5E-05 37.8 7.3 52 82-133 1-55 (166)
34 PHA03065 Hypothetical protein; 91.5 1.1 2.5E-05 41.9 8.6 89 56-148 1-93 (438)
35 PF04599 Pox_G5: Poxvirus G5 p 89.0 1 2.2E-05 42.3 6.1 89 56-148 1-91 (425)
36 COG2454 Uncharacterized conser 80.6 22 0.00048 30.3 9.7 72 70-144 57-149 (211)
37 PF05687 DUF822: Plant protein 77.0 8.6 0.00019 31.1 5.9 71 130-221 4-74 (150)
38 KOG2520|consensus 51.9 12 0.00025 38.2 2.7 128 10-147 5-136 (815)
39 KOG1431|consensus 41.2 1.6E+02 0.0036 26.1 7.7 92 104-214 177-271 (315)
40 PHA02994 hypothetical protein; 33.5 26 0.00057 30.1 1.6 23 126-148 102-128 (218)
41 cd00008 53EXOc 5'-3' exonuclea 32.6 33 0.00071 29.6 2.2 112 25-144 2-120 (240)
42 PF04708 Pox_F16: Poxvirus F16 31.0 29 0.00064 29.8 1.5 15 126-140 102-116 (218)
43 KOG1541|consensus 30.4 43 0.00092 29.4 2.4 89 24-129 73-161 (270)
44 COG0258 Exo 5'-3' exonuclease 28.9 35 0.00077 30.4 1.8 126 16-145 3-132 (310)
45 COG1578 Uncharacterized conser 28.7 61 0.0013 29.0 3.2 46 170-216 173-218 (285)
46 PF10652 DUF2480: Protein of u 27.7 36 0.00078 28.1 1.5 52 17-87 17-70 (167)
47 PF10652 DUF2480: Protein of u 26.3 38 0.00082 28.0 1.4 25 70-94 15-41 (167)
48 PF06574 FAD_syn: FAD syntheta 26.1 47 0.001 26.8 1.9 86 109-212 23-115 (157)
49 PHA02697 hypothetical protein; 25.6 38 0.00082 29.3 1.3 12 126-137 115-126 (255)
50 PF11977 RNase_Zc3h12a: Zc3h12 20.6 1.4E+02 0.003 23.7 3.7 47 80-132 3-49 (155)
No 1
>KOG2518|consensus
Probab=100.00 E-value=6.1e-37 Score=283.11 Aligned_cols=157 Identities=27% Similarity=0.366 Sum_probs=140.7
Q ss_pred hccccccccccccceeeccccccCcEEEeecchhhhhhhhhhh---hcCCchH-HHHHHHHHHHHHHhcCCeeEEEeeCC
Q psy12967 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE---HSSQKNM-YLRNLFFRTSYLLLLGVKPIFVLEGK 131 (222)
Q Consensus 56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~---~~~~~~~-~l~~~f~R~~~Ll~~gI~PIfVFDG~ 131 (222)
|||+||+++++++.+++|+++|+|+++|||+|+|||++...+. ..|++|. |+.+++.|+..|+.+||+||+||||.
T Consensus 1 MGI~GLlp~~k~~~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~ 80 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPIHISEYKGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGD 80 (556)
T ss_pred CCcchhHHHHHHHhhhhhHHHhcCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence 9999999999999999999999999999999999999965432 3577765 88999999999999999999999999
Q ss_pred CCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhHH------------HHHHHhCCceEEEecCCCCccCcccH
Q psy12967 132 APVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFRT------------SYLLLLGVKPIFVLEGKAPVLKHDTI 194 (222)
Q Consensus 132 ~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R~------------~lL~~~GI~p~~vapGeap~l~a~~~ 194 (222)
++|.|+.|+.+||.+|+++...+.+ .|+ +|+.+|+|+ ++|+.+|| +++||||||+
T Consensus 81 ~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nV-e~IVAPyEAD------- 152 (556)
T KOG2518|consen 81 PLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNV-EYIVAPYEAD------- 152 (556)
T ss_pred CcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCC-ceEecCcccc-------
Confidence 9999999999999999988876654 444 689999886 48899999 9999999986
Q ss_pred HHHHHHhhhhcCC---eeecCcceeeccccC
Q psy12967 195 EKRQQAQGRSAGR---NVQAGSRARLKGLQT 222 (222)
Q Consensus 195 ae~~~a~l~~~g~---~~T~DsD~~lFG~~~ 222 (222)
+|.++|++.|. +||||||+++|||++
T Consensus 153 --AQlayL~~~~~i~~IITEDSDLl~fGc~~ 181 (556)
T KOG2518|consen 153 --AQLAYLEREGIVDAIITEDSDLLVFGCKK 181 (556)
T ss_pred --chhHHHHhcCcceEEEeccccccccCchh
Confidence 58999999987 799999999999985
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.5e-36 Score=277.44 Aligned_cols=156 Identities=26% Similarity=0.357 Sum_probs=133.9
Q ss_pred hcccccccccccc----ceeeccccccCcEEEeecchhhhhhhhh----------hhhcCCchHHHHHHHHHHHHHHhcC
Q psy12967 56 MGVKDLWGILTPI----CERKPIWELQDKTIAIDLSAWICDSSTI----------AEHSSQKNMYLRNLFFRTSYLLLLG 121 (222)
Q Consensus 56 MGI~gL~~~l~~~----~~~~~i~~l~Gk~iAID~s~wl~~~~~~----------~~~~~~~~~~l~~~f~R~~~Ll~~g 121 (222)
|||+||+++|++. .+++++++|+|++||||+|+||||+.+. .++.|++|+|+.++|+|+++|+++|
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~g 80 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAG 80 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCC
Confidence 9999999999875 4789999999999999999999997542 3446888999999999999999999
Q ss_pred CeeEEEeeCCCCCCchhhHHHHHHHhhhhccCcc---cccc--chhhhhhHH------------HHHHHhCCceEEEecC
Q psy12967 122 VKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNV---QAGS--RARNLFFRT------------SYLLLLGVKPIFVLEG 184 (222)
Q Consensus 122 I~PIfVFDG~~p~~K~~t~~~Rr~~r~~~~~~~~---e~gs--~ar~lf~R~------------~lL~~~GI~p~~vapG 184 (222)
|+|||||||.+|++|..+..+|+++|+.+..... +.|+ .++.+++|+ .+|..+|| ||++|||
T Consensus 81 ikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gi-p~i~AP~ 159 (393)
T PTZ00217 81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGI-PVIEAPC 159 (393)
T ss_pred CCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCC-ceEECCc
Confidence 9999999999999999999999999987765432 3443 455666553 38899999 9999998
Q ss_pred CCCccCcccHHHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967 185 KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQ 221 (222)
Q Consensus 185 eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~ 221 (222)
|| +++||++...|. |+|+|+|+|+|||.
T Consensus 160 EA---------daq~A~L~~~g~v~~ViS~D~D~l~fg~~ 190 (393)
T PTZ00217 160 EA---------EAQCAELVKKGKVYAVATEDMDALTFGTP 190 (393)
T ss_pred CH---------HHHHHHHHHCCCeEEEeCCCcCeeecCCc
Confidence 75 689999999997 67999999999985
No 3
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=1.2e-34 Score=262.05 Aligned_cols=153 Identities=28% Similarity=0.405 Sum_probs=132.4
Q ss_pred hccccccccccccceeeccccccCcEEEeecchhhhhhhhh---------hhhcCCchHHHHHHHHHHHHHHhcCCeeEE
Q psy12967 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTI---------AEHSSQKNMYLRNLFFRTSYLLLLGVKPIF 126 (222)
Q Consensus 56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~---------~~~~~~~~~~l~~~f~R~~~Ll~~gI~PIf 126 (222)
||| |||++++ .+++++++|+|+++|||+|+||||+.+. .++.|++|+|+.++|+|+++|+++||+|||
T Consensus 1 MGi-~l~~~~~--~~~~~l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~ 77 (338)
T TIGR03674 1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKPVY 77 (338)
T ss_pred CCC-ChHHHhc--cCccCHHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeEEE
Confidence 999 9999998 7899999999999999999999997542 345689999999999999999999999999
Q ss_pred EeeCCCCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhHH------------HHHHHhCCceEEEecCCCCcc
Q psy12967 127 VLEGKAPVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFRT------------SYLLLLGVKPIFVLEGKAPVL 189 (222)
Q Consensus 127 VFDG~~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R~------------~lL~~~GI~p~~vapGeap~l 189 (222)
||||.+|++|..+..+|+++|+.+.+++.+ .++ +++++++|+ .+|+.+|| |+++|||||
T Consensus 78 VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gi-p~i~AP~EA--- 153 (338)
T TIGR03674 78 VFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGI-PYVQAPSEG--- 153 (338)
T ss_pred EECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCC-eEEECCccH---
Confidence 999999999999999999999987655542 332 455555552 48999999 999999976
Q ss_pred CcccHHHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967 190 KHDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQ 221 (222)
Q Consensus 190 ~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~ 221 (222)
+++||++...|. |+|+|+|+|+||+.
T Consensus 154 ------eaq~a~L~~~g~vd~v~S~D~D~l~fg~~ 182 (338)
T TIGR03674 154 ------EAQAAYMAKKGDVDYVGSQDYDSLLFGAP 182 (338)
T ss_pred ------HHHHHHHHHCCCeeEEecCCcCeeeecCC
Confidence 689999999886 67999999999986
No 4
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=1.9e-34 Score=258.05 Aligned_cols=156 Identities=33% Similarity=0.529 Sum_probs=130.5
Q ss_pred hccccccccccccceeeccccccCcEEEeecchhhhhhhhhhh----hcCCchHHHHHHHHHHHHHHhcCCeeEEEeeCC
Q psy12967 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE----HSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGK 131 (222)
Q Consensus 56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~----~~~~~~~~l~~~f~R~~~Ll~~gI~PIfVFDG~ 131 (222)
|||+|||++|++..++.++++|+|++||||+|+||||+.+... ..|.+++|+.++++|+.+|+++||+|||||||.
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~gk~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~~~i~pvfVFDG~ 80 (316)
T cd00128 1 MGIKGLWPLLKPVARPVHLEELRGKKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLELGIKPVFVFDGK 80 (316)
T ss_pred CchhhHHHHHHhhCCCCCHHHhCCcEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHHCCCEEEEEEcCC
Confidence 9999999999998888899999999999999999999875432 247789999999999999999999999999999
Q ss_pred CCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhH------------HHHHHHhCCceEEEecCCCCccCcccH
Q psy12967 132 APVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFR------------TSYLLLLGVKPIFVLEGKAPVLKHDTI 194 (222)
Q Consensus 132 ~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R------------~~lL~~~GI~p~~vapGeap~l~a~~~ 194 (222)
+|+.|.+|..+|+++|.++..+..+ .++ ++.++..+ ..+|+.+|| |+++|||||
T Consensus 81 ~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi-~~i~ap~EA-------- 151 (316)
T cd00128 81 PPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGI-PYIVAPYEA-------- 151 (316)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCC-CEEECCcCH--------
Confidence 9999999999999988876544332 121 12222111 148999999 899998876
Q ss_pred HHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967 195 EKRQQAQGRSAGR---NVQAGSRARLKGLQ 221 (222)
Q Consensus 195 ae~~~a~l~~~g~---~~T~DsD~~lFG~~ 221 (222)
+++||++...|. |+|+|||+|+||+.
T Consensus 152 -daq~a~l~~~g~v~~i~S~DsD~l~fg~~ 180 (316)
T cd00128 152 -EAQCAYLAKKGLVDAIITEDSDLLLFGAP 180 (316)
T ss_pred -HHHHHHHHhCCCeeEEEecCCCeeeecCc
Confidence 688999999886 68999999999986
No 5
>KOG2519|consensus
Probab=100.00 E-value=2.4e-34 Score=262.90 Aligned_cols=156 Identities=29% Similarity=0.472 Sum_probs=129.8
Q ss_pred hccccccccc----cccceeeccccccCcEEEeecchhhhhhhhhhh----hcCCchHHHHHHHHHHHHHHhcCCeeEEE
Q psy12967 56 MGVKDLWGIL----TPICERKPIWELQDKTIAIDLSAWICDSSTIAE----HSSQKNMYLRNLFFRTSYLLLLGVKPIFV 127 (222)
Q Consensus 56 MGI~gL~~~l----~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~----~~~~~~~~l~~~f~R~~~Ll~~gI~PIfV 127 (222)
|||+||.+++ .+..+..+++.|+|++||||+|+||||+..+.+ ..+++++||+++|+|+++|+++||+||||
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~V 80 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRTIRLIENGIKPVYV 80 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHHHHHHHcCCcEEEE
Confidence 9999995544 345578899999999999999999999865443 46889999999999999999999999999
Q ss_pred eeCCCCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhHH------------HHHHHhCCceEEEecCCCCccC
Q psy12967 128 LEGKAPVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFRT------------SYLLLLGVKPIFVLEGKAPVLK 190 (222)
Q Consensus 128 FDG~~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R~------------~lL~~~GI~p~~vapGeap~l~ 190 (222)
|||.+|++|+.+..+|..+|..+.....+ .+. ...+++.|. .+|.+||| |++.
T Consensus 81 fDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGI----------p~i~ 150 (449)
T KOG2519|consen 81 FDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGI----------PVLD 150 (449)
T ss_pred ECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCC----------eeec
Confidence 99999999999999999999866554433 121 345555554 38999999 5666
Q ss_pred cccHHHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967 191 HDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQ 221 (222)
Q Consensus 191 a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~ 221 (222)
||.+||||||+|+++|. ++|+|||+|.||+.
T Consensus 151 ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~ 184 (449)
T KOG2519|consen 151 APGEAEAQCAALNKAGKVYAVATEDSDALTFGAP 184 (449)
T ss_pred CCchHHHHHHHHhhcCceeeeeccccchhhccCH
Confidence 66677999999999987 68999999999974
No 6
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=99.95 E-value=3.9e-29 Score=188.89 Aligned_cols=95 Identities=39% Similarity=0.677 Sum_probs=78.8
Q ss_pred hccccccccccccc--eeeccccccCcEEEeecchhhhhhhhhhhh---c-CCchHHHHHHHHHHHHHHhcCCeeEEEee
Q psy12967 56 MGVKDLWGILTPIC--ERKPIWELQDKTIAIDLSAWICDSSTIAEH---S-SQKNMYLRNLFFRTSYLLLLGVKPIFVLE 129 (222)
Q Consensus 56 MGI~gL~~~l~~~~--~~~~i~~l~Gk~iAID~s~wl~~~~~~~~~---~-~~~~~~l~~~f~R~~~Ll~~gI~PIfVFD 129 (222)
|||+|||++|++.. ++.++++|+|++||||+|+||||+...... . ...++|+.++++|++.|+++||+||||||
T Consensus 1 MGI~gL~~~l~~~~~v~~~~~~~l~g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~PifVFD 80 (101)
T PF00752_consen 1 MGIKGLWQLLKPAAAVRKVSLSELRGKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKPIFVFD 80 (101)
T ss_dssp ---TTHHHHCHHHEGEEEEEGGGGTTCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEEEEEE-
T ss_pred CCcccHHHHHHhhccCCccCHHHhCCCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEEEEEEC
Confidence 99999999999987 899999999999999999999998643321 1 22248999999999999999999999999
Q ss_pred CCCCCCchhhHHHHHHHhhhh
Q psy12967 130 GKAPVLKHDTIEKRQQAQGRS 150 (222)
Q Consensus 130 G~~p~~K~~t~~~Rr~~r~~~ 150 (222)
|.+|+.|.+|..+|+++|++|
T Consensus 81 G~~~~~K~~~~~~R~~~r~~~ 101 (101)
T PF00752_consen 81 GKPPPLKRETIQKRRKRREEA 101 (101)
T ss_dssp -STTGGCHHHHHHHHHHHHHH
T ss_pred CCCchhhHHHHHHHHHHHhcC
Confidence 999999999999999998864
No 7
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.95 E-value=2.6e-29 Score=189.45 Aligned_cols=95 Identities=41% Similarity=0.738 Sum_probs=84.6
Q ss_pred hccccccccccccceeeccccccCcEEEeecchhhhhhhhhhh---hcCCchH-HHHHHHHHHHHHHhcCCeeEEEeeCC
Q psy12967 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE---HSSQKNM-YLRNLFFRTSYLLLLGVKPIFVLEGK 131 (222)
Q Consensus 56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~---~~~~~~~-~l~~~f~R~~~Ll~~gI~PIfVFDG~ 131 (222)
|||+|||++|++..++.++++|+|++||||+|+||||+..... ....++. |+.++|+|++.|+++||+|||||||.
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~g~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L~~~~I~PifVFDG~ 80 (99)
T smart00485 1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKPIFVFDGK 80 (99)
T ss_pred CCHhHHHHHHHHhcccCCHHHhCCceEeccHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHCCCeEEEEECCC
Confidence 9999999999999999999999999999999999999865432 1223334 99999999999999999999999999
Q ss_pred CCCCchhhHHHHHHHhhhh
Q psy12967 132 APVLKHDTIEKRQQAQGRS 150 (222)
Q Consensus 132 ~p~~K~~t~~~Rr~~r~~~ 150 (222)
+|++|..|..+|+++|+++
T Consensus 81 ~~~~K~~t~~~R~~~r~~~ 99 (99)
T smart00485 81 PPPLKSETLAKRRERREEA 99 (99)
T ss_pred CchhhHHHHHHHHHHHhcC
Confidence 9999999999999998763
No 8
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=1.3e-26 Score=231.26 Aligned_cols=101 Identities=33% Similarity=0.548 Sum_probs=91.3
Q ss_pred hccccccccccccceeeccccccCcEEEeecchhhhhhhhhhh-hcC--CchHHHHHHHHHHHHHHhcCCeeEEEeeCCC
Q psy12967 56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE-HSS--QKNMYLRNLFFRTSYLLLLGVKPIFVLEGKA 132 (222)
Q Consensus 56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~-~~~--~~~~~l~~~f~R~~~Ll~~gI~PIfVFDG~~ 132 (222)
|||+|||++|+|++++++++.|+||+||||+|+||||+...+. ..| .+++||.++|+|+|+|+++||+|||||||.+
T Consensus 1 MGI~GLw~ll~~~~r~v~le~l~Gk~vAIDasiWL~q~l~~vr~~~g~~l~n~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~ 80 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhCCeEEEechHHHHHHHHHHHHhccCCccCCHHHHHHHHHHHHHHHCCCeEEEEECCCC
Confidence 9999999999999999999999999999999999999976442 222 3578999999999999999999999999999
Q ss_pred CCCchhhHHHHHHHhhhhccCccc
Q psy12967 133 PVLKHDTIEKRQQAQGRSAGRNVQ 156 (222)
Q Consensus 133 p~~K~~t~~~Rr~~r~~~~~~~~e 156 (222)
|++|+.|+++|+++|+++...+..
T Consensus 81 p~lK~~t~~~R~~rR~~a~~~a~~ 104 (1034)
T TIGR00600 81 PLLKRQTLAKRRQRRDGASEDARK 104 (1034)
T ss_pred chHhHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999988765543
No 9
>PRK03980 flap endonuclease-1; Provisional
Probab=99.91 E-value=6.9e-25 Score=194.81 Aligned_cols=114 Identities=27% Similarity=0.433 Sum_probs=97.3
Q ss_pred hhcCCchHHHHHHHHHHHHHHhcCCeeEEEeeCCCCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhHH----
Q psy12967 98 EHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFRT---- 168 (222)
Q Consensus 98 ~~~~~~~~~l~~~f~R~~~Ll~~gI~PIfVFDG~~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R~---- 168 (222)
++.|++|+|+.++|+|+++|+++||+|||||||.+|++|.++..+|+++|+++.+++.+ .|+ .++++++|+
T Consensus 2 ~~~G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt 81 (292)
T PRK03980 2 DSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLT 81 (292)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCC
Confidence 46799999999999999999999999999999999999999999999999987665543 333 455555442
Q ss_pred --------HHHHHhCCceEEEecCCCCccCcccHHHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967 169 --------SYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQ 221 (222)
Q Consensus 169 --------~lL~~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~ 221 (222)
.+|+.+|| ||++||||| ||+||++.+.|. |+|+|||+|+||+.
T Consensus 82 ~~~~~~~k~lL~~~GI-p~i~AP~EA---------EAq~A~L~~~g~vd~V~S~D~D~l~fg~~ 135 (292)
T PRK03980 82 DEIVEDSKKLLDLMGI-PYVQAPSEG---------EAQAAYMAKKGDAWAVGSQDYDSLLFGAP 135 (292)
T ss_pred HHHHHHHHHHHHHCCC-CEEecCchH---------HHHHHHHHHCCCeEEEecCCcCeeeecCC
Confidence 38999999 888888864 789999999987 67999999999985
No 10
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.40 E-value=1.3e-12 Score=117.04 Aligned_cols=135 Identities=18% Similarity=0.240 Sum_probs=99.1
Q ss_pred eccccccCcEEEeecchhhhhhhhhh-----hhcCCc---hHHHHHHHHHHHHHHhcCCeeEEEeeCCCCCCchhhHHHH
Q psy12967 72 KPIWELQDKTIAIDLSAWICDSSTIA-----EHSSQK---NMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKR 143 (222)
Q Consensus 72 ~~i~~l~Gk~iAID~s~wl~~~~~~~-----~~~~~~---~~~l~~~f~R~~~Ll~~gI~PIfVFDG~~p~~K~~t~~~R 143 (222)
.+...+.|+.++||++.|+||+.+.. +..|.+ ..++.++++|+++..+. +.|++||||.+|.+|.++..+|
T Consensus 4 ~~~~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~-~~~~~vFD~~~~tfR~~~~~~y 82 (310)
T COG0258 4 IQLMNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEP-THPVVVFDGKPPTFRHELLEEY 82 (310)
T ss_pred ccchhccCcEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCC-CcEEEEEcCCCCcchHHHHHHH
Confidence 45567889999999999999986543 233444 45777778888888777 9999999999999999999999
Q ss_pred HHHhhh-hccCccccccchhhhhhHH----HHHHHhCCceEEEecCCCCccCcccHHHHHHHhhhhcCC---eeecCcce
Q psy12967 144 QQAQGR-SAGRNVQAGSRARNLFFRT----SYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRA 215 (222)
Q Consensus 144 r~~r~~-~~~~~~e~gs~ar~lf~R~----~lL~~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~ 215 (222)
+..|.. . ...+..+. ..+.++|+ +.+-.+|- | ..++.+++++|+. ..|. ++|+|+|+
T Consensus 83 K~~R~~~~----------p~~l~~q~~~i~~~~~~~~~-~~l~~~G~-e-add~i~t~A~~a~--~~g~~~~I~S~DkD~ 147 (310)
T COG0258 83 KANREKEM----------PDELAPQIPILTELLVALGI-PLLELMGI-E-ADDPIETLAQKAY--KKGDVVLIISGDKDL 147 (310)
T ss_pred HhCCCccC----------HHHHHHHHHHHHHHHHHhCc-HhhhcCCC-C-cchhHHHHHHHHH--hcCCeEEEEeCCcch
Confidence 988876 2 12222222 35566666 44444443 2 5667889999988 4554 68999999
Q ss_pred eeccccC
Q psy12967 216 RLKGLQT 222 (222)
Q Consensus 216 ~lFG~~~ 222 (222)
+.||+.+
T Consensus 148 lql~~~~ 154 (310)
T COG0258 148 LQLVSPN 154 (310)
T ss_pred hhhcCCC
Confidence 9999863
No 11
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.34 E-value=1.1e-13 Score=104.01 Aligned_cols=43 Identities=40% Similarity=0.754 Sum_probs=40.8
Q ss_pred CcccchhhhhhccccccCcccccCceEEEecceeeeecccccc
Q psy12967 1 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE 43 (222)
Q Consensus 1 mgv~~lw~~l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~ 43 (222)
|||+|||++|+|..++.++++|+|||||||+|+||++..+.+.
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~g~~vaIDa~~wl~~~~~~~~ 43 (99)
T smart00485 1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACR 43 (99)
T ss_pred CCHhHHHHHHHHhcccCCHHHhCCceEeccHHHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999887663
No 12
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=99.32 E-value=2.4e-13 Score=102.46 Aligned_cols=43 Identities=35% Similarity=0.671 Sum_probs=37.7
Q ss_pred Ccccchhhhhhccc--cccCcccccCceEEEecceeeeecccccc
Q psy12967 1 MGVKDLWGILTPIC--ERKPIWELQDKTIAIDLSAWICDSSTIAE 43 (222)
Q Consensus 1 mgv~~lw~~l~~~~--~~~~~~~~~~~~~~~d~s~w~~~~~~~~~ 43 (222)
|||+|||++|.|.+ ++.++++|+|++||||+|+|++|..+.+.
T Consensus 1 MGI~gL~~~l~~~~~v~~~~~~~l~g~~vaID~s~wl~~~~~~~~ 45 (101)
T PF00752_consen 1 MGIKGLWQLLKPAAAVRKVSLSELRGKRVAIDASCWLHQFLFSCR 45 (101)
T ss_dssp ---TTHHHHCHHHEGEEEEEGGGGTTCEEEEEHHHHHHHHHHHSB
T ss_pred CCcccHHHHHHhhccCCccCHHHhCCCEEEEEcHHHHHHHHHHhH
Confidence 99999999999999 99999999999999999999999877664
No 13
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.23 E-value=1.1e-12 Score=132.01 Aligned_cols=54 Identities=26% Similarity=0.438 Sum_probs=46.6
Q ss_pred CcccchhhhhhccccccCcccccCceEEEecceeeeecccccc--------ccccchhhHHh
Q psy12967 1 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE--------HSSQKNMYLRA 54 (222)
Q Consensus 1 mgv~~lw~~l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~--------~~~~~~~~~r~ 54 (222)
|||+|||++|.|+++++++++|+|||||||+||||||+..++. +.++.++|.|.
T Consensus 1 MGI~GLw~ll~~~~r~v~le~l~Gk~vAIDasiWL~q~l~~vr~~~g~~l~n~hl~g~f~Ri 62 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRL 62 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhCCeEEEechHHHHHHHHHHHHhccCCccCCHHHHHHHHHH
Confidence 9999999999999999999999999999999999999988663 24455555555
No 14
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=99.08 E-value=3.6e-10 Score=97.98 Aligned_cols=127 Identities=13% Similarity=0.099 Sum_probs=87.3
Q ss_pred cEEEeecchhhhhhhhhh----hh-cCCchHHHHHHHHHHHHHHhcC--CeeEEEeeCCCCCCchhhHHHHHHHhhhhcc
Q psy12967 80 KTIAIDLSAWICDSSTIA----EH-SSQKNMYLRNLFFRTSYLLLLG--VKPIFVLEGKAPVLKHDTIEKRQQAQGRSAG 152 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~~----~~-~~~~~~~l~~~f~R~~~Ll~~g--I~PIfVFDG~~p~~K~~t~~~Rr~~r~~~~~ 152 (222)
+.+.||++..+||+.+.. +. .|.++.++.+++.++.++++.. ..+++||||..+..+.......+..|...-
T Consensus 2 ~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p- 80 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKKMP- 80 (240)
T ss_pred cEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCCCC-
Confidence 468999999999986533 22 5788999999999999998544 789999999988888887777665554311
Q ss_pred CccccccchhhhhhHH-HHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCcceeecc
Q psy12967 153 RNVQAGSRARNLFFRT-SYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKG 219 (222)
Q Consensus 153 ~~~e~gs~ar~lf~R~-~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG 219 (222)
+.....+... ..|..+|| |++.+|| ||+.+.+ ..+.+....|. ++|+|+|.+.++
T Consensus 81 ------~~l~~q~~~~~~~l~~~gi-~~i~~~~~EADD~ia-----~la~~~~~~g~~~~I~S~DkD~~ql~ 140 (240)
T cd00008 81 ------EELREQIPLIKELLEALGI-PVLEIEGYEADDVIG-----TLAKKAEAEGYKVVIVSGDKDLLQLV 140 (240)
T ss_pred ------HHHHHHHHHHHHHHHHCCC-CEEecCCcCHHHHHH-----HHHHHHHHcCCeEEEEeCCCChhhhC
Confidence 1111222222 47889999 8888876 7765321 11111223343 689999999885
No 15
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.06 E-value=8.1e-11 Score=87.96 Aligned_cols=40 Identities=30% Similarity=0.257 Sum_probs=31.6
Q ss_pred HHhCCceEEEecCCCCccCcccHHHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967 172 LLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQ 221 (222)
Q Consensus 172 ~~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~ 221 (222)
+++|| ||++||||| ++|||+|++.|. |+|+|||+|+|||+
T Consensus 1 ~~~gv-~~i~AP~EA---------eAq~A~L~~~g~vd~V~t~DsD~l~fG~~ 43 (94)
T PF00867_consen 1 RLMGV-PYIVAPYEA---------EAQCAYLERNGLVDAVITEDSDLLLFGAP 43 (94)
T ss_dssp HHHT--EEEE-SS-H---------HHHHHHHHHTTSSSEEE-SSSHHHHTT-S
T ss_pred CCCCC-eEEEcCchH---------HHHHHHHHHhcceeEEEecCCCEEeeCCC
Confidence 47899 999999875 799999999998 78999999999996
No 16
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.01 E-value=1.9e-10 Score=82.43 Aligned_cols=40 Identities=28% Similarity=0.272 Sum_probs=35.5
Q ss_pred HhCCceEEEecCCCCccCcccHHHHHHHhhhhcCC---eeecCcceeeccccC
Q psy12967 173 LLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQT 222 (222)
Q Consensus 173 ~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~~ 222 (222)
.+|| ||++||||| |+|||++++.|. |+|+|+|+|+||+.+
T Consensus 2 ~~gi-~~i~AP~eA---------eAq~A~L~~~g~vdav~s~D~D~llfG~~~ 44 (73)
T smart00484 2 LMGI-PYIVAPYEA---------EAQCAYLAKSGLVDAIITEDSDLLLFGAPR 44 (73)
T ss_pred cCCC-eEEEcCCcH---------HHHHHHHHhCCCeeEEEcCccceEecCCcE
Confidence 5799 999999875 899999999998 689999999999963
No 17
>smart00475 53EXOc 5'-3' exonuclease.
Probab=98.99 E-value=2.6e-09 Score=93.76 Aligned_cols=127 Identities=12% Similarity=0.099 Sum_probs=84.9
Q ss_pred EEEeecchhhhhhhhh----hhhcCCchHHHHHHHHHHHHHHhcC--CeeEEEeeCCCCCCchhhHHHHHHHhhhhccCc
Q psy12967 81 TIAIDLSAWICDSSTI----AEHSSQKNMYLRNLFFRTSYLLLLG--VKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRN 154 (222)
Q Consensus 81 ~iAID~s~wl~~~~~~----~~~~~~~~~~l~~~f~R~~~Ll~~g--I~PIfVFDG~~p~~K~~t~~~Rr~~r~~~~~~~ 154 (222)
-+.||++..+||+.+. .++.|.+|.++.+++.++.++++.- =.+++|||+..+.+..+.....+..|....+
T Consensus 3 lllIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~pe-- 80 (259)
T smart00475 3 LLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPD-- 80 (259)
T ss_pred EEEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccchhHHHHhCCCCCCH--
Confidence 4899999999997653 3456888999999999999998532 2349999998777766666665555442211
Q ss_pred cccccchhhhhhH-HHHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCcceeeccc
Q psy12967 155 VQAGSRARNLFFR-TSYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGL 220 (222)
Q Consensus 155 ~e~gs~ar~lf~R-~~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~ 220 (222)
.....+.. ...|..+|| |++.+|| ||+.+.+ ..+.+....|. ++|+|+|.+.+++
T Consensus 81 -----~L~~q~~~~~~~l~~~gi-~~i~~~g~EADD~ia-----tla~~~~~~g~~~~IvS~DkDl~ql~~ 140 (259)
T smart00475 81 -----ELLEQIPLIKELLDALGI-PVLEVEGYEADDVIA-----TLAKKAEAEGYEVRIVSGDKDLLQLVS 140 (259)
T ss_pred -----HHHHHHHHHHHHHHHCCC-CEEeeCCcCHHHHHH-----HHHHHHHhCCCeEEEEeCCCcHhhcCC
Confidence 11111211 147899999 8988887 8876432 11112222343 6799999998864
No 18
>PRK14976 5'-3' exonuclease; Provisional
Probab=98.93 E-value=6.9e-09 Score=92.07 Aligned_cols=128 Identities=11% Similarity=0.021 Sum_probs=89.4
Q ss_pred cEEEeecchhhhhhhhh--------hhhcCCchHHHHHHHHHHHHHHhc--CCeeEEEeeCCCCCCchhhHHHHHHHhhh
Q psy12967 80 KTIAIDLSAWICDSSTI--------AEHSSQKNMYLRNLFFRTSYLLLL--GVKPIFVLEGKAPVLKHDTIEKRQQAQGR 149 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~--------~~~~~~~~~~l~~~f~R~~~Ll~~--gI~PIfVFDG~~p~~K~~t~~~Rr~~r~~ 149 (222)
+.+.||++..+||+.+. .++.|.++.++.+++..+.++++. .-.+++|||+..+.++.+.....+..|..
T Consensus 4 ~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~ 83 (281)
T PRK14976 4 KALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKK 83 (281)
T ss_pred cEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCC
Confidence 46899999999996443 245688899999999999998843 35789999998888888887777666553
Q ss_pred hccCccccccchhhhhhH-HHHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCcceeeccc
Q psy12967 150 SAGRNVQAGSRARNLFFR-TSYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGL 220 (222)
Q Consensus 150 ~~~~~~e~gs~ar~lf~R-~~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~ 220 (222)
.-+ .....+.. ..+|..+|| |++.+|| ||+.+.+.. +.+....|. ++|.|.|.+-+..
T Consensus 84 ~p~-------~l~~q~~~i~~~l~~~gi-~~~~~~g~EADDviatl-----a~~~~~~g~~v~IvS~DkDl~ql~~ 146 (281)
T PRK14976 84 TPE-------SLISQIPLLKKILKLAGI-KWEEQPGYEADDLIGSL-----AKKLSKQNITVLIYSSDKDLLQLVN 146 (281)
T ss_pred CCH-------HHHHHHHHHHHHHHHCCC-CEEecCCcCHHHHHHHH-----HHHHHHCCCeEEEEeCCCCcCccCC
Confidence 211 11111111 147899999 8999987 887653321 222333343 6899999998865
No 19
>KOG2519|consensus
Probab=98.78 E-value=1.5e-09 Score=100.37 Aligned_cols=54 Identities=30% Similarity=0.495 Sum_probs=48.5
Q ss_pred Ccccch----hhhhhccccccCcccccCceEEEecceeeeeccccccc---------cccchhhHHh
Q psy12967 1 MGVKDL----WGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEH---------SSQKNMYLRA 54 (222)
Q Consensus 1 mgv~~l----w~~l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~~---------~~~~~~~~r~ 54 (222)
|||+|| |+.+.|+-+..|+++++|||||||+|.||+|+..+... .++.++|+|+
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt 67 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRT 67 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHH
Confidence 999999 68889999999999999999999999999999887752 6778888887
No 20
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=98.72 E-value=1.6e-09 Score=97.14 Aligned_cols=43 Identities=35% Similarity=0.673 Sum_probs=41.0
Q ss_pred CcccchhhhhhccccccCcccccCceEEEecceeeeecccccc
Q psy12967 1 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE 43 (222)
Q Consensus 1 mgv~~lw~~l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~ 43 (222)
|||+|||++|+|.+++.++++|+||+||||+|+||+++.+++.
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~gk~laID~~~~l~r~~~a~~ 43 (316)
T cd00128 1 MGIKGLWPLLKPVARPVHLEELRGKKVAIDASIWLYQFLKACR 43 (316)
T ss_pred CchhhHHHHHHhhCCCCCHHHhCCcEEEecHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999888764
No 21
>KOG2520|consensus
Probab=98.70 E-value=1.5e-08 Score=99.90 Aligned_cols=44 Identities=23% Similarity=0.173 Sum_probs=39.6
Q ss_pred HHHHHhCCceEEEecCCCCccCcccHHHHHHHhhhhcCC---eeecCcceeeccccC
Q psy12967 169 SYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGLQT 222 (222)
Q Consensus 169 ~lL~~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~~~ 222 (222)
.+|..+|| |||+||+|| |||||.++.-++ +||+|||.|+||+++
T Consensus 473 ElL~~fGI-PyI~APmEA---------EAQCa~Le~~~LvdGiITDDSDV~LFGg~~ 519 (815)
T KOG2520|consen 473 ELLRLFGI-PYIIAPMEA---------EAQCAFLEQLNLVDGIITDDSDVFLFGGTR 519 (815)
T ss_pred HHHHHcCC-ceecccccH---------HHHHHHHHHcCCcceeecccccceeeccch
Confidence 49999999 999998875 899999999887 799999999999973
No 22
>PRK05755 DNA polymerase I; Provisional
Probab=98.65 E-value=7.9e-08 Score=97.09 Aligned_cols=127 Identities=17% Similarity=0.139 Sum_probs=87.9
Q ss_pred cEEEeecchhhhhhhhhh-----hhcCCchHHHHHHHHHHHHHHhcCCee---EEEeeCCCCCCchhhHHHHHHHhhhhc
Q psy12967 80 KTIAIDLSAWICDSSTIA-----EHSSQKNMYLRNLFFRTSYLLLLGVKP---IFVLEGKAPVLKHDTIEKRQQAQGRSA 151 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~~-----~~~~~~~~~l~~~f~R~~~Ll~~gI~P---IfVFDG~~p~~K~~t~~~Rr~~r~~~~ 151 (222)
+.+.||++..+||+.+.. +..|.++.++.+++.++.+++ ...+| ++|||+..+..+......++..|...-
T Consensus 3 ~~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~-~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~~p 81 (880)
T PRK05755 3 TLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLL-KEEKPTHVAVAFDAKGKTFRHELYPEYKANRPPMP 81 (880)
T ss_pred eEEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHH-HhcCCCEEEEEEECCCCccccccCHHHhCCCCCCc
Confidence 457999999999986543 346888999999999999988 34445 999999888888887777766655321
Q ss_pred cCccccccchhhhhhHH-HHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCcceeeccc
Q psy12967 152 GRNVQAGSRARNLFFRT-SYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGL 220 (222)
Q Consensus 152 ~~~~e~gs~ar~lf~R~-~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~ 220 (222)
. .....+..+ .+|..+|| |++.+|| ||+.+.+ ..+.+....|. ++|+|.|.+-+++
T Consensus 82 ~-------~l~~q~~~~~~~l~~~gi-~~~~~~g~EADD~ia-----~la~~~~~~~~~~~i~S~DkD~~ql~~ 142 (880)
T PRK05755 82 E-------DLREQIPLIRELLRALGI-PLLELEGYEADDVIG-----TLAKQAEAAGYEVLIVTGDKDLLQLVD 142 (880)
T ss_pred H-------HHHHHHHHHHHHHHHCCC-CEEeeCCccHHHHHH-----HHHHHHHhCCCcEEEEcCCCChhhhCC
Confidence 1 112222222 37899999 9999997 8876532 11222223343 7899999998764
No 23
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.65 E-value=4e-09 Score=97.60 Aligned_cols=43 Identities=23% Similarity=0.234 Sum_probs=39.1
Q ss_pred Ccccchhhhhhcc----ccccCcccccCceEEEecceeeeecccccc
Q psy12967 1 MGVKDLWGILTPI----CERKPIWELQDKTIAIDLSAWICDSSTIAE 43 (222)
Q Consensus 1 mgv~~lw~~l~~~----~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~ 43 (222)
|||+|||++|.+. -+++++++|.||+||||+|+||||+.+++.
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~ 47 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIR 47 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcc
Confidence 9999999999876 588999999999999999999999876653
No 24
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.56 E-value=2.6e-07 Score=93.31 Aligned_cols=125 Identities=14% Similarity=0.130 Sum_probs=84.9
Q ss_pred EEeecchhhhhhhhhh------hhcCCchHHHHHHHHHHHHHHhcCCee---EEEeeCCCCCCchhhHHHHHHHhhhhcc
Q psy12967 82 IAIDLSAWICDSSTIA------EHSSQKNMYLRNLFFRTSYLLLLGVKP---IFVLEGKAPVLKHDTIEKRQQAQGRSAG 152 (222)
Q Consensus 82 iAID~s~wl~~~~~~~------~~~~~~~~~l~~~f~R~~~Ll~~gI~P---IfVFDG~~p~~K~~t~~~Rr~~r~~~~~ 152 (222)
+.||++.++||+.+.. ++.|.+|.++.+|+.++.++++. .+| ++|||+..+.++.+....-+..|...-
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~-~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~P- 79 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKE-EKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTP- 79 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHh-cCCCEEEEEEcCCCCcchHHHHHHHHhCCCCCh-
Confidence 5799999999975432 45788999999999999999853 245 999999988887766666655544321
Q ss_pred CccccccchhhhhhHH-HHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCcceeeccc
Q psy12967 153 RNVQAGSRARNLFFRT-SYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRARLKGL 220 (222)
Q Consensus 153 ~~~e~gs~ar~lf~R~-~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~lFG~ 220 (222)
+.....+..+ .+|.++|| |++..|| ||+.+.+ ..+.+....|. ++|.|.|++-+..
T Consensus 80 ------e~l~~Q~~~i~~~l~~~gi-~~i~~~g~EADDiIa-----tla~~~~~~g~~v~IvS~DkDllQLv~ 140 (887)
T TIGR00593 80 ------EELIEQIPLIKELLDALGI-PILEVEGYEADDVIA-----TLAKQAEKEGYEVRIISGDKDLLQLVS 140 (887)
T ss_pred ------HHHHHHHHHHHHHHHHCCC-cEEeeCCccHHHHHH-----HHHHHHHhCCCcEEEEECCCChhhcCC
Confidence 1122222222 37899999 8888887 8876522 11222233443 6899999987654
No 25
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=98.39 E-value=5.2e-08 Score=88.59 Aligned_cols=39 Identities=28% Similarity=0.333 Sum_probs=36.8
Q ss_pred CcccchhhhhhccccccCcccccCceEEEecceeeeeccccc
Q psy12967 1 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA 42 (222)
Q Consensus 1 mgv~~lw~~l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~ 42 (222)
||| |||++|. .+++++++++||+||||+|+||+|+.++.
T Consensus 1 MGi-~l~~~~~--~~~~~l~~~~gk~vaIDas~~L~r~~~a~ 39 (338)
T TIGR03674 1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQFLSSI 39 (338)
T ss_pred CCC-ChHHHhc--cCccCHHHhCCCEEEEeHHHHHHHHHHHH
Confidence 999 9999999 79999999999999999999999987765
No 26
>KOG2518|consensus
Probab=97.99 E-value=1.7e-06 Score=81.56 Aligned_cols=54 Identities=24% Similarity=0.446 Sum_probs=47.8
Q ss_pred CcccchhhhhhccccccCcccccCceEEEecceeeeeccccccc----cccchhhHHh
Q psy12967 1 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEH----SSQKNMYLRA 54 (222)
Q Consensus 1 mgv~~lw~~l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~~----~~~~~~~~r~ 54 (222)
||++||-.+|.|+.+++++.+++|++||||.++|||+....|+. ..-+..|+.+
T Consensus 1 MGI~GLlp~~k~~~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y 58 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPIHISEYKGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQF 58 (556)
T ss_pred CCcchhHHHHHHHhhhhhHHHhcCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHH
Confidence 99999999999999999999999999999999999999999853 4444566665
No 27
>PRK09482 flap endonuclease-like protein; Provisional
Probab=97.44 E-value=0.0019 Score=56.80 Aligned_cols=124 Identities=13% Similarity=0.041 Sum_probs=72.5
Q ss_pred cEEEeecchhhhhhhhhhh-hcCCchHHHHHHHHHHHHHH-hcCC-eeEEEeeCCCCC-CchhhHHHHHHHhhhhccCcc
Q psy12967 80 KTIAIDLSAWICDSSTIAE-HSSQKNMYLRNLFFRTSYLL-LLGV-KPIFVLEGKAPV-LKHDTIEKRQQAQGRSAGRNV 155 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~~~-~~~~~~~~l~~~f~R~~~Ll-~~gI-~PIfVFDG~~p~-~K~~t~~~Rr~~r~~~~~~~~ 155 (222)
+-+-||++..+||+-+... ..|. +..+.+|+.-+.+++ +++- .-+++||+..+. .-+.+ .-...+..-.
T Consensus 4 ~llLiDg~~l~~R~~~a~~~~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~------l~p~YKa~R~ 76 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQPSPNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQ------LLPDYKAGRK 76 (256)
T ss_pred eEEEEeCcHHHHHHHhCCCCCCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHH------HhHHHhcCCC
Confidence 3588999999999754332 3455 677888888888887 5554 457799997543 11222 1112111111
Q ss_pred ccccchhhhhhHH-HHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCccee
Q psy12967 156 QAGSRARNLFFRT-SYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRAR 216 (222)
Q Consensus 156 e~gs~ar~lf~R~-~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~ 216 (222)
+.-+.....+..+ ..|..+|| |++..|| ||+.+-+.. |. +....|. ++|.|.|.+
T Consensus 77 ~~Pe~l~~Q~~~i~~~l~~~gi-~~~~~~g~EADDvIatl-a~----~~~~~~~~v~I~S~DKDl~ 136 (256)
T PRK09482 77 PMPEALQQGLPAIRAAFEELGI-DSWHADGNEADDLIATL-AV----KVAQAGHQATIVSTDKGYC 136 (256)
T ss_pred CCcHHHHHHHHHHHHHHHhCCC-CEeccCCcCHHHHHHHH-HH----HHHHCCCeEEEEECCCCcc
Confidence 1111223333222 47888999 8888888 888763322 22 2223332 579999975
No 28
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=97.37 E-value=0.0042 Score=51.18 Aligned_cols=115 Identities=13% Similarity=0.138 Sum_probs=65.8
Q ss_pred EEEeecchhhhhhhh------hhhhcCCchHHHHHHHHHHHHHH-hcC-CeeEEEeeCCCC--------CCchhhHHHHH
Q psy12967 81 TIAIDLSAWICDSST------IAEHSSQKNMYLRNLFFRTSYLL-LLG-VKPIFVLEGKAP--------VLKHDTIEKRQ 144 (222)
Q Consensus 81 ~iAID~s~wl~~~~~------~~~~~~~~~~~l~~~f~R~~~Ll-~~g-I~PIfVFDG~~p--------~~K~~t~~~Rr 144 (222)
-+-||++.-+||+.+ +.++.|.++..+.+++.-+.+++ .+. =..+++||+..+ ..|+. |.
T Consensus 3 llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKan----R~ 78 (169)
T PF02739_consen 3 LLLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKAN----RK 78 (169)
T ss_dssp EEEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHH----HH
T ss_pred EEEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhC----CC
Confidence 478999999999754 23456888889999888887777 333 367889999854 23322 21
Q ss_pred HHhhhhccCccccccchhhhh-hHHHHHHHhCCceEEEec-CCCCccCcccHHHHHHHhhhhcCC---eeecCccee
Q psy12967 145 QAQGRSAGRNVQAGSRARNLF-FRTSYLLLLGVKPIFVLE-GKAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRAR 216 (222)
Q Consensus 145 ~~r~~~~~~~~e~gs~ar~lf-~R~~lL~~~GI~p~~vap-Geap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~ 216 (222)
...+. ....+ .-...+..+|+ +++..| +||+.+- -..+.+....|. ++|.|.|.+
T Consensus 79 ~~p~~-----------l~~q~~~i~~~l~~~gi-~~~~~~g~EADDvI-----atla~~~~~~~~~v~IvS~DkD~~ 138 (169)
T PF02739_consen 79 PMPEE-----------LIPQLPYIKELLEALGI-PVLEVPGYEADDVI-----ATLAKKASEEGFEVIIVSGDKDLL 138 (169)
T ss_dssp HHHHH-----------HHHHHHHHHHHHHHTTS-EEEEETTB-HHHHH-----HHHHHHHHHTTCEEEEE-SSGGGG
T ss_pred CCCHH-----------HHHHHHHHHHHHHHCCC-CEecCCCCcHHHHH-----HHHHhhhccCCCEEEEEcCCCCHH
Confidence 11111 11111 11246789999 555554 4555432 222233333333 679999975
No 29
>PRK03980 flap endonuclease-1; Provisional
Probab=96.62 E-value=0.0026 Score=56.94 Aligned_cols=47 Identities=38% Similarity=0.721 Sum_probs=41.3
Q ss_pred ccccchhhhhhHHHHHHHhCCceEEEecCCCCccCcccHHHHHHHhh
Q psy12967 156 QAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQG 202 (222)
Q Consensus 156 e~gs~ar~lf~R~~lL~~~GI~p~~vapGeap~l~a~~~ae~~~a~l 202 (222)
+.+++..++|.|+..|...||+|+|||||.+|.+|....++|+..+.
T Consensus 6 ~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~ 52 (292)
T PRK03980 6 RITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVRE 52 (292)
T ss_pred cCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHH
Confidence 35678899999999999999999999999999999998888887553
No 30
>PHA00439 exonuclease
Probab=96.37 E-value=0.054 Score=48.39 Aligned_cols=122 Identities=9% Similarity=-0.023 Sum_probs=67.1
Q ss_pred cEEEeecchhhhhhhhhh-----------hhcCCchHHHHHHHHHHHHHHhc----CCeeE-EEeeCCCCCCchhhHHHH
Q psy12967 80 KTIAIDLSAWICDSSTIA-----------EHSSQKNMYLRNLFFRTSYLLLL----GVKPI-FVLEGKAPVLKHDTIEKR 143 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~~-----------~~~~~~~~~l~~~f~R~~~Ll~~----gI~PI-fVFDG~~p~~K~~t~~~R 143 (222)
+.+-||++..+||+.+.. +..|.+|..+.+|+.-+.++++. .-.+| ++||+. +.. |
T Consensus 7 ~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~~-~tf-------R 78 (286)
T PHA00439 7 GVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTDS-VNW-------R 78 (286)
T ss_pred cEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECCC-CCh-------H
Confidence 458899999999986543 34577888888888778888733 44444 569942 222 2
Q ss_pred HHHhhhhccCccccccchhhhh-hHHHHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcC----CeeecCccee
Q psy12967 144 QQAQGRSAGRNVQAGSRARNLF-FRTSYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAG----RNVQAGSRAR 216 (222)
Q Consensus 144 r~~r~~~~~~~~e~gs~ar~lf-~R~~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g----~~~T~DsD~~ 216 (222)
++.-...+..-....+. ..++ ....++..+|+ |++..|| ||+.+-+ +.|. +....| .++|.|.|.+
T Consensus 79 ~elyp~YKanR~~~p~~-~~~~~~i~el~~~~gi-~~i~~~G~EADDvIg-tla~----~~~~~g~~~vvIvS~DKDl~ 150 (286)
T PHA00439 79 KEVVPTYKANRKAKRKP-VGYRKFLEELMAREEW-KSILEPGLEGDDVMG-IIGT----NPSLFGFKKAVLVSCDKDFK 150 (286)
T ss_pred hhhhhHhcCCCCCCCCc-hhhHHHHHHHHHhCCC-CEEeeCCccHHHHHH-HHHH----HHHHCCCCeEEEEeCCCCHh
Confidence 22222111111000001 1122 12246777999 7676666 8876532 1111 122233 2679999864
No 31
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=95.87 E-value=0.0077 Score=52.38 Aligned_cols=93 Identities=16% Similarity=0.188 Sum_probs=47.1
Q ss_pred hccccccccccc-cc---eeeccccc--cCcEEEeecchhhhhhhhhhhh-cCCch-HHHHHHHHHHHHHHh--cCCee-
Q psy12967 56 MGVKDLWGILTP-IC---ERKPIWEL--QDKTIAIDLSAWICDSSTIAEH-SSQKN-MYLRNLFFRTSYLLL--LGVKP- 124 (222)
Q Consensus 56 MGI~gL~~~l~~-~~---~~~~i~~l--~Gk~iAID~s~wl~~~~~~~~~-~~~~~-~~l~~~f~R~~~Ll~--~gI~P- 124 (222)
|||+||+.+|.. +. +.+.-... .=--+-||...-||.+.+.... ..... .-+..+|..+..|+. ..-+.
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~~i~~~id~l~~~v~P~k~l 80 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQRIFNYIDRLVRIVRPRKLL 80 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS----SHHHHHHHHHHHHHHHHHHH-ESSEE
T ss_pred CCHHHHHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCcccCCCccHHHHHHHHHHHHHHhheeecCceEE
Confidence 999999999974 22 22111110 1123889999999998543211 11111 234445555555542 22233
Q ss_pred EEEeeCCCCCCchhhHHHHHHHhh
Q psy12967 125 IFVLEGKAPVLKHDTIEKRQQAQG 148 (222)
Q Consensus 125 IfVFDG~~p~~K~~t~~~Rr~~r~ 148 (222)
++-+||.+|.+|..++.+||-+..
T Consensus 81 ~iavDGvaP~AKm~qQR~RRf~~~ 104 (237)
T PF03159_consen 81 YIAVDGVAPRAKMNQQRSRRFKSA 104 (237)
T ss_dssp EEE---S--HHHHHHHHHHHHHHH
T ss_pred EEEcCCCCCchHHHHHHHHHHHHh
Confidence 579999999999998877765443
No 32
>PHA02567 rnh RnaseH; Provisional
Probab=95.56 E-value=0.088 Score=47.41 Aligned_cols=128 Identities=11% Similarity=0.067 Sum_probs=64.1
Q ss_pred cEEEeecchhhhhhhhh--hhhcCCchHHHHHHHHHHH-HHH-h---cCCeeEEEeeCCCCCCchhh-HHHHHHHhhhhc
Q psy12967 80 KTIAIDLSAWICDSSTI--AEHSSQKNMYLRNLFFRTS-YLL-L---LGVKPIFVLEGKAPVLKHDT-IEKRQQAQGRSA 151 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~--~~~~~~~~~~l~~~f~R~~-~Ll-~---~gI~PIfVFDG~~p~~K~~t-~~~Rr~~r~~~~ 151 (222)
.-+-||+|.-++++.+. .++.+.++..++.++.+.. .+. . ..-..+++||+.....-+.+ ...=+..|....
T Consensus 15 ~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~~P 94 (304)
T PHA02567 15 GVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKDR 94 (304)
T ss_pred CEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCCCCC
Confidence 45889999999998543 3445666777766444433 333 2 22235889998742222222 111111111100
Q ss_pred cCccccccchhhhhh-----HHHHHHHhCCceEEEecC-CCCccCcccHHHHHHHhhhhcCC---eeecCccee
Q psy12967 152 GRNVQAGSRARNLFF-----RTSYLLLLGVKPIFVLEG-KAPVLKHDTIEKRQQAQGRSAGR---NVQAGSRAR 216 (222)
Q Consensus 152 ~~~~e~gs~ar~lf~-----R~~lL~~~GI~p~~vapG-eap~l~a~~~ae~~~a~l~~~g~---~~T~DsD~~ 216 (222)
+. ..-+.-.++. ...++..+|+ +++..|| ||+.+-+ +.|. +....|. ++|.|.|.+
T Consensus 95 ee---l~~q~~~l~~~l~~ii~el~~~~gi-~~l~~~g~EADDvIg-TLA~----k~~~~g~~VvIvS~DKDl~ 159 (304)
T PHA02567 95 EE---SPWDWEGLFEAINKIVDEIKENMPY-KVMKIDKAEADDIIA-VLTK----KFSAEGRPVLIVSSDGDFT 159 (304)
T ss_pred hH---HHHHHHHhhhhHHHHHHHHHHHCCC-CEEEeCCccHHHHHH-HHHH----HHHhCCCcEEEEeCCCChh
Confidence 00 0000001111 1136778899 7777666 8887533 1222 2233342 679999974
No 33
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=92.22 E-value=0.71 Score=37.82 Aligned_cols=52 Identities=17% Similarity=0.082 Sum_probs=30.4
Q ss_pred EEeecchhhhhhhhhhhhcCC-chHHHH-HHHHHHHHHH-hcCCeeEEEeeCCCC
Q psy12967 82 IAIDLSAWICDSSTIAEHSSQ-KNMYLR-NLFFRTSYLL-LLGVKPIFVLEGKAP 133 (222)
Q Consensus 82 iAID~s~wl~~~~~~~~~~~~-~~~~l~-~~f~R~~~Ll-~~gI~PIfVFDG~~p 133 (222)
|-||+|.-||....+...... .-.+-+ .+...+..+. ..|.+-++||||...
T Consensus 1 LlIDGYNli~~~~~l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~~~ 55 (166)
T PF05991_consen 1 LLIDGYNLIHAWPELRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAYKV 55 (166)
T ss_pred CeEcchhhhCCCHHHHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCCcC
Confidence 469999999986443322211 111222 2333444443 677999999999743
No 34
>PHA03065 Hypothetical protein; Provisional
Probab=91.52 E-value=1.1 Score=41.92 Aligned_cols=89 Identities=17% Similarity=0.084 Sum_probs=56.7
Q ss_pred hccccccccccccceeeccc---cccCcEEEeecchhhhhhhhhhhhcCCchHHHHH-HHHHHHHHHhcCCeeEEEeeCC
Q psy12967 56 MGVKDLWGILTPICERKPIW---ELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRN-LFFRTSYLLLLGVKPIFVLEGK 131 (222)
Q Consensus 56 MGI~gL~~~l~~~~~~~~i~---~l~Gk~iAID~s~wl~~~~~~~~~~~~~~~~l~~-~f~R~~~Ll~~gI~PIfVFDG~ 131 (222)
|||+.|-.+|-..+.-..++ .=.++-|-||........++-+.+ ...|+. +..|+..+....=+.++..|-+
T Consensus 1 MGIKNLKtLLL~~gsL~~~~~~~~~~~~~iFVD~ms~fmsiAysv~~----~~eL~~~~~~~iq~w~~~~gkVtlFvDRG 76 (438)
T PHA03065 1 MGIKNLKTLLLETGSLTKLDNNLKDRFNGIFVDTMSVFMSIAYSVNN----LDELRSTFEEYVQQWVKKAGKVTLFVDRG 76 (438)
T ss_pred CchhhHHHHHHhcCCcccccccccccCceEEEechhhhhhhhhhhCC----HHHHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence 99999999997655322221 112356999998876554432221 234443 4567777754444555566888
Q ss_pred CCCCchhhHHHHHHHhh
Q psy12967 132 APVLKHDTIEKRQQAQG 148 (222)
Q Consensus 132 ~p~~K~~t~~~Rr~~r~ 148 (222)
..+.|....++||+...
T Consensus 77 ~I~IK~~lReKRr~a~~ 93 (438)
T PHA03065 77 SIPIKQSLREKRRKASK 93 (438)
T ss_pred ccchhhHHHHHHHHHHH
Confidence 99999999888876544
No 35
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=88.98 E-value=1 Score=42.29 Aligned_cols=89 Identities=19% Similarity=0.101 Sum_probs=60.3
Q ss_pred hccccccccccccce-eeccccccCcEEEeecchhhhhhhhhhhhcCCchHHHHH-HHHHHHHHHhcCCeeEEEeeCCCC
Q psy12967 56 MGVKDLWGILTPICE-RKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRN-LFFRTSYLLLLGVKPIFVLEGKAP 133 (222)
Q Consensus 56 MGI~gL~~~l~~~~~-~~~i~~l~Gk~iAID~s~wl~~~~~~~~~~~~~~~~l~~-~f~R~~~Ll~~gI~PIfVFDG~~p 133 (222)
|||+.|-.+|-..+. ...-....++-|-||..+..+-.++.+.+ ...|.. +..++..+...+=+..+..|-+..
T Consensus 1 MGIKNLK~lLl~~gsL~~i~~~~~~~~ifVD~msif~tiAysv~s----~~eL~~~~~~~i~~w~~~~~~VtlFvDRG~I 76 (425)
T PF04599_consen 1 MGIKNLKALLLETGSLKKIDNIEKNNEIFVDTMSIFMTIAYSVNS----LDELRNSFEEYIQQWIKNNGKVTLFVDRGSI 76 (425)
T ss_pred CchhHHHHHHHhcCCceeccCCCCCccEEEEcchhhhhhhhhhCC----HHHHHHHHHHHHHHHHhcCCeEEEEEecCcc
Confidence 999999999986553 22222334477999998877665543322 224443 456677776555566777799999
Q ss_pred CCchhhHHHHHHHhh
Q psy12967 134 VLKHDTIEKRQQAQG 148 (222)
Q Consensus 134 ~~K~~t~~~Rr~~r~ 148 (222)
+.|....+|||+.-.
T Consensus 77 ~iK~~lReKRr~a~k 91 (425)
T PF04599_consen 77 NIKEPLREKRRKALK 91 (425)
T ss_pred chhhHHHHHHHHHHH
Confidence 999999888876544
No 36
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=80.63 E-value=22 Score=30.33 Aligned_cols=72 Identities=18% Similarity=0.174 Sum_probs=42.7
Q ss_pred eeeccccccCcEEEeecchhhhhhhhh-------h------hh---cC-----CchHHHHHHHHHHHHHHhcCCeeEEEe
Q psy12967 70 ERKPIWELQDKTIAIDLSAWICDSSTI-------A------EH---SS-----QKNMYLRNLFFRTSYLLLLGVKPIFVL 128 (222)
Q Consensus 70 ~~~~i~~l~Gk~iAID~s~wl~~~~~~-------~------~~---~~-----~~~~~l~~~f~R~~~Ll~~gI~PIfVF 128 (222)
+...++.++|+.+.||++.-|---.++ + +- +| +.+.. .+---+..+-+.+++-+..+
T Consensus 57 k~~~~~~~rg~~l~iDGyNvLItleSl~~g~~vlcdDg~iRDl~~~~gkyk~~E~t~~--Al~lil~~lk~~~~k~vi~L 134 (211)
T COG2454 57 KRMKINSLRGQDLVIDGYNVLITLESLLKGEAVLCDDGVIRDLRGVQGKYKINEKTDK--ALDLLLEFLKDVEPKSVIFL 134 (211)
T ss_pred hhccCCCcccceEEEechhhhhhHHHHhcCcEEEecCchhhhhhhhccchhhhhHHHH--HHHHHHHHHHHcCCceEEEE
Confidence 567888999999999999876533221 1 10 11 11111 11111234458999988888
Q ss_pred eCCCCCCchhhHHHHH
Q psy12967 129 EGKAPVLKHDTIEKRQ 144 (222)
Q Consensus 129 DG~~p~~K~~t~~~Rr 144 (222)
++.+ ..|+++...|-
T Consensus 135 ~d~~-vs~SGel~~~i 149 (211)
T COG2454 135 FDAP-VSKSGELAGRI 149 (211)
T ss_pred eCCC-CCccHHHHHHH
Confidence 8764 44677766553
No 37
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=76.99 E-value=8.6 Score=31.08 Aligned_cols=71 Identities=27% Similarity=0.339 Sum_probs=44.9
Q ss_pred CCCCCCchhhHHHHHHHhhhhccCccccccchhhhhhHHHHHHHhCCceEEEecCCCCccCcccHHHHHHHhhhhcCCee
Q psy12967 130 GKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNV 209 (222)
Q Consensus 130 G~~p~~K~~t~~~Rr~~r~~~~~~~~e~gs~ar~lf~R~~lL~~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~~~ 209 (222)
|..|..|..+..|||++|..+. +.++|. -|+..|- |-.|.-| ...|=.-|.+..+|-+|
T Consensus 4 ~r~pt~kErEnnk~RERrRRAI---------aakIfa---GLR~~Gn---y~Lp~~a------D~NeVLkALc~eAGw~V 62 (150)
T PF05687_consen 4 GRRPTWKERENNKRRERRRRAI---------AAKIFA---GLRAHGN---YKLPKHA------DNNEVLKALCREAGWTV 62 (150)
T ss_pred cccccHhhhHHHHHHHHHHHHH---------HHHHHH---HHHHhcC---CCCCCcC------CHHHHHHHHHHhCCEEE
Confidence 3478899999999998888764 234443 5788886 1222222 23333335555667788
Q ss_pred ecCcceeecccc
Q psy12967 210 QAGSRARLKGLQ 221 (222)
Q Consensus 210 T~DsD~~lFG~~ 221 (222)
.+|...+--|++
T Consensus 63 e~DGTtyr~~~~ 74 (150)
T PF05687_consen 63 EPDGTTYRKGCK 74 (150)
T ss_pred ccCCCeeccCCC
Confidence 888887766654
No 38
>KOG2520|consensus
Probab=51.89 E-value=12 Score=38.24 Aligned_cols=128 Identities=17% Similarity=0.130 Sum_probs=85.7
Q ss_pred hhccccccCcccccCceEEEecceeeeeccccccccccchhhHH----hhhccccccccccccceeeccccccCcEEEee
Q psy12967 10 LTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLR----AIMGVKDLWGILTPICERKPIWELQDKTIAID 85 (222)
Q Consensus 10 l~~~~~~~~~~~~~~~~~~~d~s~w~~~~~~~~~~~~~~~~~~r----~~MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID 85 (222)
++|++...+.++.+++-.+|| |..+..-+. -.++..-.++ -.||+.-+|++|++....++. .+.+.|++
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~~~~~~~~s~~~~~l~~~~~~~~p---~~~~~a~~ 77 (815)
T KOG2520|consen 5 LEPTATEQPLAEGGSKLGLID---GSYAKKAAE-IDDQPAPLLSKLEGEKMGVSTIWEFLKPSSPDVTP---LELRAAVI 77 (815)
T ss_pred ccchheeeccccCccceeeee---hhhccceee-eccccchhhhhhhccccccceeccccCccccCCCC---chhhHHHH
Confidence 899999999999999999999 776544333 1112222223 389999999999987765543 23456777
Q ss_pred cchhhhhhhhhhhhcCCchHHHHHHHHHHHHHHhcCCeeEEEeeCCCCCCchhhHHHHHHHh
Q psy12967 86 LSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQ 147 (222)
Q Consensus 86 ~s~wl~~~~~~~~~~~~~~~~l~~~f~R~~~Ll~~gI~PIfVFDG~~p~~K~~t~~~Rr~~r 147 (222)
...|.....+... ......+.+-.|...++.+-+.+..++|+....+|......+....
T Consensus 78 ~~~k~~~~~~~e~---~d~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~s~~d~~~d~~~~~~ 136 (815)
T KOG2520|consen 78 DFQKRQNRSPDEK---IDKANGKLFEDRKLQAIRISISSGSRNDSEAKSIKDSDIDSKQESK 136 (815)
T ss_pred HHHHhcCCChhhh---ccHHHHHHHHhhhhhhhhhhccccccchhhhcchhhccchhhhhcc
Confidence 7777755432111 1112333333466778888889999999998888887766655443
No 39
>KOG1431|consensus
Probab=41.18 E-value=1.6e+02 Score=26.08 Aligned_cols=92 Identities=18% Similarity=0.133 Sum_probs=62.7
Q ss_pred hHH-HHHHHHHHHHHHhcCCeeEEEeeCCCCCCchhhHHHHHHHhhhhccCccccccchhhhhhHHHHHHHhCCceEEEe
Q psy12967 104 NMY-LRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVL 182 (222)
Q Consensus 104 ~~~-l~~~f~R~~~Ll~~gI~PIfVFDG~~p~~K~~t~~~Rr~~r~~~~~~~~e~gs~ar~lf~R~~lL~~~GI~p~~va 182 (222)
++| |-++++|.......|-.++.||-...| .| +--- . .....+|-. .+=...|+-|+++.
T Consensus 177 ~sHVlPali~r~h~ak~~gtd~~~VwGsG~P--------lR----qFiy-----s-~DLA~l~i~-vlr~Y~~vEpiils 237 (315)
T KOG1431|consen 177 NSHVLPALIHRFHEAKRNGTDELTVWGSGSP--------LR----QFIY-----S-DDLADLFIW-VLREYEGVEPIILS 237 (315)
T ss_pred cccchHHHHHHHHHHHhcCCceEEEecCCCh--------HH----HHhh-----H-hHHHHHHHH-HHHhhcCccceEec
Confidence 445 557899999999999999999977754 11 1000 0 000111110 12355699999999
Q ss_pred cCCCCccCcccHHHHHHHhhhhcCC--eeecCcc
Q psy12967 183 EGKAPVLKHDTIEKRQQAQGRSAGR--NVQAGSR 214 (222)
Q Consensus 183 pGeap~l~a~~~ae~~~a~l~~~g~--~~T~DsD 214 (222)
-||.+++..+..||+........|. +.|.-||
T Consensus 238 ~ge~~EVtI~e~aeaV~ea~~F~G~l~~DttK~D 271 (315)
T KOG1431|consen 238 VGESDEVTIREAAEAVVEAVDFTGKLVWDTTKSD 271 (315)
T ss_pred cCccceeEHHHHHHHHHHHhCCCceEEeeccCCC
Confidence 9999999999999999988888887 3466665
No 40
>PHA02994 hypothetical protein; Provisional
Probab=33.49 E-value=26 Score=30.10 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=16.0
Q ss_pred EEeeCCCCCCchhhH----HHHHHHhh
Q psy12967 126 FVLEGKAPVLKHDTI----EKRQQAQG 148 (222)
Q Consensus 126 fVFDG~~p~~K~~t~----~~Rr~~r~ 148 (222)
++|||.||++|.-+. .-|..-|+
T Consensus 102 l~fDG~PPsFr~v~~dv~~~~RkkirD 128 (218)
T PHA02994 102 LAFDGIPPSFRMVNIDVKIYNRKKIKD 128 (218)
T ss_pred eeeccCCCcceeecchHHHHHHHHHHH
Confidence 579999999998554 34444444
No 41
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=32.58 E-value=33 Score=29.59 Aligned_cols=112 Identities=17% Similarity=0.163 Sum_probs=56.6
Q ss_pred ceEEEecceeeeecccccccccc--chhhHHhhhccc-cccccccccceeeccccccCcEEEeecc--hhhhhhhh-hhh
Q psy12967 25 KTIAIDLSAWICDSSTIAEHSSQ--KNMYLRAIMGVK-DLWGILTPICERKPIWELQDKTIAIDLS--AWICDSST-IAE 98 (222)
Q Consensus 25 ~~~~~d~s~w~~~~~~~~~~~~~--~~~~~r~~MGI~-gL~~~l~~~~~~~~i~~l~Gk~iAID~s--~wl~~~~~-~~~ 98 (222)
+.+.||.|..++++-++...... .+..-..+.|+- -|+.+++.. . -..-.++.|.. .|-++... ...
T Consensus 2 ~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~----~---p~~~~~~fD~~~~~~R~~l~p~YK~ 74 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEY----K---PTYVAVVFDAGGKTFRHELYPEYKA 74 (240)
T ss_pred cEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhc----C---CCeEEEEEeCCCCcccccccHHHHc
Confidence 46899999999987776532111 111111122211 233333211 1 12235788875 67666432 111
Q ss_pred hcCCchHHHHHHHHHHHHHH-hcCCeeEEEeeCCCCCCchhhHHHHH
Q psy12967 99 HSSQKNMYLRNLFFRTSYLL-LLGVKPIFVLEGKAPVLKHDTIEKRQ 144 (222)
Q Consensus 99 ~~~~~~~~l~~~f~R~~~Ll-~~gI~PIfVFDG~~p~~K~~t~~~Rr 144 (222)
...+....+...+..+..++ ..|| |++..+|-.-.-=.++.+++.
T Consensus 75 ~R~~~p~~l~~q~~~~~~~l~~~gi-~~i~~~~~EADD~ia~la~~~ 120 (240)
T cd00008 75 NRKKMPEELREQIPLIKELLEALGI-PVLEIEGYEADDVIGTLAKKA 120 (240)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCC-CEEecCCcCHHHHHHHHHHHH
Confidence 12222346666677777665 7898 777777642221234555543
No 42
>PF04708 Pox_F16: Poxvirus F16 protein; InterPro: IPR006798 This entry represents the Poxvirus F16 proteins.
Probab=30.97 E-value=29 Score=29.85 Aligned_cols=15 Identities=13% Similarity=0.536 Sum_probs=12.3
Q ss_pred EEeeCCCCCCchhhH
Q psy12967 126 FVLEGKAPVLKHDTI 140 (222)
Q Consensus 126 fVFDG~~p~~K~~t~ 140 (222)
++|||.||++|.-..
T Consensus 102 L~fDG~pP~Fr~v~~ 116 (218)
T PF04708_consen 102 LAFDGSPPSFRPVNM 116 (218)
T ss_pred eEecccCCcceEecc
Confidence 569999999998554
No 43
>KOG1541|consensus
Probab=30.36 E-value=43 Score=29.44 Aligned_cols=89 Identities=17% Similarity=0.231 Sum_probs=57.1
Q ss_pred CceEEEecceeeeeccccccccccchhhHHhhhccccccccccccceeeccccccCcEEEeecchhhhhhhhhhhhcCCc
Q psy12967 24 DKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQK 103 (222)
Q Consensus 24 ~~~~~~d~s~w~~~~~~~~~~~~~~~~~~r~~MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~~~~~~ 103 (222)
-.-|+||+|-=|.+. +.+ ...++.++.+-|| .||- ...-.|.| .|.|-|-.||+.+.. +...|
T Consensus 73 h~wiGvDiSpsML~~--a~~-~e~egdlil~DMG-~Glp---------frpGtFDg-~ISISAvQWLcnA~~---s~~~P 135 (270)
T KOG1541|consen 73 HQWIGVDISPSMLEQ--AVE-RELEGDLILCDMG-EGLP---------FRPGTFDG-VISISAVQWLCNADK---SLHVP 135 (270)
T ss_pred ceEEeecCCHHHHHH--HHH-hhhhcCeeeeecC-CCCC---------CCCCccce-EEEeeeeeeecccCc---cccCh
Confidence 345778887655432 222 5566788888888 5542 12233444 488888899988742 22335
Q ss_pred hHHHHHHHHHHHHHHhcCCeeEEEee
Q psy12967 104 NMYLRNLFFRTSYLLLLGVKPIFVLE 129 (222)
Q Consensus 104 ~~~l~~~f~R~~~Ll~~gI~PIfVFD 129 (222)
...|+.||--+-.++..|-+.||=|=
T Consensus 136 ~~Rl~~FF~tLy~~l~rg~raV~QfY 161 (270)
T KOG1541|consen 136 KKRLLRFFGTLYSCLKRGARAVLQFY 161 (270)
T ss_pred HHHHHHHhhhhhhhhccCceeEEEec
Confidence 55677777767778888888888663
No 44
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=28.89 E-value=35 Score=30.42 Aligned_cols=126 Identities=13% Similarity=0.042 Sum_probs=67.2
Q ss_pred ccCcccccCceEEEecceeeeeccccccccccchhhHHhhhccccccccccccceeeccccccCcEEEeecchhhhhhhh
Q psy12967 16 RKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSST 95 (222)
Q Consensus 16 ~~~~~~~~~~~~~~d~s~w~~~~~~~~~~~~~~~~~~r~~MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~ 95 (222)
..++....|+.++||.|.|++++-++............+- .+.|+...|....+.. +.....++.|+.-=.+|.+.
T Consensus 3 ~~~~~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~-~~~~~~~~l~~~~~~~---~~~~~~~vFD~~~~tfR~~~ 78 (310)
T COG0258 3 EIQLMNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTG-AVSGFLGMLYRLIRLL---EPTHPVVVFDGKPPTFRHEL 78 (310)
T ss_pred cccchhccCcEEEEechHHHHHHHHhcchhcCCCCCCCcc-HHHHHHHHHHHHHHhc---CCCcEEEEEcCCCCcchHHH
Confidence 4567788999999999999998877663321111111100 2223333332211111 11445688888554555432
Q ss_pred hh---hhcCC-chHHHHHHHHHHHHHHhcCCeeEEEeeCCCCCCchhhHHHHHH
Q psy12967 96 IA---EHSSQ-KNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145 (222)
Q Consensus 96 ~~---~~~~~-~~~~l~~~f~R~~~Ll~~gI~PIfVFDG~~p~~K~~t~~~Rr~ 145 (222)
.. ....+ +...+..-+-++..++..-..+.+-..|-+-..=.+|.++...
T Consensus 79 ~~~yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~ 132 (310)
T COG0258 79 LEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY 132 (310)
T ss_pred HHHHHhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH
Confidence 21 12233 3345555555666665444447777788775555677766554
No 45
>COG1578 Uncharacterized conserved protein [Function unknown]
Probab=28.70 E-value=61 Score=28.98 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=40.0
Q ss_pred HHHHhCCceEEEecCCCCccCcccHHHHHHHhhhhcCCeeecCccee
Q psy12967 170 YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRAR 216 (222)
Q Consensus 170 lL~~~GI~p~~vapGeap~l~a~~~ae~~~a~l~~~g~~~T~DsD~~ 216 (222)
.++.+|.+++++.-|. |.+-..++..+..+.+.....++|++||..
T Consensus 173 ~ik~~~~~vv~vVrg~-PIlnDaT~EDak~~~i~~i~~vittG~~~v 218 (285)
T COG1578 173 VIKELGKKVVVVVRGG-PILNDATMEDAKEAGIDEIAKVITTGSDIV 218 (285)
T ss_pred HHHhcCCceEEEEcCC-ceechhhHHHHHHcCcchhheeecCCCCcc
Confidence 6899999999999996 888889999999999888888999888863
No 46
>PF10652 DUF2480: Protein of unknown function (DUF2480); InterPro: IPR018914 All the members of this family are uncharacterised proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (5.3.1.9 from EC). This could not, however, be confirmed.
Probab=27.71 E-value=36 Score=28.09 Aligned_cols=52 Identities=19% Similarity=0.328 Sum_probs=35.2
Q ss_pred cCcccc--cCceEEEecceeeeeccccccccccchhhHHhhhccccccccccccceeeccccccCcEEEeecc
Q psy12967 17 KPIWEL--QDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLS 87 (222)
Q Consensus 17 ~~~~~~--~~~~~~~d~s~w~~~~~~~~~~~~~~~~~~r~~MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s 87 (222)
..||++ .|.|+.+|+|=||+|..-. +..=||. ..+..+++.|.|+-|||-.|
T Consensus 17 fDLedyyp~g~r~~~Dik~~L~~GliL------kEKdFR~-------------~lk~~DWsqY~~~~Vai~CS 70 (167)
T PF10652_consen 17 FDLEDYYPKGERVVFDIKDWLFEGLIL------KEKDFRE-------------FLKEHDWSQYQDKYVAIYCS 70 (167)
T ss_pred eeHHHhCCCCcEEEEecHHHHhhhhhh------hhHHHHH-------------HHHhcCHHHhCCcEEEEEcc
Confidence 345554 8999999999999973322 2222332 12456788999999998654
No 47
>PF10652 DUF2480: Protein of unknown function (DUF2480); InterPro: IPR018914 All the members of this family are uncharacterised proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (5.3.1.9 from EC). This could not, however, be confirmed.
Probab=26.32 E-value=38 Score=27.97 Aligned_cols=25 Identities=8% Similarity=0.343 Sum_probs=20.5
Q ss_pred eeeccccc--cCcEEEeecchhhhhhh
Q psy12967 70 ERKPIWEL--QDKTIAIDLSAWICDSS 94 (222)
Q Consensus 70 ~~~~i~~l--~Gk~iAID~s~wl~~~~ 94 (222)
...++++| .|.|+.+|.+.|||+|.
T Consensus 15 itfDLedyyp~g~r~~~Dik~~L~~Gl 41 (167)
T PF10652_consen 15 ITFDLEDYYPKGERVVFDIKDWLFEGL 41 (167)
T ss_pred eEeeHHHhCCCCcEEEEecHHHHhhhh
Confidence 35567776 58999999999999984
No 48
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=26.11 E-value=47 Score=26.76 Aligned_cols=86 Identities=12% Similarity=0.066 Sum_probs=45.7
Q ss_pred HHHHHHHHHH-hcCCeeE-EEeeCCCCCCchhhHHHHHHHhhhhccCccccccchhhhhhHHHHHHHhCCceEEEecCCC
Q psy12967 109 NLFFRTSYLL-LLGVKPI-FVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKA 186 (222)
Q Consensus 109 ~~f~R~~~Ll-~~gI~PI-fVFDG~~p~~K~~t~~~Rr~~r~~~~~~~~e~gs~ar~lf~R~~lL~~~GI~p~~vapGea 186 (222)
.++.+++..- +++..++ +.||..|...... . .........-.|...|..+||..+++.|-+.
T Consensus 23 ~Li~~~~~~a~~~~~~~~v~tF~~~P~~~~~~---------~-------~~~~~l~s~~ek~~~l~~~Gvd~~~~~~F~~ 86 (157)
T PF06574_consen 23 KLIKKAVEIAKEKGLKSVVLTFDPHPKEVLNP---------D-------KPPKLLTSLEEKLELLESLGVDYVIVIPFTE 86 (157)
T ss_dssp HHHHHHHHHHHHCT-EEEEEEESS-CHHHHSC---------T-------CCGGBSS-HHHHHHHHHHTTESEEEEE-CCC
T ss_pred HHHHHHhhhhhhcccceEEEEcccCHHHHhcC---------C-------CcccCCCCHHHHHHHHHHcCCCEEEEecchH
Confidence 4567777664 7888884 6899876322110 0 0001134455677899999998888988863
Q ss_pred CccCcccHHHHHHHh-----hhhcCCeeecC
Q psy12967 187 PVLKHDTIEKRQQAQ-----GRSAGRNVQAG 212 (222)
Q Consensus 187 p~l~a~~~ae~~~a~-----l~~~g~~~T~D 212 (222)
. + +...++.-... ++....|+.+|
T Consensus 87 ~-~-~~ls~~~Fi~~iL~~~l~~~~ivvG~D 115 (157)
T PF06574_consen 87 E-F-ANLSPEDFIEKILKEKLNVKHIVVGED 115 (157)
T ss_dssp H-H-CCS-HHHHHHHHCCCHCTEEEEEEETT
T ss_pred H-H-HcCCHHHHHHHHHHhcCCccEEEEccC
Confidence 2 2 22344444443 33333356666
No 49
>PHA02697 hypothetical protein; Provisional
Probab=25.55 E-value=38 Score=29.29 Aligned_cols=12 Identities=17% Similarity=0.385 Sum_probs=11.0
Q ss_pred EEeeCCCCCCch
Q psy12967 126 FVLEGKAPVLKH 137 (222)
Q Consensus 126 fVFDG~~p~~K~ 137 (222)
|+|||.||.+|.
T Consensus 115 L~fDGsPPsFK~ 126 (255)
T PHA02697 115 FYVDASPSRFKP 126 (255)
T ss_pred eEeccCCCcccc
Confidence 679999999998
No 50
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=20.59 E-value=1.4e+02 Score=23.73 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=25.8
Q ss_pred cEEEeecchhhhhhhhhhhhcCCchHHHHHHHHHHHHHHhcCCeeEEEeeCCC
Q psy12967 80 KTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKA 132 (222)
Q Consensus 80 k~iAID~s~wl~~~~~~~~~~~~~~~~l~~~f~R~~~Ll~~gI~PIfVFDG~~ 132 (222)
+.|.||++.--+... ..+ +....++..-+..+.+.|.+++.|||-.-
T Consensus 3 r~VVIDG~NVA~~~~-----~~~-~f~~~~i~~~v~~~~~rG~~~v~v~~~~~ 49 (155)
T PF11977_consen 3 RPVVIDGSNVAYSHG-----NQK-FFSVRGIQIAVEYFKSRGHEVVVVFPPNY 49 (155)
T ss_dssp --EEEEHHHHHHHHT-----TTT-SEEHHHHHHHHHHHHHTT---EEEEEEGG
T ss_pred CEEEEeCHHHHhhcC-----CCC-CcCHHHHHHHHHHHHHcCCCeEEEEcchh
Confidence 568999998744211 111 12334444445568899999999999664
Done!