Query psy14294
Match_columns 314
No_of_seqs 187 out of 1134
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 16:08:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14294.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14294hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00128 XPG Xeroderma pigmento 100.0 3.4E-39 7.3E-44 308.2 18.9 188 125-314 1-206 (316)
2 PTZ00217 flap endonuclease-1; 100.0 4.2E-39 9.1E-44 316.3 17.9 187 125-314 1-218 (393)
3 TIGR03674 fen_arch flap struct 100.0 3.6E-38 7.8E-43 304.5 18.7 185 125-313 1-218 (338)
4 KOG2518|consensus 100.0 5.1E-39 1.1E-43 317.6 12.7 185 125-312 1-202 (556)
5 KOG2519|consensus 100.0 7.4E-34 1.6E-38 278.0 10.0 186 125-313 1-211 (449)
6 PRK03980 flap endonuclease-1; 100.0 1.1E-30 2.4E-35 247.9 15.6 145 167-313 3-171 (292)
7 TIGR00600 rad2 DNA excision re 100.0 1E-27 2.2E-32 256.1 19.9 125 2-127 90-226 (1034)
8 smart00485 XPGN Xeroderma pigm 99.9 1.2E-22 2.6E-27 163.3 7.0 94 125-219 1-98 (99)
9 PF00752 XPG_N: XPG N-terminal 99.9 4E-22 8.6E-27 160.5 8.5 95 125-220 1-101 (101)
10 smart00484 XPGI Xeroderma pigm 99.8 4.5E-20 9.8E-25 141.6 7.0 66 248-313 2-70 (73)
11 PF00867 XPG_I: XPG I-region; 99.8 3.9E-20 8.4E-25 148.0 4.9 67 247-313 1-76 (94)
12 TIGR00600 rad2 DNA excision re 99.8 1.6E-19 3.4E-24 193.6 8.5 95 125-220 1-98 (1034)
13 KOG2520|consensus 99.7 1.1E-18 2.4E-23 182.3 6.7 90 225-314 454-543 (815)
14 smart00475 53EXOc 5'-3' exonuc 99.7 9.6E-17 2.1E-21 150.3 14.0 153 148-314 3-167 (259)
15 cd00008 53EXOc 5'-3' exonuclea 99.7 4.4E-16 9.6E-21 144.2 14.0 149 148-313 3-163 (240)
16 COG0258 Exo 5'-3' exonuclease 99.7 1E-16 2.3E-21 153.2 8.7 161 145-313 10-177 (310)
17 PRK14976 5'-3' exonuclease; Pr 99.6 3.3E-15 7.1E-20 141.5 14.4 154 147-314 4-172 (281)
18 TIGR00593 pola DNA polymerase 99.5 9.7E-14 2.1E-18 149.0 13.5 152 149-314 2-166 (887)
19 PRK05755 DNA polymerase I; Pro 99.5 9.2E-14 2E-18 149.5 13.4 151 147-313 3-167 (880)
20 PF02739 5_3_exonuc_N: 5'-3' e 99.3 3.9E-12 8.5E-17 112.2 7.9 152 148-314 3-169 (169)
21 PRK09482 flap endonuclease-lik 99.3 6.3E-11 1.4E-15 111.0 13.3 151 146-314 3-163 (256)
22 PHA00439 exonuclease 98.9 9.3E-09 2E-13 97.7 12.4 128 147-289 7-155 (286)
23 PF12813 XPG_I_2: XPG domain c 98.9 2.5E-09 5.5E-14 99.7 7.1 78 236-314 3-97 (246)
24 PHA02567 rnh RnaseH; Provision 98.6 6E-07 1.3E-11 86.0 13.0 129 146-287 14-162 (304)
25 PF03159 XRN_N: XRN 5'-3' exon 98.1 1.9E-05 4.1E-10 73.5 8.9 160 125-288 1-223 (237)
26 PHA03065 Hypothetical protein; 95.8 0.17 3.6E-06 50.7 12.7 158 125-288 1-204 (438)
27 PF04599 Pox_G5: Poxvirus G5 p 95.7 0.17 3.8E-06 50.8 12.5 158 125-288 1-202 (425)
28 PF05991 NYN_YacP: YacP-like N 95.0 0.094 2E-06 46.1 7.4 53 149-203 1-55 (166)
29 COG5366 Protein involved in pr 91.5 0.048 1E-06 55.1 -0.5 67 242-309 134-203 (531)
30 PF11977 RNase_Zc3h12a: Zc3h12 80.3 8.2 0.00018 33.3 7.4 46 147-201 3-48 (155)
31 COG2454 Uncharacterized conser 79.7 12 0.00025 34.5 8.3 117 139-292 60-193 (211)
32 PF05411 Peptidase_C32: Equine 58.7 4.1 8.8E-05 34.5 0.6 52 93-144 18-74 (127)
33 KOG2044|consensus 50.7 1.4E+02 0.003 33.0 10.4 145 149-297 51-256 (931)
34 TIGR02765 crypto_DASH cryptoch 50.4 33 0.00071 34.3 5.6 18 240-257 86-103 (429)
35 COG5049 XRN1 5'-3' exonuclease 49.3 1.4E+02 0.0029 32.7 10.0 140 146-288 29-227 (953)
36 PF04019 DUF359: Protein of un 45.1 56 0.0012 27.5 5.4 91 185-290 3-95 (121)
37 cd08556 GDPD Glycerophosphodie 43.3 43 0.00093 28.5 4.6 39 240-279 150-188 (189)
38 PF01927 Mut7-C: Mut7-C RNAse 43.2 28 0.00062 29.7 3.5 46 238-285 8-54 (147)
39 KOG2045|consensus 39.0 2.3E+02 0.0049 32.2 9.9 139 149-288 32-213 (1493)
40 TIGR00114 lumazine-synth 6,7-d 37.9 73 0.0016 27.4 5.1 46 233-278 13-65 (138)
41 TIGR00028 Mtu_PIN_fam Mycobact 37.8 33 0.00072 27.8 3.0 36 259-295 105-140 (142)
42 PRK01160 hypothetical protein; 37.6 1.2E+02 0.0026 27.3 6.6 92 185-290 52-148 (178)
43 PRK10674 deoxyribodipyrimidine 35.7 1.3E+02 0.0028 30.7 7.4 19 239-257 85-103 (472)
44 PF00885 DMRL_synthase: 6,7-di 35.6 1E+02 0.0022 26.6 5.7 46 233-278 16-68 (144)
45 PF05687 DUF822: Plant protein 34.4 1.6E+02 0.0034 25.8 6.5 71 202-291 6-76 (150)
46 cd04236 AAK_NAGS-Urea AAK_NAGS 34.0 56 0.0012 31.1 4.2 53 152-204 18-80 (271)
47 COG0258 Exo 5'-3' exonuclease 32.9 45 0.00097 32.0 3.4 38 233-270 92-130 (310)
48 cd01971 Nitrogenase_VnfN_like 32.3 1.7E+02 0.0037 29.3 7.6 18 184-201 178-196 (427)
49 cd01422 MGS Methylglyoxal synt 31.3 85 0.0018 25.7 4.3 37 243-279 37-77 (115)
50 cd00532 MGS-like MGS-like doma 30.8 61 0.0013 26.2 3.4 36 243-278 35-74 (112)
51 PRK12419 riboflavin synthase s 30.4 94 0.002 27.4 4.7 48 231-278 21-75 (158)
52 TIGR02766 crypt_chrom_pln cryp 30.1 1.5E+02 0.0033 30.1 6.8 35 238-272 75-117 (475)
53 PF01850 PIN: PIN domain; Int 29.3 59 0.0013 25.2 3.0 47 232-284 70-116 (121)
54 TIGR00305 probable toxin-antit 29.3 36 0.00079 27.3 1.8 29 257-285 85-113 (114)
55 PRK05234 mgsA methylglyoxal sy 29.1 77 0.0017 27.2 3.8 36 243-278 42-81 (142)
56 PF14377 DUF4414: Domain of un 29.0 22 0.00049 28.9 0.5 29 85-113 40-68 (108)
57 cd00316 Oxidoreductase_nitroge 28.5 2.2E+02 0.0047 27.6 7.4 20 183-202 170-190 (399)
58 PF09372 PRANC: PRANC domain; 28.3 26 0.00056 27.6 0.8 19 92-110 69-87 (97)
59 cd01424 MGS_CPS_II Methylglyox 26.5 89 0.0019 24.8 3.6 36 243-278 36-73 (110)
60 PLN02404 6,7-dimethyl-8-ribity 26.4 1.4E+02 0.0031 25.8 5.0 47 232-278 19-72 (141)
61 PRK14487 cbb3-type cytochrome 26.4 64 0.0014 30.0 3.0 15 258-272 194-208 (217)
62 PF13919 ASXH: Asx homology do 26.3 24 0.00052 30.3 0.2 23 90-112 39-61 (138)
63 PF02677 DUF208: Uncharacteriz 24.6 3.7E+02 0.008 24.1 7.5 56 184-265 15-70 (176)
64 PRK00061 ribH 6,7-dimethyl-8-r 24.4 1.4E+02 0.0031 26.0 4.7 46 233-278 25-77 (154)
65 cd08562 GDPD_EcUgpQ_like Glyce 23.3 1.4E+02 0.003 26.5 4.7 38 241-279 190-227 (229)
66 PF03009 GDPD: Glycerophosphor 22.9 1.2E+02 0.0025 26.7 4.0 41 241-282 213-255 (256)
67 COG0548 ArgB Acetylglutamate k 22.8 91 0.002 29.8 3.4 27 176-202 19-45 (265)
68 cd01966 Nitrogenase_NifN_1 Nit 22.0 3E+02 0.0066 27.5 7.2 20 183-202 175-201 (417)
69 cd01965 Nitrogenase_MoFe_beta_ 21.9 3E+02 0.0064 27.5 7.1 15 185-199 176-190 (428)
70 cd08568 GDPD_TmGDE_like Glycer 21.7 1.3E+02 0.0029 26.9 4.2 42 240-283 184-225 (226)
71 PF11770 GAPT: GRB2-binding ad 21.7 62 0.0013 28.4 1.9 13 46-58 144-156 (158)
72 PF06792 UPF0261: Uncharacteri 21.7 1.8E+02 0.0038 29.6 5.3 45 233-277 194-240 (403)
73 PRK09454 ugpQ cytoplasmic glyc 21.5 1.4E+02 0.0029 27.5 4.3 44 240-284 199-242 (249)
74 smart00851 MGS MGS-like domain 21.4 1E+02 0.0023 23.6 3.0 37 243-279 23-62 (90)
75 TIGR00288 conserved hypothetic 21.3 1.2E+02 0.0027 26.7 3.7 63 241-308 70-138 (160)
76 PF01399 PCI: PCI domain; Int 21.0 2.2E+02 0.0049 21.5 4.9 41 243-287 64-104 (105)
77 PRK00124 hypothetical protein; 20.3 2.1E+02 0.0045 25.1 4.9 50 257-311 54-103 (151)
No 1
>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=3.4e-39 Score=308.23 Aligned_cols=188 Identities=40% Similarity=0.588 Sum_probs=163.7
Q ss_pred CCcccccccccccc---cccccCCCCEEEeeHHHHHHHHHHHhhhhC--CCCCchHHHHHHHHHHHHHHhCCCeeEEEee
Q psy14294 125 MPQNDQHSMLEFRC---NIVINKLLVDLISDVSIWLHQLTKGTHDLA--GGSVPNAHLIGLYHRICKLLFFKIKPVFVFD 199 (314)
Q Consensus 125 m~i~~l~~~l~~~~---~Ls~~~~g~rIaIDas~WL~q~~~a~~~~~--G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFD 199 (314)
|||+|||+++.+.+ +|+.++ |++|||||++||||++++++... |+..+ +++.+|++++..|+++||+||||||
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~-gk~laID~~~~l~r~~~a~~~~~~~~g~~~-~~l~~~~~rl~~L~~~~i~pvfVFD 78 (316)
T cd00128 1 MGIKGLWPLLKPVARPVHLEELR-GKKVAIDASIWLYQFLKACRQELGSGGETT-SHLQGFFYRTCRLLELGIKPVFVFD 78 (316)
T ss_pred CchhhHHHHHHhhCCCCCHHHhC-CcEEEecHHHHHHHHHHHhhhhccCCCCCc-HHHHHHHHHHHHHHHCCCEEEEEEc
Confidence 89999999999776 577887 99999999999999998885432 33333 3999999999999999999999999
Q ss_pred CCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHH
Q psy14294 200 GGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASL 267 (314)
Q Consensus 200 G~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L 267 (314)
|.+++.|..+..+|+.++.++.. ++.++.+++..+++.++..++++|+.+||||++||||||||||+|
T Consensus 79 G~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l 158 (316)
T cd00128 79 GKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYL 158 (316)
T ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHH
Confidence 99999999999998877665321 223344566788999999999999999999999999999999999
Q ss_pred HhcCCeeEEEcCCccEEeecCCeeeeeccCCC-CcEEEEehhhhhhcC
Q psy14294 268 ELGNHTQGVITDDSDIWLFGARTVYKNFFDKK-SHVLRYTAPDIRYYF 314 (314)
Q Consensus 268 ~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~-~~v~~y~~~~i~~~~ 314 (314)
++.|+||+|+|+|||+|+||+++||++++..+ .++++|+.+++..+|
T Consensus 159 ~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~l 206 (316)
T cd00128 159 AKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKEL 206 (316)
T ss_pred HhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHHc
Confidence 99999999999999999999999999999876 589999999997754
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=4.2e-39 Score=316.33 Aligned_cols=187 Identities=30% Similarity=0.403 Sum_probs=163.9
Q ss_pred CCcccccccccccc-------cccccCCCCEEEeeHHHHHHHHHHHhhh---------hCCCCCchHHHHHHHHHHHHHH
Q psy14294 125 MPQNDQHSMLEFRC-------NIVINKLLVDLISDVSIWLHQLTKGTHD---------LAGGSVPNAHLIGLYHRICKLL 188 (314)
Q Consensus 125 m~i~~l~~~l~~~~-------~Ls~~~~g~rIaIDas~WL~q~~~a~~~---------~~G~~~~~~~l~~f~~rL~~Ll 188 (314)
|||+||++++.+.+ +|+.+. |++|||||++||||++++++. ..|.++ +|+.+|++|+..|+
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~-gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t--~~l~g~~~r~~~Ll 77 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYF-GRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVT--SHISGLFNRTIRLL 77 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhC-CcEEEEeHHHHHHHHHHHcccccccccchhccCCcc--HHHHHHHHHHHHHH
Confidence 89999999998652 677777 999999999999999988753 234444 49999999999999
Q ss_pred hCCCeeEEEeeCCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcccHHHHHHHHHHHHHhCCceEec
Q psy14294 189 FFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQELLQLFGVPFIVA 256 (314)
Q Consensus 189 ~~gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~A 256 (314)
++||+|||||||.+|+.|..+..+|+..|.++.+ ++.++.+++..+++.++..++++|+.+|||||+|
T Consensus 78 ~~gikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~A 157 (393)
T PTZ00217 78 EAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEA 157 (393)
T ss_pred HCCCCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEEC
Confidence 9999999999999999999999999888775532 2345667788999999999999999999999999
Q ss_pred cchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccCC---CCcEEEEehhhhhhcC
Q psy14294 257 PGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDK---KSHVLRYTAPDIRYYF 314 (314)
Q Consensus 257 P~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~---~~~v~~y~~~~i~~~~ 314 (314)
|||||||||+|++.|+||+|+|+|+|+|+||++++|++++.. +.++++|+.+++...|
T Consensus 158 P~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~ 218 (393)
T PTZ00217 158 PCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEEL 218 (393)
T ss_pred CcCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHh
Confidence 999999999999999999999999999999999999999863 3478999999987653
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=3.6e-38 Score=304.54 Aligned_cols=185 Identities=28% Similarity=0.330 Sum_probs=161.7
Q ss_pred CCcccccccccccc-cccccCCCCEEEeeHHHHHHHHHHHhhh--------hCCCCCchHHHHHHHHHHHHHHhCCCeeE
Q psy14294 125 MPQNDQHSMLEFRC-NIVINKLLVDLISDVSIWLHQLTKGTHD--------LAGGSVPNAHLIGLYHRICKLLFFKIKPV 195 (314)
Q Consensus 125 m~i~~l~~~l~~~~-~Ls~~~~g~rIaIDas~WL~q~~~a~~~--------~~G~~~~~~~l~~f~~rL~~Ll~~gI~PI 195 (314)
||| +||+++..+. +++.++ |++|||||++||||++++++. ..|.++. |+.++++++..|+++||+||
T Consensus 1 MGi-~l~~~~~~~~~~l~~~~-gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~--~l~g~~~~~~~ll~~~i~Pv 76 (338)
T TIGR03674 1 MGV-DLRDLLAKEEIELEDLS-GKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITS--HLSGLFYRTINLLENGIKPV 76 (338)
T ss_pred CCC-ChHHHhccCccCHHHhC-CCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcH--HHHHHHHHHHHHHHCCCeEE
Confidence 899 9999999653 888888 999999999999999988753 3455543 99999999999999999999
Q ss_pred EEeeCCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHH
Q psy14294 196 FVFDGGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQ 263 (314)
Q Consensus 196 FVFDG~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq 263 (314)
|||||.+|+.|..+..+|+..|.++.+ ++.++.+++..++++++..++++|+.+||||++||||||||
T Consensus 77 ~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq 156 (338)
T TIGR03674 77 YVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQ 156 (338)
T ss_pred EEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHH
Confidence 999999999999999999887776433 22344667788999999999999999999999999999999
Q ss_pred HHHHHhcCCeeEEEcCCccEEeecCCeeeeeccCCCC------------cEEEEehhhhhhc
Q psy14294 264 CASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS------------HVLRYTAPDIRYY 313 (314)
Q Consensus 264 ~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~------------~v~~y~~~~i~~~ 313 (314)
||+|++.|+||+|+|+|+|+|+||+++|+++++..++ ..++|+.+++.+.
T Consensus 157 ~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~ 218 (338)
T TIGR03674 157 AAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSE 218 (338)
T ss_pred HHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHH
Confidence 9999999999999999999999999999999987664 4677888887654
No 4
>KOG2518|consensus
Probab=100.00 E-value=5.1e-39 Score=317.61 Aligned_cols=185 Identities=26% Similarity=0.293 Sum_probs=164.6
Q ss_pred CCcccccccccccc---cccccCCCCEEEeeHHHHHHHHHHHhhh--hCCCCCchHHHHHHHHHHHHHHhCCCeeEEEee
Q psy14294 125 MPQNDQHSMLEFRC---NIVINKLLVDLISDVSIWLHQLTKGTHD--LAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFD 199 (314)
Q Consensus 125 m~i~~l~~~l~~~~---~Ls~~~~g~rIaIDas~WL~q~~~a~~~--~~G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFD 199 (314)
|||.||-+.+.+.+ +++.++ |++||||+++|||++..+|.. ..|.|+. .|+..|+++++.|+.+||+||+|||
T Consensus 1 MGI~GLlp~~k~~~~~~hi~~~~-g~tvavD~y~WLhrg~~~Ca~el~~~~pT~-ryi~y~ik~v~lL~~~gikPilVFD 78 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPIHISEYK-GKTVAVDGYCWLHRGALACAEKLAKGKPTD-RYIQFFIKRVKLLLSYGIKPILVFD 78 (556)
T ss_pred CCcchhHHHHHHHhhhhhHHHhc-CceEEEehhhHHhhhHHhHHHHHhcCCChH-HHHHHHHHHHHHHHhcCCeEEEEec
Confidence 89999999999876 777777 999999999999999998853 5777875 4999999999999999999999999
Q ss_pred CCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHH
Q psy14294 200 GGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASL 267 (314)
Q Consensus 200 G~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L 267 (314)
|.+.|.|..|..+|+.+|.+... ++..+.+++..|+++|+..++++|+..||+||+||||||||+|||
T Consensus 79 G~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL 158 (556)
T KOG2518|consen 79 GDPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYL 158 (556)
T ss_pred CCCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHH
Confidence 99999999999999888775321 234456789999999999999999999999999999999999999
Q ss_pred HhcCCeeEEEcCCccEEeecCCeeeeeccCCCCcEEEEehhhhhh
Q psy14294 268 ELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRY 312 (314)
Q Consensus 268 ~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~~v~~y~~~~i~~ 312 (314)
.+.|+||+|||+|||+++|||++||++++..| .+..|+.+++..
T Consensus 159 ~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G-~~le~~~~~l~~ 202 (556)
T KOG2518|consen 159 EREGIVDAIITEDSDLLVFGCKKVIFKMDSFG-NGLEINRSKLPE 202 (556)
T ss_pred HhcCcceEEEeccccccccCchhheeeccCCC-CcccccHhhhhh
Confidence 99999999999999999999999999999865 666667776654
No 5
>KOG2519|consensus
Probab=100.00 E-value=7.4e-34 Score=277.96 Aligned_cols=186 Identities=32% Similarity=0.438 Sum_probs=157.4
Q ss_pred CCcccc---cccccccc----cccccCCCCEEEeeHHHHHHHHHHHhhh---hCCCCCchHHHHHHHHHHHHHHhCCCee
Q psy14294 125 MPQNDQ---HSMLEFRC----NIVINKLLVDLISDVSIWLHQLTKGTHD---LAGGSVPNAHLIGLYHRICKLLFFKIKP 194 (314)
Q Consensus 125 m~i~~l---~~~l~~~~----~Ls~~~~g~rIaIDas~WL~q~~~a~~~---~~G~~~~~~~l~~f~~rL~~Ll~~gI~P 194 (314)
|||+|| |.-+.+.| ++-.+. |++|||||++||||++.+++. ..|.++ +||.++|+|+..|+++||+|
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~-~kkVAID~s~~lyqfl~~v~~~~~~~~~~~--~HL~g~f~Rt~~l~~~gi~P 77 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFF-GKKVAIDASMWLYQFLIVVRSCRNEAGEPT--SHLMGMFYRTIRLIENGIKP 77 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhc-CceEEEecceeHhhHhhhhccccccCCCch--HHHHHHHHHHHHHHHcCCcE
Confidence 899999 44455555 555555 899999999999999988764 344443 49999999999999999999
Q ss_pred EEEeeCCCccchhhhhhhhhhhhHHHH------------HHhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHH
Q psy14294 195 VFVFDGGVPQLKKQTISTLEKDRDQLL------------LERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEA 262 (314)
Q Consensus 195 IFVFDG~~~~~K~~t~~kR~~~r~~~~------------~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADA 262 (314)
||||||.+|+.|..+..+|...|.++. ....++.++...++..+..+|..+|..|||||+.||+||+|
T Consensus 78 v~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEA 157 (449)
T KOG2519|consen 78 VYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEA 157 (449)
T ss_pred EEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHH
Confidence 999999999999999999987765332 12344556667788888899999999999999999999999
Q ss_pred HHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccC---CCCcEEEEehhhhhhc
Q psy14294 263 QCASLELGNHTQGVITDDSDIWLFGARTVYKNFFD---KKSHVLRYTAPDIRYY 313 (314)
Q Consensus 263 q~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~---~~~~v~~y~~~~i~~~ 313 (314)
|||+|++.|.|++++|+|||.+.||++.+++++.. .+.+|.+|++++|.+-
T Consensus 158 qCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~ 211 (449)
T KOG2519|consen 158 QCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEG 211 (449)
T ss_pred HHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHH
Confidence 99999999999999999999999999999999874 3359999999998753
No 6
>PRK03980 flap endonuclease-1; Provisional
Probab=99.97 E-value=1.1e-30 Score=247.87 Aligned_cols=145 Identities=30% Similarity=0.443 Sum_probs=129.2
Q ss_pred hCCCCCchHHHHHHHHHHHHHHhCCCeeEEEeeCCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcc
Q psy14294 167 LAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTI 234 (314)
Q Consensus 167 ~~G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i 234 (314)
..|.++. |+.+||+|+..|+++||+|||||||.+|+.|..+..+|+..|.++.+ ++.++.+++..+
T Consensus 3 ~~G~~Ts--~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~v 80 (292)
T PRK03980 3 SKGRITS--HLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRL 80 (292)
T ss_pred CCCcCcH--HHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccC
Confidence 4677764 99999999999999999999999999999999999999888876542 234556778889
Q ss_pred cHHHHHHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccCCCC------------cE
Q psy14294 235 TEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS------------HV 302 (314)
Q Consensus 235 ~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~------------~v 302 (314)
+++++..++++|+.+|||||+||||||||||+|++.|+||+|+|+|+|+|+||+++||++++..++ ..
T Consensus 81 t~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~ 160 (292)
T PRK03980 81 TDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKP 160 (292)
T ss_pred CHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999987653 46
Q ss_pred EEEehhhhhhc
Q psy14294 303 LRYTAPDIRYY 313 (314)
Q Consensus 303 ~~y~~~~i~~~ 313 (314)
++|+.+++...
T Consensus 161 e~~~~~~vl~~ 171 (292)
T PRK03980 161 ELIELEEVLKE 171 (292)
T ss_pred eeeeHHHHHHH
Confidence 78999888754
No 7
>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=99.95 E-value=1e-27 Score=256.08 Aligned_cols=125 Identities=30% Similarity=0.528 Sum_probs=100.5
Q ss_pred hhhhhhhHhhhhhHHHHHHHHHHHHHHHHHHHHhcCC---CCCCCCCCCC-ccccceecCCCCCCccCCccccCCChHHH
Q psy14294 2 QRKTLKSKAASNADKVRSDLLKNLLEQQLLNDVLGKN---EMALPPPSVS-REVDMFELPPAPAQTVQDEEEDSDSDDTE 77 (314)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (314)
.||++|+++..+|++|.++||++++||||+++|++.+ .+++|..+.- |++|+|+||+||..+..|..+.++.+..+
T Consensus 90 ~R~~rR~~a~~~a~~~~~~ll~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~d~y~lp~l~~~~~~D~Rims~~E~ee 169 (1034)
T TIGR00600 90 KRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKSTPEALPSVQQVPRPQDLYVLPPLPEEEKHSSEEESEKEWEE 169 (1034)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCcccccccccccccCCCccCCCCCCCCCCCcccccHHHHHH
Confidence 5999999999999999999999999999999999663 2233333333 79999999999977777766665444333
Q ss_pred -HHH-------HhcCCCccccccccccCCCcchhhHHHHHHHhhccccccccccCCCc
Q psy14294 78 -AKF-------RYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQ 127 (314)
Q Consensus 78 -~~~-------~~~~~~~~~~~s~~~~~~p~~~~~~~~~~~~e~~~~~~w~~i~~m~i 127 (314)
+.+ .++||++||++|++|.+||+++||+|||+||+++++.| ..++.||-
T Consensus 170 ~~~q~~~~~~~~~~d~~~ID~~S~~F~sLP~~~qyeILs~lRlrSRlRm-eQLeemfp 226 (1034)
T TIGR00600 170 RMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRR-TLFEAMPE 226 (1034)
T ss_pred HHHHhhcccccccCChhhcCCCCHHHHhCCHHHHHHHHHHHHHHHHHHH-HHHhhcCC
Confidence 222 24899999999999999999999999999999988877 65666643
No 8
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.87 E-value=1.2e-22 Score=163.33 Aligned_cols=94 Identities=36% Similarity=0.619 Sum_probs=81.8
Q ss_pred CCcccccccccccc---cccccCCCCEEEeeHHHHHHHHHHHhhhhCCCCCch-HHHHHHHHHHHHHHhCCCeeEEEeeC
Q psy14294 125 MPQNDQHSMLEFRC---NIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPN-AHLIGLYHRICKLLFFKIKPVFVFDG 200 (314)
Q Consensus 125 m~i~~l~~~l~~~~---~Ls~~~~g~rIaIDas~WL~q~~~a~~~~~G~~~~~-~~l~~f~~rL~~Ll~~gI~PIFVFDG 200 (314)
|||++||+++.+.+ ++..++ |++|||||++|||+++.+++...+.+..+ .++.++++++..|+++||+|||||||
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~-g~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L~~~~I~PifVFDG 79 (99)
T smart00485 1 MGIKGLWPLLKPVVREVPLEALR-GKTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKPIFVFDG 79 (99)
T ss_pred CCHhHHHHHHHHhcccCCHHHhC-CceEeccHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence 89999999999864 777777 99999999999999998886544444322 39999999999999999999999999
Q ss_pred CCccchhhhhhhhhhhhHH
Q psy14294 201 GVPQLKKQTISTLEKDRDQ 219 (314)
Q Consensus 201 ~~~~~K~~t~~kR~~~r~~ 219 (314)
..++.|..|..+|++.|++
T Consensus 80 ~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 80 KPPPLKSETLAKRRERREE 98 (99)
T ss_pred CCchhhHHHHHHHHHHHhc
Confidence 9999999999999887764
No 9
>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=99.87 E-value=4e-22 Score=160.55 Aligned_cols=95 Identities=35% Similarity=0.578 Sum_probs=75.3
Q ss_pred CCcccccccccccc-----cccccCCCCEEEeeHHHHHHHHHHHhhhhCCCCC-chHHHHHHHHHHHHHHhCCCeeEEEe
Q psy14294 125 MPQNDQHSMLEFRC-----NIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSV-PNAHLIGLYHRICKLLFFKIKPVFVF 198 (314)
Q Consensus 125 m~i~~l~~~l~~~~-----~Ls~~~~g~rIaIDas~WL~q~~~a~~~~~G~~~-~~~~l~~f~~rL~~Ll~~gI~PIFVF 198 (314)
|||+|||+++.+.+ +++.+. |++|||||++|||+++.+++...+... ..+++.++++++..|+.+||.|||||
T Consensus 1 MGI~gL~~~l~~~~~v~~~~~~~l~-g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~PifVF 79 (101)
T PF00752_consen 1 MGIKGLWQLLKPAAAVRKVSLSELR-GKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKPIFVF 79 (101)
T ss_dssp ---TTHHHHCHHHEGEEEEEGGGGT-TCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEEEEEE
T ss_pred CCcccHHHHHHhhccCCccCHHHhC-CCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEEEEEE
Confidence 89999999999865 555566 999999999999999888754322222 13599999999999999999999999
Q ss_pred eCCCccchhhhhhhhhhhhHHH
Q psy14294 199 DGGVPQLKKQTISTLEKDRDQL 220 (314)
Q Consensus 199 DG~~~~~K~~t~~kR~~~r~~~ 220 (314)
||.+|+.|..|..+|+++|+++
T Consensus 80 DG~~~~~K~~~~~~R~~~r~~~ 101 (101)
T PF00752_consen 80 DGKPPPLKRETIQKRRKRREEA 101 (101)
T ss_dssp --STTGGCHHHHHHHHHHHHHH
T ss_pred CCCCchhhHHHHHHHHHHHhcC
Confidence 9999999999999999888763
No 10
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.81 E-value=4.5e-20 Score=141.62 Aligned_cols=66 Identities=41% Similarity=0.632 Sum_probs=61.7
Q ss_pred HhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccCCCC---cEEEEehhhhhhc
Q psy14294 248 LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS---HVLRYTAPDIRYY 313 (314)
Q Consensus 248 ~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~---~v~~y~~~~i~~~ 313 (314)
.+||||++||||||||||+|+++|+||+|+|+|+|+|+||++++|++++..++ .+..++.+++.+.
T Consensus 2 ~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~ 70 (73)
T smart00484 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKE 70 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999886 7888888887654
No 11
>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=99.80 E-value=3.9e-20 Score=147.99 Aligned_cols=67 Identities=46% Similarity=0.618 Sum_probs=56.2
Q ss_pred HHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeecc-CC-C-------CcEEEEehhhhhhc
Q psy14294 247 QLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFF-DK-K-------SHVLRYTAPDIRYY 313 (314)
Q Consensus 247 k~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~-~~-~-------~~v~~y~~~~i~~~ 313 (314)
+.+||||++||||||||||||+++|+||+|+|+|||+|+||+++||++++ .. + ..+++|+.++|.+.
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 76 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKE 76 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHH
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHH
Confidence 57899999999999999999999999999999999999999999999997 33 2 47999999998764
No 12
>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=99.79 E-value=1.6e-19 Score=193.62 Aligned_cols=95 Identities=43% Similarity=0.762 Sum_probs=87.2
Q ss_pred CCcccccccccccc---cccccCCCCEEEeeHHHHHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHhCCCeeEEEeeCC
Q psy14294 125 MPQNDQHSMLEFRC---NIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGG 201 (314)
Q Consensus 125 m~i~~l~~~l~~~~---~Ls~~~~g~rIaIDas~WL~q~~~a~~~~~G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFDG~ 201 (314)
|||+|||.++.+.+ +|..+. |++||||+|+||||++.+|++..|.++.++||.+||+|++.|+.+||+|||||||.
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~ 79 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLE-GKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGG 79 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhC-CeEEEechHHHHHHHHHHHHhccCCccCCHHHHHHHHHHHHHHHCCCeEEEEECCC
Confidence 99999999999876 666666 99999999999999999998878887777899999999999999999999999999
Q ss_pred CccchhhhhhhhhhhhHHH
Q psy14294 202 VPQLKKQTISTLEKDRDQL 220 (314)
Q Consensus 202 ~~~~K~~t~~kR~~~r~~~ 220 (314)
+|+.|+.|..+|+++|.++
T Consensus 80 ~p~lK~~t~~~R~~rR~~a 98 (1034)
T TIGR00600 80 APLLKRQTLAKRRQRRDGA 98 (1034)
T ss_pred CchHhHHHHHHHHHHHHHH
Confidence 9999999999998888764
No 13
>KOG2520|consensus
Probab=99.75 E-value=1.1e-18 Score=182.28 Aligned_cols=90 Identities=52% Similarity=0.799 Sum_probs=84.6
Q ss_pred cccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccCCCCcEEE
Q psy14294 225 GKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLR 304 (314)
Q Consensus 225 ~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~~v~~ 304 (314)
++..+.+.+++..|+.+|+++|+.+|||||+||+|||||||.|.+.++||||||+|||+|+||+++||+|++..+++|+.
T Consensus 454 ~~~~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~knk~ve~ 533 (815)
T KOG2520|consen 454 YIQSRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKNKYVEK 533 (815)
T ss_pred HHHhccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcCcccee
Confidence 44456677899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EehhhhhhcC
Q psy14294 305 YTAPDIRYYF 314 (314)
Q Consensus 305 y~~~~i~~~~ 314 (314)
|.+.+|++-|
T Consensus 534 y~~~di~kel 543 (815)
T KOG2520|consen 534 YQLDDIEKEL 543 (815)
T ss_pred eehHHHHHHH
Confidence 9999998754
No 14
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.71 E-value=9.6e-17 Score=150.34 Aligned_cols=153 Identities=17% Similarity=0.149 Sum_probs=112.5
Q ss_pred EEEeeHHHHHHHHHHHhh---hhCCCCCchHHHHHHHHHHHHHHhC--CCeeEEEeeCCCccchhhhhhhhhhhhHHHHH
Q psy14294 148 DLISDVSIWLHQLTKGTH---DLAGGSVPNAHLIGLYHRICKLLFF--KIKPVFVFDGGVPQLKKQTISTLEKDRDQLLL 222 (314)
Q Consensus 148 rIaIDas~WL~q~~~a~~---~~~G~~~~~~~l~~f~~rL~~Ll~~--gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~~~ 222 (314)
-+.|||++++||++++.. ...|.++. ++.+|++.+..+++. .-++++||||..+..+++....
T Consensus 3 lllIDg~~~i~R~~~a~~~l~~~~G~~t~--a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l~p~---------- 70 (259)
T smart00475 3 LLLVDGSSLAFRAYFALPPLKNSKGEPTN--AVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPE---------- 70 (259)
T ss_pred EEEEeCcHHHHHHHHCCCcccCCCCCccc--HHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccchhHH----------
Confidence 478999999999988753 34677764 899999999888763 3456999998655442222111
Q ss_pred Hhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHhc----CCeeEEEcCCccEEeecCCeeee-ec
Q psy14294 223 ERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLELG----NHTQGVITDDSDIWLFGARTVYK-NF 295 (314)
Q Consensus 223 ~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~~----g~vdaViS~DSD~llfG~~~Vi~-~l 295 (314)
+|..|. ++.....++..++++|+.+|||++.+| ||||++||+|++. |+...|+|+|+|+++++.+.|.. ..
T Consensus 71 --YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~ 148 (259)
T smart00475 71 --YKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDP 148 (259)
T ss_pred --HHhCCCCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEec
Confidence 333443 344455667889999999999999988 6999999999974 77778999999999999876543 22
Q ss_pred cCCCCcEEEEehhhhhhcC
Q psy14294 296 FDKKSHVLRYTAPDIRYYF 314 (314)
Q Consensus 296 ~~~~~~v~~y~~~~i~~~~ 314 (314)
....+..++|+.+.+...|
T Consensus 149 ~~~~~~~~~~~~~~v~~~~ 167 (259)
T smart00475 149 TKGIKEFELYTPENVIEKY 167 (259)
T ss_pred cCCCCccEEEcHHHHHHHh
Confidence 2222245789988886543
No 15
>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=99.68 E-value=4.4e-16 Score=144.19 Aligned_cols=149 Identities=17% Similarity=0.101 Sum_probs=110.1
Q ss_pred EEEeeHHHHHHHHHHHhhh---h-CCCCCchHHHHHHHHHHHHHHhC--CCeeEEEeeCCCccchhhhhhhhhhhhHHHH
Q psy14294 148 DLISDVSIWLHQLTKGTHD---L-AGGSVPNAHLIGLYHRICKLLFF--KIKPVFVFDGGVPQLKKQTISTLEKDRDQLL 221 (314)
Q Consensus 148 rIaIDas~WL~q~~~a~~~---~-~G~~~~~~~l~~f~~rL~~Ll~~--gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~~ 221 (314)
.+.|||++++||++++... . .|.++. ++.+|+.++..+++. ..+++|||||..+..++.....
T Consensus 3 ~llIDg~~l~yr~~~a~~~~~~~~~g~~t~--ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~--------- 71 (240)
T cd00008 3 LLLIDGSSLAYRAYFALPPLKNSPKGLPTN--AVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPE--------- 71 (240)
T ss_pred EEEEEChHHHHHHHHCCCCcCCCCCCcCch--HHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHH---------
Confidence 5899999999999887642 2 566654 899999999888764 4789999999755554443322
Q ss_pred HHhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHh----cCCeeEEEcCCccEEeecCCeeeeec
Q psy14294 222 LERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLEL----GNHTQGVITDDSDIWLFGARTVYKNF 295 (314)
Q Consensus 222 ~~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~----~g~vdaViS~DSD~llfG~~~Vi~~l 295 (314)
+|..|. .+.....++..++++|+.+|||++.+| +|||++||+|++ .|....|+|.|+|++++..+.|...-
T Consensus 72 ---YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~ 148 (240)
T cd00008 72 ---YKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVS 148 (240)
T ss_pred ---HHcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEe
Confidence 333443 344556778899999999999999998 699999999995 47777899999999999766543321
Q ss_pred cCCCCcEEEEehhhhhhc
Q psy14294 296 FDKKSHVLRYTAPDIRYY 313 (314)
Q Consensus 296 ~~~~~~v~~y~~~~i~~~ 313 (314)
.. ....++.+.+..+
T Consensus 149 ~~---~~~~i~~~~v~~~ 163 (240)
T cd00008 149 PM---KKKLVTEENVIEK 163 (240)
T ss_pred CC---CceEEeHHHHHHH
Confidence 11 2345666665443
No 16
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.67 E-value=1e-16 Score=153.25 Aligned_cols=161 Identities=19% Similarity=0.184 Sum_probs=116.3
Q ss_pred CCCEEEeeHHHHHHHHHHHhh----hhCCCCCchHHHHHHHHHHHHHHh--CCCeeEEEeeCCCccchhhhhhhhhhhhH
Q psy14294 145 LLVDLISDVSIWLHQLTKGTH----DLAGGSVPNAHLIGLYHRICKLLF--FKIKPVFVFDGGVPQLKKQTISTLEKDRD 218 (314)
Q Consensus 145 ~g~rIaIDas~WL~q~~~a~~----~~~G~~~~~~~l~~f~~rL~~Ll~--~gI~PIFVFDG~~~~~K~~t~~kR~~~r~ 218 (314)
++..++|||++|+||+++++. ...|.++. .+.+|...+..+++ ..++|++||||.++..|.++..+|+..|.
T Consensus 10 ~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~--~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~ 87 (310)
T COG0258 10 SGKLLLIDGSSLLYRALHALPQPLGNPLGDPTG--AVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANRE 87 (310)
T ss_pred cCcEEEEechHHHHHHHHhcchhcCCCCCCCcc--HHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCC
Confidence 478999999999999998873 23555543 45555554444332 23999999999888888888887776665
Q ss_pred H-HHHHhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccC
Q psy14294 219 Q-LLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFD 297 (314)
Q Consensus 219 ~-~~~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~ 297 (314)
. .- ..+..+...+++.+....+.+|..+|+| +.+|.|+.||+|+ +.|.+.+|+|+|+|+++|+++++..-...
T Consensus 88 ~~~p---~~l~~q~~~i~~~~~~~~~~~l~~~G~e-add~i~t~A~~a~--~~g~~~~I~S~DkD~lql~~~~~~~~~~~ 161 (310)
T COG0258 88 KEMP---DELAPQIPILTELLVALGIPLLELMGIE-ADDPIETLAQKAY--KKGDVVLIISGDKDLLQLVSPNVLVINGK 161 (310)
T ss_pred ccCH---HHHHHHHHHHHHHHHHhCcHhhhcCCCC-cchhHHHHHHHHH--hcCCeEEEEeCCcchhhhcCCCcEEEecc
Confidence 4 21 1223344556677777788888888988 8888999999998 78999999999999999999986544444
Q ss_pred CCCcEEEEehhhhhhc
Q psy14294 298 KKSHVLRYTAPDIRYY 313 (314)
Q Consensus 298 ~~~~v~~y~~~~i~~~ 313 (314)
.+.....++...+...
T Consensus 162 ~~~~~~~~~~~~~~e~ 177 (310)
T COG0258 162 KGEPEKFLDLEEVEEK 177 (310)
T ss_pred CCCCcccCCHHHHHHH
Confidence 4433225666655543
No 17
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.64 E-value=3.3e-15 Score=141.53 Aligned_cols=154 Identities=18% Similarity=0.133 Sum_probs=112.0
Q ss_pred CEEEeeHHHHHHHHHHHh-------hhhCCCCCchHHHHHHHHHHHHHHhC--CCeeEEEeeCCCccchhhhhhhhhhhh
Q psy14294 147 VDLISDVSIWLHQLTKGT-------HDLAGGSVPNAHLIGLYHRICKLLFF--KIKPVFVFDGGVPQLKKQTISTLEKDR 217 (314)
Q Consensus 147 ~rIaIDas~WL~q~~~a~-------~~~~G~~~~~~~l~~f~~rL~~Ll~~--gI~PIFVFDG~~~~~K~~t~~kR~~~r 217 (314)
+.+.|||++++||++++. ....|.++. ++.+|++.+..+++. .-++++||||..+..+.+....
T Consensus 4 ~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~--a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~----- 76 (281)
T PRK14976 4 KALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTN--AIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDE----- 76 (281)
T ss_pred cEEEEeCcHHHHHHHHccCccCCCccCCCCCCch--HHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHH-----
Confidence 457999999999988774 234677664 899999999888763 4689999999655544433322
Q ss_pred HHHHHHhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHhc----CCeeEEEcCCccEEeecCCee
Q psy14294 218 DQLLLERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLELG----NHTQGVITDDSDIWLFGARTV 291 (314)
Q Consensus 218 ~~~~~~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~~----g~vdaViS~DSD~llfG~~~V 291 (314)
+|..|. .+.....++..++++|+.+|||++.+| +|||+.||+|++. |.--.|+|.|+|++++..+.|
T Consensus 77 -------YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v 149 (281)
T PRK14976 77 -------YKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENT 149 (281)
T ss_pred -------HhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCe
Confidence 333443 344456678889999999999999999 6999999999864 544469999999999998754
Q ss_pred eeeccCCCCcEEEEehhhhhhcC
Q psy14294 292 YKNFFDKKSHVLRYTAPDIRYYF 314 (314)
Q Consensus 292 i~~l~~~~~~v~~y~~~~i~~~~ 314 (314)
.......+....+|+.+++...|
T Consensus 150 ~~~~~~~~~~~~~~~~~~v~~~~ 172 (281)
T PRK14976 150 DVLLKKKGTSHFILNTNNFFELY 172 (281)
T ss_pred EEEEecCCCCcEEEcHHHHHHHh
Confidence 33222222235678888766543
No 18
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.52 E-value=9.7e-14 Score=148.98 Aligned_cols=152 Identities=18% Similarity=0.191 Sum_probs=111.3
Q ss_pred EEeeHHHHHHHHHHHhh-----hhCCCCCchHHHHHHHHHHHHHHhC--CCeeEEEeeCCCccchhhhhhhhhhhhHHHH
Q psy14294 149 LISDVSIWLHQLTKGTH-----DLAGGSVPNAHLIGLYHRICKLLFF--KIKPVFVFDGGVPQLKKQTISTLEKDRDQLL 221 (314)
Q Consensus 149 IaIDas~WL~q~~~a~~-----~~~G~~~~~~~l~~f~~rL~~Ll~~--gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~~ 221 (314)
+.|||++++||+++++. ...|.|+. ++.+|++++..+++. .-+.+|||||..+..+.+....
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~--av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~~~~~--------- 70 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTN--AVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAE--------- 70 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEec--HHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHHHHHH---------
Confidence 57999999999988763 34677764 899999999888863 3455999999665543332221
Q ss_pred HHhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHhc----CCeeEEEcCCccEEeecCCeeeeec
Q psy14294 222 LERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLELG----NHTQGVITDDSDIWLFGARTVYKNF 295 (314)
Q Consensus 222 ~~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~~----g~vdaViS~DSD~llfG~~~Vi~~l 295 (314)
+|..|. ++.....++..++++|+.+|||++.+| ||||++||+|++. |+...|+|.|.|++++..+.|....
T Consensus 71 ---YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~ 147 (887)
T TIGR00593 71 ---YKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLI 147 (887)
T ss_pred ---HHhCCCCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEe
Confidence 343443 344556678899999999999999999 6999999999974 7777899999999999987553221
Q ss_pred cCCCCcEEEEehhhhhhcC
Q psy14294 296 FDKKSHVLRYTAPDIRYYF 314 (314)
Q Consensus 296 ~~~~~~v~~y~~~~i~~~~ 314 (314)
...+...+.|+.+.+..+|
T Consensus 148 ~~~~~~~~~~~~~~v~~~~ 166 (887)
T TIGR00593 148 PKGKTSFTEITPEYVVEKY 166 (887)
T ss_pred ccCCCCceEEcHHHHHHHh
Confidence 1212145568888776543
No 19
>PRK05755 DNA polymerase I; Provisional
Probab=99.52 E-value=9.2e-14 Score=149.45 Aligned_cols=151 Identities=17% Similarity=0.143 Sum_probs=111.8
Q ss_pred CEEEeeHHHHHHHHHHHh----hhhCCCCCchHHHHHHHHHHHHHHh-C-CCeeEEEeeCCCccchhhhhhhhhhhhHHH
Q psy14294 147 VDLISDVSIWLHQLTKGT----HDLAGGSVPNAHLIGLYHRICKLLF-F-KIKPVFVFDGGVPQLKKQTISTLEKDRDQL 220 (314)
Q Consensus 147 ~rIaIDas~WL~q~~~a~----~~~~G~~~~~~~l~~f~~rL~~Ll~-~-gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~ 220 (314)
+-+.|||++++||++++. ....|.++. ++.+|+.++..++. + .-+.+|||||..+..++.....
T Consensus 3 ~~~liDg~~~~~r~~~a~~~~~~~~~g~~~~--a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~~~~-------- 72 (880)
T PRK05755 3 TLLLIDGSSLLFRAFYALLPTLRNSDGLPTG--AVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPE-------- 72 (880)
T ss_pred eEEEEeCcHHHHHHHHCCCCcccCCCCCccc--HHHHHHHHHHHHHHhcCCCEEEEEEECCCCccccccCHH--------
Confidence 457999999999998876 234676664 89999999988874 2 3445999999655454443322
Q ss_pred HHHhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHh----cCCeeEEEcCCccEEeecCCee--e
Q psy14294 221 LLERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLEL----GNHTQGVITDDSDIWLFGARTV--Y 292 (314)
Q Consensus 221 ~~~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~----~g~vdaViS~DSD~llfG~~~V--i 292 (314)
+|..|. .+.....++..++++|+.+||+++.+| ||||++||+|++ .|....|+|.|+|++++..+.| +
T Consensus 73 ----YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~ 148 (880)
T PRK05755 73 ----YKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLL 148 (880)
T ss_pred ----HhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEe
Confidence 333443 344456678889999999999999999 699999999995 4778899999999999998754 3
Q ss_pred eeccCCCCcEEEEehhhhhhc
Q psy14294 293 KNFFDKKSHVLRYTAPDIRYY 313 (314)
Q Consensus 293 ~~l~~~~~~v~~y~~~~i~~~ 313 (314)
..++ ++....|+.+.+..+
T Consensus 149 ~~~~--~~~~~~~~~~~v~~~ 167 (880)
T PRK05755 149 DTMG--VSKNEELDPEEVVEK 167 (880)
T ss_pred eccC--CCCCeEEcHHHHHHH
Confidence 3322 234567888877654
No 20
>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=99.32 E-value=3.9e-12 Score=112.23 Aligned_cols=152 Identities=20% Similarity=0.233 Sum_probs=104.7
Q ss_pred EEEeeHHHHHHHHHHHhh-----hhCCCCCchHHHHHHHHHHHHHHh-C-CCeeEEEeeCCCccchhhhhhhhhhhhHHH
Q psy14294 148 DLISDVSIWLHQLTKGTH-----DLAGGSVPNAHLIGLYHRICKLLF-F-KIKPVFVFDGGVPQLKKQTISTLEKDRDQL 220 (314)
Q Consensus 148 rIaIDas~WL~q~~~a~~-----~~~G~~~~~~~l~~f~~rL~~Ll~-~-gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~ 220 (314)
-+.|||++.+||.++++. ...|.++. .+.+|+..+..++. . .-.+++|||+..+ ..|.+...
T Consensus 3 llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~--ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~-~fR~~l~p-------- 71 (169)
T PF02739_consen 3 LLLIDGNSLLFRAYYALPKDPLRNSDGEPTN--AIYGFLRMLLKLLKDFKPDYVVVAFDSKGP-TFRKELYP-------- 71 (169)
T ss_dssp EEEEEHHHHHHHCCCCCTTST-BETTSEB-H--HHHHHHHHHHHHHHHTTEEEEEEEEEBSSC-HHHHHCCT--------
T ss_pred EEEEechHHHHHHHHhhccCCCcCCCCCChH--HHHHHHHHHHHHHHHcCCceEEEEecCCCc-chHHHHHH--------
Confidence 367899999999987764 34676764 89999998887765 3 3579999999765 33322221
Q ss_pred HHHhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHhc----CCeeEEEcCCccEEeecCC--eee
Q psy14294 221 LLERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLELG----NHTQGVITDDSDIWLFGAR--TVY 292 (314)
Q Consensus 221 ~~~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~~----g~vdaViS~DSD~llfG~~--~Vi 292 (314)
-+|..|. .+..+..++..++++|..+|++++..| +|||..+|.|++. |.--.|+|.|.|++..=.+ .|+
T Consensus 72 ---~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~ 148 (169)
T PF02739_consen 72 ---EYKANRKPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVY 148 (169)
T ss_dssp ---TTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEE
T ss_pred ---HHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEE
Confidence 1222332 222344556789999999999999998 9999999999973 4444799999999998777 333
Q ss_pred eeccCCCCcEEEEehhhhhhcC
Q psy14294 293 KNFFDKKSHVLRYTAPDIRYYF 314 (314)
Q Consensus 293 ~~l~~~~~~v~~y~~~~i~~~~ 314 (314)
.++.......+|+.+.+..+|
T Consensus 149 -~~~~~~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 149 -LLDPGKKKFKVYDPEEVEEKY 169 (169)
T ss_dssp -EEETTTTCS-EB-HHHHHHHT
T ss_pred -EeecCCCCCEEEcHHHHhhcC
Confidence 333334577889988887765
No 21
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.27 E-value=6.3e-11 Score=111.00 Aligned_cols=151 Identities=19% Similarity=0.158 Sum_probs=103.2
Q ss_pred CCEEEeeHHHHHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHh-C-CCeeEEEeeCCCcc-chhhhhhhhhhhhHHHHH
Q psy14294 146 LVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLF-F-KIKPVFVFDGGVPQ-LKKQTISTLEKDRDQLLL 222 (314)
Q Consensus 146 g~rIaIDas~WL~q~~~a~~~~~G~~~~~~~l~~f~~rL~~Ll~-~-gI~PIFVFDG~~~~-~K~~t~~kR~~~r~~~~~ 222 (314)
.+-+.|||++.+||++++.....|. ++ .+.+|++.+..+++ + .=+.+++|||..+. .-|.+...
T Consensus 3 ~~llLiDg~~l~~R~~~a~~~~~g~--t~-av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~l~p---------- 69 (256)
T PRK09482 3 NHLLIIDALNLIRRIHAVQPSPNDI--NA-CVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQLLP---------- 69 (256)
T ss_pred CeEEEEeCcHHHHHHHhCCCCCCCc--ch-HHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHHHhH----------
Confidence 3457899999999988776434555 33 89999988887765 4 44689999995432 12222211
Q ss_pred Hhcccccc-cCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHhc----CCeeEEEcCCccEEeecCCeee-eec
Q psy14294 223 ERGKQTRL-ASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLELG----NHTQGVITDDSDIWLFGARTVY-KNF 295 (314)
Q Consensus 223 ~~~k~~r~-~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~~----g~vdaViS~DSD~llfG~~~Vi-~~l 295 (314)
.+|..|. .+.....++..++++|..+||+++..| +|||..||.|++. |.--.|+|.|.|+++.=.+.|. .+.
T Consensus 70 -~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~ 148 (256)
T PRK09482 70 -DYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDY 148 (256)
T ss_pred -HHhcCCCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEec
Confidence 2454553 455566777889999999999999999 6999999999863 4333689999999876443332 222
Q ss_pred cCCCCcEEEEehhhhhhcC
Q psy14294 296 FDKKSHVLRYTAPDIRYYF 314 (314)
Q Consensus 296 ~~~~~~v~~y~~~~i~~~~ 314 (314)
. ..++|+.+.+..+|
T Consensus 149 ~----~~~~~~~~~v~~~~ 163 (256)
T PRK09482 149 F----QKRWLDAPFIEQEF 163 (256)
T ss_pred c----ccccCCHHHHHHHh
Confidence 1 12356666665543
No 22
>PHA00439 exonuclease
Probab=98.94 E-value=9.3e-09 Score=97.67 Aligned_cols=128 Identities=14% Similarity=0.013 Sum_probs=91.9
Q ss_pred CEEEeeHHHHHHHHHHHhh----------hhCCCCCchHHHHHHHHHHHHHHh-----CCCeeEEEeeCCCccchhhhhh
Q psy14294 147 VDLISDVSIWLHQLTKGTH----------DLAGGSVPNAHLIGLYHRICKLLF-----FKIKPVFVFDGGVPQLKKQTIS 211 (314)
Q Consensus 147 ~rIaIDas~WL~q~~~a~~----------~~~G~~~~~~~l~~f~~rL~~Ll~-----~gI~PIFVFDG~~~~~K~~t~~ 211 (314)
.-+.|||++++||.++++. ...|.++. ++.+|++.|..+++ ..=..+++||+. + ..|.+..
T Consensus 7 ~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~--A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~~-~-tfR~ely 82 (286)
T PHA00439 7 GVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAK--ARQILEDSIKSYKTRKKAWKDAPIVLAFTDS-V-NWRKEVV 82 (286)
T ss_pred cEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeecc--HHHHHHHHHHHHHHhhccCCCCeEEEEECCC-C-ChHhhhh
Confidence 3578999999999998872 23566654 78999998888874 344567789952 2 2233322
Q ss_pred hhhhhhHHHHHHhcccccccCcccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHh----cCC-eeEEEcCCccEEe
Q psy14294 212 TLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLEL----GNH-TQGVITDDSDIWL 285 (314)
Q Consensus 212 kR~~~r~~~~~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~----~g~-vdaViS~DSD~ll 285 (314)
. .+|..|........+...+++++..+||+++..| +|||..+|.|++ .|+ --.|+|.|.|++.
T Consensus 83 p-----------~YKanR~~~p~~~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~Q 151 (286)
T PHA00439 83 P-----------TYKANRKAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKT 151 (286)
T ss_pred h-----------HhcCCCCCCCCchhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhh
Confidence 1 2566665433335567788999999999999888 899999999986 354 3369999999998
Q ss_pred ecCC
Q psy14294 286 FGAR 289 (314)
Q Consensus 286 fG~~ 289 (314)
.-..
T Consensus 152 Lv~~ 155 (286)
T PHA00439 152 IPNC 155 (286)
T ss_pred cCcc
Confidence 8533
No 23
>PF12813 XPG_I_2: XPG domain containing
Probab=98.91 E-value=2.5e-09 Score=99.73 Aligned_cols=78 Identities=26% Similarity=0.305 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHHHh---CCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecC--Ceeeeec---cCCC--------
Q psy14294 236 EQMSREAQELLQLF---GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA--RTVYKNF---FDKK-------- 299 (314)
Q Consensus 236 ~~~i~~~~~lLk~l---GV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~--~~Vi~~l---~~~~-------- 299 (314)
+-++..++++|+.+ |++++++|+|||..||.++++. .++|+|+|||+|+|+. +..|.+| .+..
T Consensus 3 ~f~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~-~~~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~ 81 (246)
T PF12813_consen 3 PFLVPAFIEALRESWRYGVPVVQCPGEADRECAALARKW-GCPVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGS 81 (246)
T ss_pred cchHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHc-CCeEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCC
Confidence 34667899999999 9999999999999999999654 4499999999999998 5555444 3333
Q ss_pred -CcEEEEehhhhhhcC
Q psy14294 300 -SHVLRYTAPDIRYYF 314 (314)
Q Consensus 300 -~~v~~y~~~~i~~~~ 314 (314)
-.+.+|+.+.|+++|
T Consensus 82 ~i~~~~y~~~~i~~~l 97 (246)
T PF12813_consen 82 YISAKVYSPDKICKRL 97 (246)
T ss_pred eeEEEEEcHHHHHHHc
Confidence 266779999999876
No 24
>PHA02567 rnh RnaseH; Provisional
Probab=98.61 E-value=6e-07 Score=85.98 Aligned_cols=129 Identities=13% Similarity=0.012 Sum_probs=83.5
Q ss_pred CCEEEeeHHHHHHHHHHHh-hhhCCCCCchHHH-HHHHHHHHHHHh----CCCeeEEEeeCCCccchhhhhhhhhhhhHH
Q psy14294 146 LVDLISDVSIWLHQLTKGT-HDLAGGSVPNAHL-IGLYHRICKLLF----FKIKPVFVFDGGVPQLKKQTISTLEKDRDQ 219 (314)
Q Consensus 146 g~rIaIDas~WL~q~~~a~-~~~~G~~~~~~~l-~~f~~rL~~Ll~----~gI~PIFVFDG~~~~~K~~t~~kR~~~r~~ 219 (314)
..-+.||+|..+++.+.+. ....|.++ + .+ ..++..|..+.. ..-+.+++||+...+..|.....
T Consensus 14 ~~~~LiDgs~i~~~~~~a~l~~~~~~~~-~-~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp------- 84 (304)
T PHA02567 14 EGVNLIDFSQIIIATIMANFKPKDKINE-A-MVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAW------- 84 (304)
T ss_pred CCEEEEehHHHHHHHHHhhCCCCCCCcH-H-HHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhh-------
Confidence 4468899999999988774 22335444 2 45 346666655443 33347999998532222222211
Q ss_pred HHHHhccccccc-Ccc--------cHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHh----cCCeeEEEcCCccEEe
Q psy14294 220 LLLERGKQTRLA-STI--------TEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLEL----GNHTQGVITDDSDIWL 285 (314)
Q Consensus 220 ~~~~~~k~~r~~-~~i--------~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~----~g~vdaViS~DSD~ll 285 (314)
.+|..|.. +.. +..+-..+.+++..+||+++..| +|||..+|.|++ .|.--.|+|.|.|++.
T Consensus 85 ----~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~Q 160 (304)
T PHA02567 85 ----YYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQ 160 (304)
T ss_pred ----HhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhh
Confidence 24444432 221 22222457888899999999988 799999999996 3543479999999998
Q ss_pred ec
Q psy14294 286 FG 287 (314)
Q Consensus 286 fG 287 (314)
.=
T Consensus 161 Lv 162 (304)
T PHA02567 161 LH 162 (304)
T ss_pred cc
Confidence 83
No 25
>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=98.05 E-value=1.9e-05 Score=73.55 Aligned_cols=160 Identities=17% Similarity=0.175 Sum_probs=83.8
Q ss_pred CCccccccccccccccccc-----C---CCCEEEeeHHHHHHHHHHHhhhhCCCC-CchHHHHHHHHHHHHHHh--CCCe
Q psy14294 125 MPQNDQHSMLEFRCNIVIN-----K---LLVDLISDVSIWLHQLTKGTHDLAGGS-VPNAHLIGLYHRICKLLF--FKIK 193 (314)
Q Consensus 125 m~i~~l~~~l~~~~~Ls~~-----~---~g~rIaIDas~WL~q~~~a~~~~~G~~-~~~~~l~~f~~rL~~Ll~--~gI~ 193 (314)
|||-+|+.|+..+-+.... . .=-.+.||.++.+|.+...... ..+ +....+..++..+..|.. ..-+
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~--~~~~~~~~~~~~i~~~id~l~~~v~P~k 78 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDS--SIPKTEEEIFQRIFNYIDRLVRIVRPRK 78 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS------SHHHHHHHHHHHHHHHHHHH-ESS
T ss_pred CCHHHHHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCccc--CCCccHHHHHHHHHHHHHHhheeecCce
Confidence 8999999999977544311 1 0124889999999987543321 111 122245667767766654 3333
Q ss_pred -eEEEeeCCCccchhhhhhhhhhhhHH-HH---H-------Hh-------------cccccccCcccH--HHHHHHHHH-
Q psy14294 194 -PVFVFDGGVPQLKKQTISTLEKDRDQ-LL---L-------ER-------------GKQTRLASTITE--QMSREAQEL- 245 (314)
Q Consensus 194 -PIFVFDG~~~~~K~~t~~kR~~~r~~-~~---~-------~~-------------~k~~r~~~~i~~--~~i~~~~~l- 245 (314)
.++.+||..|..|..++..||-+... .. . .. .++... .++| +....+.+.
T Consensus 79 ~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn--~ITPGT~FM~~l~~~L 156 (237)
T PF03159_consen 79 LLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSN--CITPGTEFMEKLSDAL 156 (237)
T ss_dssp EEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GG--GSSTTSHHHHHHHHHH
T ss_pred EEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccccc--eeccCCHHHHHHHHHH
Confidence 36899999999999988777643321 10 0 00 011111 2222 112222222
Q ss_pred -------HHH----hCCceEec----cchHHHHHHHHHhc---------CCeeEEEcCCccEEeecC
Q psy14294 246 -------LQL----FGVPFIVA----PGEAEAQCASLELG---------NHTQGVITDDSDIWLFGA 288 (314)
Q Consensus 246 -------Lk~----lGV~~I~A----P~EADAq~A~L~~~---------g~vdaViS~DSD~llfG~ 288 (314)
+.. -++.+|.+ |||+|--+....+. +....|+|.|+|+++++-
T Consensus 157 ~~~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L 223 (237)
T PF03159_consen 157 RYYIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSL 223 (237)
T ss_dssp HHHHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHH
T ss_pred HHHHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHH
Confidence 211 15678876 69999988766552 467889999999999874
No 26
>PHA03065 Hypothetical protein; Provisional
Probab=95.79 E-value=0.17 Score=50.74 Aligned_cols=158 Identities=14% Similarity=0.111 Sum_probs=100.0
Q ss_pred CCccccccccccccccccc-----CCCCEEEeeHHHHHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHhCCCeeEEEee
Q psy14294 125 MPQNDQHSMLEFRCNIVIN-----KLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFD 199 (314)
Q Consensus 125 m~i~~l~~~l~~~~~Ls~~-----~~g~rIaIDas~WL~q~~~a~~~~~G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFD 199 (314)
|||+.|.+++-..+-|... .+..-|-||+.+...-..++|.+.. .....|..++..|....=+.++..|
T Consensus 1 MGIKNLKtLLL~~gsL~~~~~~~~~~~~~iFVD~ms~fmsiAysv~~~~------eL~~~~~~~iq~w~~~~gkVtlFvD 74 (438)
T PHA03065 1 MGIKNLKTLLLETGSLTKLDNNLKDRFNGIFVDTMSVFMSIAYSVNNLD------ELRSTFEEYVQQWVKKAGKVTLFVD 74 (438)
T ss_pred CchhhHHHHHHhcCCcccccccccccCceEEEechhhhhhhhhhhCCHH------HHHHHHHHHHHHHHhcCCcEEEEEe
Confidence 8999999999888744322 2245699999999988877774311 1334577788888554445555557
Q ss_pred CCCccchhhhhhhhhhhhHH-HH---------H--------------Hhc-----ccccccCcc----cHHHHHHHHHHH
Q psy14294 200 GGVPQLKKQTISTLEKDRDQ-LL---------L--------------ERG-----KQTRLASTI----TEQMSREAQELL 246 (314)
Q Consensus 200 G~~~~~K~~t~~kR~~~r~~-~~---------~--------------~~~-----k~~r~~~~i----~~~~i~~~~~lL 246 (314)
-+..+.|.....+|++.... .. . +.+ |..+..... ...+-..+-+.|
T Consensus 75 RG~I~IK~~lReKRr~a~~~~~kRK~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~~fLa~~~nlk~~l~~~L 154 (438)
T PHA03065 75 RGSIPIKQSLREKRRKASKNTIKRKREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQLFLANSNNLKRLLESAL 154 (438)
T ss_pred cCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHcchhhHHHHHHHHH
Confidence 77888999888887643221 10 0 000 000100000 112222345567
Q ss_pred HHh--CCceEecc-chHHHHHHHHHh-----cCCeeEEEcCCccEEeecC
Q psy14294 247 QLF--GVPFIVAP-GEAEAQCASLEL-----GNHTQGVITDDSDIWLFGA 288 (314)
Q Consensus 247 k~l--GV~~I~AP-~EADAq~A~L~~-----~g~vdaViS~DSD~llfG~ 288 (314)
..+ +|..+-+. -+||-.+-.=++ +|-=-.++|.|.|+++|.+
T Consensus 155 ~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s 204 (438)
T PHA03065 155 ARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSS 204 (438)
T ss_pred HhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEe
Confidence 777 89999888 688877665554 4755579999999999985
No 27
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=95.69 E-value=0.17 Score=50.76 Aligned_cols=158 Identities=14% Similarity=0.099 Sum_probs=101.2
Q ss_pred CCccccccccccccccccc---CCCCEEEeeHHHHHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHhCCCeeEEEeeCC
Q psy14294 125 MPQNDQHSMLEFRCNIVIN---KLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGG 201 (314)
Q Consensus 125 m~i~~l~~~l~~~~~Ls~~---~~g~rIaIDas~WL~q~~~a~~~~~G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFDG~ 201 (314)
|||+.|.+.+-..+-|... ..+.-|-||+.+..+-..+.|.+.. .-...|..++..|...+=+.++..|-+
T Consensus 1 MGIKNLK~lLl~~gsL~~i~~~~~~~~ifVD~msif~tiAysv~s~~------eL~~~~~~~i~~w~~~~~~VtlFvDRG 74 (425)
T PF04599_consen 1 MGIKNLKALLLETGSLKKIDNIEKNNEIFVDTMSIFMTIAYSVNSLD------ELRNSFEEYIQQWIKNNGKVTLFVDRG 74 (425)
T ss_pred CchhHHHHHHHhcCCceeccCCCCCccEEEEcchhhhhhhhhhCCHH------HHHHHHHHHHHHHHhcCCeEEEEEecC
Confidence 8899999888877733322 2256699999999988877774311 134567788899977666777777888
Q ss_pred CccchhhhhhhhhhhhHHHH-------H-----------------Hhc-----ccccccCcc----cHHHHHHHHHHHHH
Q psy14294 202 VPQLKKQTISTLEKDRDQLL-------L-----------------ERG-----KQTRLASTI----TEQMSREAQELLQL 248 (314)
Q Consensus 202 ~~~~K~~t~~kR~~~r~~~~-------~-----------------~~~-----k~~r~~~~i----~~~~i~~~~~lLk~ 248 (314)
..+.|.....+|++...... + +.. +..+....+ ...+-..+.++|..
T Consensus 75 ~I~iK~~lReKRr~a~k~~~~RK~~~i~~l~~~~~~ld~~d~~yeEikt~~~lki~K~~F~~fla~~~n~k~~l~~~L~~ 154 (425)
T PF04599_consen 75 SINIKEPLREKRRKALKNTIKRKREEIENLEDCIKNLDVDDEFYEEIKTDLELKIQKLSFQLFLANSNNLKTILESSLSR 154 (425)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHh
Confidence 99999998888854322110 0 000 000100000 11112234455555
Q ss_pred h--CCceEecc-chHHHHHHHHHh-----cCCeeEEEcCCccEEeecC
Q psy14294 249 F--GVPFIVAP-GEAEAQCASLEL-----GNHTQGVITDDSDIWLFGA 288 (314)
Q Consensus 249 l--GV~~I~AP-~EADAq~A~L~~-----~g~vdaViS~DSD~llfG~ 288 (314)
+ +|..+-+. .+||-.+-+=++ +|-=-.++|.|.|+++|.+
T Consensus 155 ~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss 202 (425)
T PF04599_consen 155 LKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSS 202 (425)
T ss_pred ccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeee
Confidence 5 89999888 788887766554 4755579999999999986
No 28
>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=95.03 E-value=0.094 Score=46.14 Aligned_cols=53 Identities=21% Similarity=0.165 Sum_probs=31.0
Q ss_pred EEeeHHHHHHHHHHHhhhhC-CCCCchHHHHHHHHHHHHHHh-CCCeeEEEeeCCCc
Q psy14294 149 LISDVSIWLHQLTKGTHDLA-GGSVPNAHLIGLYHRICKLLF-FKIKPVFVFDGGVP 203 (314)
Q Consensus 149 IaIDas~WL~q~~~a~~~~~-G~~~~~~~l~~f~~rL~~Ll~-~gI~PIFVFDG~~~ 203 (314)
|.|||++.||..- .+.... ...+. ..-..|+..|..+.. .|.+.++||||...
T Consensus 1 LlIDGYNli~~~~-~l~~~~~~~~l~-~aR~~Li~~L~~y~~~~~~~v~VVFDa~~~ 55 (166)
T PF05991_consen 1 LLIDGYNLIHAWP-ELRSLAERGDLE-AARERLIEMLSEYAQFSGYEVIVVFDAYKV 55 (166)
T ss_pred CeEcchhhhCCCH-HHHhhcCcCCHH-HHHHHHHHHHHHHhcccCCEEEEEEeCCcC
Confidence 4799999999741 222211 11221 123345555554443 68999999999653
No 29
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=91.46 E-value=0.048 Score=55.08 Aligned_cols=67 Identities=25% Similarity=0.301 Sum_probs=55.3
Q ss_pred HHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeecC-CeeeeeccCCCC--cEEEEehhh
Q psy14294 242 AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA-RTVYKNFFDKKS--HVLRYTAPD 309 (314)
Q Consensus 242 ~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG~-~~Vi~~l~~~~~--~v~~y~~~~ 309 (314)
.-.++...||.|+++||-|..|||||+...+|+++.+ -+|.+++.+ ++.|..+....+ ++.+|...+
T Consensus 134 ~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~ 203 (531)
T COG5366 134 ASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAFG-PSDILLLDGVDRIILDMSFGSDKPPLDVFHVPR 203 (531)
T ss_pred ccccccccceEEEehhhHHHHHHHHHHHHHHHHhcCC-chHhHHHhhhhhheeecccCCCCCCCcccccch
Confidence 4567888999999999999999999999999999998 599999975 788776655433 777777665
No 30
>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=80.27 E-value=8.2 Score=33.26 Aligned_cols=46 Identities=13% Similarity=-0.060 Sum_probs=27.4
Q ss_pred CEEEeeHHHHHHHHHHHhhhhCCCCCchHHHHHHHHHHHHHHhCCCeeEEEeeCC
Q psy14294 147 VDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGG 201 (314)
Q Consensus 147 ~rIaIDas~WL~q~~~a~~~~~G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFDG~ 201 (314)
..|.|||++--+... .+... .+.++..-+..|.+.|.++++||+-.
T Consensus 3 r~VVIDG~NVA~~~~------~~~~f---~~~~i~~~v~~~~~rG~~~v~v~~~~ 48 (155)
T PF11977_consen 3 RPVVIDGSNVAYSHG------NQKFF---SVRGIQIAVEYFKSRGHEVVVVFPPN 48 (155)
T ss_dssp --EEEEHHHHHHHHT------TTTSE---EHHHHHHHHHHHHHTT---EEEEEEG
T ss_pred CEEEEeCHHHHhhcC------CCCCc---CHHHHHHHHHHHHHcCCCeEEEEcch
Confidence 469999999755221 11111 35566666788999999999999963
No 31
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=79.73 E-value=12 Score=34.47 Aligned_cols=117 Identities=22% Similarity=0.101 Sum_probs=66.3
Q ss_pred cccccCCCCEEEeeHHHHHHHHHHHh------------hhhC---CCCCchHHH-HHHHHHHHHHHhCCCeeEEEeeCCC
Q psy14294 139 NIVINKLLVDLISDVSIWLHQLTKGT------------HDLA---GGSVPNAHL-IGLYHRICKLLFFKIKPVFVFDGGV 202 (314)
Q Consensus 139 ~Ls~~~~g~rIaIDas~WL~q~~~a~------------~~~~---G~~~~~~~l-~~f~~rL~~Ll~~gI~PIFVFDG~~ 202 (314)
+++-++ |+.++|||++.|--.-..+ ++.. |..-.+... ..+--.+..+.+.+++-+.+++|.+
T Consensus 60 ~~~~~r-g~~l~iDGyNvLItleSl~~g~~vlcdDg~iRDl~~~~gkyk~~E~t~~Al~lil~~lk~~~~k~vi~L~d~~ 138 (211)
T COG2454 60 KINSLR-GQDLVIDGYNVLITLESLLKGEAVLCDDGVIRDLRGVQGKYKINEKTDKALDLLLEFLKDVEPKSVIFLFDAP 138 (211)
T ss_pred cCCCcc-cceEEEechhhhhhHHHHhcCcEEEecCchhhhhhhhccchhhhhHHHHHHHHHHHHHHHcCCceEEEEeCCC
Confidence 455555 8999999999886432211 1111 111000011 1122223566778998777777744
Q ss_pred ccchhhhhhhhhhhhHHHHHHhcccccccCcccHHHHHHHHHHHHHhCCce-EeccchHHHHHHHHHhcCCeeEEEcCCc
Q psy14294 203 PQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPF-IVAPGEAEAQCASLELGNHTQGVITDDS 281 (314)
Q Consensus 203 ~~~K~~t~~kR~~~r~~~~~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~-I~AP~EADAq~A~L~~~g~vdaViS~DS 281 (314)
. .|..+ +...+.+.++++|||. +..---||..+..+. +|.|.|+
T Consensus 139 v-s~SGe----------------------------l~~~i~~~mK~~~I~g~~~lvk~~D~eLk~~e------~VaTsD~ 183 (211)
T COG2454 139 V-SKSGE----------------------------LAGRIEEKMKSLGIPGEASLVKNADFELKELE------VVATSDS 183 (211)
T ss_pred C-CccHH----------------------------HHHHHHHHHHhcCCCceeEeccCcCHHHHhcC------ceeecCe
Confidence 3 23322 3334667789999983 333456677776322 6899888
Q ss_pred cEEeecCCeee
Q psy14294 282 DIWLFGARTVY 292 (314)
Q Consensus 282 D~llfG~~~Vi 292 (314)
.+++.+++|.
T Consensus 184 -~IIdsv~~vV 193 (211)
T COG2454 184 -GIIDSVKRVV 193 (211)
T ss_pred -eeeeehhHHH
Confidence 6677766554
No 32
>PF05411 Peptidase_C32: Equine arteritis virus putative proteinase; InterPro: IPR008742 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases corresponds to MEROPS peptidase family C32 (clan CA). The type example is equine arteritis virus-type cysteine proteinase (porcine reproductive and respiratory syndrome virus), which is involved in viral polyprotein processing [].; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 3MTV_A.
Probab=58.66 E-value=4.1 Score=34.52 Aligned_cols=52 Identities=13% Similarity=0.203 Sum_probs=35.1
Q ss_pred ccccCCCcchhhHHHHHHHhhccccccccccC-----CCcccccccccccccccccC
Q psy14294 93 EQFSALPPDMRHEILTELLEQRKLSSWHKMHE-----MPQNDQHSMLEFRCNIVINK 144 (314)
Q Consensus 93 ~~~~~~p~~~~~~~~~~~~e~~~~~~w~~i~~-----m~i~~l~~~l~~~~~Ls~~~ 144 (314)
+=|..||.+++++=+.-..-+-|++.||.-.+ +.++||..+..+.+++.+.+
T Consensus 18 ~lF~~~~~~~~~~E~~~A~~fGYqt~~GV~GkYLqrRLqv~GLraV~d~~G~~~v~a 74 (127)
T PF05411_consen 18 SLFPGLPWEVQREEIRLAVQFGYQTKWGVPGKYLQRRLQVNGLRAVVDPYGPIHVYA 74 (127)
T ss_dssp GGG-SS-HHHHHHHHHHHHHSS-SSTT-B-SHHHHHHHHTTTEEEEE-TT-SEEEEE
T ss_pred HHcCCCChHHhHHHHHHHHHhCcccCCCCccHHHHHHHHhcCeeEEECCCCCEEEEE
Confidence 34888999998887777777899999998665 47888888888777766654
No 33
>KOG2044|consensus
Probab=50.72 E-value=1.4e+02 Score=32.99 Aligned_cols=145 Identities=17% Similarity=0.245 Sum_probs=79.4
Q ss_pred EEeeHHHHHHHHHHHhhhhCCCCC---chHHHHHHHH---HHHHHHhCCCeeEEEeeCCCccchhhhhhhhhhhhH-HHH
Q psy14294 149 LISDVSIWLHQLTKGTHDLAGGSV---PNAHLIGLYH---RICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRD-QLL 221 (314)
Q Consensus 149 IaIDas~WL~q~~~a~~~~~G~~~---~~~~l~~f~~---rL~~Ll~~gI~PIFVFDG~~~~~K~~t~~kR~~~r~-~~~ 221 (314)
+.+|..+-+|-+ ..+.+.|. ...-+..+|. ||-.+.+=.--++.-.||..|..|......|+=+.. ++.
T Consensus 51 LYLDMNGIIHPC----~HPEdkPaP~tedEm~~avFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaa 126 (931)
T KOG2044|consen 51 LYLDMNGIIHPC----THPEDKPAPETEDEMFVAVFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAA 126 (931)
T ss_pred eeeecCcccccC----CCCCCCCCCccHHHHHHHHHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhhHHH
Confidence 566666666544 33333332 1112333333 444444444456777899999999988777653221 111
Q ss_pred ----------HHh---ccc------cc--ccCcccH--HHHHHHHHHHHHh------------CCceEec----cchHHH
Q psy14294 222 ----------LER---GKQ------TR--LASTITE--QMSREAQELLQLF------------GVPFIVA----PGEAEA 262 (314)
Q Consensus 222 ----------~~~---~k~------~r--~~~~i~~--~~i~~~~~lLk~l------------GV~~I~A----P~EADA 262 (314)
++. .+. .. .+..||| +....+-..|+-. ||.+|.+ |+|+|-
T Consensus 127 e~~~e~e~~ree~~~~G~~lpp~~~~e~fDSNcITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEH 206 (931)
T KOG2044|consen 127 EKEAEIERLREEFEAEGKFLPPKVKKETFDSNCITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEH 206 (931)
T ss_pred HHHHHHHHHHHHHHhcCCcCCchhhccccccCccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchh
Confidence 000 000 00 1222332 2222333333221 7788864 799999
Q ss_pred HHHHHHhc---------CCeeEEEcCCccEEeecCC------eeeeeccC
Q psy14294 263 QCASLELG---------NHTQGVITDDSDIWLFGAR------TVYKNFFD 297 (314)
Q Consensus 263 q~A~L~~~---------g~vdaViS~DSD~llfG~~------~Vi~~l~~ 297 (314)
-+....+. +-.+++++-|.|+++.|.- .|+|....
T Consensus 207 KIM~yIR~QR~~P~~dPNT~HclyGlDADLImLgLATHE~hF~IlRE~~~ 256 (931)
T KOG2044|consen 207 KIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLGLATHEPHFSILREEFF 256 (931)
T ss_pred HHHHHHHHccCCCCCCCCceeeeecCCccceeeeccccCCceEEeeeeec
Confidence 88876653 3578899999999999953 36665444
No 34
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=50.36 E-value=33 Score=34.25 Aligned_cols=18 Identities=22% Similarity=0.285 Sum_probs=12.5
Q ss_pred HHHHHHHHHhCCceEecc
Q psy14294 240 REAQELLQLFGVPFIVAP 257 (314)
Q Consensus 240 ~~~~~lLk~lGV~~I~AP 257 (314)
..+.++++..||..|.+.
T Consensus 86 ~vl~~L~~~~~~~~V~~~ 103 (429)
T TIGR02765 86 DVLPELIKELGVRTVFLH 103 (429)
T ss_pred HHHHHHHHHhCCCEEEEe
Confidence 346677777788777665
No 35
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=49.25 E-value=1.4e+02 Score=32.74 Aligned_cols=140 Identities=19% Similarity=0.227 Sum_probs=78.0
Q ss_pred CCEEEeeHHHHHHHHHHHhhhhCCC-C-CchHHHHHHHHHHHHHHh---CCCeeEEEeeCCCccchhhhhhhhhhhhH-H
Q psy14294 146 LVDLISDVSIWLHQLTKGTHDLAGG-S-VPNAHLIGLYHRICKLLF---FKIKPVFVFDGGVPQLKKQTISTLEKDRD-Q 219 (314)
Q Consensus 146 g~rIaIDas~WL~q~~~a~~~~~G~-~-~~~~~l~~f~~rL~~Ll~---~gI~PIFVFDG~~~~~K~~t~~kR~~~r~-~ 219 (314)
+--+.+|..+-+|-+.+.- .|. | +...-+..+|..+..++. =.--.+.-.||..|..|...+..|+=+.. .
T Consensus 29 ~DNLYLDMNgIlH~CtHp~---d~~~petEeEm~~aVf~Yidhil~~irPrKllymAVDGvAPRAKMNQQRaRRFRsAkd 105 (953)
T COG5049 29 FDNLYLDMNGILHNCTHPN---DGSPPETEEEMYKAVFEYIDHILLKIRPRKLLYMAVDGVAPRAKMNQQRARRFRSAKD 105 (953)
T ss_pred cceeEEecccccccCCCCC---CCCCCCCHHHHHHHHHHHHHHHHHhcCcceEEEEEecccCchhhhhHHHHHhhhhhhh
Confidence 3458899888887653221 122 2 122233444444444433 23335667899999999987766643221 1
Q ss_pred ---HHH--H---------h--------------cccccccCcccHHHHHHHHHHHHH------------hCCceEec---
Q psy14294 220 ---LLL--E---------R--------------GKQTRLASTITEQMSREAQELLQL------------FGVPFIVA--- 256 (314)
Q Consensus 220 ---~~~--~---------~--------------~k~~r~~~~i~~~~i~~~~~lLk~------------lGV~~I~A--- 256 (314)
+.. + . .++...|+..-+.....+-..|.- .+|.+|.+
T Consensus 106 a~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~fDSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~ 185 (953)
T COG5049 106 ASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKFDSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHL 185 (953)
T ss_pred hHHHHhhccccccccchhccccCCccchhhhhhccccccCCCCCChHHHHHHHHHHHHHHhhhcCCccceeEEEEEecCc
Confidence 110 0 0 011112222111222223333322 26777764
Q ss_pred -cchHHHHHHHHHhc---------CCeeEEEcCCccEEeecC
Q psy14294 257 -PGEAEAQCASLELG---------NHTQGVITDDSDIWLFGA 288 (314)
Q Consensus 257 -P~EADAq~A~L~~~---------g~vdaViS~DSD~llfG~ 288 (314)
|||+|--+..+-+. +-.++|.+-|.|+++.|.
T Consensus 186 vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGL 227 (953)
T COG5049 186 VPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGL 227 (953)
T ss_pred CCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeec
Confidence 79999998877763 457789999999999995
No 36
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=45.12 E-value=56 Score=27.49 Aligned_cols=91 Identities=22% Similarity=0.303 Sum_probs=51.7
Q ss_pred HHHHhCCCee-EEEeeCCCccchhhhhhhhhhhhHHHHHHhcccccccCcccHHHHHHHHHHHHHhCCceE-eccchHHH
Q psy14294 185 CKLLFFKIKP-VFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFI-VAPGEAEA 262 (314)
Q Consensus 185 ~~Ll~~gI~P-IFVFDG~~~~~K~~t~~kR~~~r~~~~~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I-~AP~EADA 262 (314)
..|+++|+.| +.|+||.. ||........... ..-+-....+.++.+.+..+++.+.. |-++. .-.||=|
T Consensus 3 ~~ll~~g~~P~laIvD~kT---kR~~~~~~~~~~~----~~i~v~NPpG~It~el~~ai~~a~~~-~~~~~I~V~GEED- 73 (121)
T PF04019_consen 3 YNLLEAGIIPDLAIVDGKT---KREPVVEEVRKFY----RVIEVKNPPGTITEELIEAIKKALES-GKPVVIFVDGEED- 73 (121)
T ss_pred HHHHhCCCCCCEEEEeCcc---cccCCcccccCCc----eEEEEECCCCcccHHHHHHHHHHHhC-CCCEEEEEeChHH-
Confidence 4688999996 78999963 2322111000000 00011223567899999988888755 44433 3445544
Q ss_pred HHHHHHhcCCeeEEEcCCccEEeecCCe
Q psy14294 263 QCASLELGNHTQGVITDDSDIWLFGART 290 (314)
Q Consensus 263 q~A~L~~~g~vdaViS~DSD~llfG~~~ 290 (314)
|+.|-. ..+.++..+++||.+.
T Consensus 74 -L~~lPa-----il~aP~gs~V~YGQP~ 95 (121)
T PF04019_consen 74 -LAVLPA-----ILYAPEGSVVLYGQPG 95 (121)
T ss_pred -HHHHHH-----HHhCCCCCEEEECCCC
Confidence 444441 2455677799999874
No 37
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=43.30 E-value=43 Score=28.50 Aligned_cols=39 Identities=21% Similarity=0.156 Sum_probs=31.9
Q ss_pred HHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcC
Q psy14294 240 REAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITD 279 (314)
Q Consensus 240 ~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~ 279 (314)
..+.+.++..|++++.-...-..+..++...| ||+|+|+
T Consensus 150 ~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD 188 (189)
T cd08556 150 PELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITD 188 (189)
T ss_pred HHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecC
Confidence 45677888899999988877777888888788 7899995
No 38
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=43.25 E-value=28 Score=29.74 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHhCCceEeccchHHHHHHHHHhc-CCeeEEEcCCccEEe
Q psy14294 238 MSREAQELLQLFGVPFIVAPGEAEAQCASLELG-NHTQGVITDDSDIWL 285 (314)
Q Consensus 238 ~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~-g~vdaViS~DSD~ll 285 (314)
|+..+-..|+.+|+..+..+...|..+..++++ |-+ ++|.|.+++-
T Consensus 8 ~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~Ri--llTrd~~l~~ 54 (147)
T PF01927_consen 8 MLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGRI--LLTRDRDLLK 54 (147)
T ss_pred CHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCeE--EEECCHHHHH
Confidence 445678899999999999998899999999964 554 9999998654
No 39
>KOG2045|consensus
Probab=39.05 E-value=2.3e+02 Score=32.18 Aligned_cols=139 Identities=22% Similarity=0.268 Sum_probs=75.6
Q ss_pred EEeeHHHHHHHHHHHhhhhCCCCCc-hHHHHHHHHHHHHHHhCCCee----EEEeeCCCccchhhhhhhhhhhhH-HHHH
Q psy14294 149 LISDVSIWLHQLTKGTHDLAGGSVP-NAHLIGLYHRICKLLFFKIKP----VFVFDGGVPQLKKQTISTLEKDRD-QLLL 222 (314)
Q Consensus 149 IaIDas~WL~q~~~a~~~~~G~~~~-~~~l~~f~~rL~~Ll~~gI~P----IFVFDG~~~~~K~~t~~kR~~~r~-~~~~ 222 (314)
+.+|..+-||.+-+...+.-..+++ ...+..+|.-+..|-. -|+| ..-.||..|..|......|+=+.. .+..
T Consensus 32 LYLDMNgIlHNCsH~nDddvt~rLtEeEif~~IfnYIdhLf~-~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~ 110 (1493)
T KOG2045|consen 32 LYLDMNGILHNCSHPNDDDVTFRLTEEEIFQEIFNYIDHLFY-LIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQ 110 (1493)
T ss_pred eeeecccccccCCCCCCCccCcCCCHHHHHHHHHHHHHHHHH-hhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHH
Confidence 7889988888764322221111222 1133445555544433 2444 445699999999988777653322 1211
Q ss_pred Hhccc---------cc-ccCcccHH--HHHHHHHHHHHh------------CCceEe----ccchHHHHHHHHHhc----
Q psy14294 223 ERGKQ---------TR-LASTITEQ--MSREAQELLQLF------------GVPFIV----APGEAEAQCASLELG---- 270 (314)
Q Consensus 223 ~~~k~---------~r-~~~~i~~~--~i~~~~~lLk~l------------GV~~I~----AP~EADAq~A~L~~~---- 270 (314)
...|+ .+ .+..|+|. ....+.+-|..+ ++.+|. +|||+|--+.-.-+.
T Consensus 111 qlaKA~enGe~~p~erFDSNcITPGTeFM~rl~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq 190 (1493)
T KOG2045|consen 111 QLAKAAENGELRPHERFDSNCITPGTEFMVRLQEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQ 190 (1493)
T ss_pred HHHHHHhccccCcccccccCCCCCcHHHHHHHHHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcC
Confidence 11111 11 13334432 222233333322 677774 689999988766542
Q ss_pred -----CCeeEEEcCCccEEeecC
Q psy14294 271 -----NHTQGVITDDSDIWLFGA 288 (314)
Q Consensus 271 -----g~vdaViS~DSD~llfG~ 288 (314)
+-=+++++=|-|+++.|.
T Consensus 191 ~dydpNTRHClYGLDADLImLGL 213 (1493)
T KOG2045|consen 191 PDYDPNTRHCLYGLDADLIMLGL 213 (1493)
T ss_pred CCCCCCcceeecccchhhheeee
Confidence 234568899999999984
No 40
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=37.88 E-value=73 Score=27.35 Aligned_cols=46 Identities=24% Similarity=0.270 Sum_probs=36.6
Q ss_pred cccHHHHHHHHHHHHHhCCc-----eEecc--chHHHHHHHHHhcCCeeEEEc
Q psy14294 233 TITEQMSREAQELLQLFGVP-----FIVAP--GEAEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 233 ~i~~~~i~~~~~lLk~lGV~-----~I~AP--~EADAq~A~L~~~g~vdaViS 278 (314)
.++..|...+.+.|+..|++ .+..| +|-=-.+..|++.|-.|+|++
T Consensus 13 ~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~ 65 (138)
T TIGR00114 13 DITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIA 65 (138)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 56778888999999999875 66778 677777778888777788775
No 41
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=37.79 E-value=33 Score=27.77 Aligned_cols=36 Identities=17% Similarity=0.114 Sum_probs=27.3
Q ss_pred hHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeec
Q psy14294 259 EAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNF 295 (314)
Q Consensus 259 EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l 295 (314)
-+|+.++..+..+- +.++|.|.|+-.|+.-.++.++
T Consensus 105 ~~D~~i~a~A~~~~-~~lvT~D~~f~~~~~~~i~~P~ 140 (142)
T TIGR00028 105 VTDAHLAALAREHG-AELVTFDRGFARFAGIRWRDPL 140 (142)
T ss_pred chHHHHHHHHHHcC-CEEEecCCCccccCCCeeeCCC
Confidence 48999998887654 5889999998767766666554
No 42
>PRK01160 hypothetical protein; Provisional
Probab=37.63 E-value=1.2e+02 Score=27.26 Aligned_cols=92 Identities=18% Similarity=0.216 Sum_probs=52.5
Q ss_pred HHHHhCCCeeEE-EeeCCCccchhhhhhhhh-hhhHHHHHHhcccccccCcccHHHHHHHHHHHHH--hCCce-Eeccch
Q psy14294 185 CKLLFFKIKPVF-VFDGGVPQLKKQTISTLE-KDRDQLLLERGKQTRLASTITEQMSREAQELLQL--FGVPF-IVAPGE 259 (314)
Q Consensus 185 ~~Ll~~gI~PIF-VFDG~~~~~K~~t~~kR~-~~r~~~~~~~~k~~r~~~~i~~~~i~~~~~lLk~--lGV~~-I~AP~E 259 (314)
..|+++|+.|-+ |+||.. ||......- ..... .-+-....+.++.+.++.+++.+.. -|.++ |.-.|
T Consensus 52 ~~ll~~g~~P~laIvD~kT---kR~~~~~~i~~~~~~----~i~V~NPpGtIt~el~~ai~~a~~~~~~~~~~~I~VdG- 123 (178)
T PRK01160 52 ENLLRVGLKPFLAIYDLKT---KRREYKPSIFEHEEV----SITVRNPPGTITLALLRAIKKAFSLIERGKKVRIEVNG- 123 (178)
T ss_pred HHHHHCCCCCCEEEEeCcc---ccCCCcccccccccc----EEEEECCCCcccHHHHHHHHHHHHhhhcCCeEEEEEcC-
Confidence 567899999977 999953 333211100 00000 0111234568899999988888542 35553 33344
Q ss_pred HHHHHHHHHhcCCeeEEEcCCccEEeecCCe
Q psy14294 260 AEAQCASLELGNHTQGVITDDSDIWLFGART 290 (314)
Q Consensus 260 ADAq~A~L~~~g~vdaViS~DSD~llfG~~~ 290 (314)
|-.+|.|-. ..+.+...+++||-|.
T Consensus 124 -EEDLa~lP~-----il~aP~gs~VlYGQP~ 148 (178)
T PRK01160 124 -EEDLAVIPA-----VLYAPLGTVVAYGQPD 148 (178)
T ss_pred -hHHHHHHHH-----HHhcCCCCEEEeCCCC
Confidence 445565552 2344567799999863
No 43
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=35.71 E-value=1.3e+02 Score=30.68 Aligned_cols=19 Identities=11% Similarity=0.017 Sum_probs=13.1
Q ss_pred HHHHHHHHHHhCCceEecc
Q psy14294 239 SREAQELLQLFGVPFIVAP 257 (314)
Q Consensus 239 i~~~~~lLk~lGV~~I~AP 257 (314)
...+.++++..+|..|.+.
T Consensus 85 ~~vl~~l~~~~~i~~v~~~ 103 (472)
T PRK10674 85 VEWLKQFCQQHQVTHLFYN 103 (472)
T ss_pred HHHHHHHHHHcCCCEEEEe
Confidence 3446777778888777665
No 44
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=35.63 E-value=1e+02 Score=26.57 Aligned_cols=46 Identities=28% Similarity=0.294 Sum_probs=38.0
Q ss_pred cccHHHHHHHHHHHHHhCC-----ceEecc--chHHHHHHHHHhcCCeeEEEc
Q psy14294 233 TITEQMSREAQELLQLFGV-----PFIVAP--GEAEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 233 ~i~~~~i~~~~~lLk~lGV-----~~I~AP--~EADAq~A~L~~~g~vdaViS 278 (314)
.+...+...+.+.|+..|+ ..+..| +|-=-.+..|.+.|-+|+|+.
T Consensus 16 ~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~ 68 (144)
T PF00885_consen 16 EITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIA 68 (144)
T ss_dssp HHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEE
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEE
Confidence 4667788889999999987 677777 788888889998888888876
No 45
>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=34.35 E-value=1.6e+02 Score=25.84 Aligned_cols=71 Identities=11% Similarity=0.093 Sum_probs=41.8
Q ss_pred CccchhhhhhhhhhhhHHHHHHhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCc
Q psy14294 202 VPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDS 281 (314)
Q Consensus 202 ~~~~K~~t~~kR~~~r~~~~~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DS 281 (314)
.+..|..++.+|++++..+ +...|..-|+..|---+-.-.+-...|+.||++ +-.|+-+|.
T Consensus 6 ~pt~kErEnnk~RERrRRA-----------------IaakIfaGLR~~Gny~Lp~~aD~NeVLkALc~e--AGw~Ve~DG 66 (150)
T PF05687_consen 6 RPTWKERENNKRRERRRRA-----------------IAAKIFAGLRAHGNYKLPKHADNNEVLKALCRE--AGWTVEPDG 66 (150)
T ss_pred cccHhhhHHHHHHHHHHHH-----------------HHHHHHHHHHHhcCCCCCCcCCHHHHHHHHHHh--CCEEEccCC
Confidence 4556666666665554432 222345556666654454555666677777765 224677788
Q ss_pred cEEeecCCee
Q psy14294 282 DIWLFGARTV 291 (314)
Q Consensus 282 D~llfG~~~V 291 (314)
..|=-|++..
T Consensus 67 Ttyr~~~~~~ 76 (150)
T PF05687_consen 67 TTYRKGCKPP 76 (150)
T ss_pred CeeccCCCCC
Confidence 8887666654
No 46
>cd04236 AAK_NAGS-Urea AAK_NAGS-Urea: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the urea cycle found in animals. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate; NAG is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Ureogenic NAGS activity is dependent on the concentration of glutamate (substrate) and arginine (activator). Domain architecture of ureogenic NAGS consists of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal DUF619 domain. Members of this CD belong to the protein superfamily, the Amino Acid Kinase Family (AAKF).
Probab=33.97 E-value=56 Score=31.11 Aligned_cols=53 Identities=15% Similarity=0.178 Sum_probs=36.1
Q ss_pred eHHHHHHHHHHHhh--h-------hCCCCCc-hHHHHHHHHHHHHHHhCCCeeEEEeeCCCcc
Q psy14294 152 DVSIWLHQLTKGTH--D-------LAGGSVP-NAHLIGLYHRICKLLFFKIKPVFVFDGGVPQ 204 (314)
Q Consensus 152 Das~WL~q~~~a~~--~-------~~G~~~~-~~~l~~f~~rL~~Ll~~gI~PIFVFDG~~~~ 204 (314)
++..||.+|..... . .+|..+. ...+..+...+..|...|++||+|.-|.+.-
T Consensus 18 e~~~~l~~f~~~~~~~~~~f~VIK~GG~~~~~~~~~~~l~~dla~L~~lGl~~VlVHGggp~i 80 (271)
T cd04236 18 EARYWLTQFQIAMPNDWPAFAVLEVDHSVFRSLEMVQSLSFGLAFLQRMDMKLLVVMGLSAPD 80 (271)
T ss_pred HHHHHHHHhhccCCCCCCCEEEEEEChhhhcCchhHHHHHHHHHHHHHCCCeEEEEeCCChHH
Confidence 45678877743211 1 1333332 2367789999999999999999999997643
No 47
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=32.89 E-value=45 Score=31.96 Aligned_cols=38 Identities=21% Similarity=0.187 Sum_probs=32.6
Q ss_pred cccHHHHHHHHHHHHHhCCceEecc-chHHHHHHHHHhc
Q psy14294 233 TITEQMSREAQELLQLFGVPFIVAP-GEAEAQCASLELG 270 (314)
Q Consensus 233 ~i~~~~i~~~~~lLk~lGV~~I~AP-~EADAq~A~L~~~ 270 (314)
.-....+..+.+++..+|++++..+ +|||+.++.+++.
T Consensus 92 ~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~ 130 (310)
T COG0258 92 DELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQK 130 (310)
T ss_pred HHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHH
Confidence 3445566788999999999999888 9999999999975
No 48
>cd01971 Nitrogenase_VnfN_like Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like. This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protien for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.
Probab=32.31 E-value=1.7e+02 Score=29.25 Aligned_cols=18 Identities=22% Similarity=0.174 Sum_probs=13.6
Q ss_pred HHH-HHhCCCeeEEEeeCC
Q psy14294 184 ICK-LLFFKIKPVFVFDGG 201 (314)
Q Consensus 184 L~~-Ll~~gI~PIFVFDG~ 201 (314)
+.. |...|++++.||.+.
T Consensus 178 lk~lL~~~Gl~v~~~~~~~ 196 (427)
T cd01971 178 IKRVLEGIGLKVNILFGPE 196 (427)
T ss_pred HHHHHHHCCCeEEEEECCC
Confidence 444 445999999999864
No 49
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=31.34 E-value=85 Score=25.71 Aligned_cols=37 Identities=22% Similarity=0.139 Sum_probs=28.1
Q ss_pred HHHHHH-hCCceEe---ccchHHHHHHHHHhcCCeeEEEcC
Q psy14294 243 QELLQL-FGVPFIV---APGEAEAQCASLELGNHTQGVITD 279 (314)
Q Consensus 243 ~~lLk~-lGV~~I~---AP~EADAq~A~L~~~g~vdaViS~ 279 (314)
-+.|+. .|+++-. .|.|++.+++.+-++|.+|+|+.-
T Consensus 37 a~~L~~~~Gi~v~~vk~~~~~g~~~i~~~i~~g~i~~VInt 77 (115)
T cd01422 37 GLLIQEATGLTVNRMKSGPLGGDQQIGALIAEGEIDAVIFF 77 (115)
T ss_pred HHHHHHhhCCcEEEEecCCCCchhHHHHHHHcCceeEEEEc
Confidence 345666 7887642 237999999999999999998653
No 50
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=30.81 E-value=61 Score=26.15 Aligned_cols=36 Identities=19% Similarity=0.172 Sum_probs=27.9
Q ss_pred HHHHHHhCCceE--eccch-HHHHHHHHHhc-CCeeEEEc
Q psy14294 243 QELLQLFGVPFI--VAPGE-AEAQCASLELG-NHTQGVIT 278 (314)
Q Consensus 243 ~~lLk~lGV~~I--~AP~E-ADAq~A~L~~~-g~vdaViS 278 (314)
-+.|+..||++. ..+.| +++++..+-++ |.+|.||.
T Consensus 35 a~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn 74 (112)
T cd00532 35 SRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVIN 74 (112)
T ss_pred HHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEE
Confidence 355677898864 44566 78999999999 99999886
No 51
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=30.44 E-value=94 Score=27.43 Aligned_cols=48 Identities=15% Similarity=0.171 Sum_probs=37.8
Q ss_pred cCcccHHHHHHHHHHHHHhC-----CceEecc--chHHHHHHHHHhcCCeeEEEc
Q psy14294 231 ASTITEQMSREAQELLQLFG-----VPFIVAP--GEAEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 231 ~~~i~~~~i~~~~~lLk~lG-----V~~I~AP--~EADAq~A~L~~~g~vdaViS 278 (314)
...++..++.-+.+.|+..| |.++..| +|-=..+..|++.|..|+|+.
T Consensus 21 n~~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIa 75 (158)
T PRK12419 21 HADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVA 75 (158)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 34577888889999999999 5677788 677777778888887777765
No 52
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=30.09 E-value=1.5e+02 Score=30.07 Aligned_cols=35 Identities=3% Similarity=-0.018 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhCCceEeccc--h-----HHHHHHHHHh-cCC
Q psy14294 238 MSREAQELLQLFGVPFIVAPG--E-----AEAQCASLEL-GNH 272 (314)
Q Consensus 238 ~i~~~~~lLk~lGV~~I~AP~--E-----ADAq~A~L~~-~g~ 272 (314)
....+.++++..||..|.+-. + -|..+...++ .|.
T Consensus 75 ~~~~l~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~~~gi 117 (475)
T TIGR02766 75 TVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQGI 117 (475)
T ss_pred HHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHcCC
Confidence 445578888889998775442 2 3555565554 444
No 53
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=29.31 E-value=59 Score=25.23 Aligned_cols=47 Identities=30% Similarity=0.282 Sum_probs=36.2
Q ss_pred CcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEE
Q psy14294 232 STITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIW 284 (314)
Q Consensus 232 ~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~l 284 (314)
..++.+....+.++....+ ..-+|+.++.++...-+..|+|.|.|+.
T Consensus 70 ~~~~~~~~~~~~~~~~~~~------~~~~Da~~~a~A~~~~~~~v~T~D~~f~ 116 (121)
T PF01850_consen 70 LPITSEVFERAAELMRKYG------LDFADALIAATAKENGAPLVVTFDKDFR 116 (121)
T ss_dssp EEBCHHHHHHHHHHHHHHH------SSHHHHHHHHHHHHHT-EEE-ESSHHHH
T ss_pred ccchhHHHHHHHHHHHhcc------CChhHHHHHHHHHHcCCEEEEECCcCHH
Confidence 3467788888888888877 7788999999998766767779999853
No 54
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=29.29 E-value=36 Score=27.28 Aligned_cols=29 Identities=14% Similarity=0.329 Sum_probs=23.2
Q ss_pred cchHHHHHHHHHhcCCeeEEEcCCccEEe
Q psy14294 257 PGEAEAQCASLELGNHTQGVITDDSDIWL 285 (314)
Q Consensus 257 P~EADAq~A~L~~~g~vdaViS~DSD~ll 285 (314)
+-..|+-+...+..+-+|+++|.|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 45567777778888889999999999763
No 55
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=29.07 E-value=77 Score=27.17 Aligned_cols=36 Identities=17% Similarity=0.102 Sum_probs=28.0
Q ss_pred HHHHHHh-CCceEeccch---HHHHHHHHHhcCCeeEEEc
Q psy14294 243 QELLQLF-GVPFIVAPGE---AEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 243 ~~lLk~l-GV~~I~AP~E---ADAq~A~L~~~g~vdaViS 278 (314)
-+.|+.. |+++-.-.+| ++.+++.+-++|.+++||.
T Consensus 42 a~~L~~~~Gi~v~~vi~~~~gg~~~i~~~I~~g~i~lVIn 81 (142)
T PRK05234 42 GGLIQEATGLDVTRLLSGPLGGDQQIGALIAEGKIDMLIF 81 (142)
T ss_pred HHHHHhccCCeeEEEEcCCCCCchhHHHHHHcCceeEEEE
Confidence 4556777 8886544555 7899999999999999976
No 56
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=28.99 E-value=22 Score=28.90 Aligned_cols=29 Identities=34% Similarity=0.620 Sum_probs=23.5
Q ss_pred CCccccccccccCCCcchhhHHHHHHHhh
Q psy14294 85 LHSVDINSEQFSALPPDMRHEILTELLEQ 113 (314)
Q Consensus 85 ~~~~~~~s~~~~~~p~~~~~~~~~~~~e~ 113 (314)
+..-.|..+-+.+||+++|-|||....-.
T Consensus 40 ~~~~~I~pefL~ALP~diR~EVl~qe~~~ 68 (108)
T PF14377_consen 40 PQPSQIDPEFLAALPPDIREEVLAQERRE 68 (108)
T ss_pred CCccccCHHHHHhCCHHHHHHHHHHHHHH
Confidence 44556777999999999999999876554
No 57
>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molec
Probab=28.54 E-value=2.2e+02 Score=27.60 Aligned_cols=20 Identities=30% Similarity=0.468 Sum_probs=14.6
Q ss_pred HHHH-HHhCCCeeEEEeeCCC
Q psy14294 183 RICK-LLFFKIKPVFVFDGGV 202 (314)
Q Consensus 183 rL~~-Ll~~gI~PIFVFDG~~ 202 (314)
.+.. |...|++++.+|++..
T Consensus 170 el~~ll~~~G~~v~~~~~~~~ 190 (399)
T cd00316 170 ELKRLLEEMGIRVNALFDGGT 190 (399)
T ss_pred HHHHHHHHcCCcEEEEcCCCC
Confidence 3444 4569999999999843
No 58
>PF09372 PRANC: PRANC domain; InterPro: IPR018272 This presumed domain is found at the C terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin, C-terminal) domain is also found on its own in some proteins []. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.
Probab=28.27 E-value=26 Score=27.62 Aligned_cols=19 Identities=26% Similarity=0.508 Sum_probs=16.6
Q ss_pred cccccCCCcchhhHHHHHH
Q psy14294 92 SEQFSALPPDMRHEILTEL 110 (314)
Q Consensus 92 s~~~~~~p~~~~~~~~~~~ 110 (314)
+.-+..||+|+|+.||.-|
T Consensus 69 ~~~w~~LP~EIk~~Il~~L 87 (97)
T PF09372_consen 69 NNYWNILPIEIKYKILEYL 87 (97)
T ss_pred CCchhhCCHHHHHHHHHcC
Confidence 5789999999999999744
No 59
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=26.53 E-value=89 Score=24.84 Aligned_cols=36 Identities=25% Similarity=0.280 Sum_probs=28.3
Q ss_pred HHHHHHhCCce--EeccchHHHHHHHHHhcCCeeEEEc
Q psy14294 243 QELLQLFGVPF--IVAPGEAEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 243 ~~lLk~lGV~~--I~AP~EADAq~A~L~~~g~vdaViS 278 (314)
-+.|+..|+++ +..+.+++.++..+-++|.+|.|+.
T Consensus 36 ~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn 73 (110)
T cd01424 36 AKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVIN 73 (110)
T ss_pred HHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEE
Confidence 35577788885 4445678899999999999999987
No 60
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=26.43 E-value=1.4e+02 Score=25.76 Aligned_cols=47 Identities=17% Similarity=0.237 Sum_probs=36.8
Q ss_pred CcccHHHHHHHHHHHHHhCC-----ceEecc--chHHHHHHHHHhcCCeeEEEc
Q psy14294 232 STITEQMSREAQELLQLFGV-----PFIVAP--GEAEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 232 ~~i~~~~i~~~~~lLk~lGV-----~~I~AP--~EADAq~A~L~~~g~vdaViS 278 (314)
..++..++.-+.+.|+..|+ .++.-| +|-=..+..|++.|..|+|++
T Consensus 19 ~~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIa 72 (141)
T PLN02404 19 EIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILC 72 (141)
T ss_pred HHHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 35777888899999999996 566677 777777778888776777775
No 61
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=26.39 E-value=64 Score=29.97 Aligned_cols=15 Identities=27% Similarity=0.091 Sum_probs=13.0
Q ss_pred chHHHHHHHHHhcCC
Q psy14294 258 GEAEAQCASLELGNH 272 (314)
Q Consensus 258 ~EADAq~A~L~~~g~ 272 (314)
-|.||.+|||++.|.
T Consensus 194 te~~AliAYLq~LG~ 208 (217)
T PRK14487 194 TEMDALIAYLQSLGT 208 (217)
T ss_pred cHHHHHHHHHHHhcc
Confidence 789999999998773
No 62
>PF13919 ASXH: Asx homology domain
Probab=26.33 E-value=24 Score=30.32 Aligned_cols=23 Identities=39% Similarity=0.644 Sum_probs=21.1
Q ss_pred cccccccCCCcchhhHHHHHHHh
Q psy14294 90 INSEQFSALPPDMRHEILTELLE 112 (314)
Q Consensus 90 ~~s~~~~~~p~~~~~~~~~~~~e 112 (314)
||.+.|.+||++-+.+||.=+-+
T Consensus 39 ~N~~tw~~L~~eeq~eLl~LLP~ 61 (138)
T PF13919_consen 39 LNPETWSCLPEEEQQELLKLLPE 61 (138)
T ss_pred hCHHHHhcCCHHHHHHHHHhCCC
Confidence 57899999999999999998777
No 63
>PF02677 DUF208: Uncharacterized BCR, COG1636; InterPro: IPR003828 This entry describes proteins of unknown function.
Probab=24.56 E-value=3.7e+02 Score=24.12 Aligned_cols=56 Identities=13% Similarity=0.034 Sum_probs=36.9
Q ss_pred HHHHHhCCCeeEEEeeCCCccchhhhhhhhhhhhHHHHHHhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHH
Q psy14294 184 ICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQ 263 (314)
Q Consensus 184 L~~Ll~~gI~PIFVFDG~~~~~K~~t~~kR~~~r~~~~~~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq 263 (314)
+..|...|+.|.+-|=.++.--.. +..+|. ..++++.+.+||++|.++|+-+.-
T Consensus 15 ~~~L~~~g~~vt~~fyNPNIhP~~-Ey~~R~-------------------------~~~~~~~~~~~i~~i~~~Y~~~~w 68 (176)
T PF02677_consen 15 LERLREEGFDVTGYFYNPNIHPYE-EYERRL-------------------------EELKRFAEKLGIPLIEGDYDPEEW 68 (176)
T ss_pred HHHHHHCCCCeEEEEeCCCCCcHH-HHHHHH-------------------------HHHHHHHHHcCCCEEecCCCHHHH
Confidence 477888999999999887632211 222222 235667777789998888876654
Q ss_pred HH
Q psy14294 264 CA 265 (314)
Q Consensus 264 ~A 265 (314)
+.
T Consensus 69 ~~ 70 (176)
T PF02677_consen 69 LR 70 (176)
T ss_pred HH
Confidence 43
No 64
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=24.44 E-value=1.4e+02 Score=26.02 Aligned_cols=46 Identities=24% Similarity=0.268 Sum_probs=35.2
Q ss_pred cccHHHHHHHHHHHHHhCC-----ceEecc--chHHHHHHHHHhcCCeeEEEc
Q psy14294 233 TITEQMSREAQELLQLFGV-----PFIVAP--GEAEAQCASLELGNHTQGVIT 278 (314)
Q Consensus 233 ~i~~~~i~~~~~lLk~lGV-----~~I~AP--~EADAq~A~L~~~g~vdaViS 278 (314)
.++..+...+.+.|+..|| ..+.-| +|-=..+..|++.+-.|+|++
T Consensus 25 ~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIa 77 (154)
T PRK00061 25 FITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIA 77 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEE
Confidence 5677888899999999994 556677 676667778887777777775
No 65
>cd08562 GDPD_EcUgpQ_like Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two distinct GP-GDEs. UgpQ gene from the E. coli ugp operon codes for a cytosolic phosphodiesterase GlpQ, which is the prototype of this family. Various glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG)
Probab=23.26 E-value=1.4e+02 Score=26.52 Aligned_cols=38 Identities=24% Similarity=0.207 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcC
Q psy14294 241 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITD 279 (314)
Q Consensus 241 ~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~ 279 (314)
.+.+.++..|+++..-.--...++.+|...| ||+|+|+
T Consensus 190 ~~v~~~~~~g~~v~~wTvn~~~~~~~~~~~g-VdgiiTD 227 (229)
T cd08562 190 EQVKALKDAGYKLLVYTVNDPARAAELLEWG-VDAIFTD 227 (229)
T ss_pred HHHHHHHHCCCEEEEEeCCCHHHHHHHHHCC-CCEEEcC
Confidence 4667788899999887766667778888777 7899995
No 66
>PF03009 GDPD: Glycerophosphoryl diester phosphodiesterase family; InterPro: IPR004129 Glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol) all of which are are hydrolysed by this enzyme.; GO: 0008889 glycerophosphodiester phosphodiesterase activity, 0006071 glycerol metabolic process; PDB: 3I10_A 2P76_H 2OOG_F 3KS6_D 3KS5_A 2PZ0_B 1YDY_B 1T8Q_A 1O1Z_A 3L12_B ....
Probab=22.86 E-value=1.2e+02 Score=26.75 Aligned_cols=41 Identities=20% Similarity=0.092 Sum_probs=28.2
Q ss_pred HHHHHHHHhCCceEeccchHH--HHHHHHHhcCCeeEEEcCCcc
Q psy14294 241 EAQELLQLFGVPFIVAPGEAE--AQCASLELGNHTQGVITDDSD 282 (314)
Q Consensus 241 ~~~~lLk~lGV~~I~AP~EAD--Aq~A~L~~~g~vdaViS~DSD 282 (314)
.+.+.++..|+.++.--..=+ +...++...| ||+|+|++-|
T Consensus 213 ~~v~~~~~~g~~v~~wtvn~~~~~~~~~l~~~g-vdgIiTD~P~ 255 (256)
T PF03009_consen 213 RLVQEAHKAGLKVYVWTVNDPDVEDMKRLLDLG-VDGIITDFPD 255 (256)
T ss_dssp HHHHHHHHTT-EEEEBSB-SHSHHHHHHHHHHT--SEEEES-HH
T ss_pred HHHHHHHHCCCEEEEEecCCcHHHHHHHHHhCC-CCEEEEcCCC
Confidence 466778999999998775555 7777777665 7899997543
No 67
>COG0548 ArgB Acetylglutamate kinase [Amino acid transport and metabolism]
Probab=22.84 E-value=91 Score=29.77 Aligned_cols=27 Identities=33% Similarity=0.400 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHhCCCeeEEEeeCCC
Q psy14294 176 HLIGLYHRICKLLFFKIKPVFVFDGGV 202 (314)
Q Consensus 176 ~l~~f~~rL~~Ll~~gI~PIFVFDG~~ 202 (314)
.+..|+..+..|...|++||+|..|.+
T Consensus 19 l~~~~~~di~lL~~~G~~~VvVHGggp 45 (265)
T COG0548 19 LLEAFASDIALLKSVGIRPVVVHGGGP 45 (265)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEeCCch
Confidence 367788889999999999999999986
No 68
>cd01966 Nitrogenase_NifN_1 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
Probab=22.01 E-value=3e+02 Score=27.55 Aligned_cols=20 Identities=20% Similarity=0.595 Sum_probs=13.7
Q ss_pred HHHHH-HhCCCeeEEE------eeCCC
Q psy14294 183 RICKL-LFFKIKPVFV------FDGGV 202 (314)
Q Consensus 183 rL~~L-l~~gI~PIFV------FDG~~ 202 (314)
.++.| ...|++++.| |||..
T Consensus 175 eik~lL~~~Gl~v~~l~d~s~~~d~~~ 201 (417)
T cd01966 175 ELKDIIEAFGLEPIILPDLSGSLDGHL 201 (417)
T ss_pred HHHHHHHHcCCceEEecCcccccCCCC
Confidence 44444 4589999998 66754
No 69
>cd01965 Nitrogenase_MoFe_beta_like Nitrogenase_MoFe_beta_like: Nitrogenase MoFe protein, beta subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. This group contains the beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having alpha and beta subunits similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (Fe
Probab=21.88 E-value=3e+02 Score=27.48 Aligned_cols=15 Identities=27% Similarity=0.421 Sum_probs=11.7
Q ss_pred HHHHhCCCeeEEEee
Q psy14294 185 CKLLFFKIKPVFVFD 199 (314)
Q Consensus 185 ~~Ll~~gI~PIFVFD 199 (314)
..|...|++++.|||
T Consensus 176 ~lL~~~Gl~v~~~~~ 190 (428)
T cd01965 176 RILEAFGLEPIILPD 190 (428)
T ss_pred HHHHHcCCCEEEecC
Confidence 344569999999986
No 70
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=21.75 E-value=1.3e+02 Score=26.95 Aligned_cols=42 Identities=29% Similarity=0.395 Sum_probs=30.3
Q ss_pred HHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccE
Q psy14294 240 REAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDI 283 (314)
Q Consensus 240 ~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~ 283 (314)
..+.+.++..|+++..---.-..++.+|. .+ ||+|+|++-|.
T Consensus 184 ~~~v~~~~~~G~~v~~WTvn~~~~~~~l~-~~-vdgiiTD~p~~ 225 (226)
T cd08568 184 VELLRLLRKLGLKIVLWTVNDPELVPKLK-GL-VDGVITDDVEK 225 (226)
T ss_pred HHHHHHHHHCCCEEEEEcCCCHHHHHHHH-hh-CCEEEccCccc
Confidence 45667788899999887654445556665 46 99999976543
No 71
>PF11770 GAPT: GRB2-binding adapter (GAPT); InterPro: IPR021082 This entry represents a family of transmembrane proteins which bind the growth factor receptor-bound protein 2 (GRB2) in B cells []. In contrast to other transmembrane adaptor proteins, GAPT, which this entry represents, is not phosphorylated upon BCR ligation. It associates with GRB2 constitutively through its proline-rich region [].
Probab=21.74 E-value=62 Score=28.44 Aligned_cols=13 Identities=31% Similarity=0.687 Sum_probs=9.8
Q ss_pred CCCccccceecCC
Q psy14294 46 SVSREVDMFELPP 58 (314)
Q Consensus 46 ~~~~~~~~~~~~~ 58 (314)
.+.-++|||+||+
T Consensus 144 ~~pqdEDIYILPD 156 (158)
T PF11770_consen 144 EVPQDEDIYILPD 156 (158)
T ss_pred CCCCccceEecCC
Confidence 3445679999997
No 72
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=21.70 E-value=1.8e+02 Score=29.56 Aligned_cols=45 Identities=20% Similarity=0.203 Sum_probs=40.1
Q ss_pred cccHHHHHHHHHHHHHhCCceE--eccchHHHHHHHHHhcCCeeEEE
Q psy14294 233 TITEQMSREAQELLQLFGVPFI--VAPGEAEAQCASLELGNHTQGVI 277 (314)
Q Consensus 233 ~i~~~~i~~~~~lLk~lGV~~I--~AP~EADAq~A~L~~~g~vdaVi 277 (314)
-++..-+..+++.|...|++++ .|-+-+-.-+-.|.+.|.+|+|+
T Consensus 194 GvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li~~G~~~~Vl 240 (403)
T PF06792_consen 194 GVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLIREGQFDGVL 240 (403)
T ss_pred CCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHHHcCCcEEEE
Confidence 4678888999999999999877 47799999999999999999887
No 73
>PRK09454 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional
Probab=21.54 E-value=1.4e+02 Score=27.49 Aligned_cols=44 Identities=18% Similarity=0.151 Sum_probs=32.4
Q ss_pred HHHHHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEE
Q psy14294 240 REAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIW 284 (314)
Q Consensus 240 ~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~l 284 (314)
..+.+.++..|+++..--.--..++.+|...| ||+|+|+.-|.+
T Consensus 199 ~~~v~~~~~~g~~v~~WTvn~~~~~~~l~~~G-VdgIiTD~p~~~ 242 (249)
T PRK09454 199 EARVAALKAAGLRILVYTVNDPARARELLRWG-VDCICTDRIDLI 242 (249)
T ss_pred HHHHHHHHHCCCEEEEEeCCCHHHHHHHHHcC-CCEEEeCChHhc
Confidence 35678889999998877655555666777666 789999877643
No 74
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=21.42 E-value=1e+02 Score=23.58 Aligned_cols=37 Identities=16% Similarity=0.091 Sum_probs=26.5
Q ss_pred HHHHHHhCCce---EeccchHHHHHHHHHhcCCeeEEEcC
Q psy14294 243 QELLQLFGVPF---IVAPGEAEAQCASLELGNHTQGVITD 279 (314)
Q Consensus 243 ~~lLk~lGV~~---I~AP~EADAq~A~L~~~g~vdaViS~ 279 (314)
-++|+..||++ +..++++...+..+.++|.+|+|+..
T Consensus 23 a~~L~~~Gi~~~~~~~ki~~~~~~i~~~i~~g~id~VIn~ 62 (90)
T smart00851 23 AKFLREAGLPVKTLHPKVHGGILAILDLIKNGEIDLVINT 62 (90)
T ss_pred HHHHHHCCCcceeccCCCCCCCHHHHHHhcCCCeEEEEEC
Confidence 35677889985 33346655557778889999999874
No 75
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=21.34 E-value=1.2e+02 Score=26.69 Aligned_cols=63 Identities=16% Similarity=0.210 Sum_probs=42.5
Q ss_pred HHHHHHHHhCCceEeccchHHHHHHH--H--HhcC--CeeEEEcCCccEEeecCCeeeeeccCCCCcEEEEehh
Q psy14294 241 EAQELLQLFGVPFIVAPGEAEAQCAS--L--ELGN--HTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAP 308 (314)
Q Consensus 241 ~~~~lLk~lGV~~I~AP~EADAq~A~--L--~~~g--~vdaViS~DSD~llfG~~~Vi~~l~~~~~~v~~y~~~ 308 (314)
.+++.|..+|+..+...+..|-.++- | ...+ .+-+++|.|+||- .++..+...|+.|.+|..+
T Consensus 70 ~l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~-----~Lv~~lre~G~~V~v~g~~ 138 (160)
T TIGR00288 70 KLIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFL-----PVINKAKENGKETIVIGAE 138 (160)
T ss_pred HHHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHH-----HHHHHHHHCCCEEEEEeCC
Confidence 35788999999988777877777762 2 2123 3345789999974 3555566667777777643
No 76
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=21.03 E-value=2.2e+02 Score=21.46 Aligned_cols=41 Identities=15% Similarity=0.160 Sum_probs=32.7
Q ss_pred HHHHHHhCCceEeccchHHHHHHHHHhcCCeeEEEcCCccEEeec
Q psy14294 243 QELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 287 (314)
Q Consensus 243 ~~lLk~lGV~~I~AP~EADAq~A~L~~~g~vdaViS~DSD~llfG 287 (314)
.++-+.++++. .|++..++.+-.+|.+.|-|..-+-++.|+
T Consensus 64 ~~ia~~l~~~~----~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 64 SEIAKALQLSE----EEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHHTCCH----HHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHHhccch----HHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 34455566655 899999999999999999999888888775
No 77
>PRK00124 hypothetical protein; Validated
Probab=20.29 E-value=2.1e+02 Score=25.08 Aligned_cols=50 Identities=18% Similarity=0.089 Sum_probs=29.4
Q ss_pred cchHHHHHHHHHhcCCeeEEEcCCccEEeecCCeeeeeccCCCCcEEEEehhhhh
Q psy14294 257 PGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIR 311 (314)
Q Consensus 257 P~EADAq~A~L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~~v~~y~~~~i~ 311 (314)
+-.||..++.++..| |.|||.|-=+----..+...-++-. .+.|+-+.|.
T Consensus 54 ~D~AD~~Iv~~~~~g--DiVIT~Di~LAa~~l~Kga~vl~pr---G~~yt~~nI~ 103 (151)
T PRK00124 54 FDAADNEIVQLAEKG--DIVITQDYGLAALALEKGAIVLNPR---GYIYTNDNID 103 (151)
T ss_pred CChHHHHHHHhCCCC--CEEEeCCHHHHHHHHHCCCEEECCC---CcCCCHHHHH
Confidence 368888888888887 7799988633222223333333333 3555555553
Done!