Query 038444
Match_columns 300
No_of_seqs 131 out of 222
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 11:07:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038444.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038444hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04005 Hus1: Hus1-like prote 100.0 3.6E-73 7.8E-78 531.0 30.7 276 1-300 1-292 (292)
2 KOG3999 Checkpoint 9-1-1 compl 100.0 1.1E-63 2.5E-68 447.0 22.3 266 1-300 1-283 (284)
3 PLN00057 proliferating cell nu 99.7 1.2E-13 2.6E-18 127.8 27.6 242 2-296 1-251 (263)
4 TIGR00590 pcna proliferating c 99.6 2.6E-13 5.6E-18 125.3 26.9 242 2-296 1-251 (259)
5 PHA03383 PCNA-like protein; Pr 99.6 6.6E-13 1.4E-17 122.8 25.7 239 1-296 6-257 (262)
6 PTZ00113 proliferating cell nu 99.6 1.8E-12 3.8E-17 120.6 27.0 234 2-287 1-237 (275)
7 cd00577 PCNA Proliferating Cel 99.5 2.4E-11 5.3E-16 109.5 24.3 228 15-297 8-244 (248)
8 PTZ00483 proliferating cell nu 99.5 2.7E-11 5.9E-16 112.1 24.8 228 2-287 1-235 (264)
9 PRK01115 DNA polymerase slidin 99.0 5.6E-07 1.2E-11 81.9 25.7 225 3-287 2-226 (247)
10 KOG1636 DNA polymerase delta p 98.9 7.2E-08 1.6E-12 86.0 17.4 243 3-296 2-251 (260)
11 PF00705 PCNA_N: Proliferating 98.9 9.9E-08 2.1E-12 79.1 15.8 106 3-136 2-107 (127)
12 PF02144 Rad1: Repair protein 98.6 1.8E-05 3.9E-10 73.8 21.4 250 3-295 2-274 (275)
13 PF04139 Rad9: Rad9; InterPro 98.0 0.00076 1.6E-08 61.8 18.4 226 16-287 1-233 (252)
14 PF02747 PCNA_C: Proliferating 96.8 0.044 9.5E-07 45.2 13.1 113 168-297 7-126 (128)
15 PRK01115 DNA polymerase slidin 94.7 0.76 1.7E-05 41.6 12.7 83 16-116 141-223 (247)
16 cd00140 beta_clamp Beta clamp 93.9 5.8 0.00013 37.5 22.7 189 22-269 78-269 (365)
17 COG0592 DnaN DNA polymerase sl 93.0 0.93 2E-05 43.9 10.6 76 15-95 70-145 (364)
18 PF02747 PCNA_C: Proliferating 92.0 5.9 0.00013 32.4 14.1 107 3-135 7-118 (128)
19 PF02768 DNA_pol3_beta_3: DNA 89.4 7.5 0.00016 31.1 10.9 67 27-117 34-100 (121)
20 TIGR00590 pcna proliferating c 84.4 34 0.00073 31.5 13.9 96 15-134 143-243 (259)
21 PF00712 DNA_pol3_beta: DNA po 83.1 22 0.00048 28.5 10.8 101 78-210 3-103 (120)
22 cd00577 PCNA Proliferating Cel 81.3 38 0.00082 29.9 12.9 86 16-117 140-225 (248)
23 PHA03383 PCNA-like protein; Pr 79.9 36 0.00077 31.6 12.0 98 14-133 149-248 (262)
24 PTZ00483 proliferating cell nu 78.8 37 0.0008 31.6 11.7 93 14-132 148-241 (264)
25 PLN00057 proliferating cell nu 78.3 56 0.0012 30.1 13.5 96 16-133 144-242 (263)
26 PTZ00113 proliferating cell nu 76.7 66 0.0014 30.1 13.3 98 14-133 144-244 (275)
27 PF02144 Rad1: Repair protein 74.4 74 0.0016 29.5 15.2 152 29-208 120-273 (275)
28 PRK14941 DNA polymerase III su 61.0 1.6E+02 0.0035 28.4 13.5 109 77-218 2-115 (374)
29 KOG2810 Checkpoint 9-1-1 compl 56.4 15 0.00032 36.1 4.1 84 6-93 4-87 (394)
30 PRK14943 DNA polymerase III su 44.3 2.9E+02 0.0064 26.4 11.6 66 28-117 288-353 (374)
31 PRK14947 DNA polymerase III su 43.8 3E+02 0.0065 26.8 11.1 72 28-130 286-357 (384)
32 PRK05643 DNA polymerase III su 41.6 3.1E+02 0.0068 26.0 20.4 149 18-209 74-229 (367)
33 PRK14941 DNA polymerase III su 40.9 3.1E+02 0.0067 26.4 10.7 67 28-117 281-347 (374)
34 smart00480 POL3Bc DNA polymera 40.8 3.2E+02 0.0069 25.8 21.6 208 18-285 58-272 (345)
35 PRK14945 DNA polymerase III su 39.6 3.4E+02 0.0075 25.8 20.3 206 18-285 73-285 (362)
36 PRK14942 DNA polymerase III su 39.4 3.6E+02 0.0079 26.1 11.1 70 28-128 286-355 (373)
37 PRK06673 DNA polymerase III su 38.9 1.8E+02 0.0039 28.2 8.7 71 18-94 203-277 (376)
38 PF02282 Herpes_UL42: DNA poly 36.9 1.2E+02 0.0026 26.0 6.3 58 4-69 2-62 (156)
39 PRK07761 DNA polymerase III su 35.8 4E+02 0.0087 25.5 11.2 67 27-117 280-346 (376)
40 PRK05643 DNA polymerase III su 34.5 4.1E+02 0.0088 25.2 12.1 66 28-117 280-345 (367)
41 PRK14940 DNA polymerase III su 32.6 4.6E+02 0.0099 25.2 11.8 66 28-117 279-344 (367)
42 KOG1636 DNA polymerase delta p 30.4 4.4E+02 0.0095 24.3 10.0 88 13-117 142-233 (260)
43 cd00140 beta_clamp Beta clamp 30.3 4.6E+02 0.0099 24.5 11.8 66 28-117 279-344 (365)
44 smart00480 POL3Bc DNA polymera 30.2 4.7E+02 0.01 24.6 11.5 65 29-117 263-327 (345)
45 TIGR00663 dnan DNA polymerase 29.2 5E+02 0.011 24.6 10.7 94 4-128 255-349 (367)
46 PF04139 Rad9: Rad9; InterPro 29.2 4.3E+02 0.0092 23.8 9.4 88 15-117 139-230 (252)
47 PRK14942 DNA polymerase III su 27.2 3.2E+02 0.0069 26.4 8.3 129 29-201 220-350 (373)
48 PRK14947 DNA polymerase III su 25.7 4E+02 0.0088 25.9 8.7 141 19-201 203-350 (384)
49 PRK14943 DNA polymerase III su 23.8 6.2E+02 0.013 24.1 9.6 135 28-201 211-352 (374)
50 PRK14944 DNA polymerase III su 23.7 4.6E+02 0.0099 25.4 8.6 61 28-94 216-276 (375)
51 PRK14945 DNA polymerase III su 22.3 6.8E+02 0.015 23.8 13.0 130 29-200 208-338 (362)
52 PRK14940 DNA polymerase III su 20.2 7.7E+02 0.017 23.6 12.0 140 18-201 199-343 (367)
No 1
>PF04005 Hus1: Hus1-like protein; InterPro: IPR007150 Hus1, Rad1, and Rad9 are three evolutionarily conserved proteins required for checkpoint control in fission yeast. These proteins are known to form a stable complex in vivo []. Hus1-Rad1-Rad9 complex may form a PCNA-like ring structure, and could function as a sliding clamp during checkpoint control.; PDB: 3A1J_B 3G65_C 3GGR_B.
Probab=100.00 E-value=3.6e-73 Score=530.95 Aligned_cols=276 Identities=32% Similarity=0.495 Sum_probs=199.6
Q ss_pred CeeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEE
Q 038444 1 MKFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAI 80 (300)
Q Consensus 1 MkFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev 80 (300)
|||||++.|. .+|++++++++||+|.|+|||||++++||++..+++|+|+||+++++.+|++|+|||.++|+|+||+
T Consensus 1 MKFka~i~~~---~~~~~~~~~~~kl~k~~vlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~~F~~y~i~s~~~N~I~le~ 77 (292)
T PF04005_consen 1 MKFKATISDI---KLFKKFVSTISKLGKRCVLRLTPERLHFISTSDDSDGIQVWCELPQDSLFSEYRIQSASENEIYLEV 77 (292)
T ss_dssp -EEEEEEE-H---HHHHHHHHHHHHH-SEEEEEE-SSEEEEEEE-SSTT--EEEEEEEGGGT-SEEEEE-SSSS-EEEEE
T ss_pred CcceEEecCH---HHHHHHHHHHHHhhCEEEEEEeCCEEEEEEecCCCCeEEEEEEEChhhcCcccEEEeCCCCEEEEEE
Confidence 9999999983 5569999999999999999999999999988779999999999999999999999999999999999
Q ss_pred ehHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEEC-----ceeEEEEEeecCcccChhhhc
Q 038444 81 DISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKG-----YKSAVIQDVPISKPLSRAQGL 155 (300)
Q Consensus 81 ~~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g-----~~~~v~hdvPV~~vl~~~~~~ 155 (300)
++++|+||||++.+ +.+++|||+||+ +.|||+|++++ .++.|+||||| +++++++|+
T Consensus 78 ~~~~L~raLrs~~~-----------a~~~~ikL~kk~------~~p~L~~~~~~~~~~~~~~~v~hdiPV-~vl~~~~~~ 139 (292)
T PF04005_consen 78 NIDSLLRALRSADN-----------ASSVKIKLTKKG------RMPCLSFEITGTSSSGRSRIVVHDIPV-RVLPRREWE 139 (292)
T ss_dssp EHHHHHHHHCTCSS-----------CSEEEEEEE-S-------SSSEEEEEEEE--SSST-EEEEEEEEB-EE--GGGGG
T ss_pred cHHHHHHHHHhhcc-----------CceeEEehhhcc------CCcEEEEEEEeeccCCCccEEEEECCe-EecCHHHHH
Confidence 99999999999998 569999999996 48999999984 34699999999 699999999
Q ss_pred hhhhhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCC---
Q 038444 156 ELQTALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAP--- 232 (300)
Q Consensus 156 ~l~eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~--- 232 (300)
+|+||++ +.|+++|+||+++.|++++||||++|++++|+||++|+|+|.|+++.|+|+|+|+||.++++.+.+.
T Consensus 140 ~~~eP~~---~~~dv~i~LP~l~~l~~~veR~k~~s~~v~i~an~~G~L~L~v~t~~~~v~t~~~~L~~~~~~~~~~~~~ 216 (292)
T PF04005_consen 140 ELQEPMV---PDPDVSIYLPPLKQLRSIVERMKNLSDYVTISANMNGELRLSVETDSVSVETEFRGLENPPLDPAELNTV 216 (292)
T ss_dssp GGS----------SEEEE-S-HHHHHHHHHHHHTT-SEEEEEE-SSS-EEEEEE-SSEEEEEEE-S--------------
T ss_pred Hhhhccc---CCCCEEEECCCHHHHHHHHHHHhccCceEEEEEECCCcEEEEEEeCcEEEEEEECCCCCCcccccccccc
Confidence 9999987 7899999999999999999999999999999999999999999999999999999999987633211
Q ss_pred -CccccccccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE-EE------EEEEEEeccCC
Q 038444 233 -SEDRNLSAQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC-LT------VIFQFFIPGTR 300 (300)
Q Consensus 233 -~~~~~~~~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~-~~------~~l~y~ip~~~ 300 (300)
..+++..+++..+++.+++++++|+||+|+|++||++++++|++|+|||.|+++| ++ ++|+|||||+|
T Consensus 217 ~~~~~~~~~~~~~~~~~~~~~~~sV~Vd~K~~~~~l~~~~~~p~~vi~~I~~~~~~vl~~~~~~~~~l~yyip~~~ 292 (292)
T PF04005_consen 217 DQLPSEDDSDSDQQEERDPEEFASVRVDIKDLAKFLKSHQLSPSRVICCICHNKALVLHVYLDEDVSLTYYIPAVR 292 (292)
T ss_dssp ----------SSSSS-------EEEEEEHHHHHHHHHH--S--SEEEEEEETTTEEEEEEEE-TTEEEEEEEE---
T ss_pred ccccccccccccccccCCCCcEEEEEEEHHHHHHhhCccccCCCEEEEEEccCCeEEEEEEEcCCEEEEEEEeccC
Confidence 1111111111222345566899999999999999999999999999999999988 43 56999999997
No 2
>KOG3999 consensus Checkpoint 9-1-1 complex, HUS1 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=100.00 E-value=1.1e-63 Score=446.96 Aligned_cols=266 Identities=41% Similarity=0.593 Sum_probs=242.0
Q ss_pred CeeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEe-eecCCCceEEEEEEccCCCcCeeEeeec--CCCeEE
Q 038444 1 MKFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLH-NLLSGEGIQCVAQFHKETLFDDYRISSQ--NEDCIA 77 (300)
Q Consensus 1 MkFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~-~~~~~~g~qvw~~l~~~~lF~ey~ieS~--~~N~I~ 77 (300)
|||||.+.|.++..+|++++++++||+|.|+|||+|++|+||+ ...+++|+|+||++.++.+|++|+|+|. ++|+|+
T Consensus 1 MKFka~l~d~~~l~~f~ril~al~Kl~K~C~l~l~~e~lnFI~c~~~~~~~~~~ws~~~~e~iF~dy~m~s~~p~~e~I~ 80 (284)
T KOG3999|consen 1 MKFKALLQDNAVLLLFTRILPALDKLGKNCHLRLTKEHLNFIHCDLLDGGSVQVWSQLEKEVIFDDYRMESQNPNNEEIN 80 (284)
T ss_pred CchhhhhccchHHHHHHHHHHHHHHhhhceEEEecccceEEEEecccCCCceEEEEeeehhhcchhheeeccCCCcceEE
Confidence 9999999999999999999999999999999999999999997 4569999999999999999999999988 889999
Q ss_pred EEEehHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEE-------ECceeEEEEEeecCcccC
Q 038444 78 FAIDISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFET-------KGYKSAVIQDVPISKPLS 150 (300)
Q Consensus 78 lev~~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~-------~g~~~~v~hdvPV~~vl~ 150 (300)
||++.+.|.||||++.+. +.++++||+||+. ||++..+ +| ++.|+||||| ++++
T Consensus 81 L~v~~~nl~rAlrs~~~g----------~~~lklKLskk~~-------p~~t~~~~~lt~~a~~-s~iVtHdIPI-tii~ 141 (284)
T KOG3999|consen 81 LEVDSANLYRALRSLVGG----------ANRLKLKLSKKQF-------PCLTVSVEVLTFEAKG-SRIVTHDIPI-TIIS 141 (284)
T ss_pred EEecHHHHHHHHHHhcCc----------ccceEEEehhccC-------CCceeeeeeecccccc-CceeEecCCe-EEec
Confidence 999999999999999874 7889999999984 6555444 34 5899999999 5999
Q ss_pred hhhhchhhhhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccC
Q 038444 151 RAQGLELQTALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAV 230 (300)
Q Consensus 151 ~~~~~~l~eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~ 230 (300)
+++|.+|+||.. +.||.+|+||+++.|+++||+|||+|+.+.++||++|+|+++++++++.|+|+|++|.+++...+
T Consensus 142 ~s~w~~~~~P~v---p~~dl~I~lP~l~~lk~~vdk~Knis~~l~~tan~~GeLqv~v~~e~~~vtt~Fq~L~~~~~~s~ 218 (284)
T KOG3999|consen 142 RSYWSEYQEPLV---PAPDLSIQLPDLNQLKSFVDKMKNISDVLNVTANKSGELQVSVSIELIRVTTEFQDLSNPPLKSS 218 (284)
T ss_pred HHHhhhhcCcCC---CCCCcceeCCCHHHHHHHHHHhhcccceEEEEEecCceEEEEEEEeeEEEEEEhhhccCCCCCCc
Confidence 999999999987 88999999999999999999999999999999999999999999999999999999998765443
Q ss_pred CCCccccccccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeEE-------EEEEEEEeccCC
Q 038444 231 APSEDRNLSAQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGACL-------TVIFQFFIPGTR 300 (300)
Q Consensus 231 ~~~~~~~~~~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~~-------~~~l~y~ip~~~ 300 (300)
.+.+ +|..| ++++|++|+|+++.||.+.+..+..+.|+|..+++++ +++|||||||++
T Consensus 219 s~~e-------dr~~e-----~~a~~~ld~r~~~~~~~s~~~~~~~l~c~i~~~~~v~~~~~~~~dvvL~y~vp~~~ 283 (284)
T KOG3999|consen 219 SPVE-------DRSAE-----ARAEVALDSRDASSFFVSVQVFSTSLQCNITKNDSVHYGIAPQEDVVLQYIVPAVS 283 (284)
T ss_pred cccc-------ccChh-----hhhhheehhhhHHHHHHHhhcCcceeEEeeccCceEEEeeccCccEEEEEEecccc
Confidence 3333 23334 6899999999999999999999999999999999885 599999999985
No 3
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=99.66 E-value=1.2e-13 Score=127.79 Aligned_cols=242 Identities=12% Similarity=0.173 Sum_probs=177.6
Q ss_pred eeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEe
Q 038444 2 KFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAID 81 (300)
Q Consensus 2 kFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~ 81 (300)
-|+|++.+. ..||+++.+|+++-++|.+.+|++.+.+.. ..++.-.++-..|+.+ .|++|+|+. ++.+-++
T Consensus 1 Mf~a~~~~a---~~~k~i~~ai~~lvde~~~~~t~~Gi~~~a-mD~s~Valv~l~l~~~-~F~eY~~d~----~~~~gv~ 71 (263)
T PLN00057 1 MLEARLVQG---SLLKKVLEAIKDLVSDANFDCSETGLSLQA-MDSSHVALVALLLRAD-GFEHYRCDR----NLSMGIN 71 (263)
T ss_pred CeEEEEcch---HHHHHHHHHHHHHhheeEEEEcCCeEEEEE-EcCCcEEEEEEEeChh-cCeEEecCC----ceEEEEE
Confidence 099999987 346999999999999999999999999854 4567888999999999 999999986 5788999
Q ss_pred hHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECce--eEEEEEeecCcccChhhhchhhh
Q 038444 82 ISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYK--SAVIQDVPISKPLSRAQGLELQT 159 (300)
Q Consensus 82 ~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~--~~v~hdvPV~~vl~~~~~~~l~e 159 (300)
.+.|.++||.+.+ .+.++|+....+ -.|.+.+++.+ +.-...+|. +... .+++..
T Consensus 72 l~~l~kiLk~~~~-----------~d~l~l~~~~~~--------~~l~i~~~~~~~~~~~~f~l~l---~d~~-~e~l~i 128 (263)
T PLN00057 72 LANMSKILKCAGN-----------DDIITIKADDGG--------DTVTFMFESPKQDRISDFELKL---MDID-SEHLGI 128 (263)
T ss_pred HHHHHHHHhccCC-----------CCEEEEEecCCC--------CEEEEEEEcCCCceEEEEEEEe---eecC-cccCCC
Confidence 9999999999986 688999865543 46777777644 333444555 3332 245655
Q ss_pred hhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCcccccc
Q 038444 160 ALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLS 239 (300)
Q Consensus 160 P~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~ 239 (300)
|. ...++.+.||+ ..|++++..+..+||.|+|+++ .+.+.|+.+.+..+....++.=. +.+..+..
T Consensus 129 P~----~e~~~~v~m~s-~~f~~~~kdl~~vsd~v~i~~~-~~~~~f~~~Gd~g~~~~~l~~~~--------~~~~~~~~ 194 (263)
T PLN00057 129 PE----TEYSAIVRMPS-AEFQRICKDLSSIGDTVVISVT-KEGVKFSTSGDIGTANIVLRQNT--------TVDKPEEK 194 (263)
T ss_pred CC----CceeEEEEEEH-HHHHHHHHHHHHcCCEEEEEEe-CCEEEEEEEecCcEEEEEEecCC--------CCCCccce
Confidence 63 23345777998 8999999999999999999995 56799999988888777776411 00000000
Q ss_pred ccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE-EE------EEEEEEe
Q 038444 240 AQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC-LT------VIFQFFI 296 (300)
Q Consensus 240 ~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~-~~------~~l~y~i 296 (300)
. .....+.++..-.++-|..|.+.-.+ .+.|.+.+.++..+ +. ..++||+
T Consensus 195 ----~--~i~~~e~~~~~y~l~YL~~~~Ka~~l-s~~V~i~~~~~~Pl~l~y~l~~~g~l~f~L 251 (263)
T PLN00057 195 ----T--VIEMQEPVSLTFALRYLNSFTKATPL-SDTVTLSLSKELPVVVEYKIAEMGYIRYYL 251 (263)
T ss_pred ----E--EEEecCceEEEEhHHHHHHhhccccC-CCeEEEEEcCCCCEEEEEEeCCCeEEEEEE
Confidence 0 00011346777888888888876544 56889999999877 42 4556665
No 4
>TIGR00590 pcna proliferating cell nuclear antigen (pcna). All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.64 E-value=2.6e-13 Score=125.26 Aligned_cols=242 Identities=12% Similarity=0.154 Sum_probs=177.5
Q ss_pred eeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEe
Q 038444 2 KFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAID 81 (300)
Q Consensus 2 kFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~ 81 (300)
-|+|++.+. ..||+++.+|+++-++|.+.+|++.+.+.. ..++.-.++-..|+.+ .|++|+|+. +..+-++
T Consensus 1 Mfea~~~~a---~~~k~i~eai~~lv~e~~~~~t~~Gi~~~a-mD~s~Valv~l~l~~~-~F~~Y~~d~----~~~~gv~ 71 (259)
T TIGR00590 1 MFEARLEQA---SLLKKILEAIKDLVNDANFDCSESGISLQA-MDSSHVSLVSLTLRSE-GFDTYRCDR----NLALGVN 71 (259)
T ss_pred CeEEEEccH---HHHHHHHHHHHHHhceeeEEECCCeEEEEE-EcCCcEEEEEEEcCHH-hCceEecCC----ceEEEEE
Confidence 199999987 346999999999999999999999999864 4567888999999988 999999986 4688899
Q ss_pred hHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeE--EEEEeecCcccChhhhchhhh
Q 038444 82 ISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSA--VIQDVPISKPLSRAQGLELQT 159 (300)
Q Consensus 82 ~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~--v~hdvPV~~vl~~~~~~~l~e 159 (300)
.+.|.++||.+.+ .+.++|++...+ ..|.|.+++.+.. -...+|. +.. +.+++..
T Consensus 72 l~~l~kiLk~~~~-----------~d~l~l~~~~~~--------~~l~i~~~~~~~~~~~~f~l~l---~d~-~~e~l~i 128 (259)
T TIGR00590 72 LTSLSKILKCANN-----------EDIVTLKAEDNA--------DTLILVFESPKQDKISDYELKL---MDI-DVEHLGI 128 (259)
T ss_pred HHHHHHHHhccCC-----------CCEEEEEecCCC--------CEEEEEEEcCCCCeEEEEEEEe---eec-ccccCCC
Confidence 9999999999986 688888764443 4577877754433 3344554 332 2245555
Q ss_pred hhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCcccccc
Q 038444 160 ALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLS 239 (300)
Q Consensus 160 P~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~ 239 (300)
|. ...++.+.||+ ..|+.++..+..+||.|+|+++ .+.+.|..+.+..+..+.+++-.-. ..|.+.
T Consensus 129 P~----~e~~~~v~m~s-~~f~~~~kdl~~v~d~v~i~~~-~~~~~f~~~Gd~g~~~~~~~~~~~~----~~~~~~---- 194 (259)
T TIGR00590 129 PE----QEYDCVVEMPS-SEFARICRDLSQFSDSVVISCT-KEGVKFSAKGDIGSGNVKLKQTSDT----DKEEEA---- 194 (259)
T ss_pred CC----CceeEEEEEEH-HHHHHHHHHHHHcCCEEEEEEe-CCEEEEEEEecccEEEEEEecCCCC----CCCcce----
Confidence 63 22445777998 8999999999999999999996 5679999999888888887753210 000000
Q ss_pred ccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE-EE------EEEEEEe
Q 038444 240 AQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC-LT------VIFQFFI 296 (300)
Q Consensus 240 ~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~-~~------~~l~y~i 296 (300)
......+.++.+-.++-|..|.+.-.+ .+.|.+.+.++..+ +. ..++||+
T Consensus 195 ------~~i~~~~~~~~~y~l~YL~~~~Ka~~l-s~~V~l~~~~~~Pl~l~y~i~~~g~l~f~l 251 (259)
T TIGR00590 195 ------VTIEMKEPVTLTFAIKYLNLFTKATPL-SDRVTLSMSNDVPLVVEYKIKDMGFLRFFL 251 (259)
T ss_pred ------EEEEecCceeeeeeHHHHHHhhhhccC-CCeEEEEEcCCCCEEEEEEeCCCeEEEEEE
Confidence 000111345667788888888876544 56889999998876 42 5666775
No 5
>PHA03383 PCNA-like protein; Provisional
Probab=99.60 E-value=6.6e-13 Score=122.75 Aligned_cols=239 Identities=12% Similarity=0.161 Sum_probs=178.5
Q ss_pred CeeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEE
Q 038444 1 MKFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAI 80 (300)
Q Consensus 1 MkFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev 80 (300)
|-|+|++.+. .+||+++.++++|-++|.+.++++.+.+.. ..++.-..+-..|+.+ .|++|+|+. .+.+=+
T Consensus 6 ~mfe~~~~~a---~~~K~iieai~~lv~e~~f~~t~~Gi~lqa-mD~shVaLv~l~L~~~-~F~~Y~~d~----~~~iGv 76 (262)
T PHA03383 6 VLFHIRTIQG---SVIKSLFDVLKEILHDVNIFFRPTGVYISA-LDGAKVSLVHMKLDAE-SFEEYHCDQ----TYEIGV 76 (262)
T ss_pred EEEEEEecch---HHHHHHHHHHHHHhceEEEEECCCcEEEEE-ECCCcEEEEEEEeCHH-hCceEecCC----ceEEEE
Confidence 5699999987 446999999999999999999999999965 4466777888889998 999999997 556789
Q ss_pred ehHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECce--eEEEEEeecCcccChhhhchhh
Q 038444 81 DISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYK--SAVIQDVPISKPLSRAQGLELQ 158 (300)
Q Consensus 81 ~~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~--~~v~hdvPV~~vl~~~~~~~l~ 158 (300)
+.+.|.++||.+.+ .+.+.|++...+ .-.|.|.++|.+ +.-...+|. +.... +++.
T Consensus 77 ~~~~l~KILk~a~~-----------~D~l~l~~~~~~-------~~~l~i~~~~~~~~~~~~f~l~L---idi~~-e~l~ 134 (262)
T PHA03383 77 NVSNMFKLLRTAGS-----------HDSILFRYLKNS-------PHFLEITIQNFEKNSLTKFQLKL---IEIDS-SRIE 134 (262)
T ss_pred EHHHHHHHHhccCC-----------CCEEEEEecCCC-------CCEEEEEEEeCCCCcEEEEEEEc---cccCc-ccCC
Confidence 99999999999987 688999865444 237888887654 334455555 33222 5566
Q ss_pred hhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEE----EeecceEEeEEeccccccccccCCCCc
Q 038444 159 TALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQ----ISTTLITLGAEFRKLLVIGEKAVAPSE 234 (300)
Q Consensus 159 eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~----v~t~~v~v~t~~~~L~~~~~~~~~~~~ 234 (300)
+|- ...++.+.||+ ..|++++..+..+||.++|+++ .+.+.|. .+.|.....+.+..... ....
T Consensus 135 iP~----~e~~~~v~m~s-~~f~~i~kdl~~igD~v~i~~~-~~~v~f~~~~~~~Gd~~~~~~~~~~~~~------~~v~ 202 (262)
T PHA03383 135 VPD----VEFDTIIILPS-NYFQRLCRDMSNITDDLEITKK-GKEVSFRSDYTCVTDFASQETIIGDSDN------GQIT 202 (262)
T ss_pred CCC----CCccEEEEEEH-HHHHHHHHHHHHcCCeEEEEEe-CCEEEEEEcccccccccceEEEecCCCC------CceE
Confidence 663 23456888998 9999999999999999999995 4559998 77776666666543321 0000
Q ss_pred cccccccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE-EE------EEEEEEe
Q 038444 235 DRNLSAQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC-LT------VIFQFFI 296 (300)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~-~~------~~l~y~i 296 (300)
.. + .+.++....+|-|..|.++..+ .+.|.+.+.++..+ +. ..+.|||
T Consensus 203 -------~~--~----~~~~~~~ysl~YL~~~~Ka~~l-s~~V~i~l~~d~Pl~ley~i~~~G~l~fyL 257 (262)
T PHA03383 203 -------CN--E----SPDYTGKFSLKYLTSFTKASGM-SSSVEIYLKESNPLILKYNVGSLGNLKFVI 257 (262)
T ss_pred -------Ee--c----CCceEEEEeHHHHHHhhccccC-CCeEEEEEcCCCCEEEEEEeCCCcEEEEEE
Confidence 00 0 1246788899999999986555 55888999988877 42 4667776
No 6
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=99.59 E-value=1.8e-12 Score=120.59 Aligned_cols=234 Identities=12% Similarity=0.143 Sum_probs=172.4
Q ss_pred eeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEe
Q 038444 2 KFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAID 81 (300)
Q Consensus 2 kFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~ 81 (300)
-|+|++.+. .+||+++.+|.+|-.++.+.++++-+.+.. ..++.-..+-..|+.+ .|++|+|+. ++.+=++
T Consensus 1 Mfea~~~~a---~~~K~i~eal~~lv~e~~f~~t~~Gi~lqa-mD~shVaLv~l~l~~~-~FeeY~cd~----~~~lGvn 71 (275)
T PTZ00113 1 MLEAKLNNA---SVLRRLFECIKDLVSDGNIDFDETGLKLQA-LDGNHVALVHLKLHDS-GFSHYRCDR----ERALGIN 71 (275)
T ss_pred CeEEEeccH---HHHHHHHHHHHHHhceEEEEECCCeEEEEE-ECCCcEEEEEEEeCHH-hCeEEecCC----CcEEEEE
Confidence 099999987 346999999999999999999999999865 4466777888889998 999999997 4677899
Q ss_pred hHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECcee--EEEEEeecCcccChhh-hchhh
Q 038444 82 ISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKS--AVIQDVPISKPLSRAQ-GLELQ 158 (300)
Q Consensus 82 ~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~--~v~hdvPV~~vl~~~~-~~~l~ 158 (300)
.+.|.++||.+.+ .+.+.|+.... ...|.|.+.+... .-...+|. +.... ...++
T Consensus 72 ~~~l~KILk~~~~-----------~D~l~l~~~~~--------~~~l~i~~~~~~~~~~~~f~l~L---~di~~e~~~iP 129 (275)
T PTZ00113 72 IASVTKVFKLCSN-----------NDSVLIQSEED--------KDNINFVFENNVEDKVSSFSLKL---MSIEQDALSIP 129 (275)
T ss_pred HHHHHHHHHhCCC-----------CCEEEEEEcCC--------CCEEEEEEEcCCCceEEEEEEEc---cccCccccCCC
Confidence 9999999999987 68899985333 2578888887654 44455555 32222 12233
Q ss_pred hhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccc
Q 038444 159 TALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNL 238 (300)
Q Consensus 159 eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~ 238 (300)
||. ...++.+.||+ ..|+.++..+..+||.|+|+++ .+.+.+..+.+..+..+.++.-. |..+++.
T Consensus 130 e~~----~e~~~~v~m~s-~~f~~i~rdl~~vgd~V~i~~~-~~~v~f~a~Gd~g~~~i~l~~~~--------~~~~~~~ 195 (275)
T PTZ00113 130 ENE----EGFDAEVTLSS-KELTNICRQMNEFSDTVKIEID-SNSIKFTTQGDLGDGEVVLKPRP--------PTSEDDC 195 (275)
T ss_pred CCC----CCccEEEEEEH-HHHHHHHHHHHHcCCEEEEEEe-CCEEEEEEeccCcEEEEEEecCC--------CCCCccc
Confidence 331 13456788998 9999999999999999999995 55699999999888877776421 1111000
Q ss_pred cccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE
Q 038444 239 SAQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC 287 (300)
Q Consensus 239 ~~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~ 287 (300)
.- .....+.++....+|-|..|.++..+ .+.|.+.+.++..+
T Consensus 196 ~~------~~~v~~~~~~~ysl~YL~~f~Ka~~l-s~~V~l~l~~d~Pl 237 (275)
T PTZ00113 196 GV------TIKVRKPIKQSYATKYLNMFAKSGCL-SDVVTLGLSDNRPI 237 (275)
T ss_pred eE------EEEecCceeeEEhHHHHHHhhccccC-CCeEEEEEcCCCCE
Confidence 00 00011356778899999999986555 45888888888766
No 7
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Probab=99.48 E-value=2.4e-11 Score=109.49 Aligned_cols=228 Identities=16% Similarity=0.212 Sum_probs=165.1
Q ss_pred HHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccc
Q 038444 15 LEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVS 94 (300)
Q Consensus 15 l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~ 94 (300)
.|++++.+++++.+.|.+.++++.+.++.+. .....++|+.++.+ +|++|+++ +++.+.++...|..+||.+..
T Consensus 8 ~l~~~~~~l~~i~~~v~~~~~~~gl~~~a~d-~~r~~~~~~~l~~~-~F~~y~~~----~~~~~~i~~k~l~~~lk~~~~ 81 (248)
T cd00577 8 LLKKIVDALSKLVDEANFDITEDGISLQAMD-SSHVALVSLFLPKE-LFEEYRCD----EEISLGVNLKSLLKILKCAGN 81 (248)
T ss_pred HHHHHHHHHHHHhcEEeEEECCCceEEEEEc-CCcEEEEEEEechh-hCeEEecC----CceEEEEEHHHHHHHHhhCCC
Confidence 3589999999999999999999999998643 33457999999877 99999998 589999999999999999975
Q ss_pred ccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEc
Q 038444 95 ICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQV 174 (300)
Q Consensus 95 ~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~l 174 (300)
.+.+.|++.++ +.|.|.+......+.+.+.+ +++....+ ++..|. ...+..+.|
T Consensus 82 -----------~~~v~i~~~~~---------~~l~i~~~~~~~~~~~~~~~-~li~~~~~-~~~~~~----~~~~~~i~i 135 (248)
T cd00577 82 -----------EDCVTLRADDE---------DPLKILFESSKGDVTSEFSL-KLMDIDSE-QLPIPE----LEYDATVTL 135 (248)
T ss_pred -----------CCEEEEEecCC---------CeEEEEEEcCCCceEEEEEE-EccccCcc-cCCCCC----CceeEEEEE
Confidence 56677777544 35666666443356677777 46665554 344331 445568889
Q ss_pred CChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeec-c-eEEeEEeccccccccccCCCCccccccccchhhhhcCCCC
Q 038444 175 PDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTT-L-ITLGAEFRKLLVIGEKAVAPSEDRNLSAQTRSERAISRGD 252 (300)
Q Consensus 175 P~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~-~-v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (300)
|+ +.|+.+++|+..+++.++|.++.++ |.|+..++ . ......+.+.... +.-..++
T Consensus 136 ~~-~~L~~~i~~~~~~~~~i~i~~~~~~-l~lss~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~ 193 (248)
T cd00577 136 PS-DELKDIVRDLESISDSVTISASKDG-FKFSAEGELGGASVTLLPKDSDLL--------------------VTIECSE 193 (248)
T ss_pred EH-HHHHHHHHHHHHcCCEEEEEEcCCE-EEEEEeecCCceEEEEecCCCCce--------------------EEEEeCC
Confidence 98 9999999999999999999996654 88888765 2 2333333322210 0001124
Q ss_pred eEEEEEechhHHhhccccccCCcEEEEEEECCCeE-EE------EEEEEEec
Q 038444 253 AQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC-LT------VIFQFFIP 297 (300)
Q Consensus 253 ~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~-~~------~~l~y~ip 297 (300)
..++..+.|-|..++..-.. .+.|.+.+..++.+ +. ..++||+.
T Consensus 194 ~~~~~fn~~yL~~~l~~~~~-s~~v~i~~~~~~p~~i~~~~~~~~~~~f~la 244 (248)
T cd00577 194 PVSSTYSLKYLKDFTKAAPL-SDKVTLSFGSDGPLSLEFKIADGGHLTFYLA 244 (248)
T ss_pred ceEEEEhHHHHHHHhhhccc-CCeEEEEEcCCCCEEEEEEcCCCcEEEEEEc
Confidence 67899999999999986544 56888888887666 31 45566653
No 8
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=99.48 E-value=2.7e-11 Score=112.10 Aligned_cols=228 Identities=10% Similarity=0.120 Sum_probs=165.5
Q ss_pred eeeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEe
Q 038444 2 KFKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAID 81 (300)
Q Consensus 2 kFrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~ 81 (300)
-|+|++. . .+||+++.++++|-.+|.+.++++.+.+.. ..++.-..+-..|+.+ .|++|+|+. +..+=++
T Consensus 1 Mfea~~~-a---~~lK~i~eai~~lv~e~~f~~~e~Gi~lqA-mD~shVaLV~l~L~~~-~Fe~Y~cd~----~~~lGin 70 (264)
T PTZ00483 1 MFECRLD-G---MFLRRLFETLKDICTDVSIDCSENGLKMQA-MDNSHISLIHLNLAPD-FFQLYRCDK----PCVLGLN 70 (264)
T ss_pred CeEEEEe-H---HHHHHHHHHHHHHhheeEEEECCCcEEEEE-ECCCcEEEEEEEcCHH-hCeEEecCC----CeEEEEE
Confidence 0999995 3 557999999999999999999999999865 4566778888899998 999999998 4457899
Q ss_pred hHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECce-------eEEEEEeecCcccChhhh
Q 038444 82 ISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYK-------SAVIQDVPISKPLSRAQG 154 (300)
Q Consensus 82 ~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~-------~~v~hdvPV~~vl~~~~~ 154 (300)
.+.|.++||.+.+ .+.+.|+..... ....+.+.+.+.. +.-...+|. +....
T Consensus 71 l~~l~KiLk~a~~-----------~D~l~l~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~f~l~L---idi~~- 129 (264)
T PTZ00483 71 ISFMLKILSVVKE-----------KSTIYLFRGDNT------EDPVLNIRIIEEEGQNSLESDSLEAQVKL---INVQR- 129 (264)
T ss_pred HHHHHHHHhhcCC-----------CCEEEEEeccCC------CCceEEEEEeccccccccccceEEEEEEc---cccCc-
Confidence 9999999999987 678888633222 1356665554332 333455555 33222
Q ss_pred chhhhhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCc
Q 038444 155 LELQTALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSE 234 (300)
Q Consensus 155 ~~l~eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~ 234 (300)
+++..|- ...++.+.||+ ..|++++..++.+||.|+|+++ .+.+.|..+++..+..+.++. . .+.-
T Consensus 130 e~l~iP~----~e~~~~v~m~s-~~f~~i~kdl~~vsD~v~i~~~-~~~v~f~a~Gd~~~~~~~l~~-~-------~~~v 195 (264)
T PTZ00483 130 EHLEIPQ----CEYHCKCVMNS-KKFQEFAKYLHSIGDTVSISMK-KDEMRLETEGEGIKASKQFHN-D-------VGDV 195 (264)
T ss_pred ccCCCCC----CCccEEEEEEH-HHHHHHHHHHHHcCCEEEEEEE-CCEEEEEEeecCcEEEEEEcc-C-------CCce
Confidence 5566663 23456888998 9999999999999999999995 566999999998877777641 1 0000
Q ss_pred cccccccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE
Q 038444 235 DRNLSAQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC 287 (300)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~ 287 (300)
.. + ..+-++-...+|-|..|.++..+ .+.|.+.+.++..+
T Consensus 196 ~~---------~---~~~~v~~~fsl~YL~~f~Ka~~l-sd~V~i~l~~~~Pl 235 (264)
T PTZ00483 196 RV---------T---STESLSQEFATRYLVLFSKATSL-ADEVSINLSAGIPL 235 (264)
T ss_pred EE---------E---ecCcchheehHHHHHHhhccccC-CCeEEEEEcCCCCE
Confidence 00 0 00234455677888888886555 45888899888776
No 9
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=98.99 E-value=5.6e-07 Score=81.88 Aligned_cols=225 Identities=12% Similarity=0.106 Sum_probs=153.1
Q ss_pred eeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEeh
Q 038444 3 FKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDI 82 (300)
Q Consensus 3 FrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~ 82 (300)
|+|++.+.+ . |++++.++.++...+.+.++++.+.++.+. ...-.++...++.+ .|++|++.- ...+-++.
T Consensus 2 ~~~~~~~~~--~-lk~i~~~i~~l~~~v~~~~~~~~l~~~atD-~~Rla~~~~~~~~~-~f~~~~~~~----~~~~~v~l 72 (247)
T PRK01115 2 MKAVYPDAK--D-FKYIIDAISKLVDEAKFKFTEDGIRLRALD-PAKVAMVDLELPKE-AFEEYEVDE----EEKIGVDL 72 (247)
T ss_pred eEEEecchH--H-HHHHHHHHHHHhceEEEEECCCcEEEEEEC-CccEEEEEEEeCHH-hCccEecCC----CeEEEEEH
Confidence 799999874 4 589999999999999999999999997643 23445667777765 899999875 23477999
Q ss_pred HHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhc
Q 038444 83 SLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALD 162 (300)
Q Consensus 83 ~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~ 162 (300)
..|.+.||.+.. .+.++|.+.+.+ ..+.|.+.+ +...+...+ ++-....+ .+.|-
T Consensus 73 ~~l~~il~~~~~-----------~~~v~i~~~~~~--------~~l~~~~~~-~~~~~~~~~---Lieg~~p~-~~v~p- 127 (247)
T PRK01115 73 EDLKKILKRAKK-----------GDKLELELDEEE--------NKLKITFGG-EKTREFSLP---LLDVSSEE-PPEPN- 127 (247)
T ss_pred HHHHHHHhhCCC-----------CCEEEEEEcCCC--------CEEEEEEec-CcEEEEEEE---eeccCCCC-CCCCC-
Confidence 999999999854 467888876543 467787776 222333333 34333322 22220
Q ss_pred ccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccccccc
Q 038444 163 MAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLSAQT 242 (300)
Q Consensus 163 ~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~ 242 (300)
...+..+.|+. ..|+..++|+..+++.++|+.+ +|.|.|+..++ .....+...-. +.. .
T Consensus 128 ---~~~~~~i~~~~-~~l~~~~~r~~~~~~~v~i~~~-~~~l~lsa~~~-g~a~~~i~~~~------~~~-~-------- 186 (247)
T PRK01115 128 ---LELPVKAVILG-DDLKDAIKDAELVSDHIELEAD-EDKFYIEAEGE-GEDEVELSLDS------GPL-I-------- 186 (247)
T ss_pred ---CcccEEEEEEH-HHHHHHHHHHHhcCCeEEEEEe-CCEEEEEEEeC-CceEEEEecCC------Cce-E--------
Confidence 22345777888 9999999999999999999995 66788877664 33222222100 000 0
Q ss_pred hhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE
Q 038444 243 RSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC 287 (300)
Q Consensus 243 ~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~ 287 (300)
+ -...+..++..+.|-|..+|+.... .+.|.+.+.++..+
T Consensus 187 ---~-~~g~e~~~i~fn~~YL~d~lk~~~~-~~~V~l~~~~~~P~ 226 (247)
T PRK01115 187 ---E-LSVEEPAKSSYSLDYLKDMVKATSA-SDEVTIEFGSDMPL 226 (247)
T ss_pred ---E-EEecCceeEEEhHHHHHHhhccccC-CCeEEEEECCCCCE
Confidence 0 0000246889999999999984322 35888888777766
No 10
>KOG1636 consensus DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair]
Probab=98.95 E-value=7.2e-08 Score=86.05 Aligned_cols=243 Identities=13% Similarity=0.196 Sum_probs=176.4
Q ss_pred eeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEeh
Q 038444 3 FKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDI 82 (300)
Q Consensus 3 FrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~ 82 (300)
|-|++... .|+|+|+.++.-|-..+.+.-+.+.+.+..- ..+.-..|-..+..+ .|+.|||+- .+.|=+++
T Consensus 2 ~Earl~q~---sLlKkIlealkdlV~~a~fdcse~GislQaM-D~SHValvsl~l~s~-~F~~yRCDR----nl~lG~~L 72 (260)
T KOG1636|consen 2 LEARLVQA---SLLKKILEALKDLVNDANFDCSETGISLQAM-DSSHVALVSLLLRSE-GFEKYRCDR----NLSLGMNL 72 (260)
T ss_pred chhHHHHH---HHHHHHHHHHHHHHhccCcccccCceEEEEe-cccceEEEEEEeecc-ccceeccCC----ccccccCH
Confidence 55666654 4569999999999999999999999888642 233444445555666 999999997 89999999
Q ss_pred HHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhc
Q 038444 83 SLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALD 162 (300)
Q Consensus 83 ~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~ 162 (300)
.+|.++||-|.+ .+.+++|-..+. -.+++.+++.+..=+.|.-+ |++. -+.++|.-|-
T Consensus 73 ~slsKiLkcann-----------ed~~Tlkaed~~--------dti~l~fe~~~~dki~dy~l-KLmd-iD~ehl~IPe- 130 (260)
T KOG1636|consen 73 KSLSKILKCANN-----------EDTVTLKAEDNP--------DTITLMFESPKQDKIADYEL-KLMD-IDSEHLGIPE- 130 (260)
T ss_pred HHHHHHHccccC-----------CCceEEEeecCC--------ceEEEEEECCCCCcceeeEE-Eeee-ccHHHcCCCc-
Confidence 999999999986 688999988775 46677777776677788888 6554 3446665442
Q ss_pred ccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccccccc
Q 038444 163 MAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLSAQT 242 (300)
Q Consensus 163 ~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~ 242 (300)
..-+..+.||+ .++..+...+..+||.|.|.+++.| ++|....|..+-.+.++...... .|.+ ...
T Consensus 131 ---~dy~~~~~mPa-~EF~ricrdls~f~Dsv~I~~tkeg-v~F~~~Gdig~asi~l~~~~~~d----~~e~--av~--- 196 (260)
T KOG1636|consen 131 ---QDYDAVVTMPA-GEFSRICRDLSTFSDSVVISATKEG-VKFSAKGDIGTASITLSQCTAVD----KPEE--AVK--- 196 (260)
T ss_pred ---ccceEEEEccH-HHHHHHHHHHhhhcCeEEEEEecce-eEEEecccccceeEEEccCCCCC----Cccc--eEE---
Confidence 12234677998 8999999999999999999997665 78888888777777776544211 0100 000
Q ss_pred hhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeEE-------EEEEEEEe
Q 038444 243 RSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGACL-------TVIFQFFI 296 (300)
Q Consensus 243 ~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~~-------~~~l~y~i 296 (300)
..-.+-++.+..+|-+..|-++--+ .++|-+.+..+..++ ..-++||+
T Consensus 197 -----iE~~~pVtltfa~kYln~ftKatpL-s~rV~lsls~~~P~~vey~i~~~g~lr~YL 251 (260)
T KOG1636|consen 197 -----IEMNEPVTLTFALKYLNQFTKATPL-SDRVTLSLSSEVPVVVEYKIEDMGHLRYYL 251 (260)
T ss_pred -----EEecCcchhhhHHHHHHHhhccccc-cceEEEEecCCCcEEEEEecccCceEEEEE
Confidence 0011356777888888888876444 578889998888775 26788886
No 11
>PF00705 PCNA_N: Proliferating cell nuclear antigen, N-terminal domain; InterPro: IPR022648 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1U76_E 2ZVK_B 1VYJ_A 1UL1_B 3P87_D 2ZVM_C 2ZVL_A 1AXC_C 3VKX_A 3TBL_B ....
Probab=98.90 E-value=9.9e-08 Score=79.12 Aligned_cols=106 Identities=16% Similarity=0.238 Sum_probs=89.7
Q ss_pred eeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEeh
Q 038444 3 FKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDI 82 (300)
Q Consensus 3 FrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~ 82 (300)
|+|++.++ .+||+++.++++|-.++.+.++++.+.+.. ..++.-..+-..++.+ .|++|+|+. ++.+-++.
T Consensus 2 fea~~~~a---~~~K~i~eal~~lv~e~~f~~~~~Gi~~~a-mD~s~Valv~l~l~~~-~F~~Y~~d~----~~~igvnl 72 (127)
T PF00705_consen 2 FEAKFSDA---SLFKKIFEALKDLVDEANFEFTEDGISLQA-MDPSHVALVDLELPSE-AFEEYRCDK----ELSIGVNL 72 (127)
T ss_dssp EEEEESSH---HHHHHHHHHHTTTCSEEEEEEESSEEEEEE-E-TTSSEEEEEEEEGG-GSSEEEESS----SEEEEEEH
T ss_pred eEEEEcch---HHHHHHHHHHHHHhhEEEEEEccCCEEEEE-ECCCcEEEEEEEechh-cceEEEcCC----CEEEEEEH
Confidence 89999987 346999999999999999999999999965 4566788888999988 999999985 78999999
Q ss_pred HHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECce
Q 038444 83 SLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYK 136 (300)
Q Consensus 83 ~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~ 136 (300)
+.|.++||++.+ .+.+.|+.... ...|.+.+++.+
T Consensus 73 ~~l~kiLk~~~~-----------~D~l~l~~~~~--------~~~l~i~~~~~~ 107 (127)
T PF00705_consen 73 SDLKKILKRAKK-----------DDSLELESDEE--------PDKLNIVFENEK 107 (127)
T ss_dssp HHHHHHHTTSST-----------TSEEEEEEESS--------SSEEEEEEEETT
T ss_pred HHHHHHHhhccC-----------CCEEEEEEeCC--------CCEEEEEEEcCC
Confidence 999999999997 68899987544 367777776544
No 12
>PF02144 Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IPR003021 REC1 of Ustilago maydis plays a key role in regulating the genetic system of the fungus. REC1 mutants are very sensitive to UV light. Mutation leads to a complex phenotype with alterations in DNA repair, recombination, mutagenesis, meiosis and cell division []. The predicted product of the REC1 gene is a polypeptide of 522 amino acid residues with molecular mass 57kDa. The protein shows 3'--5' exonuclease activity, but only in cells over-expressing REC1 []. While it is distinguishable from the major bacterial nucleases, the protein has certain enzymatic features in common with epsilon, the proof-reading exonuclease subunit of Escherichia coli DNA polymerase III holoenzyme []. The rad1 gene of Schizosaccharomyces pombe comprises three exons and encodes a 37kDa protein that exhibits partial similarity to the REC1 gene of U. maydis []. The two genes share putative functional similarities in their respective organisms.; GO: 0003684 damaged DNA binding, 0008853 exodeoxyribonuclease III activity, 0006281 DNA repair, 0005634 nucleus; PDB: 3G65_B 3GGR_C 3A1J_C.
Probab=98.56 E-value=1.8e-05 Score=73.76 Aligned_cols=250 Identities=17% Similarity=0.205 Sum_probs=148.5
Q ss_pred eeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEe---------eecCC
Q 038444 3 FKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRI---------SSQNE 73 (300)
Q Consensus 3 FrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~i---------eS~~~ 73 (300)
|.|++.+. +.| .+++.+|.-.. .|.+.++++.+.|... .+..+|+-+-++.+ +|++|.+ +..++
T Consensus 2 f~A~~~~~--~~l-~~lL~~I~~~~-~a~v~is~~Gi~~~vE--~~~~~qa~a~l~k~-LF~~Y~~~~~~~~~~~~~~~~ 74 (275)
T PF02144_consen 2 FSASTSNV--RHL-YQLLKCIAFKN-KATVEISEDGIKFTVE--DSKSIQASAFLDKS-LFSEYTFNPPPDADDDDEEEE 74 (275)
T ss_dssp EEEEES-T--HHH-HHHHHTT-SSS-EEEEEEETTEEEEEEE--ETTTEEEEEEEEGG-GSSEEEE------------SS
T ss_pred eEEEECCH--HHH-HHHHHhcccCC-eEEEEEcCCEEEEEEE--CCcEEEEEEEEChh-hceEEEEeccccccccccCCC
Confidence 89999976 454 68888888777 6999999999999663 67999999999988 9999999 23456
Q ss_pred CeEEEEEehHHHHHHHhccccccccccccCC---------CCceEEEEEeecCCCCCCCCCce-EEEEEECceeEEEEEe
Q 038444 74 DCIAFAIDISLLQRAVRSGVSICSEIGAAGS---------AANRLQIKLVKKLPPNCTQAMPF-LTFETKGYKSAVIQDV 143 (300)
Q Consensus 74 N~I~lev~~~~L~raLrsa~~~~~~~~~~~~---------~a~~v~ikL~kk~~~~~~~~~P~-L~~~~~g~~~~v~hdv 143 (300)
..+.|++++..|+.+|.-...+...++.++. ......++|.=.+. ..|+ |.++-.| ++-++
T Consensus 75 ~~~~F~I~L~~LlecL~ifg~~~~~~~~~~~~~~~~~~~~~~~~~~~~lsY~g~-----G~pL~l~led~g----v~t~c 145 (275)
T PF02144_consen 75 DEVSFGINLSALLECLNIFGSSDSSSSSSSSGGDPSRNNASGEPTSCRLSYPGE-----GSPLVLILEDSG----VTTTC 145 (275)
T ss_dssp S-EEEEEEHHHHHHHHTTT-SS--TT-----------------EEEEEEEESSS-----CCEEEEEEEETT----EEEEE
T ss_pred CceEEEEEhHHHHHHHHHhCCCCCccccccccccccccccccCCceEEEEEcCC-----CCeEEEEEEeCC----EEEEE
Confidence 8999999999999999998765322110000 01124555554431 1453 4444422 23333
Q ss_pred ecCcccChhhhchhhhhhcccCCCCC-eEEEcCChhhHHHHHHhhhcc-CCEEEEEEEcC--CeEEEEEeecceEEeEEe
Q 038444 144 PISKPLSRAQGLELQTALDMAQDIPP-TLVQVPDLNQLQNFVHRMKHV-GDLLNVSIYKY--GDLHLQISTTLITLGAEF 219 (300)
Q Consensus 144 PV~~vl~~~~~~~l~eP~~~~~~~p~-~~i~lP~l~~l~~ivdR~k~~-~~~v~i~an~~--G~L~l~v~t~~v~v~t~~ 219 (300)
-+ +..-+.+..++. .+ ..+- ..+.|.+ ..|+..+..+... ++.++|.++.. ..|+|....+....++.|
T Consensus 146 ~i-~T~~~~~~~d~~--f~---~~~~~~kiimks-~~L~~al~eL~~~~~~~l~i~~s~~~~p~f~l~s~G~~G~s~v~f 218 (275)
T PF02144_consen 146 EI-RTYEPDDPLDFP--FD---RSDVVNKIIMKS-DWLRDALSELDWSNSEELTIYISPPDKPHFRLSSKGPLGSSKVDF 218 (275)
T ss_dssp EE-EEE----------------TTTEEEEEEEEH-HHHHHHHHTT-TS-CSEEEEEE-S-SSSSEEEEEEETTEEEEEEE
T ss_pred EE-EEecCCcccCcc--cc---cccceeEEEEEh-HHHHHHHHHHhhccCCeEEEEEEeCCCCEEEEEEEcCCCeEEEEE
Confidence 33 233333322332 11 1111 2456766 7899999999999 89999999884 789999998888888888
Q ss_pred ccccccccccCCCCccccccccchhhhhcCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeEEEEEEEEE
Q 038444 220 RKLLVIGEKAVAPSEDRNLSAQTRSERAISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGACLTVIFQFF 295 (300)
Q Consensus 220 ~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~~~~~l~y~ 295 (300)
..=.-.-+. -+.. ...+...-+-..+.|.+.+.+-.+ .+++.+-+..++.+ ++||.
T Consensus 219 p~~~~~le~----f~~~------------~~~~~~~~~Y~f~~i~~~~kAl~~-ssKv~ir~d~~GlL---s~Q~m 274 (275)
T PF02144_consen 219 PNDSDVLET----FECY------------DGEEPVISRYKFSLIKKAMKALKI-SSKVSIRIDENGLL---SLQFM 274 (275)
T ss_dssp -TTSTSEEE----EEE----------------S-EEEEEEHHHHCCHHHHHTT-SSEEEEEEESSS-E---EEEEE
T ss_pred CCCCCceeE----EEEe------------ccCceEEEEEeHHHHHHHHHHhhh-ccEEEEEeCCCcEE---EEEEe
Confidence 752200000 0000 000233444777777777775333 57888888888743 44444
No 13
>PF04139 Rad9: Rad9; InterPro: IPR007268 Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage.; GO: 0006281 DNA repair; PDB: 3GGR_A 3G65_A 3A1J_A.
Probab=98.00 E-value=0.00076 Score=61.80 Aligned_cols=226 Identities=15% Similarity=0.193 Sum_probs=125.0
Q ss_pred HHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccc
Q 038444 16 EKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSI 95 (300)
Q Consensus 16 ~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~ 95 (300)
|.+.+++++|++++..+-.+++.|.+-. ...+...-.-..+..+ +|++|.-....+..+.+.+..-+++.++|+....
T Consensus 1 f~ral~~Lskigeel~ie~~~~~L~l~a-vNss~Sa~~~~~F~~~-FF~~y~~~~~~~~~~~~~i~~K~~l~vfr~~~~~ 78 (252)
T PF04139_consen 1 FARALQCLSKIGEELYIEITEDGLSLRA-VNSSRSAYAQFRFSKS-FFDKYQADSDSQDSFSCKISMKSLLSVFRSLSTL 78 (252)
T ss_dssp HHHHHHHHHTT-SEEEEEEETTEEEEEE-E-TTSSEEEEEEETGG-GSSEEE--SSSS----EEEEHHHHHHHHSSCTCC
T ss_pred CHHHHHHHHhhCCeEEEEEcCCeEEEEE-ECccccEEEEEEEChH-HhhhhcccCCCCCcEEEEEEchhhhhhhcccccc
Confidence 4688999999999999999999999963 2333444444445655 9999944455567889999999999999975521
Q ss_pred cccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECce-eEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEc
Q 038444 96 CSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYK-SAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQV 174 (300)
Q Consensus 96 ~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~-~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~l 174 (300)
.. +-+.+.|++... ..-|.+++.... ..-+|.+|.. .-..-. ..+... ..|. .+.+
T Consensus 79 ~~-------~Ve~c~i~i~~~--------~~~L~~~l~c~~gI~Kt~~l~~~-~~~~~~-a~~d~~-----~~~n-~l~~ 135 (252)
T PF04139_consen 79 EK-------NVESCEISIDND--------ESRLIFQLFCKNGIIKTYNLPYE-ECESLQ-AVFDKE-----SCPN-YLVI 135 (252)
T ss_dssp HH-------CEEEEEEEE-TT--------SSEEEEEEEEGGGEEEEEEEE-C-E----------GG-----GSSE-EEEE
T ss_pred cc-------ceeEEEEEEcCC--------CcEEEEEEEeccceEEEEEEEEE-eccccc-cccchh-----cCCc-eEEE
Confidence 00 257788999322 456888876443 4567888883 221111 111100 1122 4556
Q ss_pred CChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecce-----EEeEEeccccccccccCCCCccccccccchhhhhcC
Q 038444 175 PDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLI-----TLGAEFRKLLVIGEKAVAPSEDRNLSAQTRSERAIS 249 (300)
Q Consensus 175 P~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v-----~v~t~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 (300)
++ +.|+.+++-+..=-+.+++..+. +.+.+.--++.. .+.|+-. + .+.+=+. -..
T Consensus 136 ~~-~~l~~~l~~f~~~~eeitl~~~~-~~v~~~s~~~~~~~~~~~l~t~v~---i------~~~ef~~----~~~----- 195 (252)
T PF04139_consen 136 SP-RLLKDLLDHFPSSTEEITLEVTD-DKVSFKSYTEEIQDSKQPLSTEVT---I------STEEFDE----YNV----- 195 (252)
T ss_dssp EH-HHHHHHHTTS-TT--EEEEEEEC-TCEEEEEE-----SSS---EEEEE---E-------GGGSSE----EE------
T ss_pred Ch-HHHHHHHhhcCCChhhEEEEecC-CEEEEEeecccccccccceEEEEE---E------ehHhcce----EEc-----
Confidence 66 88999999988755788888755 666665422211 1111100 0 0000000 001
Q ss_pred CCCeEEEEEechhHHhhccccccCCcEEEEEEE-CCCeE
Q 038444 250 RGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIA-PQGAC 287 (300)
Q Consensus 250 ~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~-~~~~~ 287 (300)
++...+++.+|.|..+++-....-..+-++.. +++.+
T Consensus 196 -~~~~~itF~lKefka~l~~ae~~~~~i~~~f~~pG~Pi 233 (252)
T PF04139_consen 196 -QEDTDITFSLKEFKAILSFAESLSLPISIYFDNPGRPI 233 (252)
T ss_dssp --TT-EEEEEHHHHHHHHHHHHHTTEEEEEEESSTTS-E
T ss_pred -CCCCEEEEEeHHHHHHHHHHHhcCCcEEEEECCCCCcE
Confidence 12379999999999998864433445556664 44444
No 14
>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....
Probab=96.83 E-value=0.044 Score=45.20 Aligned_cols=113 Identities=14% Similarity=0.188 Sum_probs=82.2
Q ss_pred CCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccccccchhhhh
Q 038444 168 PPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLSAQTRSERA 247 (300)
Q Consensus 168 p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (300)
.+..+.||+ ..+++++..+..+||.|+|.++. +.+.|..+.|..+..+.++.-... ..+.+ . -.
T Consensus 7 ~~~~v~m~S-~~f~~~~kdl~~v~d~v~i~~~~-~~~~f~~~Gd~~~~~v~~~~~~~~----~~~~~----~------~~ 70 (128)
T PF02747_consen 7 YDATVTMPS-SEFKKICKDLSSVGDTVTISADK-DSVIFSAEGDIGSAEVEFKETESS----EDDEE----L------IE 70 (128)
T ss_dssp -SEEEEEEH-HHHHHHHHHHHTTCSEEEEEEET-TEEEEEEEESSEEEEEEEEEEEEE----TTCTC----E------SE
T ss_pred ceEEEEEEH-HHHHHHHHHHHhcCCEEEEEEeC-CEEEEEEEeccCcEEEEEeecccc----ccccc----c------ce
Confidence 356788998 89999999999999999999975 569999999988888777653310 00000 0 00
Q ss_pred cCCCCeEEEEEechhHHhhccccccCCcEEEEEEECCCeE-EE------EEEEEEec
Q 038444 248 ISRGDAQSVQVSVKHFSKSLQCHLAKPDCAFFGIAPQGAC-LT------VIFQFFIP 297 (300)
Q Consensus 248 ~~~~~~~~V~Vd~k~l~~~L~~~~~~p~~v~~~i~~~~~~-~~------~~l~y~ip 297 (300)
....+.++....+|-|..|..+-.+ .+.|.+.+.++..+ +. ..++||+.
T Consensus 71 i~~~~~~~~~fsl~YL~~~~Ka~~l-s~~V~l~l~~~~Pl~l~f~~~~~g~l~f~LA 126 (128)
T PF02747_consen 71 IEVKEPVSSSFSLDYLNDFSKAAPL-SDEVTLELGEDMPLKLEFELADGGSLKFYLA 126 (128)
T ss_dssp EEESSEEEEEEEHHHHHHHGGGGGT-TSEEEEEEETTSEEEEEEEETTTEEEEEEE-
T ss_pred eeeccceeeEEeHHHHHhhhccccC-CceEEEEEcCCCCEEEEEEeCCCeEEEEEEc
Confidence 1111457788999999999986544 67999999999877 42 67888874
No 15
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=94.65 E-value=0.76 Score=41.55 Aligned_cols=83 Identities=8% Similarity=0.077 Sum_probs=63.9
Q ss_pred HHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccc
Q 038444 16 EKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSI 95 (300)
Q Consensus 16 ~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~ 95 (300)
|.+++.-++-+++.+.|.++++.+.|.... + +..........+ .|.+|..+. .+...++...|..+||.+..
T Consensus 141 l~~~~~r~~~~~~~v~i~~~~~~l~lsa~~-~-g~a~~~i~~~~~-~~~~~~g~e----~~~i~fn~~YL~d~lk~~~~- 212 (247)
T PRK01115 141 LKDAIKDAELVSDHIELEADEDKFYIEAEG-E-GEDEVELSLDSG-PLIELSVEE----PAKSSYSLDYLKDMVKATSA- 212 (247)
T ss_pred HHHHHHHHHhcCCeEEEEEeCCEEEEEEEe-C-CceEEEEecCCC-ceEEEEecC----ceeEEEhHHHHHHhhccccC-
Confidence 479999999999999999999999986544 3 555555555544 666677643 57788899999999998874
Q ss_pred cccccccCCCCceEEEEEeec
Q 038444 96 CSEIGAAGSAANRLQIKLVKK 116 (300)
Q Consensus 96 ~~~~~~~~~~a~~v~ikL~kk 116 (300)
++.++|++...
T Consensus 213 ----------~~~V~l~~~~~ 223 (247)
T PRK01115 213 ----------SDEVTIEFGSD 223 (247)
T ss_pred ----------CCeEEEEECCC
Confidence 57899999654
No 16
>cd00140 beta_clamp Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.
Probab=93.93 E-value=5.8 Score=37.53 Aligned_cols=189 Identities=12% Similarity=0.074 Sum_probs=103.6
Q ss_pred HHHhcC-CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccccccccc
Q 038444 22 ALDKMG-KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIG 100 (300)
Q Consensus 22 ~i~kl~-k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~ 100 (300)
.+.++. ..+.+.+..+.+.|.. ++....+.+-...-|.+|.-. ++.-.++++.+.|.++|+.+....+..
T Consensus 78 i~k~l~~~~v~i~~~~~~l~i~~-----g~~~~~~~~~~~~~fP~~~~~---~~~~~~~i~~~~l~~~l~~v~~~~~~~- 148 (365)
T cd00140 78 IVRKLPDEEVTLETEENRLTIKS-----GKSRFSLNTLPAEEFPELPEI---ENGSSFTIPASELKELIKKTAFAVSTD- 148 (365)
T ss_pred HHHhCCCCcEEEEEcCCEEEEEE-----CcEEEEEcCCCHHHCCCCCCC---CCCcEEEECHHHHHHHHhhEEEEecCc-
Confidence 344443 6788888888777754 455666665543368887765 445688999999999999987542210
Q ss_pred ccCCCCc-e-EEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEcCChh
Q 038444 101 AAGSAAN-R-LQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQVPDLN 178 (300)
Q Consensus 101 ~~~~~a~-~-v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~lP~l~ 178 (300)
+.. . --|+|.-.+ ..|.+...+..+.....+++. .- ..++..+.+|. +
T Consensus 149 ----~~~~~l~gI~~~~~~--------~~l~l~atD~~~~~~~~~~~~-~~----------------~~~~~~~~i~~-~ 198 (365)
T cd00140 149 ----ETRPILNGVLLEIED--------NKLRAVATDGHRLALREIELE-SG----------------AEEDFNVIVPR-K 198 (365)
T ss_pred ----cCcccceEEEEEEEC--------CEEEEEEEcCceEEEEEeecC-CC----------------CccCceEEEec-h
Confidence 010 0 124444333 356666555555556666662 10 01245566776 5
Q ss_pred hHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccccccchhhhhcCCCCeEEEEE
Q 038444 179 QLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLSAQTRSERAISRGDAQSVQV 258 (300)
Q Consensus 179 ~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~V 258 (300)
.|..++..++.-++.++|..+. +.+.+.. +...+.+.--+-..|.. . .- .+. ....++.|
T Consensus 199 ~l~~l~k~l~~~~~~v~i~~~~-~~l~i~~--~~~~~~~~li~~~yP~~------~-~~------ip~----~~~~~~~i 258 (365)
T cd00140 199 TLNELLKLLEDDDEEVEISISE-NQILFKL--GNTTFTSRLIEGEFPDY------E-RV------IPK----EFEKSLTV 258 (365)
T ss_pred HHHHHHHhccCCCCcEEEEEeC-CEEEEEE--CCEEEEEEEEeeECCCc------h-hc------CCC----CCcEEEEE
Confidence 5555555554324678887744 3444444 33332222111111111 0 00 000 02468889
Q ss_pred echhHHhhccc
Q 038444 259 SVKHFSKSLQC 269 (300)
Q Consensus 259 d~k~l~~~L~~ 269 (300)
+.+.|.+.++-
T Consensus 259 ~~~~L~~~l~~ 269 (365)
T cd00140 259 DREELLEALKR 269 (365)
T ss_pred EHHHHHHHHHH
Confidence 99999888864
No 17
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]
Probab=93.03 E-value=0.93 Score=43.94 Aligned_cols=76 Identities=17% Similarity=0.336 Sum_probs=58.8
Q ss_pred HHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccc
Q 038444 15 LEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVS 94 (300)
Q Consensus 15 l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~ 94 (300)
.++.+..++++|-..+++.++.+...... ...+..-..--.++.+ -|.+|.+.... +.+.++.+.|.++++++..
T Consensus 70 ~~k~l~dii~~L~de~~~~~~~~~~~~~~-i~~~~s~f~l~~lp~e-~Fp~~~~~~~~---~~~~l~~~~Lk~ii~~~~f 144 (364)
T COG0592 70 PAKKLLDIISKLPDEAVFLVTEDGISLLA-VDSGKSAFVLLTLPAE-DFPEYPVDEEE---VEFGLPTELLKKIIKRTKF 144 (364)
T ss_pred EhHHHHHHHHhCCCCceEEEEecCCceEE-EecCceEEEcCCCCHH-HCCCCCCCCcC---ceEEecHHHHHHHHhheee
Confidence 35889999999999999999999875211 1233444455556777 89999988744 7899999999999999987
Q ss_pred c
Q 038444 95 I 95 (300)
Q Consensus 95 ~ 95 (300)
+
T Consensus 145 a 145 (364)
T COG0592 145 A 145 (364)
T ss_pred c
Confidence 4
No 18
>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....
Probab=92.00 E-value=5.9 Score=32.42 Aligned_cols=107 Identities=14% Similarity=0.181 Sum_probs=71.9
Q ss_pred eeEEecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCC-CcC---eeEeeecCCCeEEE
Q 038444 3 FKAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKET-LFD---DYRISSQNEDCIAF 78 (300)
Q Consensus 3 FrA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~-lF~---ey~ieS~~~N~I~l 78 (300)
|.|++.=.. ..|++++..++.++..+.+..+++.+.|...+ +....=..+.... ..+ ...++. ++.+..
T Consensus 7 ~~~~v~m~S--~~f~~~~kdl~~v~d~v~i~~~~~~~~f~~~G---d~~~~~v~~~~~~~~~~~~~~~~i~~--~~~~~~ 79 (128)
T PF02747_consen 7 YDATVTMPS--SEFKKICKDLSSVGDTVTISADKDSVIFSAEG---DIGSAEVEFKETESSEDDEELIEIEV--KEPVSS 79 (128)
T ss_dssp -SEEEEEEH--HHHHHHHHHHHTTCSEEEEEEETTEEEEEEEE---SSEEEEEEEEEEEEETTCTCESEEEE--SSEEEE
T ss_pred ceEEEEEEH--HHHHHHHHHHHhcCCEEEEEEeCCEEEEEEEe---ccCcEEEEEeeccccccccccceeee--ccceee
Confidence 445544332 34699999999999999999999999996543 2222222222110 111 123332 246788
Q ss_pred EEehHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCc-eEEEEEECc
Q 038444 79 AIDISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMP-FLTFETKGY 135 (300)
Q Consensus 79 ev~~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P-~L~~~~~g~ 135 (300)
+++.+.|....|.+.- ++.++|+|.... | .|.|.+.+.
T Consensus 80 ~fsl~YL~~~~Ka~~l-----------s~~V~l~l~~~~--------Pl~l~f~~~~~ 118 (128)
T PF02747_consen 80 SFSLDYLNDFSKAAPL-----------SDEVTLELGEDM--------PLKLEFELADG 118 (128)
T ss_dssp EEEHHHHHHHGGGGGT-----------TSEEEEEEETTS--------EEEEEEEETTT
T ss_pred EEeHHHHHhhhccccC-----------CceEEEEEcCCC--------CEEEEEEeCCC
Confidence 9999999999987765 789999999875 7 477887654
No 19
>PF02768 DNA_pol3_beta_3: DNA polymerase III beta subunit, C-terminal domain; InterPro: IPR022635 This entry describes the C-terminal domain of the beta chain of DNA polymerase III. This is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3P16_A 3RB9_B 2AVT_B 2XUR_B 3Q4K_A 3BEP_A 3D1G_A 1UNN_B 3Q4J_D 2POL_A ....
Probab=89.40 E-value=7.5 Score=31.12 Aligned_cols=67 Identities=10% Similarity=0.119 Sum_probs=47.0
Q ss_pred CCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCC
Q 038444 27 GKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAA 106 (300)
Q Consensus 27 ~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a 106 (300)
.+.+.|.|+++++.+-... .+..+..-+++.+ |. ++.+.+-+|...|.-+|++.. +
T Consensus 34 ~~~v~l~~~~~~l~l~~~~--~~~g~~~e~i~~~-----~~-----g~~~~i~fN~~yL~d~L~~~~------------~ 89 (121)
T PF02768_consen 34 NNPVKLSFSDNQLTLSSQS--SEIGEAEEEIPIE-----YE-----GEPLEIAFNPKYLLDALKAID------------G 89 (121)
T ss_dssp TGEEEEEEETTEEEEEEEE--TTTEEEEEEEE-E-----EE-----ES-EEEEEEHHHHHHHHHCC-------------S
T ss_pred CceEEEEEECCEEEEEEcC--CCCceEEEEEeee-----ec-----CCceEEEECHHHHHHHHhhcC------------C
Confidence 3578899999999985432 2333555544433 22 457899999999999999986 4
Q ss_pred ceEEEEEeecC
Q 038444 107 NRLQIKLVKKL 117 (300)
Q Consensus 107 ~~v~ikL~kk~ 117 (300)
+.+.|+++...
T Consensus 90 ~~V~l~~~~~~ 100 (121)
T PF02768_consen 90 EEVTLEFSDPS 100 (121)
T ss_dssp SEEEEEESSTT
T ss_pred CEEEEEEcCCC
Confidence 67999998775
No 20
>TIGR00590 pcna proliferating cell nuclear antigen (pcna). All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.39 E-value=34 Score=31.53 Aligned_cols=96 Identities=13% Similarity=0.174 Sum_probs=67.4
Q ss_pred HHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccC--CCcCe--eEeeecCCCeEEEEEehHHHHHHHh
Q 038444 15 LEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKE--TLFDD--YRISSQNEDCIAFAIDISLLQRAVR 90 (300)
Q Consensus 15 l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~--~lF~e--y~ieS~~~N~I~lev~~~~L~raLr 90 (300)
-|++++.-++.++..+.+..+++.+.|...+ +....-.+++.+ ..-++ ..++ .++.+.-....+.|....|
T Consensus 143 ~f~~~~kdl~~v~d~v~i~~~~~~~~f~~~G---d~g~~~~~~~~~~~~~~~~~~~~i~--~~~~~~~~y~l~YL~~~~K 217 (259)
T TIGR00590 143 EFARICRDLSQFSDSVVISCTKEGVKFSAKG---DIGSGNVKLKQTSDTDKEEEAVTIE--MKEPVTLTFAIKYLNLFTK 217 (259)
T ss_pred HHHHHHHHHHHcCCEEEEEEeCCEEEEEEEe---cccEEEEEEecCCCCCCCcceEEEE--ecCceeeeeeHHHHHHhhh
Confidence 3589999999999999999999999997543 223444445433 11111 1222 2346777889999999999
Q ss_pred ccccccccccccCCCCceEEEEEeecCCCCCCCCCc-eEEEEEEC
Q 038444 91 SGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMP-FLTFETKG 134 (300)
Q Consensus 91 sa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P-~L~~~~~g 134 (300)
.+.- ++.++|+|.... | .|.|.+.+
T Consensus 218 a~~l-----------s~~V~l~~~~~~--------Pl~l~y~i~~ 243 (259)
T TIGR00590 218 ATPL-----------SDRVTLSMSNDV--------PLVVEYKIKD 243 (259)
T ss_pred hccC-----------CCeEEEEEcCCC--------CEEEEEEeCC
Confidence 6664 788999999986 6 46677653
No 21
>PF00712 DNA_pol3_beta: DNA polymerase III beta subunit, N-terminal domain; InterPro: IPR022634 This entry describes the N-terminal domain of the beta chain of DNA polymerase III. This is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication from an RNA primer, nucleotide triphosphate (dNTP) residues being added to the 5'-end of the growing DNA chain.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3P16_A 3RB9_B 2AWA_C 1VPK_A 2XUR_B 3Q4K_A 3BEP_A 3D1G_A 1UNN_B 3Q4J_D ....
Probab=83.15 E-value=22 Score=28.46 Aligned_cols=101 Identities=14% Similarity=0.211 Sum_probs=64.9
Q ss_pred EEEehHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchh
Q 038444 78 FAIDISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLEL 157 (300)
Q Consensus 78 lev~~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l 157 (300)
|.++.+.|.++|+.+.+..+.-++. .---.+++.-++ -.|.+...+....+.+.+|+. +.
T Consensus 3 f~i~k~~L~~~l~~v~~~i~~k~~~---piL~~ili~a~~--------~~l~l~atD~e~~i~~~i~~~-~~-------- 62 (120)
T PF00712_consen 3 FTINKEELLKALSKVSKVIPSKSTI---PILSNILIEAKD--------NKLTLTATDLEISIRTTIPAE-IE-------- 62 (120)
T ss_dssp EEEEHHHHHHHHHHHHTCSSSSSSS---GGGGEEEEEEET--------TEEEEEEE-SSEEEEEEEETE-EE--------
T ss_pred EEEEHHHHHHHHHHHHhhhCCCCCh---HHhccEEEEEeC--------CEEEEEEEcCeEEEEEEEece-ee--------
Confidence 6788999999999988753321110 111234444443 367777777788999999994 33
Q ss_pred hhhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEee
Q 038444 158 QTALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQIST 210 (300)
Q Consensus 158 ~eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t 210 (300)
.+ +-.+.+|+ +.|..++.+|.. ++.|+|+.+. +.+.+..+.
T Consensus 63 ~~---------~G~~~v~a-k~l~~ivk~lp~-~~~I~i~~~~-~~l~I~~~~ 103 (120)
T PF00712_consen 63 EE---------EGSILVPA-KKLFDIVKKLPD-DEEITIEVEE-NKLTIKSGK 103 (120)
T ss_dssp EE----------EEEEEEH-HHHHHHHHHSSS-TSEEEEEEET-TEEEEEETT
T ss_pred cC---------CeEEEEEh-HHHHHHHHhCCC-CCeEEEEEeC-CEEEEEECC
Confidence 11 23566776 777788877776 4579998855 677777433
No 22
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Probab=81.26 E-value=38 Score=29.90 Aligned_cols=86 Identities=8% Similarity=0.096 Sum_probs=59.8
Q ss_pred HHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccc
Q 038444 16 EKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSI 95 (300)
Q Consensus 16 ~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~ 95 (300)
|++++.-++-++....+.++++++.|.... +.++.-..........+.+|... ..+...++...|..+|+....
T Consensus 140 L~~~i~~~~~~~~~i~i~~~~~~l~lss~~-~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~fn~~yL~~~l~~~~~- 213 (248)
T cd00577 140 LKDIVRDLESISDSVTISASKDGFKFSAEG-ELGGASVTLLPKDSDLLVTIECS----EPVSSTYSLKYLKDFTKAAPL- 213 (248)
T ss_pred HHHHHHHHHHcCCEEEEEEcCCEEEEEEee-cCCceEEEEecCCCCceEEEEeC----CceEEEEhHHHHHHHhhhccc-
Confidence 478888888899999999999998885433 22333333322233355444433 367788999999999999874
Q ss_pred cccccccCCCCceEEEEEeecC
Q 038444 96 CSEIGAAGSAANRLQIKLVKKL 117 (300)
Q Consensus 96 ~~~~~~~~~~a~~v~ikL~kk~ 117 (300)
++.+.|++...+
T Consensus 214 ----------s~~v~i~~~~~~ 225 (248)
T cd00577 214 ----------SDKVTLSFGSDG 225 (248)
T ss_pred ----------CCeEEEEEcCCC
Confidence 467888887774
No 23
>PHA03383 PCNA-like protein; Provisional
Probab=79.93 E-value=36 Score=31.59 Aligned_cols=98 Identities=9% Similarity=0.096 Sum_probs=65.6
Q ss_pred hHHHhHHHHHHhcCCEEEEEEecCeEEEEeee-cCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcc
Q 038444 14 LLEKRFLPALDKMGKVCHLFLTREKAYFLHNL-LSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSG 92 (300)
Q Consensus 14 ~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~-~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa 92 (300)
..|++++.-++.++..+.+.-+++.+.|-... ..++....-..+... +.=.+.-...+.+...++++.|....|.+
T Consensus 149 ~~f~~i~kdl~~igD~v~i~~~~~~v~f~~~~~~~Gd~~~~~~~~~~~---~~~~v~~~~~~~~~~~ysl~YL~~~~Ka~ 225 (262)
T PHA03383 149 NYFQRLCRDMSNITDDLEITKKGKEVSFRSDYTCVTDFASQETIIGDS---DNGQITCNESPDYTGKFSLKYLTSFTKAS 225 (262)
T ss_pred HHHHHHHHHHHHcCCeEEEEEeCCEEEEEEcccccccccceEEEecCC---CCCceEEecCCceEEEEeHHHHHHhhccc
Confidence 34699999999999999999999999996210 122222222222111 00001112245688899999999999976
Q ss_pred ccccccccccCCCCceEEEEEeecCCCCCCCCCce-EEEEEE
Q 038444 93 VSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPF-LTFETK 133 (300)
Q Consensus 93 ~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~-L~~~~~ 133 (300)
.- ++.++|+|.... |+ |.|.+.
T Consensus 226 ~l-----------s~~V~i~l~~d~--------Pl~ley~i~ 248 (262)
T PHA03383 226 GM-----------SSSVEIYLKESN--------PLILKYNVG 248 (262)
T ss_pred cC-----------CCeEEEEEcCCC--------CEEEEEEeC
Confidence 65 789999999774 74 777774
No 24
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=78.83 E-value=37 Score=31.57 Aligned_cols=93 Identities=17% Similarity=0.319 Sum_probs=63.2
Q ss_pred hHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccc
Q 038444 14 LLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGV 93 (300)
Q Consensus 14 ~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~ 93 (300)
.-|++++.-++.++..+.+..+++.+.|-..+ ++...-..+..+. .+ +.-.-+..+...+.++.|....|.+.
T Consensus 148 ~~f~~i~kdl~~vsD~v~i~~~~~~v~f~a~G---d~~~~~~~l~~~~--~~--v~~~~~~~v~~~fsl~YL~~f~Ka~~ 220 (264)
T PTZ00483 148 KKFQEFAKYLHSIGDTVSISMKKDEMRLETEG---EGIKASKQFHNDV--GD--VRVTSTESLSQEFATRYLVLFSKATS 220 (264)
T ss_pred HHHHHHHHHHHHcCCEEEEEEECCEEEEEEee---cCcEEEEEEccCC--Cc--eEEEecCcchheehHHHHHHhhcccc
Confidence 33689999999999999999999999997543 2223333333221 11 22112335556677888888888665
Q ss_pred cccccccccCCCCceEEEEEeecCCCCCCCCCce-EEEEE
Q 038444 94 SICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPF-LTFET 132 (300)
Q Consensus 94 ~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~-L~~~~ 132 (300)
- ++.|+|+|.... |+ |.|.+
T Consensus 221 l-----------sd~V~i~l~~~~--------Pl~ley~i 241 (264)
T PTZ00483 221 L-----------ADEVSINLSAGI--------PLSVKFNF 241 (264)
T ss_pred C-----------CCeEEEEEcCCC--------CEEEEEEe
Confidence 4 789999999885 74 66776
No 25
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=78.29 E-value=56 Score=30.13 Aligned_cols=96 Identities=13% Similarity=0.206 Sum_probs=67.3
Q ss_pred HHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCC--cCeeEeeecCCCeEEEEEehHHHHHHHhccc
Q 038444 16 EKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETL--FDDYRISSQNEDCIAFAIDISLLQRAVRSGV 93 (300)
Q Consensus 16 ~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~l--F~ey~ieS~~~N~I~lev~~~~L~raLrsa~ 93 (300)
|++++.-++.++..+.+..+++.+.|...+ ++...-..++.+.- -.+=.++....+.+.-....+.|....|.+.
T Consensus 144 f~~~~kdl~~vsd~v~i~~~~~~~~f~~~G---d~g~~~~~l~~~~~~~~~~~~~~i~~~e~~~~~y~l~YL~~~~Ka~~ 220 (263)
T PLN00057 144 FQRICKDLSSIGDTVVISVTKEGVKFSTSG---DIGTANIVLRQNTTVDKPEEKTVIEMQEPVSLTFALRYLNSFTKATP 220 (263)
T ss_pred HHHHHHHHHHcCCEEEEEEeCCEEEEEEEe---cCcEEEEEEecCCCCCCccceEEEEecCceEEEEhHHHHHHhhcccc
Confidence 589999999999999999999999996543 22334445543311 0110122123356788899999999999665
Q ss_pred cccccccccCCCCceEEEEEeecCCCCCCCCCc-eEEEEEE
Q 038444 94 SICSEIGAAGSAANRLQIKLVKKLPPNCTQAMP-FLTFETK 133 (300)
Q Consensus 94 ~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P-~L~~~~~ 133 (300)
- ++.++|++.... | .|.|.+.
T Consensus 221 l-----------s~~V~i~~~~~~--------Pl~l~y~l~ 242 (263)
T PLN00057 221 L-----------SDTVTLSLSKEL--------PVVVEYKIA 242 (263)
T ss_pred C-----------CCeEEEEEcCCC--------CEEEEEEeC
Confidence 4 788999999886 6 4777774
No 26
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=76.72 E-value=66 Score=30.09 Aligned_cols=98 Identities=11% Similarity=0.121 Sum_probs=68.2
Q ss_pred hHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCC--CcCeeEeeecCCCeEEEEEehHHHHHHHhc
Q 038444 14 LLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKET--LFDDYRISSQNEDCIAFAIDISLLQRAVRS 91 (300)
Q Consensus 14 ~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~--lF~ey~ieS~~~N~I~lev~~~~L~raLrs 91 (300)
.-|++++.-++.++..+.+..+++.+.|...+ +....-..++... -=++-.++-.-+..+...++++.|....|.
T Consensus 144 ~~f~~i~rdl~~vgd~V~i~~~~~~v~f~a~G---d~g~~~i~l~~~~~~~~~~~~~~~~v~~~~~~~ysl~YL~~f~Ka 220 (275)
T PTZ00113 144 KELTNICRQMNEFSDTVKIEIDSNSIKFTTQG---DLGDGEVVLKPRPPTSEDDCGVTIKVRKPIKQSYATKYLNMFAKS 220 (275)
T ss_pred HHHHHHHHHHHHcCCEEEEEEeCCEEEEEEec---cCcEEEEEEecCCCCCCccceEEEEecCceeeEEhHHHHHHhhcc
Confidence 33699999999999999999999999996533 3333344443221 001122222233577888899999999997
Q ss_pred cccccccccccCCCCceEEEEEeecCCCCCCCCCce-EEEEEE
Q 038444 92 GVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPF-LTFETK 133 (300)
Q Consensus 92 a~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~-L~~~~~ 133 (300)
+.- ++.|+|.|.... |+ |.|.+.
T Consensus 221 ~~l-----------s~~V~l~l~~d~--------Pl~ley~i~ 244 (275)
T PTZ00113 221 GCL-----------SDVVTLGLSDNR--------PIEVKYEIK 244 (275)
T ss_pred ccC-----------CCeEEEEEcCCC--------CEEEEEEec
Confidence 665 788999999885 74 777774
No 27
>PF02144 Rad1: Repair protein Rad1/Rec1/Rad17; InterPro: IPR003021 REC1 of Ustilago maydis plays a key role in regulating the genetic system of the fungus. REC1 mutants are very sensitive to UV light. Mutation leads to a complex phenotype with alterations in DNA repair, recombination, mutagenesis, meiosis and cell division []. The predicted product of the REC1 gene is a polypeptide of 522 amino acid residues with molecular mass 57kDa. The protein shows 3'--5' exonuclease activity, but only in cells over-expressing REC1 []. While it is distinguishable from the major bacterial nucleases, the protein has certain enzymatic features in common with epsilon, the proof-reading exonuclease subunit of Escherichia coli DNA polymerase III holoenzyme []. The rad1 gene of Schizosaccharomyces pombe comprises three exons and encodes a 37kDa protein that exhibits partial similarity to the REC1 gene of U. maydis []. The two genes share putative functional similarities in their respective organisms.; GO: 0003684 damaged DNA binding, 0008853 exodeoxyribonuclease III activity, 0006281 DNA repair, 0005634 nucleus; PDB: 3G65_B 3GGR_C 3A1J_C.
Probab=74.44 E-value=74 Score=29.54 Aligned_cols=152 Identities=14% Similarity=0.158 Sum_probs=85.8
Q ss_pred EEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEE--EEEehHHHHHHHhccccccccccccCCCC
Q 038444 29 VCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIA--FAIDISLLQRAVRSGVSICSEIGAAGSAA 106 (300)
Q Consensus 29 ~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~--lev~~~~L~raLrsa~~~~~~~~~~~~~a 106 (300)
.|.|....+.--|+... .++|+-.-|++..-.--+...++-.. +.+. +-+..+.|..||+-.... ++
T Consensus 120 ~~~lsY~g~G~pL~l~l-ed~gv~t~c~i~T~~~~~~~d~~f~~-~~~~~kiimks~~L~~al~eL~~~---------~~ 188 (275)
T PF02144_consen 120 SCRLSYPGEGSPLVLIL-EDSGVTTTCEIRTYEPDDPLDFPFDR-SDVVNKIIMKSDWLRDALSELDWS---------NS 188 (275)
T ss_dssp EEEEEESSSCCEEEEEE-EETTEEEEEEEEEE-----------T-TTEEEEEEEEHHHHHHHHHTT-TS----------C
T ss_pred eEEEEEcCCCCeEEEEE-EeCCEEEEEEEEEecCCcccCccccc-ccceeEEEEEhHHHHHHHHHHhhc---------cC
Confidence 57777666653343322 22888888998764333433333222 3344 445999999999998873 36
Q ss_pred ceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEcCChhhHHHHHHh
Q 038444 107 NRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQVPDLNQLQNFVHR 186 (300)
Q Consensus 107 ~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~lP~l~~l~~ivdR 186 (300)
+.+.|.+...+ .|.|.|..+|.--...-|+|-.+ .-++.+.=-.. ..+...-| .+..++++..=
T Consensus 189 ~~l~i~~s~~~-------~p~f~l~s~G~~G~s~v~fp~~~----~~le~f~~~~~---~~~~~~~Y--~f~~i~~~~kA 252 (275)
T PF02144_consen 189 EELTIYISPPD-------KPHFRLSSKGPLGSSKVDFPNDS----DVLETFECYDG---EEPVISRY--KFSLIKKAMKA 252 (275)
T ss_dssp SEEEEEE-S-S-------SSSEEEEEEETTEEEEEEE-TTS----TSEEEEEE-------S-EEEEE--EHHHHCCHHHH
T ss_pred CeEEEEEEeCC-------CCEEEEEEEcCCCeEEEEECCCC----CceeEEEEecc---CceEEEEE--eHHHHHHHHHH
Confidence 78999998853 59999999987656888888852 12233321000 11222222 23445554444
Q ss_pred hhccCCEEEEEEEcCCeEEEEE
Q 038444 187 MKHVGDLLNVSIYKYGDLHLQI 208 (300)
Q Consensus 187 ~k~~~~~v~i~an~~G~L~l~v 208 (300)
|+ ++..+.|+.+.+|-|.++.
T Consensus 253 l~-~ssKv~ir~d~~GlLs~Q~ 273 (275)
T PF02144_consen 253 LK-ISSKVSIRIDENGLLSLQF 273 (275)
T ss_dssp HT-TSSEEEEEEESSS-EEEEE
T ss_pred hh-hccEEEEEeCCCcEEEEEE
Confidence 44 6788999999999998764
No 28
>PRK14941 DNA polymerase III subunit beta; Provisional
Probab=60.96 E-value=1.6e+02 Score=28.38 Aligned_cols=109 Identities=16% Similarity=0.172 Sum_probs=64.3
Q ss_pred EEEEehHHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhch
Q 038444 77 AFAIDISLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLE 156 (300)
Q Consensus 77 ~lev~~~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~ 156 (300)
.|.++.+.|.++|..+.+..++-++-. =-..+.++. .+ -.|.+...+....+...+|+. +-
T Consensus 2 kf~i~k~~l~~~l~~v~~~v~~k~~~p-iL~~ill~a--~~--------~~l~l~atD~e~~i~~~i~~~-~~------- 62 (374)
T PRK14941 2 KFTSSIKQLQEAVNKVAQAIPAKSIDP-RFENIHLTL--EN--------GKLTLFATDGELSITAKTEVE-SS------- 62 (374)
T ss_pred EEEEEHHHHHHHHHHHHhhhcCCCchh-HhcCEEEEE--EC--------CEEEEEEECCCeEEEEEEeee-ec-------
Confidence 367899999999999877532211000 001233333 33 356666666667888888873 21
Q ss_pred hhhhhcccCCCCCeEEEcCChhhHHHHHHhhhccCCEEEEEEE-----cCCeEEEEEeecceEEeEE
Q 038444 157 LQTALDMAQDIPPTLVQVPDLNQLQNFVHRMKHVGDLLNVSIY-----KYGDLHLQISTTLITLGAE 218 (300)
Q Consensus 157 l~eP~~~~~~~p~~~i~lP~l~~l~~ivdR~k~~~~~v~i~an-----~~G~L~l~v~t~~v~v~t~ 218 (300)
+ .-.+.+|+ +.|..+|-+|.. +.|+++.. .++.+.+..+....++.+.
T Consensus 63 --~---------~G~~~v~a-~~l~~ivk~lp~--~~i~~~~~~~~~~~~~~l~I~~~~~~f~l~~~ 115 (374)
T PRK14941 63 --D---------SGNIGIRA-RTLQDFLRSMYD--TEVTFSIERQEISDHGTVHIATDKGRYKIPCL 115 (374)
T ss_pred --c---------ceEEEEEh-HHHHHHHHcCCC--CcEEEEEeccccCCCCEEEEEECCEEEEeecc
Confidence 1 23466887 666666666643 56888875 3566776665555555443
No 29
>KOG2810 consensus Checkpoint 9-1-1 complex, RAD9 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=56.41 E-value=15 Score=36.13 Aligned_cols=84 Identities=12% Similarity=0.193 Sum_probs=56.8
Q ss_pred EecCchhhhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHH
Q 038444 6 FLTDNGVNLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLL 85 (300)
Q Consensus 6 ~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L 85 (300)
++...+++.| .+.+..++|+++++.+-.+|..|.+-. .++.-.-.-|-.-...+|+.|.++-..-..- +-+.....
T Consensus 4 ~vs~~nlr~l-Arai~sLSri~~ev~iev~~~~l~l~t--~N~srSa~~~~~f~~~FF~~ydf~~~q~~~~-~~v~mK~c 79 (394)
T KOG2810|consen 4 TVSGSNLRVL-ARAIVSLSRIGEEVTIEVSPLGLCLKT--VNESRSAFSCATFKEMFFGVYDFQPPQADFG-CKVSMKFC 79 (394)
T ss_pred eeccchhHHH-HHHhhhHhhhcceeEEEEcCCeeEEEe--cccccchhhhhhhhHhhccchhcCCccccch-hhhhHHHH
Confidence 3444455665 699999999999999999999999962 1111111222223445999999984332222 44888899
Q ss_pred HHHHhccc
Q 038444 86 QRAVRSGV 93 (300)
Q Consensus 86 ~raLrsa~ 93 (300)
++++|+..
T Consensus 80 lsvFRgl~ 87 (394)
T KOG2810|consen 80 LSVFRGLL 87 (394)
T ss_pred HHHHhhhc
Confidence 99999643
No 30
>PRK14943 DNA polymerase III subunit beta; Provisional
Probab=44.33 E-value=2.9e+02 Score=26.39 Aligned_cols=66 Identities=8% Similarity=0.117 Sum_probs=43.8
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.|.|.++.+.+...... .| +.--++ .++ .++..+.+-+|...|+.||+... .+
T Consensus 288 ~~v~l~~~~~~l~i~~~~~e-~G-~~~e~i---------~~~-~~G~~~~i~fN~~yl~d~l~~~~------------~~ 343 (374)
T PRK14943 288 NSVKLKFSENLLEIASSSEG-VG-EAHESM---------AIT-YSGPELQVAFNPDFFMAPLKALT------------KD 343 (374)
T ss_pred ceEEEEEECCEEEEEEcCCC-Cc-eEEEEE---------EEE-ecCCcEEEEECHHHHHHHHhcCC------------CC
Confidence 45778999998887543222 22 111111 121 12357889999999999999986 46
Q ss_pred eEEEEEeecC
Q 038444 108 RLQIKLVKKL 117 (300)
Q Consensus 108 ~v~ikL~kk~ 117 (300)
.++|++....
T Consensus 344 ~v~l~~~~~~ 353 (374)
T PRK14943 344 EVFFELKDEM 353 (374)
T ss_pred EEEEEECCCC
Confidence 7888888765
No 31
>PRK14947 DNA polymerase III subunit beta; Provisional
Probab=43.79 E-value=3e+02 Score=26.77 Aligned_cols=72 Identities=8% Similarity=0.008 Sum_probs=47.3
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.|.|+++.|.+-.... +-| . .-++..++ -+++.+.+-+|...|.-+|+... ++
T Consensus 286 ~~v~l~~~~~~l~iss~~~-e~G-~---------a~E~i~~~-~~Ge~~~I~fN~~YL~d~L~~i~------------~~ 341 (384)
T PRK14947 286 RCTYFDFGPGELSLSAQGQ-DVG-S---------ATESLEVT-YSGDIKKIAFPTKNLIEILGHFQ------------SD 341 (384)
T ss_pred ceEEEEEeCCEEEEEEcCC-CCc-e---------EEEEEEEE-ecCCcEEEEECHHHHHHHHhcCC------------CC
Confidence 3588999999888744221 111 1 12222333 12356788899999999999986 46
Q ss_pred eEEEEEeecCCCCCCCCCceEEE
Q 038444 108 RLQIKLVKKLPPNCTQAMPFLTF 130 (300)
Q Consensus 108 ~v~ikL~kk~~~~~~~~~P~L~~ 130 (300)
.+.|++.... .|++--
T Consensus 342 ~i~l~~~~~~-------~p~~i~ 357 (384)
T PRK14947 342 KITLTLTGAE-------GPCGIT 357 (384)
T ss_pred eEEEEECCCC-------CCEEEE
Confidence 7888888775 587643
No 32
>PRK05643 DNA polymerase III subunit beta; Validated
Probab=41.64 E-value=3.1e+02 Score=25.95 Aligned_cols=149 Identities=11% Similarity=0.114 Sum_probs=77.2
Q ss_pred hHHHHHHhcCC--EEEEEEecC-eEEEEeeecCCCceEEEEEEcc--CCCcCeeEeeecCCCeEEEEEehHHHHHHHhcc
Q 038444 18 RFLPALDKMGK--VCHLFLTRE-KAYFLHNLLSGEGIQCVAQFHK--ETLFDDYRISSQNEDCIAFAIDISLLQRAVRSG 92 (300)
Q Consensus 18 ~iv~~i~kl~k--~cvlrlt~~-~l~~i~~~~~~~g~qvw~~l~~--~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa 92 (300)
.+...+.+|.. .+.+.+..+ .+.+.+. ..+ ..++. ..=|.+|.-. ++...++++.+.|.++|+..
T Consensus 74 ~l~eiik~l~~~~~i~i~~~~~~~l~i~~~-----~~~--~~l~~~~~~~fP~~~~~---~~~~~~~i~~~~l~~~i~~v 143 (367)
T PRK05643 74 KLLDIVRKLPDGAEITLELEENNRLTIKSG-----KSR--FNLPTLPAEDFPNLPEI---EEEVSFTLPQKTLKRLIEKT 143 (367)
T ss_pred HHHHHHHcCCCCCcEEEEECCCCEEEEEEC-----CEE--EEeccCCHHHCCCCCCC---CCCcEEEECHHHHHHHHhhe
Confidence 44556666754 466666553 5555331 111 22221 1146655532 34567899999999999998
Q ss_pred ccccccccccCCCCce-E-EEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCCCCe
Q 038444 93 VSICSEIGAAGSAANR-L-QIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDIPPT 170 (300)
Q Consensus 93 ~~~~~~~~~~~~~a~~-v-~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~ 170 (300)
..+.+..+ ... + -+.+..++ -.|.+...+..+.....+++. .- ...+.
T Consensus 144 ~~a~~~~~-----~~piL~gi~~~~~~--------~~l~l~aTD~~rl~~~~~~~~-~~----------------~~~~~ 193 (367)
T PRK05643 144 QFAMSTQE-----TRYYLNGVLLEIEG--------NELRAVATDGHRLAVRKLELE-EG----------------SLGDF 193 (367)
T ss_pred eEEeecCC-----ccccccEEEEEEeC--------CEEEEEEeccceeEEEEeccc-CC----------------cccCc
Confidence 76432111 110 0 13333332 246666555556666666652 10 01134
Q ss_pred EEEcCChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEe
Q 038444 171 LVQVPDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQIS 209 (300)
Q Consensus 171 ~i~lP~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~ 209 (300)
.+.+|. +.|..++..+.. .+.+.+..+ ++.+.+..+
T Consensus 194 ~~~vp~-k~l~ei~k~l~~-~~~v~i~~~-~~~~~~~~~ 229 (367)
T PRK05643 194 SVIIPR-KTLLELQKLLDD-EEPVEIFIS-DNQILFEFG 229 (367)
T ss_pred eEEEch-HHHHHHHHhcCC-CCcEEEEEe-CCEEEEEEC
Confidence 466787 666666655542 235777763 345555553
No 33
>PRK14941 DNA polymerase III subunit beta; Provisional
Probab=40.92 E-value=3.1e+02 Score=26.44 Aligned_cols=67 Identities=10% Similarity=0.088 Sum_probs=44.2
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.+.|.+..+.+..... +.|.+. -++..++- .+..+.+-+|...|.-+|+... ++
T Consensus 281 ~~v~~~~~~~~l~l~~~~~-~~g~~~---------~e~i~~~~-~G~~~~I~fN~~yl~d~L~~~~------------~~ 337 (374)
T PRK14941 281 GDIKISVEGSVLKVMAENT-NEGESA---------QEELPCSY-TGEDITIGFNSKFIEAALAHLD------------EE 337 (374)
T ss_pred CceEEEEECCEEEEEEECc-ccccce---------EEEEEeEe-CCCcEEEEEcHHHHHHHHhcCC------------CC
Confidence 4577888888887754222 222121 12333432 2357888899999999999996 46
Q ss_pred eEEEEEeecC
Q 038444 108 RLQIKLVKKL 117 (300)
Q Consensus 108 ~v~ikL~kk~ 117 (300)
.+.|++....
T Consensus 338 ~v~l~~~~~~ 347 (374)
T PRK14941 338 EIIIELSSPT 347 (374)
T ss_pred EEEEEECCCC
Confidence 7899998765
No 34
>smart00480 POL3Bc DNA polymerase III beta subunit.
Probab=40.76 E-value=3.2e+02 Score=25.78 Aligned_cols=208 Identities=13% Similarity=0.158 Sum_probs=100.9
Q ss_pred hHHHHHHhcC-CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccccc
Q 038444 18 RFLPALDKMG-KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSIC 96 (300)
Q Consensus 18 ~iv~~i~kl~-k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~ 96 (300)
.+...+.+|. ..+.+.+..+++.+.+. ++----..++.+ =|.++.. .++...++++.+.|.++++....+.
T Consensus 58 ~l~~ivk~lp~~~i~~~~~~~~l~i~~~----~~~~~l~~~~~~-~fP~~~~---~~~~~~~~i~~~~L~~~i~~v~~a~ 129 (345)
T smart00480 58 KFLDIVRKLPDKEITLSVEEDKLVITSG----KSRFNLPTLDAE-EFPELPF---IEEGVTFELPTKLLKEGIEKTAFAV 129 (345)
T ss_pred HHHHHHHhCCCCceEEEEcCCEEEEEEC----cEEEEecCCCHH-HCCCCCC---cCCCcEEEECHHHHHHHHhhEEEEE
Confidence 3445555664 34556665566555331 111111112222 3544422 2344578999999999999887643
Q ss_pred ccccccCCCCc-e-EEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEc
Q 038444 97 SEIGAAGSAAN-R-LQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQV 174 (300)
Q Consensus 97 ~~~~~~~~~a~-~-v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~l 174 (300)
+.-. .. . --|.+..++ -.|.+...+..+.....+|+. . ..++..+.+
T Consensus 130 s~~~-----~~piL~Gi~~~~~~--------~~l~lvATDg~rla~~~~~~~-~-----------------~~~~~~~iv 178 (345)
T smart00480 130 STDE-----TRPVLNGVNLEISN--------GELRLVATDGHRLAVREIKLE-S-----------------EEDDFSVII 178 (345)
T ss_pred ecCC-----CcceeeEEEEEEEC--------CEEEEEEEcCceEEEEEeccC-C-----------------CCCcceEEE
Confidence 2111 10 0 113333332 245555554445555556652 1 112345678
Q ss_pred CChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccccccchhhhhcCCCCeE
Q 038444 175 PDLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLSAQTRSERAISRGDAQ 254 (300)
Q Consensus 175 P~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 254 (300)
|. +.|..++..+..-.+.++|..+ ++.+.+..+. ..+.+.--+-..|....--| .....
T Consensus 179 P~-k~l~el~k~l~~~~~~v~i~~~-~~~~~~~~~~--~~~~~~li~g~fP~~~~vip-----------------~~~~~ 237 (345)
T smart00480 179 PR-KSLLELNKLLTDNEELVEIFIS-SNQILFETGN--VIFTSRLIDGEFPDYKRVIP-----------------KEFET 237 (345)
T ss_pred eh-HHHHHHHHhccCCCCcEEEEEe-CCEEEEEECC--EEEEEEEeeecCCCchhhCC-----------------CCCCE
Confidence 87 6666666666543356888775 4455554433 22222111111211110000 01246
Q ss_pred EEEEechhHHhhcccccc----CCcEEEEEEECCC
Q 038444 255 SVQVSVKHFSKSLQCHLA----KPDCAFFGIAPQG 285 (300)
Q Consensus 255 ~V~Vd~k~l~~~L~~~~~----~p~~v~~~i~~~~ 285 (300)
.+.|+.+.|...+.--.+ .-..|.+.+.+++
T Consensus 238 ~~~i~~~~L~~ai~rv~~~~~~~~~~v~l~~~~~~ 272 (345)
T smart00480 238 KLTVNRKELKEALKRVALLANEKNRSVKLTLEEGQ 272 (345)
T ss_pred EEEEEHHHHHHHHHHHhhhhcCCCceEEEEEeCCE
Confidence 888999999888763111 1224555665554
No 35
>PRK14945 DNA polymerase III subunit beta; Provisional
Probab=39.64 E-value=3.4e+02 Score=25.85 Aligned_cols=206 Identities=12% Similarity=0.093 Sum_probs=100.9
Q ss_pred hHHHHHHhcCC-EEEEEEecCeEEEEeeecCCCceEE-EEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccc
Q 038444 18 RFLPALDKMGK-VCHLFLTREKAYFLHNLLSGEGIQC-VAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSI 95 (300)
Q Consensus 18 ~iv~~i~kl~k-~cvlrlt~~~l~~i~~~~~~~g~qv-w~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~ 95 (300)
.+...+.+|.. .+.+.+...++.+.+. .... ...++.+ =|.++... ... .++++.+.|.++|+....+
T Consensus 73 ~l~~ivk~lp~~~i~~~~~~~~l~i~~~-----~~~~~l~~~~~~-~fP~~~~~--~~~--~~~i~~~~L~~~i~~v~~a 142 (362)
T PRK14945 73 LFFQIVRNLPGELVELEFQGGELEVRSG-----SSRTKLQTAPPE-GYPELSFP--SQG--DVRLSAGELAKALTHVRYA 142 (362)
T ss_pred CHHHHHHhCCCCcEEEEEcCCEEEEEEC-----CEEEEeccCChH-HCCCCCCC--CCc--eEEECHHHHHHHHhhEEEE
Confidence 34567777754 4667665555555431 1111 1122233 45555422 112 3699999999999998765
Q ss_pred cccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEcC
Q 038444 96 CSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQVP 175 (300)
Q Consensus 96 ~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~lP 175 (300)
.+.-.+- .--..+.+. ..+ -.|++...+..+.+..++++. . ..+..+.+|
T Consensus 143 vs~~~~~-piL~gv~l~--~~~--------~~l~lvATDg~rla~~~~~~~-~------------------~~~~~~iip 192 (362)
T PRK14945 143 ASNEEFQ-AIFRGVKLE--HSP--------QGLRAVASDGYRLAIYDLPAS-Q------------------GQGRKLVIP 192 (362)
T ss_pred Eecccch-hheeeEEEE--EeC--------CEEEEEEEccceEEEEEeccC-C------------------CCCceEEEE
Confidence 3211100 000112222 222 246666655555555566552 1 123567788
Q ss_pred ChhhHHHHHHhhhccCCEEEEEEEcCCeEEEEEeecceEEeEEeccccccccccCCCCccccccccchhhhhcCCCCeEE
Q 038444 176 DLNQLQNFVHRMKHVGDLLNVSIYKYGDLHLQISTTLITLGAEFRKLLVIGEKAVAPSEDRNLSAQTRSERAISRGDAQS 255 (300)
Q Consensus 176 ~l~~l~~ivdR~k~~~~~v~i~an~~G~L~l~v~t~~v~v~t~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 (300)
. +.|..++..+.. ++.++|..+ ++.+.+.. +...+.+.--+-..|. .. ..........
T Consensus 193 ~-k~l~el~k~l~~-~~~v~i~~~-~~~i~~~~--~~~~~~~~lidg~fP~------~~-----------~vip~~~~~~ 250 (362)
T PRK14945 193 A-RSADELVRVLKD-GDEASLALG-EGVLTLTT--GGVRMNLKLMEGEFPD------YE-----------RVIPQDFKLQ 250 (362)
T ss_pred H-HHHHHHHHhcCC-CCcEEEEEc-CCEEEEEE--CCEEEEEEeecccCCC------hh-----------hhCCCCCCEE
Confidence 7 666666666654 236777764 33444443 3333221111101111 00 0000012368
Q ss_pred EEEechhHHhhccccc--c--C-CcEEEEEEECCC
Q 038444 256 VQVSVKHFSKSLQCHL--A--K-PDCAFFGIAPQG 285 (300)
Q Consensus 256 V~Vd~k~l~~~L~~~~--~--~-p~~v~~~i~~~~ 285 (300)
+.|+.+.|...++--. . . ..+|.+.+.++.
T Consensus 251 v~i~~~~L~~~l~r~~~~~~~~~~~~v~l~~~~~~ 285 (362)
T PRK14945 251 VTLPAEALREAVNRVAVLSDRNANNRVELLVAEGR 285 (362)
T ss_pred EEEEHHHHHHHHHHHhhhhccCCCccEEEEEECCE
Confidence 8999999999886411 1 1 233556665554
No 36
>PRK14942 DNA polymerase III subunit beta; Provisional
Probab=39.43 E-value=3.6e+02 Score=26.06 Aligned_cols=70 Identities=16% Similarity=0.191 Sum_probs=46.9
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.|.|+++.+.+-... .+.| + .-++..++ -++..+.+-+|...|.-||+... ++
T Consensus 286 ~~v~l~~~~~~l~isa~~-~~~g-~---------~~e~i~~~-~~G~~~~I~fN~~ylld~L~~i~------------~~ 341 (373)
T PRK14942 286 RQVRLTFSKNNLNLFAQT-LGAS-E---------ADINMPIE-YSGEEITIAFKGEYLMDIFRSID------------DN 341 (373)
T ss_pred ceEEEEEeCCEEEEEEeC-CCcc-e---------EEEEEEEE-ecCCcEEEEECHHHHHHHHhcCC------------CC
Confidence 457788888888774422 1112 1 12233343 23457888999999999999986 46
Q ss_pred eEEEEEeecCCCCCCCCCceE
Q 038444 108 RLQIKLVKKLPPNCTQAMPFL 128 (300)
Q Consensus 108 ~v~ikL~kk~~~~~~~~~P~L 128 (300)
.+.|++.... .|++
T Consensus 342 ~v~l~~~~~~-------~P~~ 355 (373)
T PRK14942 342 EVKIEFSDSS-------SPVI 355 (373)
T ss_pred eEEEEECCCC-------CCEE
Confidence 7888888765 5775
No 37
>PRK06673 DNA polymerase III subunit beta; Validated
Probab=38.89 E-value=1.8e+02 Score=28.18 Aligned_cols=71 Identities=13% Similarity=0.122 Sum_probs=52.4
Q ss_pred hHHHHHHhc----CCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccc
Q 038444 18 RFLPALDKM----GKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGV 93 (300)
Q Consensus 18 ~iv~~i~kl----~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~ 93 (300)
+.+.-+.|+ .+.+.+.+++.++.|.. ++..+++++--. -|.+|+=-=..+....+.++...|..||+++.
T Consensus 203 k~l~el~kll~~~~~~v~i~~~~~~i~f~~-----~~~~~~srLieG-~fPdy~~vip~~~~~~v~i~r~~l~~al~Rvs 276 (376)
T PRK06673 203 ATINELLKLMNSNLEFVSIYLSESHIIFTF-----GTTTLYSRLIEG-KYPNISTLIPNEFQTVINIDRQRMLQGVDRSS 276 (376)
T ss_pred HHHHHHHHhccCCCceEEEEEeCCEEEEEE-----CCEEEEEEEecc-cCCChhhcCCCCCcEEEEEEHHHHHHHHHHHH
Confidence 334444444 34688889999988854 577888988544 78888755334567789999999999999986
Q ss_pred c
Q 038444 94 S 94 (300)
Q Consensus 94 ~ 94 (300)
-
T Consensus 277 i 277 (376)
T PRK06673 277 L 277 (376)
T ss_pred H
Confidence 4
No 38
>PF02282 Herpes_UL42: DNA polymerase processivity factor (UL42); InterPro: IPR003202 The DNA polymerase processivity factor (UL42) of Human herpesvirus 1 (HHV-1) forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerisation and makes little contribution to the catalytic activity of the polymerase.; GO: 0003677 DNA binding, 0006260 DNA replication; PDB: 1DML_G.
Probab=36.85 E-value=1.2e+02 Score=26.02 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=41.9
Q ss_pred eEEecCchhhhHHHhHHHHHHhcC---CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEee
Q 038444 4 KAFLTDNGVNLLEKRFLPALDKMG---KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRIS 69 (300)
Q Consensus 4 rA~i~d~~~~~l~~~iv~~i~kl~---k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ie 69 (300)
++.++.. .| .+++.++++++ +.+-+.+..+.+.+.++. +|.||...++.+ -|++|...
T Consensus 2 ~~~L~~~---QL-~kil~~~~~~~~~~~~~F~l~~~~gl~i~~~~---~~~~V~f~i~~~-~~~~y~w~ 62 (156)
T PF02282_consen 2 RLVLSKP---QL-NKILAVAAPLGTSLKTTFLLFSEGGLSIHSTV---GGEQVYFPIREE-GFSSYPWN 62 (156)
T ss_dssp EEEEECC---HH-HHHHHCCCCCTTTTSCEEEEECCCEEEEEECE---TTEEEEEEEECG-GCCCEE--
T ss_pred EEEEcHH---HH-HHHHHhhcccccCCCceEEEecCCcEEEEecc---CceEEEEEcCHH-HcccCccC
Confidence 3556655 43 68888888876 677777777777775533 678999999998 99999855
No 39
>PRK07761 DNA polymerase III subunit beta; Validated
Probab=35.83 E-value=4e+02 Score=25.52 Aligned_cols=67 Identities=7% Similarity=0.070 Sum_probs=43.7
Q ss_pred CCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCC
Q 038444 27 GKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAA 106 (300)
Q Consensus 27 ~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a 106 (300)
.+.+.|.+.++++.+-... .+.| +.=-++ .++ -++..+.+-+|+..|..+|+... +
T Consensus 280 ~~~v~l~~~~~~l~l~~~~-~~~G-~~~e~i---------~~~-~~Ge~~~i~fN~~yl~d~L~~~~------------~ 335 (376)
T PRK07761 280 NAPVRLEFSDGQLTLSAGG-GDDA-QASEAL---------EAD-LTGEDLTIAFNPQYLLDGLSALH------------T 335 (376)
T ss_pred CceEEEEEeCCEEEEEEcC-CCcc-eEEEEE---------EEE-ecCCcEEEEECHHHHHHHHhcCC------------C
Confidence 3557888888888774322 2222 211122 222 12346888899999999999996 4
Q ss_pred ceEEEEEeecC
Q 038444 107 NRLQIKLVKKL 117 (300)
Q Consensus 107 ~~v~ikL~kk~ 117 (300)
+.+.|++....
T Consensus 336 ~~v~l~~~~~~ 346 (376)
T PRK07761 336 PRVRFGFTTPS 346 (376)
T ss_pred CeEEEEECCCC
Confidence 67888888865
No 40
>PRK05643 DNA polymerase III subunit beta; Validated
Probab=34.45 E-value=4.1e+02 Score=25.17 Aligned_cols=66 Identities=6% Similarity=0.097 Sum_probs=43.9
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.|.++++++.+..+..+.+..+. +++ ++ ..++.+.+-++...|..+||... ++
T Consensus 280 ~~i~l~~~~~~l~~~a~~~~~g~a~~--~i~---------~~-~~g~~~~i~~n~~yL~d~l~~~~------------~~ 335 (367)
T PRK05643 280 RGVKLSLSEGQLKISANNPEQGEAEE--ELE---------VE-YSGEELEIGFNVKYLLDVLKALD------------SE 335 (367)
T ss_pred ceEEEEEeCCEEEEEEECCCCCcEEE--EEE---------EE-ecCCcEEEEEcHHHHHHHHhcCC------------CC
Confidence 45778888999888654332221222 222 11 12346888999999999999875 46
Q ss_pred eEEEEEeecC
Q 038444 108 RLQIKLVKKL 117 (300)
Q Consensus 108 ~v~ikL~kk~ 117 (300)
.++|.+....
T Consensus 336 ~v~i~~~~~~ 345 (367)
T PRK05643 336 EVRLSFNDAN 345 (367)
T ss_pred EEEEEECCCC
Confidence 7888888765
No 41
>PRK14940 DNA polymerase III subunit beta; Provisional
Probab=32.59 E-value=4.6e+02 Score=25.18 Aligned_cols=66 Identities=8% Similarity=0.100 Sum_probs=43.7
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.|.|.++.+.+-.... +-| +.- ++..++ -+++.+.+-+|...|.-||+... ++
T Consensus 279 ~~v~l~~~~~~l~l~~~~~-e~G-~~~---------e~i~~~-~~Ge~~~I~fN~~yl~d~L~~i~------------~~ 334 (367)
T PRK14940 279 RRIFLTIQQGLLTLSSQEN-EIG-DAQ---------EEIACA-YTGEEEVIALNYLYLEEPLKVFT------------SK 334 (367)
T ss_pred ceEEEEEeCCEEEEEEcCC-CCc-cEE---------EEEEEE-ecCCcEEEEECHHHHHHHHhCCC------------CC
Confidence 4577888888887743222 112 111 122222 13457888999999999999996 57
Q ss_pred eEEEEEeecC
Q 038444 108 RLQIKLVKKL 117 (300)
Q Consensus 108 ~v~ikL~kk~ 117 (300)
.+.|++....
T Consensus 335 ~v~l~~~~~~ 344 (367)
T PRK14940 335 EVQVEFTEAA 344 (367)
T ss_pred EEEEEECCCC
Confidence 7999998865
No 42
>KOG1636 consensus DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair]
Probab=30.39 E-value=4.4e+02 Score=24.32 Aligned_cols=88 Identities=14% Similarity=0.135 Sum_probs=54.9
Q ss_pred hhHHHhHHHHHHhcCCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEE-ehHHHHHHHhc
Q 038444 13 NLLEKRFLPALDKMGKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAI-DISLLQRAVRS 91 (300)
Q Consensus 13 ~~l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev-~~~~L~raLrs 91 (300)
.. |.+|+.-++.++..+++-.|.+.+.|..++..++|.-...+...- ...+..|.+|+ .+-.|-=|+|.
T Consensus 142 ~E-F~ricrdls~f~Dsv~I~~tkegv~F~~~Gdig~asi~l~~~~~~---------d~~e~av~iE~~~pVtltfa~kY 211 (260)
T KOG1636|consen 142 GE-FSRICRDLSTFSDSVVISATKEGVKFSAKGDIGTASITLSQCTAV---------DKPEEAVKIEMNEPVTLTFALKY 211 (260)
T ss_pred HH-HHHHHHHHhhhcCeEEEEEecceeEEEecccccceeEEEccCCCC---------CCccceEEEEecCcchhhhHHHH
Confidence 35 579999999999999999999999998776666554444333221 12223455555 33333333333
Q ss_pred c---ccccccccccCCCCceEEEEEeecC
Q 038444 92 G---VSICSEIGAAGSAANRLQIKLVKKL 117 (300)
Q Consensus 92 a---~~~~~~~~~~~~~a~~v~ikL~kk~ 117 (300)
. .++.+ =++.|+|.|....
T Consensus 212 ln~ftKatp-------Ls~rV~lsls~~~ 233 (260)
T KOG1636|consen 212 LNQFTKATP-------LSDRVTLSLSSEV 233 (260)
T ss_pred HHHhhcccc-------ccceEEEEecCCC
Confidence 2 22100 1688999998875
No 43
>cd00140 beta_clamp Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.
Probab=30.35 E-value=4.6e+02 Score=24.50 Aligned_cols=66 Identities=6% Similarity=0.068 Sum_probs=42.8
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAAN 107 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~ 107 (300)
+.+.|.++++++.+..+..+.+..+. +++ ++. .+..+.+-++...|..+||... .+
T Consensus 279 ~~v~l~~~~~~l~~~a~~~~~~~~~~--~~~---------~~~-~g~~~~i~~~~~yL~d~lk~~~------------~~ 334 (365)
T cd00140 279 RGVKLEISEGQLKLSANNPEIGEAEE--ELE---------VEY-EGEELEIGFNPKYLLDALKAID------------SE 334 (365)
T ss_pred ceEEEEEeCCEEEEEEcCCCCceEEE--EEE---------EEe-cCCcEEEEECHHHHHHHHhcCC------------CC
Confidence 36778899999998654322121222 222 121 2235788999999999999875 35
Q ss_pred eEEEEEeecC
Q 038444 108 RLQIKLVKKL 117 (300)
Q Consensus 108 ~v~ikL~kk~ 117 (300)
.++|.+....
T Consensus 335 ~v~i~~~~~~ 344 (365)
T cd00140 335 EVRLSFTDSN 344 (365)
T ss_pred EEEEEECCCC
Confidence 7888887653
No 44
>smart00480 POL3Bc DNA polymerase III beta subunit.
Probab=30.24 E-value=4.7e+02 Score=24.60 Aligned_cols=65 Identities=11% Similarity=0.135 Sum_probs=42.0
Q ss_pred EEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCce
Q 038444 29 VCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAANR 108 (300)
Q Consensus 29 ~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~~ 108 (300)
.+.|.|+++++.+..+..+.+ +.--++ .++- ++..+.+-+|...|..+|+... ++.
T Consensus 263 ~v~l~~~~~~l~~~a~d~~~g--~~~e~i---------~~~~-~g~~~~i~fN~~yL~d~l~~~~------------~~~ 318 (345)
T smart00480 263 SVKLTLEEGQLKLTANSPEVG--EAEEEV---------DVDY-EGEDLEIAFNPKYLLDALKALK------------SEE 318 (345)
T ss_pred eEEEEEeCCEEEEEEcCCccc--eEEEEE---------EEEe-cCCcEEEEECHHHHHHHHhcCC------------CCE
Confidence 577888888888865432222 111122 2221 1235777789999999999986 467
Q ss_pred EEEEEeecC
Q 038444 109 LQIKLVKKL 117 (300)
Q Consensus 109 v~ikL~kk~ 117 (300)
+.|++....
T Consensus 319 v~l~~~~~~ 327 (345)
T smart00480 319 IELKFTDSS 327 (345)
T ss_pred EEEEECCCC
Confidence 888887654
No 45
>TIGR00663 dnan DNA polymerase III, beta subunit. University).
Probab=29.21 E-value=5e+02 Score=24.59 Aligned_cols=94 Identities=13% Similarity=0.105 Sum_probs=0.0
Q ss_pred eEEecCchhhhHHHhHHHHHHhcCCEEEEEEecC-eEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEeh
Q 038444 4 KAFLTDNGVNLLEKRFLPALDKMGKVCHLFLTRE-KAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDI 82 (300)
Q Consensus 4 rA~i~d~~~~~l~~~iv~~i~kl~k~cvlrlt~~-~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~ 82 (300)
+.++.-.......+++.-....-.+.+.+.+..+ ++.+-....+.+ ..-++..++ .++..+.+-++.
T Consensus 255 ~~~i~~~~L~~al~rv~~~~~~~~~~v~~~~~~~~~l~i~~~~~~~g-----------~~~e~i~~~-~~g~~~~i~fN~ 322 (367)
T TIGR00663 255 SFTVNREELKEAIKRVSLLADEKRNLVLTLSENGKKLKESSDTQEIG-----------EAEEEIEVA-YDGEDLVIAFNI 322 (367)
T ss_pred EEEEeHHHHHHHHHHHHHHhcCCCceEEEEECCCCeEEEEEcCCCCc-----------cEEEEEEEE-ecCCcEEEEECH
Q ss_pred HHHHHHHhccccccccccccCCCCceEEEEEeecCCCCCCCCCceE
Q 038444 83 SLLQRAVRSGVSICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFL 128 (300)
Q Consensus 83 ~~L~raLrsa~~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L 128 (300)
..|..+|+... ++.+.|.+.... .|++
T Consensus 323 ~yL~d~l~~~~------------~~~v~l~~~~~~-------~p~~ 349 (367)
T TIGR00663 323 KYLLDALKALK------------SKEIQIQFNDPS-------KPLL 349 (367)
T ss_pred HHHHHHHhcCC------------CCEEEEEECCCC-------CCEE
No 46
>PF04139 Rad9: Rad9; InterPro: IPR007268 Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage.; GO: 0006281 DNA repair; PDB: 3GGR_A 3G65_A 3A1J_A.
Probab=29.20 E-value=4.3e+02 Score=23.79 Aligned_cols=88 Identities=16% Similarity=0.180 Sum_probs=57.4
Q ss_pred HHHhHHHHHHhcCCEEEEEEecCeEEEEeeec----CCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHh
Q 038444 15 LEKRFLPALDKMGKVCHLFLTREKAYFLHNLL----SGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVR 90 (300)
Q Consensus 15 l~~~iv~~i~kl~k~cvlrlt~~~l~~i~~~~----~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLr 90 (300)
++++++..+..=..++.+.++++++.+-+-.. ...+++.=..+..+ =|++|.+... ..+.+..-.|...|.
T Consensus 139 ~l~~~l~~f~~~~eeitl~~~~~~v~~~s~~~~~~~~~~~l~t~v~i~~~-ef~~~~~~~~----~~itF~lKefka~l~ 213 (252)
T PF04139_consen 139 LLKDLLDHFPSSTEEITLEVTDDKVSFKSYTEEIQDSKQPLSTEVTISTE-EFDEYNVQED----TDITFSLKEFKAILS 213 (252)
T ss_dssp HHHHHHTTS-TT--EEEEEEECTCEEEEEE-----SSS---EEEEEE-GG-GSSEEE--TT-----EEEEEHHHHHHHHH
T ss_pred HHHHHHhhcCCChhhEEEEecCCEEEEEeecccccccccceEEEEEEehH-hcceEEcCCC----CEEEEEeHHHHHHHH
Confidence 34677777776678999999999998874321 22566666667776 5899999974 677778888888888
Q ss_pred ccccccccccccCCCCceEEEEEeecC
Q 038444 91 SGVSICSEIGAAGSAANRLQIKLVKKL 117 (300)
Q Consensus 91 sa~~~~~~~~~~~~~a~~v~ikL~kk~ 117 (300)
-++.. ...+.|.....|
T Consensus 214 ~ae~~----------~~~i~~~f~~pG 230 (252)
T PF04139_consen 214 FAESL----------SLPISIYFDNPG 230 (252)
T ss_dssp HHHHT----------TEEEEEEESSTT
T ss_pred HHHhc----------CCcEEEEECCCC
Confidence 87753 456788887776
No 47
>PRK14942 DNA polymerase III subunit beta; Provisional
Probab=27.22 E-value=3.2e+02 Score=26.43 Aligned_cols=129 Identities=12% Similarity=0.206 Sum_probs=79.0
Q ss_pred EEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCce
Q 038444 29 VCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAANR 108 (300)
Q Consensus 29 ~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~~ 108 (300)
.+-+.++.+++.|-. ++..++|++=.. =|.+|+=-=..++...+.++...|..||+++.-.... ....
T Consensus 220 ~v~i~~~~~~i~f~~-----~~~~~~srLieG-~yPdy~~vIP~~~~~~~~v~r~~l~~al~Rv~~~~~~------~~~~ 287 (373)
T PRK14942 220 TGNIGLIDEQIYVSA-----NNIELLCKLIEG-NFPNYEQVIPKQTKFSVRISKEEFQVSLRQVLTAAEE------PSRQ 287 (373)
T ss_pred cEEEEEcCCEEEEEE-----CCEEEEEEeccc-CCCChhhhCCCCCCeEEEEeHHHHHHHHHHHHHHhhc------CCce
Confidence 577888888877743 567888988554 7888876655567889999999999999997532100 0233
Q ss_pred EEEEEeecCCCCCCCCCceEEEEEECce-eEEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEcCChhhHHHHHHhh
Q 038444 109 LQIKLVKKLPPNCTQAMPFLTFETKGYK-SAVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQVPDLNQLQNFVHRM 187 (300)
Q Consensus 109 v~ikL~kk~~~~~~~~~P~L~~~~~g~~-~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~lP~l~~l~~ivdR~ 187 (300)
+.+.+..+ -|.+...+.. -.....+|+ . .. =++..|-+=+ +=++|=+
T Consensus 288 v~l~~~~~----------~l~isa~~~~~g~~~e~i~~-~-~~----------------G~~~~I~fN~----~ylld~L 335 (373)
T PRK14942 288 VRLTFSKN----------NLNLFAQTLGASEADINMPI-E-YS----------------GEEITIAFKG----EYLMDIF 335 (373)
T ss_pred EEEEEeCC----------EEEEEEeCCCcceEEEEEEE-E-ec----------------CCcEEEEECH----HHHHHHH
Confidence 55555322 4455544332 234455777 2 21 0123443333 4566777
Q ss_pred hcc-CCEEEEEEEcC
Q 038444 188 KHV-GDLLNVSIYKY 201 (300)
Q Consensus 188 k~~-~~~v~i~an~~ 201 (300)
+.+ ++.|++..+..
T Consensus 336 ~~i~~~~v~l~~~~~ 350 (373)
T PRK14942 336 RSIDDNEVKIEFSDS 350 (373)
T ss_pred hcCCCCeEEEEECCC
Confidence 777 46777777543
No 48
>PRK14947 DNA polymerase III subunit beta; Provisional
Probab=25.70 E-value=4e+02 Score=25.87 Aligned_cols=141 Identities=12% Similarity=0.199 Sum_probs=84.1
Q ss_pred HHHHHHhc--CCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEee-ec--CCCeEEEEEehHHHHHHHhccc
Q 038444 19 FLPALDKM--GKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRIS-SQ--NEDCIAFAIDISLLQRAVRSGV 93 (300)
Q Consensus 19 iv~~i~kl--~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ie-S~--~~N~I~lev~~~~L~raLrsa~ 93 (300)
.+.-+.|+ ...+.+.++..++.|.. .+.+..+++++-. .-|.+|+=- .. .++...+.++.+.|..||+++.
T Consensus 203 ~l~el~kll~~~~v~i~~~~~~i~f~~---~~~~~~~~srLie-G~fPdY~~vIP~~~~~~~~~~~i~r~~l~~al~Rvs 278 (384)
T PRK14947 203 YLLELKKWLGADEIELSISEKRLFFRT---GDGKETFSLPLSY-YQYPDYMNFLSKLQGDDVSNLEVDRKECMDALDRIL 278 (384)
T ss_pred HHHHHHHhCCCCcEEEEEeCCEEEEEE---CCcEEEEEEEeee-cccCcceeeCCCCCCCCCEEEEEEHHHHHHHHHHHH
Confidence 33444444 25688889988888854 2235688888854 489998765 22 2467899999999999999986
Q ss_pred cccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECcee-EEEEEeecCcccChhhhchhhhhhcccCCCCCeEE
Q 038444 94 SICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKS-AVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLV 172 (300)
Q Consensus 94 ~~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~-~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i 172 (300)
-..+. ....+++++... -|.+...+... .....+|+. . . . ++..|
T Consensus 279 i~s~~------~~~~v~l~~~~~----------~l~iss~~~e~G~a~E~i~~~--~--------~-------G-e~~~I 324 (384)
T PRK14947 279 IFNTD------NNRCTYFDFGPG----------ELSLSAQGQDVGSATESLEVT--Y--------S-------G-DIKKI 324 (384)
T ss_pred HHhcC------CCceEEEEEeCC----------EEEEEEcCCCCceEEEEEEEE--e--------c-------C-CcEEE
Confidence 43110 123355555422 34454443322 344456662 1 1 1 23445
Q ss_pred EcCChhhHHHHHHhhhcc-CCEEEEEEEcC
Q 038444 173 QVPDLNQLQNFVHRMKHV-GDLLNVSIYKY 201 (300)
Q Consensus 173 ~lP~l~~l~~ivdR~k~~-~~~v~i~an~~ 201 (300)
-+-+ +=+.|=++.+ ++.+.+..+..
T Consensus 325 ~fN~----~YL~d~L~~i~~~~i~l~~~~~ 350 (384)
T PRK14947 325 AFPT----KNLIEILGHFQSDKITLTLTGA 350 (384)
T ss_pred EECH----HHHHHHHhcCCCCeEEEEECCC
Confidence 4444 5567777777 47788877543
No 49
>PRK14943 DNA polymerase III subunit beta; Provisional
Probab=23.76 E-value=6.2e+02 Score=24.11 Aligned_cols=135 Identities=14% Similarity=0.194 Sum_probs=78.2
Q ss_pred CEEEEEEecCeEEEEeeecCC-----CceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccccccccccc
Q 038444 28 KVCHLFLTREKAYFLHNLLSG-----EGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAA 102 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~-----~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~ 102 (300)
..+.+.+....+.|......+ ++..+.+++-.. =|.+|+=--..+....++++...|.++|+++.-.++.
T Consensus 211 ~~V~i~~~~~~~~f~~~~~~~~~~~~~~~~~~~~li~g-~fP~y~~vip~~~~~~~~i~~~~l~~al~r~~~~~~~---- 285 (374)
T PRK14943 211 GKLKIRFNDRQAAFEISIGEDSSGLANDTYLISKLVEG-NYPNYRQVIPKETKERIKLERELLLECVHRAALVSSD---- 285 (374)
T ss_pred CcEEEEEeCCEEEEEEeccccccccCCCEEEEEEEeee-cCCChHHhCCCCCCeEEEEEHHHHHHHHHHHHhhccc----
Confidence 468888888887776421111 445677777444 7888884333345678999999999999987542110
Q ss_pred CCCCceEEEEEeecCCCCCCCCCceEEEEEECcee-EEEEEeecCcccChhhhchhhhhhcccCCCCCeEEEcCChhhHH
Q 038444 103 GSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKS-AVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQVPDLNQLQ 181 (300)
Q Consensus 103 ~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~-~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~lP~l~~l~ 181 (300)
....+.+.+.++ -|.+...+... .....+|+. .. =++..|-+-+ +
T Consensus 286 --~~~~v~l~~~~~----------~l~i~~~~~e~G~~~e~i~~~--~~----------------G~~~~i~fN~----~ 331 (374)
T PRK14943 286 --KSNSVKLKFSEN----------LLEIASSSEGVGEAHESMAIT--YS----------------GPELQVAFNP----D 331 (374)
T ss_pred --CCceEEEEEECC----------EEEEEEcCCCCceEEEEEEEE--ec----------------CCcEEEEECH----H
Confidence 123355555422 34444433221 233446662 10 1234454544 5
Q ss_pred HHHHhhhccC-CEEEEEEEcC
Q 038444 182 NFVHRMKHVG-DLLNVSIYKY 201 (300)
Q Consensus 182 ~ivdR~k~~~-~~v~i~an~~ 201 (300)
-+.|=+|.+. +.|+++.+..
T Consensus 332 yl~d~l~~~~~~~v~l~~~~~ 352 (374)
T PRK14943 332 FFMAPLKALTKDEVFFELKDE 352 (374)
T ss_pred HHHHHHhcCCCCEEEEEECCC
Confidence 5677778874 7788888653
No 50
>PRK14944 DNA polymerase III subunit beta; Provisional
Probab=23.72 E-value=4.6e+02 Score=25.38 Aligned_cols=61 Identities=7% Similarity=0.060 Sum_probs=47.1
Q ss_pred CEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccc
Q 038444 28 KVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVS 94 (300)
Q Consensus 28 k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~ 94 (300)
..+-+.+...++.|.. ++..+++++--. =|.+|+=-=..+....+.++...|..||+++.-
T Consensus 216 ~~v~i~~~~~~i~f~~-----~~~~~~srLieG-~fPdy~~viP~~~~~~~~i~r~~l~~al~Rvsl 276 (375)
T PRK14944 216 KNLKIYSDSKKIFLKI-----DNLWFQTSLLEG-NYPQIQEIKLTNFPFSIHLNKDDLMKALERVSL 276 (375)
T ss_pred CcEEEEEcCCEEEEEE-----CCEEEEEEeecc-cCCChhhhCCCCCCeEEEEeHHHHHHHHHHHHH
Confidence 3578888888888854 567888888544 788886553345678899999999999999764
No 51
>PRK14945 DNA polymerase III subunit beta; Provisional
Probab=22.32 E-value=6.8e+02 Score=23.78 Aligned_cols=130 Identities=10% Similarity=0.124 Sum_probs=76.4
Q ss_pred EEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhccccccccccccCCCCce
Q 038444 29 VCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVSICSEIGAAGSAANR 108 (300)
Q Consensus 29 ~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~~~~~~~~~~~~a~~ 108 (300)
.+.+.+..+++.|.. ++....+.+-.. =|.+|.---..+....+.++.+.|.++|+++.-..+. .+.
T Consensus 208 ~v~i~~~~~~i~~~~-----~~~~~~~~lidg-~fP~~~~vip~~~~~~v~i~~~~L~~~l~r~~~~~~~-------~~~ 274 (362)
T PRK14945 208 EASLALGEGVLTLTT-----GGVRMNLKLMEG-EFPDYERVIPQDFKLQVTLPAEALREAVNRVAVLSDR-------NAN 274 (362)
T ss_pred cEEEEEcCCEEEEEE-----CCEEEEEEeecc-cCCChhhhCCCCCCEEEEEEHHHHHHHHHHHhhhhcc-------CCC
Confidence 577888878776643 445666766444 5999963322345689999999999999998753110 101
Q ss_pred EEEEEeecCCCCCCCCCceEEEEEECceeEEEEEeecCcccChhhhchhhhhhcccCCC-CCeEEEcCChhhHHHHHHhh
Q 038444 109 LQIKLVKKLPPNCTQAMPFLTFETKGYKSAVIQDVPISKPLSRAQGLELQTALDMAQDI-PPTLVQVPDLNQLQNFVHRM 187 (300)
Q Consensus 109 v~ikL~kk~~~~~~~~~P~L~~~~~g~~~~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~-p~~~i~lP~l~~l~~ivdR~ 187 (300)
-.++|.-.+ -.|.+...+........+|+ . +. .. ++..|-+-+ +-+.|=+
T Consensus 275 ~~v~l~~~~--------~~l~~~a~~~~g~a~~~i~~-~---------~~-------G~~~~~~i~fN~----~yl~d~L 325 (362)
T PRK14945 275 NRVELLVAE--------GRLRLTAEGDYGRGQEELAV-T---------QE-------GSEPAMALAYNA----RYLLDAL 325 (362)
T ss_pred ccEEEEEEC--------CEEEEEecCCCceEEEEEEE-E---------ee-------cCCCCEEEEECH----HHHHHHH
Confidence 224444443 24666554332344555776 2 11 11 346665554 4556666
Q ss_pred hccCCEEEEEEEc
Q 038444 188 KHVGDLLNVSIYK 200 (300)
Q Consensus 188 k~~~~~v~i~an~ 200 (300)
|.+.+.|+|..+.
T Consensus 326 ~~~~~~v~l~~~~ 338 (362)
T PRK14945 326 APIEGDARLGFSG 338 (362)
T ss_pred HhCCCcEEEEECC
Confidence 6766667777754
No 52
>PRK14940 DNA polymerase III subunit beta; Provisional
Probab=20.17 E-value=7.7e+02 Score=23.59 Aligned_cols=140 Identities=11% Similarity=0.209 Sum_probs=84.5
Q ss_pred hHHHHHHhc---CCEEEEEEecCeEEEEeeecCCCceEEEEEEccCCCcCeeEeeecCCCeEEEEEehHHHHHHHhcccc
Q 038444 18 RFLPALDKM---GKVCHLFLTREKAYFLHNLLSGEGIQCVAQFHKETLFDDYRISSQNEDCIAFAIDISLLQRAVRSGVS 94 (300)
Q Consensus 18 ~iv~~i~kl---~k~cvlrlt~~~l~~i~~~~~~~g~qvw~~l~~~~lF~ey~ieS~~~N~I~lev~~~~L~raLrsa~~ 94 (300)
+.+..+.|+ ...+.+.++..++.|.. ++.++.+++-.. -|.+|+--=..+....++++...|..+++++.-
T Consensus 199 k~l~~l~kll~~~~~v~i~~~~~~i~f~~-----~~~~~~~rlidg-~fPdy~~vip~~~~~~~~i~~~~L~~al~R~~~ 272 (367)
T PRK14940 199 KILGIINKKLSPEGNVTLCITSQNIFFFF-----GGYKFSSVLIEG-QFPNYKRVIPDHQERSFCVGRVELMEALKRVSL 272 (367)
T ss_pred HHHHHHHHhcCCCCcEEEEEeCCEEEEEE-----CCEEEEEEEccc-cccchHhhCCCCCCEEEEEEHHHHHHHHHHHHH
Confidence 445567776 34577888888877743 567888887655 788887442233567889999999999999765
Q ss_pred ccccccccCCCCceEEEEEeecCCCCCCCCCceEEEEEECcee-EEEEEeecCcccChhhhchhhhhhcccCCCCCeEEE
Q 038444 95 ICSEIGAAGSAANRLQIKLVKKLPPNCTQAMPFLTFETKGYKS-AVIQDVPISKPLSRAQGLELQTALDMAQDIPPTLVQ 173 (300)
Q Consensus 95 ~~~~~~~~~~~a~~v~ikL~kk~~~~~~~~~P~L~~~~~g~~~-~v~hdvPV~~vl~~~~~~~l~eP~~~~~~~p~~~i~ 173 (300)
..+. ....+++.+. + ..|.++..+... .....+|+ . . . . ++..|-
T Consensus 273 ~~~~------~~~~v~l~~~--~--------~~l~l~~~~~e~G~~~e~i~~-~-~--------~-------G-e~~~I~ 318 (367)
T PRK14940 273 LVEQ------KSRRIFLTIQ--Q--------GLLTLSSQENEIGDAQEEIAC-A-Y--------T-------G-EEEVIA 318 (367)
T ss_pred Hhcc------CCceEEEEEe--C--------CEEEEEEcCCCCccEEEEEEE-E-e--------c-------C-CcEEEE
Confidence 3110 1233555553 2 245555443322 23445666 2 1 0 1 234454
Q ss_pred cCChhhHHHHHHhhhcc-CCEEEEEEEcC
Q 038444 174 VPDLNQLQNFVHRMKHV-GDLLNVSIYKY 201 (300)
Q Consensus 174 lP~l~~l~~ivdR~k~~-~~~v~i~an~~ 201 (300)
+-+ +=+.|=+|.+ ++.|++..+..
T Consensus 319 fN~----~yl~d~L~~i~~~~v~l~~~~~ 343 (367)
T PRK14940 319 LNY----LYLEEPLKVFTSKEVQVEFTEA 343 (367)
T ss_pred ECH----HHHHHHHhCCCCCEEEEEECCC
Confidence 443 5567777777 47788877654
Done!