Query psy2363
Match_columns 156
No_of_seqs 118 out of 488
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 23:03:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2363.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2363hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1636|consensus 100.0 1.4E-38 3E-43 261.4 13.3 122 1-156 139-260 (260)
2 PF02747 PCNA_C: Proliferating 100.0 3.8E-33 8.3E-38 210.3 14.7 116 1-150 13-128 (128)
3 PTZ00113 proliferating cell nu 100.0 8E-32 1.7E-36 227.2 14.8 122 1-156 141-272 (275)
4 PLN00057 proliferating cell nu 100.0 1.1E-30 2.4E-35 218.0 15.3 122 1-156 139-260 (263)
5 TIGR00590 pcna proliferating c 100.0 2.7E-30 5.9E-35 215.1 15.4 121 1-155 139-259 (259)
6 PTZ00483 proliferating cell nu 100.0 2E-30 4.2E-35 217.6 13.4 113 1-153 145-264 (264)
7 PHA03383 PCNA-like protein; Pr 100.0 2.1E-28 4.6E-33 204.9 13.1 113 1-152 146-262 (262)
8 PRK01115 DNA polymerase slidin 99.8 1E-17 2.2E-22 136.5 14.2 112 1-152 136-247 (247)
9 cd00577 PCNA Proliferating Cel 99.6 9E-15 1.9E-19 117.2 14.0 114 1-152 135-248 (248)
10 cd00140 beta_clamp Beta clamp 98.3 1.1E-05 2.4E-10 68.3 11.0 100 2-150 259-364 (365)
11 COG0592 DnaN DNA polymerase sl 98.2 2.2E-07 4.7E-12 81.0 0.2 59 95-153 261-325 (364)
12 PRK05643 DNA polymerase III su 98.0 8.3E-05 1.8E-09 63.8 11.8 100 2-150 260-365 (367)
13 KOG3194|consensus 97.9 7.4E-05 1.6E-09 63.3 8.5 109 2-149 156-270 (279)
14 PTZ00113 proliferating cell nu 97.8 0.00058 1.3E-08 58.1 12.4 73 4-78 73-180 (275)
15 PF02144 Rad1: Repair protein 97.7 0.00044 9.5E-09 58.3 10.7 99 1-135 171-273 (275)
16 PF02768 DNA_pol3_beta_3: DNA 97.7 0.0012 2.6E-08 48.4 11.6 99 2-149 15-119 (121)
17 TIGR00590 pcna proliferating c 97.5 0.0031 6.7E-08 52.7 12.5 73 4-78 73-178 (259)
18 PF02747 PCNA_C: Proliferating 97.5 0.00017 3.8E-09 54.1 4.3 23 55-78 30-52 (128)
19 PF00705 PCNA_N: Proliferating 97.4 0.016 3.4E-07 43.8 14.4 102 2-144 8-112 (127)
20 cd00577 PCNA Proliferating Cel 97.4 0.0087 1.9E-07 47.7 13.5 110 2-152 5-116 (248)
21 PRK14945 DNA polymerase III su 96.8 0.021 4.4E-07 49.4 11.7 100 1-149 253-359 (362)
22 PF04005 Hus1: Hus1-like prote 96.8 0.054 1.2E-06 45.9 13.3 128 4-148 159-289 (292)
23 smart00480 POL3Bc DNA polymera 96.4 0.036 7.7E-07 47.4 10.2 86 2-134 242-333 (345)
24 PTZ00483 proliferating cell nu 96.4 0.0046 1E-07 52.3 4.6 24 54-78 161-184 (264)
25 PLN00057 proliferating cell nu 96.2 0.22 4.8E-06 41.7 13.8 106 3-147 9-116 (263)
26 PHA03383 PCNA-like protein; Pr 96.1 0.17 3.7E-06 42.7 12.3 108 2-148 14-124 (262)
27 PRK14947 DNA polymerase III su 96.0 0.099 2.1E-06 46.1 11.2 105 2-155 266-377 (384)
28 PRK14940 DNA polymerase III su 95.4 0.31 6.8E-06 42.4 11.8 99 2-149 259-363 (367)
29 PRK14941 DNA polymerase III su 94.8 0.47 1E-05 41.4 11.2 101 2-149 263-369 (374)
30 PRK14943 DNA polymerase III su 94.8 0.59 1.3E-05 40.4 11.6 98 2-150 268-371 (374)
31 PRK06673 DNA polymerase III su 94.8 2.6 5.7E-05 36.9 16.0 66 81-149 303-372 (376)
32 PRK14942 DNA polymerase III su 94.4 0.88 1.9E-05 39.9 11.8 99 2-149 266-370 (373)
33 KOG1636|consensus 94.3 0.068 1.5E-06 45.0 4.4 25 53-78 154-178 (260)
34 PRK07761 DNA polymerase III su 94.3 0.75 1.6E-05 39.9 11.1 101 2-149 262-371 (376)
35 PRK01115 DNA polymerase slidin 94.2 1.4 3.1E-05 35.6 12.0 109 3-153 9-118 (247)
36 PRK14946 DNA polymerase III su 94.2 0.71 1.5E-05 40.5 10.7 98 2-148 258-362 (366)
37 TIGR00663 dnan DNA polymerase 93.3 1.4 3.1E-05 37.7 11.0 99 2-149 259-364 (367)
38 PRK14944 DNA polymerase III su 92.2 2.4 5.2E-05 37.2 11.0 101 2-150 263-373 (375)
39 PF04139 Rad9: Rad9; InterPro 91.6 0.72 1.6E-05 37.9 6.7 56 93-148 193-250 (252)
40 PF04005 Hus1: Hus1-like prote 90.8 3.9 8.5E-05 34.6 10.6 99 4-138 11-115 (292)
41 PF04139 Rad9: Rad9; InterPro 84.4 3.8 8.2E-05 33.6 6.5 41 6-46 1-43 (252)
42 PF01776 Ribosomal_L22e: Ribos 70.9 6.5 0.00014 29.6 3.7 21 103-123 64-88 (112)
43 cd00140 beta_clamp Beta clamp 70.6 63 0.0014 27.1 11.0 34 102-138 194-228 (365)
44 PTZ00198 60S ribosomal protein 68.5 11 0.00024 28.9 4.4 17 106-122 80-100 (122)
45 cd02974 AhpF_NTD_N Alkyl hydro 67.6 16 0.00035 26.1 5.1 43 108-150 36-82 (94)
46 KOG3999|consensus 65.7 90 0.002 27.1 10.6 46 3-48 165-211 (284)
47 KOG2810|consensus 63.1 11 0.00025 33.9 4.3 115 4-153 11-129 (394)
48 PF06228 ChuX_HutX: Haem utili 61.3 17 0.00038 28.1 4.5 39 2-41 25-63 (141)
49 PF09095 DUF1926: Domain of un 50.1 1.1E+02 0.0023 25.9 7.8 55 19-73 125-182 (278)
50 COG0592 DnaN DNA polymerase sl 48.5 1.9E+02 0.004 25.3 10.5 50 98-150 312-362 (364)
51 COG3110 Uncharacterized protei 41.0 30 0.00065 28.8 3.0 41 111-155 63-103 (216)
52 PRK15317 alkyl hydroperoxide r 31.0 1.1E+02 0.0023 27.7 5.3 57 94-150 16-82 (517)
53 PF04045 P34-Arc: Arp2/3 compl 28.5 43 0.00093 28.2 2.1 56 96-151 122-186 (241)
54 PRK06673 DNA polymerase III su 27.3 1.6E+02 0.0035 25.6 5.6 82 2-98 264-352 (376)
55 PRK14943 DNA polymerase III su 26.5 4.1E+02 0.009 22.8 10.7 33 2-34 6-47 (374)
56 TIGR03140 AhpF alkyl hydropero 24.6 1.6E+02 0.0034 26.8 5.1 56 95-150 17-83 (515)
57 PF05517 p25-alpha: p25-alpha 22.9 29 0.00063 26.8 0.1 19 1-19 19-37 (154)
58 TIGR03170 flgA_cterm flagella 21.3 1.3E+02 0.0029 21.5 3.4 21 16-36 68-88 (122)
59 PF14977 FAM194: FAM194 protei 21.3 1.3E+02 0.0029 24.8 3.7 67 55-132 77-155 (208)
60 TIGR00663 dnan DNA polymerase 20.7 5.3E+02 0.011 21.9 10.0 34 2-35 6-48 (367)
61 PRK12618 flgA flagellar basal 20.1 1.4E+02 0.0029 22.9 3.3 21 16-36 84-104 (141)
No 1
>KOG1636|consensus
Probab=100.00 E-value=1.4e-38 Score=261.41 Aligned_cols=122 Identities=64% Similarity=1.073 Sum_probs=112.7
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|||+||+||||||+.|||+|+|.+++++|+|+++||+|+++|.+++....+++
T Consensus 139 mPa~EF~ricrdls~f~Dsv~I~~tkegv~F~~~Gdig~asi~l~~~~~~d~~--------------------------- 191 (260)
T KOG1636|consen 139 MPAGEFSRICRDLSTFSDSVVISATKEGVKFSAKGDIGTASITLSQCTAVDKP--------------------------- 191 (260)
T ss_pred ccHHHHHHHHHHHhhhcCeEEEEEecceeEEEecccccceeEEEccCCCCCCc---------------------------
Confidence 89999999999999999999999999999999999999999999887655444
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccCCCCC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN 156 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~~e~~ 156 (156)
++.|+|+|++||+|+||+|||+.|+||++||++|+|+|+++.|+.|+|++.+.|||||||||||+++++
T Consensus 192 -------e~av~iE~~~pVtltfa~kYln~ftKatpLs~rV~lsls~~~P~~vey~i~~~g~lr~YLAPKieD~e~ 260 (260)
T KOG1636|consen 192 -------EEAVKIEMNEPVTLTFALKYLNQFTKATPLSDRVTLSLSSEVPVVVEYKIEDMGHLRYYLAPKIEDEED 260 (260)
T ss_pred -------cceEEEEecCcchhhhHHHHHHHhhccccccceEEEEecCCCcEEEEEecccCceEEEEEccccCCCCC
Confidence 455667777789999999999999999999999999999999999999999999999999999998764
No 2
>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=100.00 E-value=3.8e-33 Score=210.31 Aligned_cols=116 Identities=47% Similarity=0.879 Sum_probs=100.1
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|+|++|+++||||+.|||+|+|.+++++++|+++||.|++++.+.+....+++++.
T Consensus 13 m~S~~f~~~~kdl~~v~d~v~i~~~~~~~~f~~~Gd~~~~~v~~~~~~~~~~~~~~------------------------ 68 (128)
T PF02747_consen 13 MPSSEFKKICKDLSSVGDTVTISADKDSVIFSAEGDIGSAEVEFKETESSEDDEEL------------------------ 68 (128)
T ss_dssp EEHHHHHHHHHHHHTTCSEEEEEEETTEEEEEEEESSEEEEEEEEEEEEETTCTCE------------------------
T ss_pred EEHHHHHHHHHHHHhcCCEEEEEEeCCEEEEEEEeccCcEEEEEeecccccccccc------------------------
Confidence 78999999999999999999999999999999999999999998765332222333
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeec
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
+.+++++|++.+|+++||+.|+|++++|++|+|+|++++||+|+|+++++|+|+||||||
T Consensus 69 ----------~~i~~~~~~~~~fsl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~f~~~~~g~l~f~LAPK 128 (128)
T PF02747_consen 69 ----------IEIEVKEPVSSSFSLDYLNDFSKAAPLSDEVTLELGEDMPLKLEFELADGGSLKFYLAPK 128 (128)
T ss_dssp ----------SEEEESSEEEEEEEHHHHHHHGGGGGTTSEEEEEEETTSEEEEEEEETTTEEEEEEE-BB
T ss_pred ----------ceeeeccceeeEEeHHHHHhhhccccCCceEEEEEcCCCCEEEEEEeCCCeEEEEEEcCC
Confidence 445555566666667779999999999999999999999999999999999999999998
No 3
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=99.98 E-value=8e-32 Score=227.16 Aligned_cols=122 Identities=30% Similarity=0.682 Sum_probs=106.5
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|+|++|+++||||+.|||+|+|++++++|+|+++||.|++++.+++..+.+++++.
T Consensus 141 m~s~~f~~i~rdl~~vgd~V~i~~~~~~v~f~a~Gd~g~~~i~l~~~~~~~~~~~~------------------------ 196 (275)
T PTZ00113 141 LSSKELTNICRQMNEFSDTVKIEIDSNSIKFTTQGDLGDGEVVLKPRPPTSEDDCG------------------------ 196 (275)
T ss_pred EEHHHHHHHHHHHHHcCCEEEEEEeCCEEEEEEeccCcEEEEEEecCCCCCCccce------------------------
Confidence 78999999999999999999999999999999999999999999876554333333
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCC----------CeEEEEEEeec
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD----------IGHIRYYLAPK 150 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~----------~G~l~~yLAPk 150 (156)
|++++++|++..||++||+.|+||++||++|+|+|++++||+|+|++++ .|+|+||||||
T Consensus 197 ----------~~~~v~~~~~~~ysl~YL~~f~Ka~~ls~~V~l~l~~d~Pl~ley~i~~~~~~~~~~~~~G~l~fyLAPk 266 (275)
T PTZ00113 197 ----------VTIKVRKPIKQSYATKYLNMFAKSGCLSDVVTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKFFLAPK 266 (275)
T ss_pred ----------EEEEecCceeeEEhHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeccccccccccCCccEEEEEEcCc
Confidence 4555566677777777799999999999999999999999999999962 59999999999
Q ss_pred cCCCCC
Q psy2363 151 IESDDN 156 (156)
Q Consensus 151 i~~e~~ 156 (156)
+++|++
T Consensus 267 ie~~~~ 272 (275)
T PTZ00113 267 MDDDMD 272 (275)
T ss_pred cCcccc
Confidence 998874
No 4
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=99.97 E-value=1.1e-30 Score=217.99 Aligned_cols=122 Identities=62% Similarity=1.010 Sum_probs=106.8
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|+|++|+++||||+.+||+|+|++++++++|++.||.|++++.+++..+.+++++.+.
T Consensus 139 m~s~~f~~~~kdl~~vsd~v~i~~~~~~~~f~~~Gd~g~~~~~l~~~~~~~~~~~~~~---------------------- 196 (263)
T PLN00057 139 MPSAEFQRICKDLSSIGDTVVISVTKEGVKFSTSGDIGTANIVLRQNTTVDKPEEKTV---------------------- 196 (263)
T ss_pred EEHHHHHHHHHHHHHcCCEEEEEEeCCEEEEEEEecCcEEEEEEecCCCCCCccceEE----------------------
Confidence 7899999999999999999999999999999999999999999988765433333444
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccCCCCC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN 156 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~~e~~ 156 (156)
+++++|++..|+++||+.|+||+++|++|+|+|++++||+|+|.++++|+|+||||||+++|++
T Consensus 197 ------------i~~~e~~~~~y~l~YL~~~~Ka~~ls~~V~i~~~~~~Pl~l~y~l~~~g~l~f~LAPri~~~~~ 260 (263)
T PLN00057 197 ------------IEMQEPVSLTFALRYLNSFTKATPLSDTVTLSLSKELPVVVEYKIAEMGYIRYYLAPKIEEDED 260 (263)
T ss_pred ------------EEecCceEEEEhHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeCCCeEEEEEEcCCCCCccc
Confidence 4455566666666669999999999999999999999999999999899999999999998873
No 5
>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=99.97 E-value=2.7e-30 Score=215.13 Aligned_cols=121 Identities=69% Similarity=1.106 Sum_probs=106.9
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|+|++|+++||||+.+||+|+|.+++++++|+++||.|++++.+++..+..++++.+.
T Consensus 139 m~s~~f~~~~kdl~~v~d~v~i~~~~~~~~f~~~Gd~g~~~~~~~~~~~~~~~~~~~~---------------------- 196 (259)
T TIGR00590 139 MPSSEFARICRDLSQFSDSVVISCTKEGVKFSAKGDIGSGNVKLKQTSDTDKEEEAVT---------------------- 196 (259)
T ss_pred EEHHHHHHHHHHHHHcCCEEEEEEeCCEEEEEEEecccEEEEEEecCCCCCCCcceEE----------------------
Confidence 7899999999999999999999999999999999999999999988765544444444
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccCCCC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 155 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~~e~ 155 (156)
+++++|++..|+++||+.|+||+++|++|+|+|++++||+++|.++++|+|+||||||+++|+
T Consensus 197 ------------i~~~~~~~~~y~l~YL~~~~Ka~~ls~~V~l~~~~~~Pl~l~y~i~~~g~l~f~lAPrie~~~ 259 (259)
T TIGR00590 197 ------------IEMKEPVTLTFAIKYLNLFTKATPLSDRVTLSMSNDVPLVVEYKIKDMGFLRFFLAPKIEDEE 259 (259)
T ss_pred ------------EEecCceeeeeeHHHHHHhhhhccCCCeEEEEEcCCCCEEEEEEeCCCeEEEEEEcCccCCCC
Confidence 445556666666667999999999999999999999999999999989999999999999885
No 6
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=99.97 E-value=2e-30 Score=217.56 Aligned_cols=113 Identities=33% Similarity=0.575 Sum_probs=101.2
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|+|++|+++||||+.|||+|+|.+++++|+|+++||.|++++.++.... .
T Consensus 145 m~s~~f~~i~kdl~~vsD~v~i~~~~~~v~f~a~Gd~~~~~~~l~~~~~------~------------------------ 194 (264)
T PTZ00483 145 MNSKKFQEFAKYLHSIGDTVSISMKKDEMRLETEGEGIKASKQFHNDVG------D------------------------ 194 (264)
T ss_pred EEHHHHHHHHHHHHHcCCEEEEEEECCEEEEEEeecCcEEEEEEccCCC------c------------------------
Confidence 7899999999999999999999999999999999999999988852211 1
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeC-------CCeEEEEEEeeccCC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKID-------DIGHIRYYLAPKIES 153 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~-------~~G~l~~yLAPki~~ 153 (156)
|++.+++||+++||++||+.|+||+++|++|+|+|++++||+++|+++ ++|+|+|||||||++
T Consensus 195 ----------v~~~~~~~v~~~fsl~YL~~f~Ka~~lsd~V~i~l~~~~Pl~ley~i~~~~~~~~~~G~l~fyLAPrie~ 264 (264)
T PTZ00483 195 ----------VRVTSTESLSQEFATRYLVLFSKATSLADEVSINLSAGIPLSVKFNFKDPLTDLQDSSFINFYLAPNIEE 264 (264)
T ss_pred ----------eEEEecCcchheehHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEecccccCCCCceEEEEEEccccCC
Confidence 455667788888888889999999999999999999999999999995 589999999999985
No 7
>PHA03383 PCNA-like protein; Provisional
Probab=99.96 E-value=2.1e-28 Score=204.94 Aligned_cols=113 Identities=25% Similarity=0.553 Sum_probs=99.5
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEE----EeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFS----ATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~----~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
|+|++|+++||||+.|||+|+|.+++++|+|+ ++||.|.+++.+.+.... .
T Consensus 146 m~s~~f~~i~kdl~~igD~v~i~~~~~~v~f~~~~~~~Gd~~~~~~~~~~~~~~-----~-------------------- 200 (262)
T PHA03383 146 LPSNYFQRLCRDMSNITDDLEITKKGKEVSFRSDYTCVTDFASQETIIGDSDNG-----Q-------------------- 200 (262)
T ss_pred EEHHHHHHHHHHHHHcCCeEEEEEeCCEEEEEEcccccccccceEEEecCCCCC-----c--------------------
Confidence 78999999999999999999999999999999 999999999888654321 1
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccC
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~ 152 (156)
|.+...+|++++||++||+.|+||+++|++|+|+|++++||+++|+++++|+|+|||||||.
T Consensus 201 --------------v~~~~~~~~~~~ysl~YL~~~~Ka~~ls~~V~i~l~~d~Pl~ley~i~~~G~l~fyLAPri~ 262 (262)
T PHA03383 201 --------------ITCNESPDYTGKFSLKYLTSFTKASGMSSSVEIYLKESNPLILKYNVGSLGNLKFVIAPKVS 262 (262)
T ss_pred --------------eEEecCCceEEEEeHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeCCCcEEEEEEccccC
Confidence 22333457788888888999999999999999999999999999999989999999999983
No 8
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=99.77 E-value=1e-17 Score=136.48 Aligned_cols=112 Identities=24% Similarity=0.512 Sum_probs=94.2
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|++.+|+++||+++.+++.|+|.+++++++|++.|+ |++...+..... ..+.++++
T Consensus 136 ~~~~~l~~~~~r~~~~~~~v~i~~~~~~l~lsa~~~-g~a~~~i~~~~~-----~~~~~~g~------------------ 191 (247)
T PRK01115 136 ILGDDLKDAIKDAELVSDHIELEADEDKFYIEAEGE-GEDEVELSLDSG-----PLIELSVE------------------ 191 (247)
T ss_pred EEHHHHHHHHHHHHhcCCeEEEEEeCCEEEEEEEeC-CceEEEEecCCC-----ceEEEEec------------------
Confidence 578999999999999999999999999999999998 888877754321 12334443
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~ 152 (156)
++++..|..+||..+.|+++++++|.|+|+++.|++++|.+.+.|+++||||||++
T Consensus 192 ----------------e~~~i~fn~~YL~d~lk~~~~~~~V~l~~~~~~P~~l~~~~~~~~~~~~~i~P~~~ 247 (247)
T PRK01115 192 ----------------EPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGGGKVTYLLAPRIE 247 (247)
T ss_pred ----------------CceeEEEhHHHHHHhhccccCCCeEEEEECCCCCEEEEEEeCCCeEEEEEEecccC
Confidence 34555555566999999999999999999999999999999999999999999985
No 9
>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=99.63 E-value=9e-15 Score=117.16 Aligned_cols=114 Identities=49% Similarity=0.806 Sum_probs=91.8
Q ss_pred CCcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCC
Q psy2363 1 MPSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKA 80 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~ 80 (156)
|++.+|+++|+++..+++.|+|.+++++++|++.|+.|.....+...+.. .-+...+
T Consensus 135 i~~~~L~~~i~~~~~~~~~i~i~~~~~~l~lss~~~~~~~~~~~~~~~~~----~~~~~~~------------------- 191 (248)
T cd00577 135 LPSDELKDIVRDLESISDSVTISASKDGFKFSAEGELGGASVTLLPKDSD----LLVTIEC------------------- 191 (248)
T ss_pred EEHHHHHHHHHHHHHcCCEEEEEEcCCEEEEEEeecCCceEEEEecCCCC----ceEEEEe-------------------
Confidence 57899999999999999999999999999999999866655444332210 0112223
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~ 152 (156)
.+|++..|..+||..+.|+..++++|+|+|..+.||.++|.+++.|++.|||||+++
T Consensus 192 ---------------~~~~~~~fn~~yL~~~l~~~~~s~~v~i~~~~~~p~~i~~~~~~~~~~~f~lap~~~ 248 (248)
T cd00577 192 ---------------SEPVSSTYSLKYLKDFTKAAPLSDKVTLSFGSDGPLSLEFKIADGGHLTFYLAPKIE 248 (248)
T ss_pred ---------------CCceEEEEhHHHHHHHhhhcccCCeEEEEEcCCCCEEEEEEcCCCcEEEEEEccccC
Confidence 345555556666999999999999999999999999999999989999999999974
No 10
>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=98.27 E-value=1.1e-05 Score=68.29 Aligned_cols=100 Identities=23% Similarity=0.368 Sum_probs=75.1
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEeec-ceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSATGD-IGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~gd-~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|.++++.+..+.+ .|.+..+++++++++.++ .+.+...+.. +.+.
T Consensus 259 ~~~~L~~~l~~~~~~~~~~~~~v~l~~~~~~l~~~a~~~~~~~~~~~~~~-------------~~~g------------- 312 (365)
T cd00140 259 DREELLEALKRVSLLSNEKNRGVKLEISEGQLKLSANNPEIGEAEEELEV-------------EYEG------------- 312 (365)
T ss_pred EHHHHHHHHHHHhhhhccCCceEEEEEeCCEEEEEEcCCCCceEEEEEEE-------------EecC-------------
Confidence 56889999999998876 788999999999999876 4555544321 1111
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeec
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
++++..|..+||..+.|+.+ +++|+|.++.+ .|+.+.+.- .+++.|+|+|.
T Consensus 313 --------------------~~~~i~~~~~yL~d~lk~~~-~~~v~i~~~~~~~p~~i~~~~--~~~~~~limP~ 364 (365)
T cd00140 313 --------------------EELEIGFNPKYLLDALKAID-SEEVRLSFTDSNSPVLITPED--DDNFLYLIMPV 364 (365)
T ss_pred --------------------CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEcCC--CCcEEEEEEeC
Confidence 12334444455999999876 68999999998 899998865 57899999994
No 11
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]
Probab=98.24 E-value=2.2e-07 Score=81.04 Aligned_cols=59 Identities=27% Similarity=0.299 Sum_probs=50.9
Q ss_pred ecCceeeeeehhhHHhhhhhcCCCc-eEEEEeeCCCcEEEEEEeCCC-----eEEEEEEeeccCC
Q psy2363 95 MQEPVSLNFACRYLLNFAKAAPLSN-QVCLSMSLDVPLVVEFKIDDI-----GHIRYYLAPKIES 153 (156)
Q Consensus 95 ~~~~V~l~Fa~~~L~~f~Kaa~ls~-~V~l~l~~~~Pl~v~f~i~~~-----G~l~~yLAPki~~ 153 (156)
+.++++..|.+.|++.+.+...+++ +|+|.++++.|.++++++..+ |+|.|++||++|.
T Consensus 261 l~~al~r~~~l~~~~~~~~~~~~~~~~v~i~~~~~~~g~~~eei~~~~~g~~~~I~fn~~ylld~ 325 (364)
T COG0592 261 LKEALKRVYSLSYLKDRGKKLSLADGEVKLSLGNDEPGKAEEEIDVGYTGEELKIGFNLAYLLDV 325 (364)
T ss_pred HHHHHHHHHHHHhcccCceEEEeeCCeEEEEecCCCccceEEEEEeccCCceEEEEECHHHHHHH
Confidence 4455666677777999999999998 999999999999999999864 9999999999874
No 12
>PRK05643 DNA polymerase III subunit beta; Validated
Probab=98.03 E-value=8.3e-05 Score=63.75 Aligned_cols=100 Identities=24% Similarity=0.368 Sum_probs=72.3
Q ss_pred CcHHHHHHHHHHhcc----CCeEEEEEeCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQF----GESINISCTKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~----gd~v~i~~~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|.++++-+..+ ...|.+..+++.+++++.+ +.|.+...+.- +.+
T Consensus 260 ~~~~L~~~i~rv~~~~~~~~~~i~l~~~~~~l~~~a~~~~~g~a~~~i~~-------------~~~-------------- 312 (367)
T PRK05643 260 DRKELLQALERASILSNEKSRGVKLSLSEGQLKISANNPEQGEAEEELEV-------------EYS-------------- 312 (367)
T ss_pred EHHHHHHHHHHHHHHhcCCCceEEEEEeCCEEEEEEECCCCCcEEEEEEE-------------Eec--------------
Confidence 567899999998887 3458888888999998775 56655443311 100
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeec
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
.++++..|-.+||..+.|+.. ++.|+|.|++. .|+.+.. .+.+...|+|+|.
T Consensus 313 -------------------g~~~~i~~n~~yL~d~l~~~~-~~~v~i~~~~~~~p~~i~~--~~~~~~~~limP~ 365 (367)
T PRK05643 313 -------------------GEELEIGFNVKYLLDVLKALD-SEEVRLSFNDANSPFLIRP--PDDDSFLYVIMPM 365 (367)
T ss_pred -------------------CCcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc--CCCCceEEEEEee
Confidence 013334444455999999877 88999999995 8999988 4467899999993
No 13
>KOG3194|consensus
Probab=97.88 E-value=7.4e-05 Score=63.27 Aligned_cols=109 Identities=20% Similarity=0.316 Sum_probs=88.3
Q ss_pred CcHHHHHHHHHHhccCCeEEEEEeCC--eEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccC
Q psy2363 2 PSGEFARICRDLAQFGESINISCTKE--GVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAK 79 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd~v~i~~~~~--~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k 79 (156)
.|.-+..+.+||...|+.+.|...++ .+++++-|+.|...+.+...... -=.++|.+.+.-.|-...
T Consensus 156 Kse~L~eAlkeLD~tsevl~It~s~dk~~F~L~tfG~lG~S~i~~Ps~s~~-----mEs~~~~~ev~~sy~fSl------ 224 (279)
T KOG3194|consen 156 KSEGLHEALKELDMTSEVLQITMSPDKPYFRLSTFGNLGSSHIDYPSDSSL-----MESFQCFDEVIGSYDFSL------ 224 (279)
T ss_pred hhHHHHHHHHHhhhcceeEEEEecCCCcEEEEEEecccCcceecCCCcHHH-----HHHhhhhhhhhceEeehh------
Confidence 46778999999999999999999866 99999999999999988654321 112445554455555555
Q ss_pred CCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCC-Ce---EEEEEEee
Q psy2363 80 AAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD-IG---HIRYYLAP 149 (156)
Q Consensus 80 ~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~-~G---~l~~yLAP 149 (156)
++...||..|+..|.|++...=-|.+.|-+.. .| .|.||.-|
T Consensus 225 ----------------------------i~~~tkAl~lasKv~lR~DerGvLS~qimi~~~dg~itfiefc~vp 270 (279)
T KOG3194|consen 225 ----------------------------IDKITKALKLASKVLLRMDERGVLSVQIMIQTDDGIITFIEFCMVP 270 (279)
T ss_pred ----------------------------hHHHHHHHhhhheEEEEEcCCcEEEEEEEEecCCceEEEEEEEEee
Confidence 89999999999999999999999999999964 34 67899999
No 14
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=97.78 E-value=0.00058 Score=58.06 Aligned_cols=73 Identities=16% Similarity=0.288 Sum_probs=46.8
Q ss_pred HHHHHHHHHHhccCCeEEEEE--eCCeEEEEEeecc----eeEEEEEeecCC----CCC---------------------
Q psy2363 4 GEFARICRDLAQFGESINISC--TKEGVKFSATGDI----GSANIKLAQTGN----VDK--------------------- 52 (156)
Q Consensus 4 ~~f~~i~rdl~~~gd~v~i~~--~~~~v~f~~~gd~----~~~~i~l~~~~~----~~~--------------------- 52 (156)
..|.+|+|-+ .=+|.+.++. +++.+.|.-++.. .+..+.|-.-+. ..+
T Consensus 73 ~~l~KILk~~-~~~D~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l~L~di~~e~~~iPe~~~e~~~~v~m~s~~f~~i~r 151 (275)
T PTZ00113 73 ASVTKVFKLC-SNNDSVLIQSEEDKDNINFVFENNVEDKVSSFSLKLMSIEQDALSIPENEEGFDAEVTLSSKELTNICR 151 (275)
T ss_pred HHHHHHHHhC-CCCCEEEEEEcCCCCEEEEEEEcCCCceEEEEEEEccccCccccCCCCCCCCccEEEEEEHHHHHHHHH
Confidence 4566777664 4467899877 4567888777643 334454433221 001
Q ss_pred ----CCccEEEEecCceeEEeeeeeccccc
Q psy2363 53 ----EEEAVTVEMQEPVSLNFACRYLLNFA 78 (156)
Q Consensus 53 ----~~~~v~i~~~~~~~~~fs~k~~~~~~ 78 (156)
-++.|.|+++++ +++|+++|+.|.+
T Consensus 152 dl~~vgd~V~i~~~~~-~v~f~a~Gd~g~~ 180 (275)
T PTZ00113 152 QMNEFSDTVKIEIDSN-SIKFTTQGDLGDG 180 (275)
T ss_pred HHHHcCCEEEEEEeCC-EEEEEEeccCcEE
Confidence 245788889887 8999999977766
No 15
>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=97.71 E-value=0.00044 Score=58.32 Aligned_cols=99 Identities=21% Similarity=0.308 Sum_probs=72.3
Q ss_pred CCcHHHHHHHHHHhcc-CCeEEEEEeC---CeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 1 MPSGEFARICRDLAQF-GESINISCTK---EGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~-gd~v~i~~~~---~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
|.|.-|..+++||... ++.+.|.+.. ..++|++.|+.|...+.+...... ....+|.
T Consensus 171 mks~~L~~al~eL~~~~~~~l~i~~s~~~~p~f~l~s~G~~G~s~v~fp~~~~~-----le~f~~~-------------- 231 (275)
T PF02144_consen 171 MKSDWLRDALSELDWSNSEELTIYISPPDKPHFRLSSKGPLGSSKVDFPNDSDV-----LETFECY-------------- 231 (275)
T ss_dssp EEHHHHHHHHHTT-TS-CSEEEEEE-S-SSSSEEEEEEETTEEEEEEE-TTSTS-----EEEEEE---------------
T ss_pred EEhHHHHHHHHHHhhccCCeEEEEEEeCCCCEEEEEEEcCCCeEEEEECCCCCc-----eeEEEEe--------------
Confidence 5688999999999999 8999999987 699999999999999998765432 2234444
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEE
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEF 135 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f 135 (156)
..++++.-.|-..+|+...||.++|..|.|++..+==|.+.|
T Consensus 232 -----------------~~~~~~~~~Y~f~~i~~~~kAl~~ssKv~ir~d~~GlLs~Q~ 273 (275)
T PF02144_consen 232 -----------------DGEEPVISRYKFSLIKKAMKALKISSKVSIRIDENGLLSLQF 273 (275)
T ss_dssp --------------------S-EEEEEEHHHHCCHHHHHTTSSEEEEEEESSS-EEEEE
T ss_pred -----------------ccCceEEEEEeHHHHHHHHHHhhhccEEEEEeCCCcEEEEEE
Confidence 001233333566679999999999999999998876666665
No 16
>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=97.70 E-value=0.0012 Score=48.42 Aligned_cols=99 Identities=21% Similarity=0.414 Sum_probs=69.0
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|.+++|=+..+.+ .|.+.++++.+++++.. |.|++.-.+.- ..+ .++..+.|..+|
T Consensus 15 ~r~~L~~al~Rv~~~~~~~~~~v~l~~~~~~l~l~~~~~~~g~~~e~i~~-----------~~~-g~~~~i~fN~~y--- 79 (121)
T PF02768_consen 15 DRKELLDALKRVSIISSEKNNPVKLSFSDNQLTLSSQSSEIGEAEEEIPI-----------EYE-GEPLEIAFNPKY--- 79 (121)
T ss_dssp EHHHHHHHHHHHHHHHTTTTGEEEEEEETTEEEEEEEETTTEEEEEEEE------------EEE-ES-EEEEEEHHH---
T ss_pred EHHHHHHHHHHHHHHhhcCCceEEEEEECCEEEEEEcCCCCceEEEEEee-----------eec-CCceEEEECHHH---
Confidence 34688999999998875 89999999999999974 67776654421 111 233455555555
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 149 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~-Pl~v~f~i~~~G~l~~yLAP 149 (156)
|....++.. ++.|+|.|.... |+.++= .+....+|+|-|
T Consensus 80 -------------------------------L~d~L~~~~-~~~V~l~~~~~~~p~~i~~--~~d~~~~~liMP 119 (121)
T PF02768_consen 80 -------------------------------LLDALKAID-GEEVTLEFSDPSSPILITP--EEDPDFKYLIMP 119 (121)
T ss_dssp -------------------------------HHHHHHCC--SSEEEEEESSTTS-EEEEE--TTSSCEEEEE--
T ss_pred -------------------------------HHHHHhhcC-CCEEEEEEcCCCCCEEEEe--CCCCceEEEEEe
Confidence 999999876 789999999877 987754 345567888888
No 17
>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=97.48 E-value=0.0031 Score=52.75 Aligned_cols=73 Identities=8% Similarity=0.172 Sum_probs=45.2
Q ss_pred HHHHHHHHHHhccCCeEEEEEe--CCeEEEEEeec----ceeEEEEEeecCCC---------------------------
Q psy2363 4 GEFARICRDLAQFGESINISCT--KEGVKFSATGD----IGSANIKLAQTGNV--------------------------- 50 (156)
Q Consensus 4 ~~f~~i~rdl~~~gd~v~i~~~--~~~v~f~~~gd----~~~~~i~l~~~~~~--------------------------- 50 (156)
..|.+++|-+.. +|.+.++.+ ++.+.|.-++. ..+..+.+-+-+..
T Consensus 73 ~~l~kiLk~~~~-~d~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l~l~d~~~e~l~iP~~e~~~~v~m~s~~f~~~~kdl 151 (259)
T TIGR00590 73 TSLSKILKCANN-EDIVTLKAEDNADTLILVFESPKQDKISDYELKLMDIDVEHLGIPEQEYDCVVEMPSSEFARICRDL 151 (259)
T ss_pred HHHHHHHhccCC-CCEEEEEecCCCCEEEEEEEcCCCCeEEEEEEEeeecccccCCCCCCceeEEEEEEHHHHHHHHHHH
Confidence 456666665543 688888765 46777765532 23345555442110
Q ss_pred CCCCccEEEEecCceeEEeeeeeccccc
Q psy2363 51 DKEEEAVTVEMQEPVSLNFACRYLLNFA 78 (156)
Q Consensus 51 ~~~~~~v~i~~~~~~~~~fs~k~~~~~~ 78 (156)
+.-++.|.|+++++ +++|+.+|+.|.+
T Consensus 152 ~~v~d~v~i~~~~~-~~~f~~~Gd~g~~ 178 (259)
T TIGR00590 152 SQFSDSVVISCTKE-GVKFSAKGDIGSG 178 (259)
T ss_pred HHcCCEEEEEEeCC-EEEEEEEecccEE
Confidence 00245788888877 8999999977776
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=97.45 E-value=0.00017 Score=54.15 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=17.9
Q ss_pred ccEEEEecCceeEEeeeeeccccc
Q psy2363 55 EAVTVEMQEPVSLNFACRYLLNFA 78 (156)
Q Consensus 55 ~~v~i~~~~~~~~~fs~k~~~~~~ 78 (156)
+.|.|.++++ +++|+.+|+.|++
T Consensus 30 d~v~i~~~~~-~~~f~~~Gd~~~~ 52 (128)
T PF02747_consen 30 DTVTISADKD-SVIFSAEGDIGSA 52 (128)
T ss_dssp SEEEEEEETT-EEEEEEEESSEEE
T ss_pred CEEEEEEeCC-EEEEEEEeccCcE
Confidence 4788888887 8888888866655
No 19
>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=97.40 E-value=0.016 Score=43.84 Aligned_cols=102 Identities=18% Similarity=0.243 Sum_probs=73.5
Q ss_pred CcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEE--EEEeecCCCCCCCccEEEEecCceeEEeeeeecccccC
Q psy2363 2 PSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSAN--IKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAK 79 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~--i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k 79 (156)
.++.|++++.-++.+=+.++|.++++|+++.+....--+- +.+.... --..+
T Consensus 8 ~a~~~K~i~eal~~lv~e~~f~~~~~Gi~~~amD~s~Valv~l~l~~~~-------F~~Y~------------------- 61 (127)
T PF00705_consen 8 DASLFKKIFEALKDLVDEANFEFTEDGISLQAMDPSHVALVDLELPSEA-------FEEYR------------------- 61 (127)
T ss_dssp SHHHHHHHHHHHTTTCSEEEEEEESSEEEEEEE-TTSSEEEEEEEEGGG-------SSEEE-------------------
T ss_pred chHHHHHHHHHHHHHhhEEEEEEccCCEEEEEECCCcEEEEEEEechhc-------ceEEE-------------------
Confidence 3678999999999999999999999999999985433332 2332211 11223
Q ss_pred CCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCc-EEEEEEeCCCeEEE
Q psy2363 80 AAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVP-LVVEFKIDDIGHIR 144 (156)
Q Consensus 80 ~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~P-l~v~f~i~~~G~l~ 144 (156)
+++++++.+.+.+|..+.|.++-.+.++|+..++-. |.+.|.-...++++
T Consensus 62 ---------------~d~~~~igvnl~~l~kiLk~~~~~D~l~l~~~~~~~~l~i~~~~~~~~~~~ 112 (127)
T PF00705_consen 62 ---------------CDKELSIGVNLSDLKKILKRAKKDDSLELESDEEPDKLNIVFENEKKGRVR 112 (127)
T ss_dssp ---------------ESSSEEEEEEHHHHHHHHTTSSTTSEEEEEEESSSSEEEEEEEETTSSEEE
T ss_pred ---------------cCCCEEEEEEHHHHHHHHhhccCCCEEEEEEeCCCCEEEEEEEcCCCCeEE
Confidence 334555666666699999999999999999877643 55778877777765
No 20
>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=97.37 E-value=0.0087 Score=47.74 Aligned_cols=110 Identities=19% Similarity=0.260 Sum_probs=75.8
Q ss_pred CcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecc--eeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccC
Q psy2363 2 PSGEFARICRDLAQFGESINISCTKEGVKFSATGDI--GSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAK 79 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~--~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k 79 (156)
..+.|+++++.++.+.+.|.+++.+++++|.+.... +.+.+.+... -| ..|
T Consensus 5 ~~~~l~~~~~~l~~i~~~v~~~~~~~gl~~~a~d~~r~~~~~~~l~~~--------------------~F-~~y------ 57 (248)
T cd00577 5 NAKLLKKIVDALSKLVDEANFDITEDGISLQAMDSSHVALVSLFLPKE--------------------LF-EEY------ 57 (248)
T ss_pred chHHHHHHHHHHHHHhcEEeEEECCCceEEEEEcCCcEEEEEEEechh--------------------hC-eEE------
Confidence 357899999999999999999999999999997553 2233333211 01 112
Q ss_pred CCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccC
Q psy2363 80 AAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 152 (156)
Q Consensus 80 ~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~ 152 (156)
++++++++...++.|..+.|..+-.+.|.|++..+.|+.+.|.....|.-+-|.-+-++
T Consensus 58 --------------~~~~~~~~~i~~k~l~~~lk~~~~~~~v~i~~~~~~~l~i~~~~~~~~~~~~~~~~li~ 116 (248)
T cd00577 58 --------------RCDEEISLGVNLKSLLKILKCAGNEDCVTLRADDEDPLKILFESSKGDVTSEFSLKLMD 116 (248)
T ss_pred --------------ecCCceEEEEEHHHHHHHHhhCCCCCEEEEEecCCCeEEEEEEcCCCceEEEEEEEccc
Confidence 11134455556666999999887789999999988889999887644444444444443
No 21
>PRK14945 DNA polymerase III subunit beta; Provisional
Probab=96.85 E-value=0.021 Score=49.39 Aligned_cols=100 Identities=20% Similarity=0.333 Sum_probs=68.0
Q ss_pred CCcHHHHHHHHHHhccCC-----eEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecc
Q psy2363 1 MPSGEFARICRDLAQFGE-----SINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLL 75 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd-----~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~ 75 (156)
++..+|.++++-+..+.+ .|.+...++.+++++..+.|.+...+. ++. +|
T Consensus 253 i~~~~L~~~l~r~~~~~~~~~~~~v~l~~~~~~l~~~a~~~~g~a~~~i~-------------~~~----------~G-- 307 (362)
T PRK14945 253 LPAEALREAVNRVAVLSDRNANNRVELLVAEGRLRLTAEGDYGRGQEELA-------------VTQ----------EG-- 307 (362)
T ss_pred EEHHHHHHHHHHHhhhhccCCCccEEEEEECCEEEEEecCCCceEEEEEE-------------EEe----------ec--
Confidence 356789999998887753 278888888999988877665543321 111 01
Q ss_pred cccCCCCCCcccccceEEEec-CceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy2363 76 NFAKAAPLSNQEEEAVTVEMQ-EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP 149 (156)
Q Consensus 76 ~~~k~~~~~~~~~~~V~i~~~-~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAP 149 (156)
+ +|++..|-.+||..+.|+.. ++|+|+|... .|+.+.= .+ .....|.|-|
T Consensus 308 --------------------~~~~~~i~fN~~yl~d~L~~~~--~~v~l~~~~~~~p~~i~~-~~-~~~~~~limP 359 (362)
T PRK14945 308 --------------------SEPAMALAYNARYLLDALAPIE--GDARLGFSGPTSPSVLRS-VD-DPGYLAVVVP 359 (362)
T ss_pred --------------------CCCCEEEEECHHHHHHHHHhCC--CcEEEEECCCCCCEEEEe-CC-CCcEEEEEEe
Confidence 1 24555666666999999876 4799999874 6988753 22 3446788877
No 22
>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=96.75 E-value=0.054 Score=45.94 Aligned_cols=128 Identities=16% Similarity=0.199 Sum_probs=71.9
Q ss_pred HHHHHHHHHHhccCCeEEEEEe-CCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccccc-CCC
Q psy2363 4 GEFARICRDLAQFGESINISCT-KEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFA-KAA 81 (156)
Q Consensus 4 ~~f~~i~rdl~~~gd~v~i~~~-~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~-k~~ 81 (156)
..+++++.=+..+|+.|+|+++ .+.++|..+.|..+..+.++.-..- .....+ ...+....+...+ ...
T Consensus 159 ~~l~~~veR~k~~s~~v~i~an~~G~L~L~v~t~~~~v~t~~~~L~~~-------~~~~~~--~~~~~~~~~~~~~~~~~ 229 (292)
T PF04005_consen 159 KQLRSIVERMKNLSDYVTISANMNGELRLSVETDSVSVETEFRGLENP-------PLDPAE--LNTVDQLPSEDDSDSDQ 229 (292)
T ss_dssp HHHHHHHHHHHTT-SEEEEEE-SSS-EEEEEE-SSEEEEEEE-S---------------------------------SSS
T ss_pred HHHHHHHHHHhccCceEEEEEECCCcEEEEEEeCcEEEEEEECCCCCC-------cccccc--ccccccccccccccccc
Confidence 4688999999999999999998 5669999999987777777432110 000000 0000000000000 000
Q ss_pred CCCcccccceEEEecCceeeeeehhhHHhhhhhcCCC-ceEEEEeeCCCcEEEEEEeCCCeEEEEEEe
Q psy2363 82 PLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLS-NQVCLSMSLDVPLVVEFKIDDIGHIRYYLA 148 (156)
Q Consensus 82 ~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls-~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLA 148 (156)
... .+-.+..+...-+|+|..|.+...++ ++|.+.+..+.-+.+-+-+++.+.|.|||-
T Consensus 230 ~~~--------~~~~~~~sV~Vd~K~~~~~l~~~~~~p~~vi~~I~~~~~~vl~~~~~~~~~l~yyip 289 (292)
T PF04005_consen 230 QEE--------RDPEEFASVRVDIKDLAKFLKSHQLSPSRVICCICHNKALVLHVYLDEDVSLTYYIP 289 (292)
T ss_dssp SS---------------EEEEEEHHHHHHHHHH--S--SEEEEEEETTTEEEEEEEE-TTEEEEEEEE
T ss_pred ccc--------CCCCcEEEEEEEHHHHHHhhCccccCCCEEEEEEccCCeEEEEEEEcCCEEEEEEEe
Confidence 111 12222334445566688888877787 999999999999999999988999999983
No 23
>smart00480 POL3Bc DNA polymerase III beta subunit.
Probab=96.43 E-value=0.036 Score=47.38 Aligned_cols=86 Identities=21% Similarity=0.413 Sum_probs=58.9
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|.++++-+..+.+ -|.++.+++.+++++.+ |.|.+.-.+. ++.+
T Consensus 242 ~~~~L~~ai~rv~~~~~~~~~~v~l~~~~~~l~~~a~d~~~g~~~e~i~-------------~~~~-------------- 294 (345)
T smart00480 242 NRKELKEALKRVALLANEKNRSVKLTLEEGQLKLTANSPEVGEAEEEVD-------------VDYE-------------- 294 (345)
T ss_pred EHHHHHHHHHHHhhhhcCCCceEEEEEeCCEEEEEEcCCccceEEEEEE-------------EEec--------------
Confidence 56789999998887764 47777788888887754 5555543321 1111
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCC-cEEEE
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVE 134 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~-Pl~v~ 134 (156)
.+|++..|-.+||....++.. +++|+|.|.... |+.+.
T Consensus 295 -------------------g~~~~i~fN~~yL~d~l~~~~-~~~v~l~~~~~~~p~~i~ 333 (345)
T smart00480 295 -------------------GEDLEIAFNPKYLLDALKALK-SEEIELKFTDSSSPFLIS 333 (345)
T ss_pred -------------------CCcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEE
Confidence 124444555555999999875 689999999976 99885
No 24
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=96.42 E-value=0.0046 Score=52.26 Aligned_cols=24 Identities=13% Similarity=0.104 Sum_probs=19.8
Q ss_pred CccEEEEecCceeEEeeeeeccccc
Q psy2363 54 EEAVTVEMQEPVSLNFACRYLLNFA 78 (156)
Q Consensus 54 ~~~v~i~~~~~~~~~fs~k~~~~~~ 78 (156)
++.|.|+++++ +++|+++|+.|.+
T Consensus 161 sD~v~i~~~~~-~v~f~a~Gd~~~~ 184 (264)
T PTZ00483 161 GDTVSISMKKD-EMRLETEGEGIKA 184 (264)
T ss_pred CCEEEEEEECC-EEEEEEeecCcEE
Confidence 56889999888 8999999966654
No 25
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=96.24 E-value=0.22 Score=41.73 Aligned_cols=106 Identities=11% Similarity=0.195 Sum_probs=69.0
Q ss_pred cHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCCCC
Q psy2363 3 SGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKAAP 82 (156)
Q Consensus 3 s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~~~ 82 (156)
+..|+++++-+..+=+.++|.++.+|+++.+.-....+=+ .+.+.+..=-. |
T Consensus 9 a~~~k~i~~ai~~lvde~~~~~t~~Gi~~~amD~s~Valv---------------~l~l~~~~F~e----Y--------- 60 (263)
T PLN00057 9 GSLLKKVLEAIKDLVSDANFDCSETGLSLQAMDSSHVALV---------------ALLLRADGFEH----Y--------- 60 (263)
T ss_pred hHHHHHHHHHHHHHhheeEEEEcCCeEEEEEEcCCcEEEE---------------EEEeChhcCeE----E---------
Confidence 5789999999999999999999999999998743222222 22222221111 2
Q ss_pred CCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEE-EEEE
Q psy2363 83 LSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHI-RYYL 147 (156)
Q Consensus 83 ~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l-~~yL 147 (156)
++++++++.+-+..|..+.|.++--+.++|++..+ -+|.+.|.-...|.+ +|.|
T Consensus 61 -----------~~d~~~~~gv~l~~l~kiLk~~~~~d~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l 116 (263)
T PLN00057 61 -----------RCDRNLSMGINLANMSKILKCAGNDDIITIKADDGGDTVTFMFESPKQDRISDFEL 116 (263)
T ss_pred -----------ecCCceEEEEEHHHHHHHHhccCCCCEEEEEecCCCCEEEEEEEcCCCceEEEEEE
Confidence 23334555555555888888888789999987654 356666654445664 3444
No 26
>PHA03383 PCNA-like protein; Provisional
Probab=96.07 E-value=0.17 Score=42.67 Aligned_cols=108 Identities=13% Similarity=0.227 Sum_probs=69.4
Q ss_pred CcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCCC
Q psy2363 2 PSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKAA 81 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~~ 81 (156)
.+..|++|+.-++.+=+.++|.++.+|+++.|.-...-+=+ .+.+.... | -+|
T Consensus 14 ~a~~~K~iieai~~lv~e~~f~~t~~Gi~lqamD~shVaLv---------------~l~L~~~~---F-~~Y-------- 66 (262)
T PHA03383 14 QGSVIKSLFDVLKEILHDVNIFFRPTGVYISALDGAKVSLV---------------HMKLDAES---F-EEY-------- 66 (262)
T ss_pred chHHHHHHHHHHHHHhceEEEEECCCcEEEEEECCCcEEEE---------------EEEeCHHh---C-ceE--------
Confidence 46789999999999999999999999999998843222222 22222210 1 012
Q ss_pred CCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcEEEEEEeCC--C-eEEEEEEe
Q psy2363 82 PLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD--I-GHIRYYLA 148 (156)
Q Consensus 82 ~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~--~-G~l~~yLA 148 (156)
++++++++.+-+..|..+.|.++-.+.++|+...+-|=.+.+.+.+ . ..-+|.|.
T Consensus 67 ------------~~d~~~~iGv~~~~l~KILk~a~~~D~l~l~~~~~~~~~l~i~~~~~~~~~~~~f~l~ 124 (262)
T PHA03383 67 ------------HCDQTYEIGVNVSNMFKLLRTAGSHDSILFRYLKNSPHFLEITIQNFEKNSLTKFQLK 124 (262)
T ss_pred ------------ecCCceEEEEEHHHHHHHHhccCCCCEEEEEecCCCCCEEEEEEEeCCCCcEEEEEEE
Confidence 3344555555555599999999989999998644445344444432 2 33456554
No 27
>PRK14947 DNA polymerase III subunit beta; Provisional
Probab=96.04 E-value=0.099 Score=46.05 Aligned_cols=105 Identities=19% Similarity=0.227 Sum_probs=69.3
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEe-ecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSAT-GDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~-gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|..++|=++.++. .|.+..+++.+++++. .|.|++.-.+. ++.+ |
T Consensus 266 ~r~~l~~al~Rvsi~s~~~~~~v~l~~~~~~l~iss~~~e~G~a~E~i~-------------~~~~----------G--- 319 (384)
T PRK14947 266 DRKECMDALDRILIFNTDNNRCTYFDFGPGELSLSAQGQDVGSATESLE-------------VTYS----------G--- 319 (384)
T ss_pred EHHHHHHHHHHHHHHhcCCCceEEEEEeCCEEEEEEcCCCCceEEEEEE-------------EEec----------C---
Confidence 34688899988888853 4888888888888775 35665543331 1111 1
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee-ccCCC
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP-KIESD 154 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAP-ki~~e 154 (156)
+|++..|--+||..+.++.. +++|.|+|... .|+.++ ..++. ...|.+-| |+.++
T Consensus 320 --------------------e~~~I~fN~~YL~d~L~~i~-~~~i~l~~~~~~~p~~i~-~~~~~-~~~~lIMPvr~~~~ 376 (384)
T PRK14947 320 --------------------DIKKIAFPTKNLIEILGHFQ-SDKITLTLTGAEGPCGIT-GEDDP-DYLVIVMPMKIVEE 376 (384)
T ss_pred --------------------CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEE-cCCCC-ceEEEEeceEECCC
Confidence 23344444455999999864 68999999885 699886 33333 45588999 56544
Q ss_pred C
Q psy2363 155 D 155 (156)
Q Consensus 155 ~ 155 (156)
+
T Consensus 377 ~ 377 (384)
T PRK14947 377 T 377 (384)
T ss_pred c
Confidence 3
No 28
>PRK14940 DNA polymerase III subunit beta; Provisional
Probab=95.43 E-value=0.31 Score=42.38 Aligned_cols=99 Identities=15% Similarity=0.137 Sum_probs=65.8
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEe-ecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSAT-GDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~-gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|..++|-+..+.+ .|.+..+++.+++++. .|.|++.-.+. ++.+ |
T Consensus 259 ~~~~L~~al~R~~~~~~~~~~~v~l~~~~~~l~l~~~~~e~G~~~e~i~-------------~~~~----------G--- 312 (367)
T PRK14940 259 GRVELMEALKRVSLLVEQKSRRIFLTIQQGLLTLSSQENEIGDAQEEIA-------------CAYT----------G--- 312 (367)
T ss_pred EHHHHHHHHHHHHHHhccCCceEEEEEeCCEEEEEEcCCCCccEEEEEE-------------EEec----------C---
Confidence 45788889988888742 4778888888888765 35565543321 1111 1
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP 149 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAP 149 (156)
+|++..|-.+||....++.. +++|.|+|... .|+.+.=. + .....|.+-|
T Consensus 313 --------------------e~~~I~fN~~yl~d~L~~i~-~~~v~l~~~~~~~p~~i~~~-~-~~~~~~liMP 363 (367)
T PRK14940 313 --------------------EEEVIALNYLYLEEPLKVFT-SKEVQVEFTEAAKAITLRPV-P-ETDCFHIIMP 363 (367)
T ss_pred --------------------CcEEEEECHHHHHHHHhCCC-CCEEEEEECCCCCCEEEEeC-C-CCcEEEEEEe
Confidence 23444555555999999875 68999999885 49987642 2 3456688888
No 29
>PRK14941 DNA polymerase III subunit beta; Provisional
Probab=94.84 E-value=0.47 Score=41.37 Aligned_cols=101 Identities=15% Similarity=0.254 Sum_probs=64.1
Q ss_pred CcHHHHHHHHHHhccC--CeEEEEEeCCeEEEEEee-cce-eEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccc
Q psy2363 2 PSGEFARICRDLAQFG--ESINISCTKEGVKFSATG-DIG-SANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNF 77 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~g--d~v~i~~~~~~v~f~~~g-d~~-~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~ 77 (156)
+..+|..++|-+..+. +.|++...++.+++++.+ |.| .+.-.+ .++.+ |
T Consensus 263 ~~~~L~~al~rv~~~~~~~~v~~~~~~~~l~l~~~~~~~g~~~~e~i-------------~~~~~----------G---- 315 (374)
T PRK14941 263 NRSNIYDSVKRVGRFSSIGDIKISVEGSVLKVMAENTNEGESAQEEL-------------PCSYT----------G---- 315 (374)
T ss_pred eHHHHHHHHHHHHHHccCCceEEEEECCEEEEEEECcccccceEEEE-------------EeEeC----------C----
Confidence 4678889998887764 358888888888887764 343 222111 11111 1
Q ss_pred cCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEE-eCCCeEEEEEEee
Q psy2363 78 AKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFK-IDDIGHIRYYLAP 149 (156)
Q Consensus 78 ~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~-i~~~G~l~~yLAP 149 (156)
++++..|=-+||..+.++.. +++|.|+|.+. .|+.++=. -.+.....|.+.|
T Consensus 316 -------------------~~~~I~fN~~yl~d~L~~~~-~~~v~l~~~~~~~p~~i~~~~~~~~~~~~~limP 369 (374)
T PRK14941 316 -------------------EDITIGFNSKFIEAALAHLD-EEEIIIELSSPTTAVIFKPKKEEENDDLIILVMP 369 (374)
T ss_pred -------------------CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEecCCCCCCCceEEEEee
Confidence 23444444455999999865 68999999885 59888621 1123457788888
No 30
>PRK14943 DNA polymerase III subunit beta; Provisional
Probab=94.81 E-value=0.59 Score=40.40 Aligned_cols=98 Identities=11% Similarity=0.162 Sum_probs=63.6
Q ss_pred CcHHHHHHHHHHhccC----CeEEEEEeCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFG----ESINISCTKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~g----d~v~i~~~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
+..+|.++++-+..+. ..|.+..+++.+.+++.. |.|++.-.+ .++.+ |
T Consensus 268 ~~~~l~~al~r~~~~~~~~~~~v~l~~~~~~l~i~~~~~e~G~~~e~i-------------~~~~~----------G--- 321 (374)
T PRK14943 268 ERELLLECVHRAALVSSDKSNSVKLKFSENLLEIASSSEGVGEAHESM-------------AITYS----------G--- 321 (374)
T ss_pred EHHHHHHHHHHHHhhcccCCceEEEEEECCEEEEEEcCCCCceEEEEE-------------EEEec----------C---
Confidence 4578888888877664 247788888888887753 455543222 11111 1
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEeec
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~-~~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
+|++..|=.+||....|+.. +++|+|+|.. ..|+.+.= +.. ..|.|.|-
T Consensus 322 --------------------~~~~i~fN~~yl~d~l~~~~-~~~v~l~~~~~~~p~~i~~---~~~-~~~limP~ 371 (374)
T PRK14943 322 --------------------PELQVAFNPDFFMAPLKALT-KDEVFFELKDEMSPGVFKT---LDE-FLCVIMPM 371 (374)
T ss_pred --------------------CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEec---CCC-eEEEEEee
Confidence 23444455555999999865 6899999988 56998872 233 46788873
No 31
>PRK06673 DNA polymerase III subunit beta; Validated
Probab=94.76 E-value=2.6 Score=36.85 Aligned_cols=66 Identities=21% Similarity=0.326 Sum_probs=49.1
Q ss_pred CCCCcccccceEEEe--cC-ceeeeeehhhHHhhhhhcCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEee
Q psy2363 81 APLSNQEEEAVTVEM--QE-PVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAP 149 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~--~~-~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~-~~Pl~v~f~i~~~G~l~~yLAP 149 (156)
.+..+++++.+.++. .+ |++..|--+||..+.++.. +++|.|+|.. ..|+.++= .+.....|.+.|
T Consensus 303 ~~e~G~a~e~i~~~~~~Ge~~~~I~fN~~YLld~L~~i~-~e~v~l~~~~~~~p~li~~--~~~~~~~~limP 372 (376)
T PRK06673 303 ASQIGKISETQQIDAIQGEKQLNISFDGRFMLDALRAIK-EETVTLSFSGSMRPILIEA--GTQSAAIHLISP 372 (376)
T ss_pred CCCCCcEEEEEEeeecCCCccEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc--CCCCceEEEEEe
Confidence 334466677777763 34 8999999999999999875 7899999987 46988753 223346688888
No 32
>PRK14942 DNA polymerase III subunit beta; Provisional
Probab=94.38 E-value=0.88 Score=39.87 Aligned_cols=99 Identities=18% Similarity=0.343 Sum_probs=63.7
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeeccc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLN 76 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~ 76 (156)
...+|..++|-+..+.+ .|++..+++.+++++.. +.|++...+ .++.+.
T Consensus 266 ~r~~l~~al~Rv~~~~~~~~~~v~l~~~~~~l~isa~~~~~g~~~e~i-------------~~~~~G------------- 319 (373)
T PRK14942 266 SKEEFQVSLRQVLTAAEEPSRQVRLTFSKNNLNLFAQTLGASEADINM-------------PIEYSG------------- 319 (373)
T ss_pred eHHHHHHHHHHHHHHhhcCCceEEEEEeCCEEEEEEeCCCcceEEEEE-------------EEEecC-------------
Confidence 35788999998888752 47788888888887764 344443222 111111
Q ss_pred ccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEee
Q psy2363 77 FAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAP 149 (156)
Q Consensus 77 ~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~-~~Pl~v~f~i~~~G~l~~yLAP 149 (156)
+|++..|=-+||....++.. +++|.|.|.. ..|+.+. .. +.....|.|-|
T Consensus 320 --------------------~~~~I~fN~~ylld~L~~i~-~~~v~l~~~~~~~P~~i~-~~-~~~~~~~liMP 370 (373)
T PRK14942 320 --------------------EEITIAFKGEYLMDIFRSID-DNEVKIEFSDSSSPVIFK-DP-SDPEFISVIMP 370 (373)
T ss_pred --------------------CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEE-eC-CCCceEEEEee
Confidence 23334444445999999864 6899999988 5598874 22 24456688888
No 33
>KOG1636|consensus
Probab=94.29 E-value=0.068 Score=45.04 Aligned_cols=25 Identities=12% Similarity=0.222 Sum_probs=22.7
Q ss_pred CCccEEEEecCceeEEeeeeeccccc
Q psy2363 53 EEEAVTVEMQEPVSLNFACRYLLNFA 78 (156)
Q Consensus 53 ~~~~v~i~~~~~~~~~fs~k~~~~~~ 78 (156)
-+++|.|.+++. +++|+.+|++|+|
T Consensus 154 f~Dsv~I~~tke-gv~F~~~Gdig~a 178 (260)
T KOG1636|consen 154 FSDSVVISATKE-GVKFSAKGDIGTA 178 (260)
T ss_pred hcCeEEEEEecc-eeEEEecccccce
Confidence 356899999998 9999999999999
No 34
>PRK07761 DNA polymerase III subunit beta; Validated
Probab=94.26 E-value=0.75 Score=39.91 Aligned_cols=101 Identities=20% Similarity=0.328 Sum_probs=63.6
Q ss_pred CcHHHHHHHHHHhccC---CeEEEEEeCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccc
Q psy2363 2 PSGEFARICRDLAQFG---ESINISCTKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNF 77 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~g---d~v~i~~~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~ 77 (156)
+..+|.++++-+..+. ..|.+...++.+++++.. |.|.+.-.+ .++.+.
T Consensus 262 ~~~~L~~~l~r~~~~~~~~~~v~l~~~~~~l~l~~~~~~~G~~~e~i-------------~~~~~G-------------- 314 (376)
T PRK07761 262 ETAPLIEAIKRVALVAERNAPVRLEFSDGQLTLSAGGGDDAQASEAL-------------EADLTG-------------- 314 (376)
T ss_pred EHHHHHHHHHHHHHHhcCCceEEEEEeCCEEEEEEcCCCcceEEEEE-------------EEEecC--------------
Confidence 4578888888777664 347777777888887643 455443222 111111
Q ss_pred cCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCC----CeEEEEEEee
Q psy2363 78 AKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDD----IGHIRYYLAP 149 (156)
Q Consensus 78 ~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~----~G~l~~yLAP 149 (156)
++++..|=.+||....|+.. +++|+|.|... .|+.+.=.-++ .-...|.|.|
T Consensus 315 -------------------e~~~i~fN~~yl~d~L~~~~-~~~v~l~~~~~~~p~~i~~~~~~~~~~~~~~~~limP 371 (376)
T PRK07761 315 -------------------EDLTIAFNPQYLLDGLSALH-TPRVRFGFTTPSKPALLTGQPEDDGEPSTDYRYLLMP 371 (376)
T ss_pred -------------------CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEecCcccccCCCCceEEEEEe
Confidence 23444444455999999875 68999999985 59877522111 1357888888
No 35
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=94.21 E-value=1.4 Score=35.62 Aligned_cols=109 Identities=16% Similarity=0.281 Sum_probs=64.3
Q ss_pred cHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCCCC
Q psy2363 3 SGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKAAP 82 (156)
Q Consensus 3 s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~~~ 82 (156)
.+.|+++++-+..+-+.|.++++++++++.|.-...-+-+.+. +....--.|
T Consensus 9 ~~~lk~i~~~i~~l~~~v~~~~~~~~l~~~atD~~Rla~~~~~---------------~~~~~f~~~------------- 60 (247)
T PRK01115 9 AKDFKYIIDAISKLVDEAKFKFTEDGIRLRALDPAKVAMVDLE---------------LPKEAFEEY------------- 60 (247)
T ss_pred hHHHHHHHHHHHHHhceEEEEECCCcEEEEEECCccEEEEEEE---------------eCHHhCccE-------------
Confidence 5689999999999999999999999999987632222222221 111000011
Q ss_pred CCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEeeccCC
Q psy2363 83 LSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAPKIES 153 (156)
Q Consensus 83 ~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~-~~Pl~v~f~i~~~G~l~~yLAPki~~ 153 (156)
++..|.++.-.++.|..+.|..+-.+.|+|.+.. +-++.+++ ++ +..+.+.-+.++.
T Consensus 61 -----------~~~~~~~~~v~l~~l~~il~~~~~~~~v~i~~~~~~~~l~~~~--~~-~~~~~~~~~Lieg 118 (247)
T PRK01115 61 -----------EVDEEEKIGVDLEDLKKILKRAKKGDKLELELDEEENKLKITF--GG-EKTREFSLPLLDV 118 (247)
T ss_pred -----------ecCCCeEEEEEHHHHHHHHhhCCCCCEEEEEEcCCCCEEEEEE--ec-CcEEEEEEEeecc
Confidence 1222333444444477777765556789999832 34566555 33 5555555555543
No 36
>PRK14946 DNA polymerase III subunit beta; Provisional
Probab=94.15 E-value=0.71 Score=40.46 Aligned_cols=98 Identities=14% Similarity=0.158 Sum_probs=64.3
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCCeEEEEEee-cceeEEEEEe-ecCCCCCCCccEEEEecCceeEEeeeeecc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKEGVKFSATG-DIGSANIKLA-QTGNVDKEEEAVTVEMQEPVSLNFACRYLL 75 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~~v~f~~~g-d~~~~~i~l~-~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~ 75 (156)
+..+|..++|=++.+.. .|++..+++.+++++.. |.|++...+. ... .+ .++..+.|..+|
T Consensus 258 ~r~~l~~al~Rvsl~a~~~~~~v~l~~~~~~l~lss~~~e~G~a~e~i~~~~~----------~~-Ge~~~IafN~~Y-- 324 (366)
T PRK14946 258 EKKEILDLIDKATIITPGKDNVINFSLSKNELKGYISQYESGQSNVKTKNVLR----------FS-GELAQVNVNYKY-- 324 (366)
T ss_pred EHHHHHHHHHHhheeecCCCceEEEEEcCCEEEEEEECCCCceEEEEeccccc----------cc-CCcEEEEEcHHH--
Confidence 34688999998888863 38888888999997664 6777665431 100 00 122355555555
Q ss_pred cccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEe
Q psy2363 76 NFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLA 148 (156)
Q Consensus 76 ~~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLA 148 (156)
|....++.. ++|.|+|... .|+.++ -.+.....|.+|
T Consensus 325 --------------------------------L~D~L~~i~--~~v~l~~~~~~~p~~i~--~~~~~~~~~li~ 362 (366)
T PRK14946 325 --------------------------------LKDAISVFD--KVINIFINEKKTKMLIV--SPEKKEICQLVG 362 (366)
T ss_pred --------------------------------HHHHHHhCC--CeEEEEECCCCCCEEEE--CCCCCCeEEEEE
Confidence 999999987 5699999875 598773 123344555555
No 37
>TIGR00663 dnan DNA polymerase III, beta subunit. University).
Probab=93.31 E-value=1.4 Score=37.71 Aligned_cols=99 Identities=21% Similarity=0.360 Sum_probs=61.3
Q ss_pred CcHHHHHHHHHHhccCC----eEEEEEeCC-eEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecc
Q psy2363 2 PSGEFARICRDLAQFGE----SINISCTKE-GVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLL 75 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd----~v~i~~~~~-~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~ 75 (156)
+..+|..+++-+..+.+ .|.+..+++ .+++++.+ +.|.+...+. ++.+
T Consensus 259 ~~~~L~~al~rv~~~~~~~~~~v~~~~~~~~~l~i~~~~~~~g~~~e~i~-------------~~~~------------- 312 (367)
T TIGR00663 259 NREELKEAIKRVSLLADEKRNLVLTLSENGKKLKESSDTQEIGEAEEEIE-------------VAYD------------- 312 (367)
T ss_pred eHHHHHHHHHHHHHHhcCCCceEEEEECCCCeEEEEEcCCCCccEEEEEE-------------EEec-------------
Confidence 45678888888877653 466666666 77776653 4444443221 1111
Q ss_pred cccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeC-CCcEEEEEEeCCCeEEEEEEee
Q psy2363 76 NFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHIRYYLAP 149 (156)
Q Consensus 76 ~~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~-~~Pl~v~f~i~~~G~l~~yLAP 149 (156)
.+|++..|-.+||....++.. +++|+|.+.. ..|+.+.= .+.-...|.|.|
T Consensus 313 --------------------g~~~~i~fN~~yL~d~l~~~~-~~~v~l~~~~~~~p~~i~~--~~~~~~~~limP 364 (367)
T TIGR00663 313 --------------------GEDLVIAFNIKYLLDALKALK-SKEIQIQFNDPSKPLLIEP--ENDEKITYLIMP 364 (367)
T ss_pred --------------------CCcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEec--CCCCcEEEEEEe
Confidence 124444455555999999764 5899999977 55987732 223346688888
No 38
>PRK14944 DNA polymerase III subunit beta; Provisional
Probab=92.19 E-value=2.4 Score=37.19 Aligned_cols=101 Identities=13% Similarity=0.276 Sum_probs=64.6
Q ss_pred CcHHHHHHHHHHhccCC-------eEEEEEe-CCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeee
Q psy2363 2 PSGEFARICRDLAQFGE-------SINISCT-KEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACR 72 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd-------~v~i~~~-~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k 72 (156)
+..+|..++|=++.+.. .|++... ++.+.+++.. |.|++.-.+.. +.++ .++.++.|..+
T Consensus 263 ~r~~l~~al~Rvslls~~~~~~~~~v~l~~~~~~~l~iss~~~e~G~a~e~i~~----------~~~~-Ge~~~I~fN~~ 331 (375)
T PRK14944 263 NKDDLMKALERVSLLFSKEQNNTNVVKFILTKEKSIEISSSNESLGTALEKIIP----------LKVS-ANSFEIAFNAK 331 (375)
T ss_pred eHHHHHHHHHHHHHHhccccCCCceEEEEEcCCCEEEEEEcCcccCeEEEEEec----------cccc-CCcEEEEEcHH
Confidence 35689999999999863 2888885 7788887754 66766432210 0000 12234455555
Q ss_pred ecccccCCCCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeec
Q psy2363 73 YLLNFAKAAPLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 73 ~~~~~~k~~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
| |....++.. +++|.|.|... .|+.++= .++. ...|.+-|-
T Consensus 332 Y----------------------------------L~d~L~~i~-~~~v~i~~~~~~~p~~i~~-~~~~-~~~~lImPv 373 (375)
T PRK14944 332 Y----------------------------------LEDILKVLS-VKEIVFYFDSPLKPFIVTT-LEKD-SSIHLILPI 373 (375)
T ss_pred H----------------------------------HHHHHhcCC-CCEEEEEECCCCCCEEEEc-CCCC-ceEEEEEeC
Confidence 5 999999865 68999999874 5987743 2333 345777773
No 39
>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=91.59 E-value=0.72 Score=37.88 Aligned_cols=56 Identities=20% Similarity=0.296 Sum_probs=37.4
Q ss_pred EEecCceeeeeehhhHHhhhhhc-CCCceEEEEee-CCCcEEEEEEeCCCeEEEEEEe
Q psy2363 93 VEMQEPVSLNFACRYLLNFAKAA-PLSNQVCLSMS-LDVPLVVEFKIDDIGHIRYYLA 148 (156)
Q Consensus 93 i~~~~~V~l~Fa~~~L~~f~Kaa-~ls~~V~l~l~-~~~Pl~v~f~i~~~G~l~~yLA 148 (156)
.++.+++.++|.+|-++.+...+ .++..|.+.|+ .+.|+.+++.=.+.=.+.|.||
T Consensus 193 ~~~~~~~~itF~lKefka~l~~ae~~~~~i~~~f~~pG~Pi~~~~~~~~~~~~~~vla 250 (252)
T PF04139_consen 193 YNVQEDTDITFSLKEFKAILSFAESLSLPISIYFDNPGRPILFELEQNDHFEAEFVLA 250 (252)
T ss_dssp EE--TT-EEEEEHHHHHHHHHHHHHTTEEEEEEESSTTS-EEEEEE--SSEEEEEEE-
T ss_pred EEcCCCCEEEEEeHHHHHHHHHHHhcCCcEEEEECCCCCcEEEEECCCCcEEEEEEEE
Confidence 34555677888877788888754 56778999995 5889999999324556788887
No 40
>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=90.82 E-value=3.9 Score=34.62 Aligned_cols=99 Identities=16% Similarity=0.256 Sum_probs=63.0
Q ss_pred HHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEE--ecCc-eeEEeeeeecccccCC
Q psy2363 4 GEFARICRDLAQFGESINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVE--MQEP-VSLNFACRYLLNFAKA 80 (156)
Q Consensus 4 ~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~--~~~~-~~~~fs~k~~~~~~k~ 80 (156)
..|++++.-++.++..+.+..+++.+.|...++.+. ++.+- +... +=-.|.+++
T Consensus 11 ~~~~~~~~~~~kl~k~~vlrlt~~~l~~i~~~~~~~----------------g~qvw~~l~~~~~F~~y~i~s------- 67 (292)
T PF04005_consen 11 KLFKKFVSTISKLGKRCVLRLTPERLHFISTSDDSD----------------GIQVWCELPQDSLFSEYRIQS------- 67 (292)
T ss_dssp HHHHHHHHHHHHH-SEEEEEE-SSEEEEEEE-SSTT------------------EEEEEEEGGGT-SEEEEE--------
T ss_pred HHHHHHHHHHHHhhCEEEEEEeCCEEEEEEecCCCC----------------eEEEEEEEChhhcCcccEEEe-------
Confidence 579999999999999999999999999998865111 12222 1111 111333333
Q ss_pred CCCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCC--Cc-EEEEEEeC
Q psy2363 81 APLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD--VP-LVVEFKID 138 (156)
Q Consensus 81 ~~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~--~P-l~v~f~i~ 138 (156)
.-++-|.+++-+.+|....|.+.-++.++|+|.+. .| |.+++...
T Consensus 68 -------------~~~N~I~le~~~~~L~raLrs~~~a~~~~ikL~kk~~~p~L~~~~~~~ 115 (292)
T PF04005_consen 68 -------------ASENEIYLEVNIDSLLRALRSADNASSVKIKLTKKGRMPCLSFEITGT 115 (292)
T ss_dssp -------------SSSS-EEEEEEHHHHHHHHCTCSSCSEEEEEEE-S-SSSEEEEEEEE-
T ss_pred -------------CCCCEEEEEEcHHHHHHHHHhhccCceeEEehhhccCCcEEEEEEEee
Confidence 12256777788888888888888888999999984 78 55555543
No 41
>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=84.44 E-value=3.8 Score=33.62 Aligned_cols=41 Identities=29% Similarity=0.516 Sum_probs=32.9
Q ss_pred HHHHHHHHhccCCeEEEEEeCCeEEEEEeeccee--EEEEEee
Q psy2363 6 FARICRDLAQFGESINISCTKEGVKFSATGDIGS--ANIKLAQ 46 (156)
Q Consensus 6 f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~--~~i~l~~ 46 (156)
|.|++.-|+.|||.|.|++.++++.+++-....+ +.+.+.+
T Consensus 1 f~ral~~Lskigeel~ie~~~~~L~l~avNss~Sa~~~~~F~~ 43 (252)
T PF04139_consen 1 FARALQCLSKIGEELYIEITEDGLSLRAVNSSRSAYAQFRFSK 43 (252)
T ss_dssp HHHHHHHHHTT-SEEEEEEETTEEEEEEE-TTSSEEEEEEETG
T ss_pred CHHHHHHHHhhCCeEEEEEcCCeEEEEEECccccEEEEEEECh
Confidence 7899999999999999999999999999876544 4566554
No 42
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=70.86 E-value=6.5 Score=29.59 Aligned_cols=21 Identities=29% Similarity=0.433 Sum_probs=11.7
Q ss_pred eehhhHHhhhh----hcCCCceEEE
Q psy2363 103 FACRYLLNFAK----AAPLSNQVCL 123 (156)
Q Consensus 103 Fa~~~L~~f~K----aa~ls~~V~l 123 (156)
|+-|||+|++| --.|.+-+.+
T Consensus 64 fsKrYLKYLTKKyLKK~~LRdwlrV 88 (112)
T PF01776_consen 64 FSKRYLKYLTKKYLKKNNLRDWLRV 88 (112)
T ss_dssp -SHHHHHHHHHHHHTTSSSTTTEEE
T ss_pred ccHHHHHHHHHHHHhhcchhheEEE
Confidence 34444777664 4566665554
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=70.59 E-value=63 Score=27.11 Aligned_cols=34 Identities=21% Similarity=0.195 Sum_probs=22.8
Q ss_pred eeehhhHHhhhhhcC-CCceEEEEeeCCCcEEEEEEeC
Q psy2363 102 NFACRYLLNFAKAAP-LSNQVCLSMSLDVPLVVEFKID 138 (156)
Q Consensus 102 ~Fa~~~L~~f~Kaa~-ls~~V~l~l~~~~Pl~v~f~i~ 138 (156)
.|-.+||..+.|..+ -.+.|+|.+..+ ++.+..+
T Consensus 194 ~i~~~~l~~l~k~l~~~~~~v~i~~~~~---~l~i~~~ 228 (365)
T cd00140 194 IVPRKTLNELLKLLEDDDEEVEISISEN---QILFKLG 228 (365)
T ss_pred EEechHHHHHHHhccCCCCcEEEEEeCC---EEEEEEC
Confidence 344455999998766 367899998775 4555543
No 44
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=68.46 E-value=11 Score=28.85 Aligned_cols=17 Identities=29% Similarity=0.409 Sum_probs=9.4
Q ss_pred hhHHhhhh----hcCCCceEE
Q psy2363 106 RYLLNFAK----AAPLSNQVC 122 (156)
Q Consensus 106 ~~L~~f~K----aa~ls~~V~ 122 (156)
|||+|++| -..|-|-+.
T Consensus 80 RYLKYLTKKyLKK~~LRDwlR 100 (122)
T PTZ00198 80 RYLKYLTKKYLKKKQLRDFLR 100 (122)
T ss_pred HHHHHHHHHHHhhhhhhheEE
Confidence 33888775 345555443
No 45
>cd02974 AhpF_NTD_N Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The N-terminal TRX-fold subdomain of AhpF NTD is redox inactive, but is proposed to contain an important residue that aids in the catalytic function of the redox-active CXXC motif contained in the C-terminal TRX-
Probab=67.64 E-value=16 Score=26.10 Aligned_cols=43 Identities=23% Similarity=0.243 Sum_probs=26.9
Q ss_pred HHhhh-hhcCCCceEEEEeeC---CCcEEEEEEeCCCeEEEEEEeec
Q psy2363 108 LLNFA-KAAPLSNQVCLSMSL---DVPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 108 L~~f~-Kaa~ls~~V~l~l~~---~~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
++.|. -.+.+|+.+++...+ ..|-..=..=+..+.|||+=.|-
T Consensus 36 ~~~ll~e~a~lSdkI~~~~~~~~~~~P~~~i~~~~~~~gIrF~GiP~ 82 (94)
T cd02974 36 LLELLEEIASLSDKITLEEDNDDERKPSFSINRPGEDTGIRFAGIPM 82 (94)
T ss_pred HHHHHHHHHHhCCceEEEEecCCCCCCEEEEecCCCcccEEEEecCC
Confidence 66666 477889999998765 34633222111134599998883
No 46
>KOG3999|consensus
Probab=65.73 E-value=90 Score=27.06 Aligned_cols=46 Identities=4% Similarity=0.190 Sum_probs=38.2
Q ss_pred cHHHHHHHHHHhccCCeEEEEEe-CCeEEEEEeecceeEEEEEeecC
Q psy2363 3 SGEFARICRDLAQFGESINISCT-KEGVKFSATGDIGSANIKLAQTG 48 (156)
Q Consensus 3 s~~f~~i~rdl~~~gd~v~i~~~-~~~v~f~~~gd~~~~~i~l~~~~ 48 (156)
..-+++.+.-+.++|+.++++++ .+.+.++++-+.+...+.+..-.
T Consensus 165 l~~lk~~vdk~Knis~~l~~tan~~GeLqv~v~~e~~~vtt~Fq~L~ 211 (284)
T KOG3999|consen 165 LNQLKSFVDKMKNISDVLNVTANKSGELQVSVSIELIRVTTEFQDLS 211 (284)
T ss_pred HHHHHHHHHHhhcccceEEEEEecCceEEEEEEEeeEEEEEEhhhcc
Confidence 35578899999999999999998 66699999988888888876533
No 47
>KOG2810|consensus
Probab=63.07 E-value=11 Score=33.93 Aligned_cols=115 Identities=21% Similarity=0.323 Sum_probs=68.0
Q ss_pred HHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecc--eeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeecccccCCC
Q psy2363 4 GEFARICRDLAQFGESINISCTKEGVKFSATGDI--GSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYLLNFAKAA 81 (156)
Q Consensus 4 ~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~--~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~~~~~k~~ 81 (156)
..++|++--|+.+|+.|.|+++++++.+++-.+. +-+.+.+.+.--. ..++..+ .+.|.+
T Consensus 11 r~lArai~sLSri~~ev~iev~~~~l~l~t~N~srSa~~~~~f~~~FF~-------~ydf~~~-q~~~~~---------- 72 (394)
T KOG2810|consen 11 RVLARAIVSLSRIGEEVTIEVSPLGLCLKTVNESRSAFSCATFKEMFFG-------VYDFQPP-QADFGC---------- 72 (394)
T ss_pred HHHHHHhhhHhhhcceeEEEEcCCeeEEEecccccchhhhhhhhHhhcc-------chhcCCc-cccchh----------
Confidence 3578899999999999999999999999977542 2233443332100 0011111 111111
Q ss_pred CCCcccccceEEEecCceeeeeehhhHHhhhhhcCCCceEEEEeeCCCcE-EEEEEeCC-CeEEEEEEeeccCC
Q psy2363 82 PLSNQEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPL-VVEFKIDD-IGHIRYYLAPKIES 153 (156)
Q Consensus 82 ~~~~~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~~Pl-~v~f~i~~-~G~l~~yLAPki~~ 153 (156)
-|.++|.|+=++.++-.+. +..+++..-.+.|= ++.|+|.. .|-.++|+|--.+.
T Consensus 73 ----------------~v~mK~clsvFRgl~~~~~-~~~~~~~~~~d~~s~rl~~~l~ckl~~~kt~~atl~d~ 129 (394)
T KOG2810|consen 73 ----------------KVSMKFCLSVFRGLLFFAE-STHLCESILFDAPSRRLIFTLKCKLGVGKTILATLSDT 129 (394)
T ss_pred ----------------hhhHHHHHHHHhhhccccc-ccceeeeecCCCCCcceEEEehhhhcccceEEEEeecc
Confidence 1556677444444333222 34455556667776 77778876 78889999865543
No 48
>PF06228 ChuX_HutX: Haem utilisation ChuX/HutX; InterPro: IPR010413 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2OVI_A 2PH0_B 3FM2_B 2HQV_A.
Probab=61.34 E-value=17 Score=28.13 Aligned_cols=39 Identities=23% Similarity=0.549 Sum_probs=31.2
Q ss_pred CcHHHHHHHHHHhccCCeEEEEEeCCeEEEEEeecceeEE
Q psy2363 2 PSGEFARICRDLAQFGESINISCTKEGVKFSATGDIGSAN 41 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd~v~i~~~~~~v~f~~~gd~~~~~ 41 (156)
+.+.|+.+..+|...|+ |+.-+..+.+.|..+|..-++.
T Consensus 25 ~g~~f~~ll~~l~~wG~-vt~Iv~~~~~I~E~kg~~p~g~ 63 (141)
T PF06228_consen 25 PGERFDELLEELAGWGE-VTFIVHTDGAIFEVKGPLPKGK 63 (141)
T ss_dssp EGGGHHHHHHHHTTSSE-EEEEEE-SSEEEEEEEES-SEE
T ss_pred cHHHHHHHHHHhhccCc-eEEEEEcCCEEEEEecCCCCCe
Confidence 46889999999999998 8888888888999888765443
No 49
>PF09095 DUF1926: Domain of unknown function (DUF1926); InterPro: IPR015179 Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) []. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate. This entry represents a domain found in prokaryotic alpha-amylase (3.2.1.1 from EC) and 4-alpha-glucanotransferase (2.4.1.25 from EC). This domain adopts a beta-sandwich fold, in which two layers of anti-parallel beta-sheets are arranged in a nearly parallel fashion. The exact function of this domain is, as yet, unknown, however it has been proposed that it may play a role in transglycosylation reactions []. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0003824 catalytic activity, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 1K1X_B 1K1W_A 1K1Y_A.
Probab=50.08 E-value=1.1e+02 Score=25.95 Aligned_cols=55 Identities=22% Similarity=0.392 Sum_probs=32.3
Q ss_pred eEEEEEeCCeEEEEEeecceeEEEEEeecCCCCCCCccEEEEec---CceeEEeeeee
Q psy2363 19 SINISCTKEGVKFSATGDIGSANIKLAQTGNVDKEEEAVTVEMQ---EPVSLNFACRY 73 (156)
Q Consensus 19 ~v~i~~~~~~v~f~~~gd~~~~~i~l~~~~~~~~~~~~v~i~~~---~~~~~~fs~k~ 73 (156)
.-.++..++.++|...|-+....+.|++.....+..=.|.++++ .+....|.++.
T Consensus 125 ~y~~~~~~~~v~f~r~G~~~~~~~~l~K~y~l~~~~l~V~Y~l~~~~~~~~~~f~vEi 182 (278)
T PF09095_consen 125 PYELEVNRDEVTFERDGGVEGHPITLEKRYRLTKNGLQVDYRLTESPEPISLLFGVEI 182 (278)
T ss_dssp --EEEEESSEEEEEEEEEESEEEEEEEEEEEEETTEEEEEEEEE-ESS---EEEEEEE
T ss_pred ceEEEecCCceEEEEecccccCceEEEEEEEEcCCEEEEEEEEEECCCCcceEEEEEE
Confidence 44667778889999999988888888886443222223444444 33445555554
No 50
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]
Probab=48.55 E-value=1.9e+02 Score=25.30 Aligned_cols=50 Identities=22% Similarity=0.468 Sum_probs=35.3
Q ss_pred ceeeeeehhhHHhhhhhcCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeec
Q psy2363 98 PVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 98 ~V~l~Fa~~~L~~f~Kaa~ls~~V~l~l~~~-~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
+.++.|=..|+....++-+ ++.|.+.|.+. .|+.++- .+.-...|.|.|-
T Consensus 312 ~~~I~fn~~ylld~l~~~~-~~~v~~~~~~~~~p~~i~~--~~~~~~~~~imP~ 362 (364)
T COG0592 312 ELKIGFNLAYLLDVLKALD-SEEVQFGFNDSSSPFLIRP--EENDDFKYLIMPM 362 (364)
T ss_pred eEEEEECHHHHHHHHhcCC-CCeEEEEEcCCCCcEEEEe--CCCCCceEEEEEe
Confidence 3444555555999999766 89999999874 4677766 3345588888883
No 51
>COG3110 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.02 E-value=30 Score=28.83 Aligned_cols=41 Identities=22% Similarity=0.436 Sum_probs=31.5
Q ss_pred hhhhcCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeeccCCCC
Q psy2363 111 FAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 155 (156)
Q Consensus 111 f~Kaa~ls~~V~l~l~~~~Pl~v~f~i~~~G~l~~yLAPki~~e~ 155 (156)
+.+.-.+.+...|..|+ |+.+.|+=. .-.++|. +||++++.
T Consensus 63 v~~~~~~g~d~~ly~S~--plIvtF~~~-n~~lv~~-~P~~rn~r 103 (216)
T COG3110 63 VIKTIRLGSDRRLYISP--PLIVTFNAQ-NIDLVFF-LPRLRNER 103 (216)
T ss_pred EecccCCCCceeEeecC--CEEEEEccc-chhheee-ccccccch
Confidence 34445666888888888 999999854 5678888 99998765
No 52
>PRK15317 alkyl hydroperoxide reductase subunit F; Provisional
Probab=30.97 E-value=1.1e+02 Score=27.73 Aligned_cols=57 Identities=16% Similarity=0.194 Sum_probs=34.2
Q ss_pred EecCceeeeeehh------hHHhhh-hhcCCCceEEEEeeC---CCcEEEEEEeCCCeEEEEEEeec
Q psy2363 94 EMQEPVSLNFACR------YLLNFA-KAAPLSNQVCLSMSL---DVPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 94 ~~~~~V~l~Fa~~------~L~~f~-Kaa~ls~~V~l~l~~---~~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
+|++||++.+.+. -++.|. ..+.||+.+++.... ..|...-..=++...|+|+=.|-
T Consensus 16 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~s~~i~~~~~~~~~~~p~~~~~~~~~~~~i~f~g~P~ 82 (517)
T PRK15317 16 LLERPIELVASLDDSEKSAELKELLEEIASLSDKITVEEDSLDVRKPSFSITRPGEDTGVRFAGIPM 82 (517)
T ss_pred hCCCCEEEEEEeCCCchHHHHHHHHHHHHHhCCceEEEEccCCCCCCEEEEEcCCccceEEEEecCc
Confidence 3555665544422 155666 477899999998765 35743222212235799998884
No 53
>PF04045 P34-Arc: Arp2/3 complex, 34 kD subunit p34-Arc; InterPro: IPR007188 Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits, which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc []. This family represents the p34-Arc subunit.; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 2P9L_D 2P9I_D 2P9U_D 3DXM_D 2P9N_D 1TYQ_D 3DXK_D 1K8K_D 2P9S_D 1U2V_D ....
Probab=28.48 E-value=43 Score=28.25 Aligned_cols=56 Identities=20% Similarity=0.313 Sum_probs=33.6
Q ss_pred cCceeeeeehhhHHhhhhhcCCC--ceEEEEeeC-CCcEEEEE----E-e-CCCeEEEEEEeecc
Q psy2363 96 QEPVSLNFACRYLLNFAKAAPLS--NQVCLSMSL-DVPLVVEF----K-I-DDIGHIRYYLAPKI 151 (156)
Q Consensus 96 ~~~V~l~Fa~~~L~~f~Kaa~ls--~~V~l~l~~-~~Pl~v~f----~-i-~~~G~l~~yLAPki 151 (156)
.++-...||--+|..|..|..-+ ..=.+.++. +-|+.|+= . . ++.|+++|-|-||=
T Consensus 122 ~D~~D~vigkvFLQEFvdaRr~~~~~APqvlfS~~~PPlEl~~~~~~~~~~~n~gyvTFvLfprH 186 (241)
T PF04045_consen 122 KDEDDRVIGKVFLQEFVDARRRSRQTAPQVLFSHREPPLELRGVPGARNLGDNVGYVTFVLFPRH 186 (241)
T ss_dssp SSCCHHHHHHHHHHHHHTGGGT--TTS-EEEEECSS--CGGTT-TT----STTEEEEEEEEEHHH
T ss_pred cCCCCeEeeHHHHHHHHHhccccCCCCCceeccCCCCChhHcCCCCccccCCCeEEEEEEEeccc
Confidence 34445667778899998766544 333445555 66665432 1 2 24799999999973
No 54
>PRK06673 DNA polymerase III subunit beta; Validated
Probab=27.35 E-value=1.6e+02 Score=25.64 Aligned_cols=82 Identities=15% Similarity=0.305 Sum_probs=48.1
Q ss_pred CcHHHHHHHHHHhccCC-----eEEEEE-eCCeEEEEEee-cceeEEEEEeecCCCCCCCccEEEEecCceeEEeeeeec
Q psy2363 2 PSGEFARICRDLAQFGE-----SINISC-TKEGVKFSATG-DIGSANIKLAQTGNVDKEEEAVTVEMQEPVSLNFACRYL 74 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~gd-----~v~i~~-~~~~v~f~~~g-d~~~~~i~l~~~~~~~~~~~~v~i~~~~~~~~~fs~k~~ 74 (156)
+..+|..+++=++.+.. .|++.. .++.+++++.. |.|++.-.+.-.. ++-+++..+.|..+|.
T Consensus 264 ~r~~l~~al~Rvsi~~~~~~~~~v~l~~~~~~~l~i~s~~~e~G~a~e~i~~~~----------~~Ge~~~~I~fN~~YL 333 (376)
T PRK06673 264 DRQRMLQGVDRSSLLASEWANNNVNLEIVNESTIQISSNASQIGKISETQQIDA----------IQGEKQLNISFDGRFM 333 (376)
T ss_pred EHHHHHHHHHHHHHhhccCCCCcEEEEEcCCCEEEEEEcCCCCCcEEEEEEeee----------cCCCccEEEEECHHHH
Confidence 35678888988888863 388887 67889988754 6676654332110 0011145777888873
Q ss_pred ccccCCCCCCcccccceEEEecCc
Q psy2363 75 LNFAKAAPLSNQEEEAVTVEMQEP 98 (156)
Q Consensus 75 ~~~~k~~~~~~~~~~~V~i~~~~~ 98 (156)
.=-=+.. .++.|++.+++|
T Consensus 334 ld~L~~i-----~~e~v~l~~~~~ 352 (376)
T PRK06673 334 LDALRAI-----KEETVTLSFSGS 352 (376)
T ss_pred HHHHhcC-----CCCEEEEEECCC
Confidence 3222221 234566666554
No 55
>PRK14943 DNA polymerase III subunit beta; Provisional
Probab=26.52 E-value=4.1e+02 Score=22.76 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=22.7
Q ss_pred CcHHHHHHHHHHhcc-C--------CeEEEEEeCCeEEEEEe
Q psy2363 2 PSGEFARICRDLAQF-G--------ESINISCTKEGVKFSAT 34 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~-g--------d~v~i~~~~~~v~f~~~ 34 (156)
+.++|.++++-+..+ + .-|.|++.++.+++.+.
T Consensus 6 ~~~~L~~~l~~v~~~v~~~~~~piL~gill~~~~~~l~l~aT 47 (374)
T PRK14943 6 NKDHFLNGLRQVLNVVSSKTTMPILSNVLIEAENGQISLTTT 47 (374)
T ss_pred EHHHHHHHHHHHHhHhCCCCChHHhcCEEEEEECCEEEEEEE
Confidence 456777777777654 2 24778888888888766
No 56
>TIGR03140 AhpF alkyl hydroperoxide reductase, F subunit. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP.
Probab=24.64 E-value=1.6e+02 Score=26.75 Aligned_cols=56 Identities=23% Similarity=0.368 Sum_probs=32.6
Q ss_pred ecCceeeeeeh------hhHHhhh-hhcCCCceEEEEeeC----CCcEEEEEEeCCCeEEEEEEeec
Q psy2363 95 MQEPVSLNFAC------RYLLNFA-KAAPLSNQVCLSMSL----DVPLVVEFKIDDIGHIRYYLAPK 150 (156)
Q Consensus 95 ~~~~V~l~Fa~------~~L~~f~-Kaa~ls~~V~l~l~~----~~Pl~v~f~i~~~G~l~~yLAPk 150 (156)
|++||++.+.+ .-++.|. ..+.||+.+++.... ..|...-+.=+....|+||=.|-
T Consensus 17 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~s~ki~~~~~~~~~~~~p~~~~~~~~~~~~i~f~g~P~ 83 (515)
T TIGR03140 17 LENPVTLVLSAGSHEKSKELLELLDEIASLSDKISLTQNTADTLRKPSFTILRDGADTGIRFAGIPG 83 (515)
T ss_pred cCCCEEEEEEeCCCchhHHHHHHHHHHHHhCCCeEEEEecCCcCCCCeEEEecCCcccceEEEecCC
Confidence 55555554442 1255666 477889999997654 24643222212235699998884
No 57
>PF05517 p25-alpha: p25-alpha ; InterPro: IPR008907 This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase []. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila.; PDB: 1WLM_A 1PUL_A 2JRF_A.
Probab=22.89 E-value=29 Score=26.84 Aligned_cols=19 Identities=32% Similarity=0.683 Sum_probs=15.1
Q ss_pred CCcHHHHHHHHHHhccCCe
Q psy2363 1 MPSGEFARICRDLAQFGES 19 (156)
Q Consensus 1 m~s~~f~~i~rdl~~~gd~ 19 (156)
|.+..|.++|||...++..
T Consensus 19 m~~~~F~Kl~kD~~i~d~k 37 (154)
T PF05517_consen 19 MDSKNFAKLCKDCGIIDKK 37 (154)
T ss_dssp EEHHHHHHHHHHTSS--SS
T ss_pred ccHHHHHHHHHHcCCCCCC
Confidence 6788999999999999766
No 58
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=21.32 E-value=1.3e+02 Score=21.54 Aligned_cols=21 Identities=14% Similarity=0.455 Sum_probs=18.9
Q ss_pred cCCeEEEEEeCCeEEEEEeec
Q psy2363 16 FGESINISCTKEGVKFSATGD 36 (156)
Q Consensus 16 ~gd~v~i~~~~~~v~f~~~gd 36 (156)
=||.|+|.+..+++.+++.|.
T Consensus 68 ~G~~V~i~~~~~~~~i~~~g~ 88 (122)
T TIGR03170 68 RGDTVTVIARGGGLSVTTEGK 88 (122)
T ss_pred CCCEEEEEEecCCEEEEEEEE
Confidence 389999999999999999885
No 59
>PF14977 FAM194: FAM194 protein
Probab=21.30 E-value=1.3e+02 Score=24.76 Aligned_cols=67 Identities=16% Similarity=0.156 Sum_probs=44.0
Q ss_pred ccEEEEecCceeEEeeeeeccccc-----C----CCCCCc---ccccceEEEecCceeeeeehhhHHhhhhhcCCCceEE
Q psy2363 55 EAVTVEMQEPVSLNFACRYLLNFA-----K----AAPLSN---QEEEAVTVEMQEPVSLNFACRYLLNFAKAAPLSNQVC 122 (156)
Q Consensus 55 ~~v~i~~~~~~~~~fs~k~~~~~~-----k----~~~~~~---~~~~~V~i~~~~~V~l~Fa~~~L~~f~Kaa~ls~~V~ 122 (156)
..+.+.+++..+..|..+|..-.. + +..... ++.-+|+|...+.|.++|+ .+..+++
T Consensus 77 g~~~l~l~~~gG~~~D~~G~~~k~W~W~~~~~~Pp~~pi~~klN~~i~vri~~qd~I~itF~-----------~~~~~~~ 145 (208)
T PF14977_consen 77 GNIWLVLNQEGGQYFDQKGNRVKKWNWSSHVHAPPFQPISLKLNEQIKVRILSQDKISITFT-----------AMGEQAK 145 (208)
T ss_pred CCEEEEEECCCCEEEcCCCCEEEEEecCCCCCCCccccEEEEecCcEEEEEeccceEEEEEe-----------eCCcEEE
Confidence 346666666656666555543333 1 111111 6778888888888888888 5678999
Q ss_pred EEeeCCCcEE
Q psy2363 123 LSMSLDVPLV 132 (156)
Q Consensus 123 l~l~~~~Pl~ 132 (156)
|.++..+|+.
T Consensus 146 lnvGtk~~~~ 155 (208)
T PF14977_consen 146 LNVGTKVKLV 155 (208)
T ss_pred EEecCccccC
Confidence 9999876654
No 60
>TIGR00663 dnan DNA polymerase III, beta subunit. University).
Probab=20.66 E-value=5.3e+02 Score=21.89 Aligned_cols=34 Identities=9% Similarity=0.218 Sum_probs=23.5
Q ss_pred CcHHHHHHHHHHhcc-C--------CeEEEEEeCCeEEEEEee
Q psy2363 2 PSGEFARICRDLAQF-G--------ESINISCTKEGVKFSATG 35 (156)
Q Consensus 2 ~s~~f~~i~rdl~~~-g--------d~v~i~~~~~~v~f~~~g 35 (156)
+..+|.++++-...+ + .-|-|++.++++++.+..
T Consensus 6 ~~~~L~~~l~~v~~~i~~~~~~piL~gvlle~~~~~l~l~atD 48 (367)
T TIGR00663 6 ERDDLLKELSKVQRVLSNRPTIPILSNILLEVKDDKLTITATD 48 (367)
T ss_pred EHHHHHHHHHHHHhHhcCCCchhhhcCEEEEEECCEEEEEEEC
Confidence 456777777776654 2 247788888888888763
No 61
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.09 E-value=1.4e+02 Score=22.93 Aligned_cols=21 Identities=10% Similarity=0.264 Sum_probs=19.3
Q ss_pred cCCeEEEEEeCCeEEEEEeec
Q psy2363 16 FGESINISCTKEGVKFSATGD 36 (156)
Q Consensus 16 ~gd~v~i~~~~~~v~f~~~gd 36 (156)
=|+.|+|.+..+++++++.|.
T Consensus 84 rG~~V~i~~~~ggl~i~~~G~ 104 (141)
T PRK12618 84 RNQLVPLAYRLGGLEIRTEGR 104 (141)
T ss_pred CCCEEEEEEecCCEEEEEEEE
Confidence 389999999999999999986
Done!