Query psy5572
Match_columns 62
No_of_seqs 107 out of 381
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 20:56:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5572hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00113 proliferating cell nu 99.9 1.2E-23 2.7E-28 144.2 7.7 62 1-62 201-272 (275)
2 PF02747 PCNA_C: Proliferating 99.9 2.6E-23 5.7E-28 128.3 8.3 55 2-56 74-128 (128)
3 PLN00057 proliferating cell nu 99.9 2.4E-23 5.2E-28 141.2 8.1 61 2-62 200-260 (263)
4 PTZ00483 proliferating cell nu 99.9 3.1E-23 6.8E-28 141.5 7.0 59 1-59 199-264 (264)
5 TIGR00590 pcna proliferating c 99.9 5.8E-23 1.2E-27 138.9 8.1 60 2-61 200-259 (259)
6 PHA03383 PCNA-like protein; Pr 99.9 3.4E-22 7.3E-27 136.1 7.8 57 2-58 206-262 (262)
7 KOG1636|consensus 99.9 1.7E-22 3.8E-27 137.0 6.0 61 1-61 199-259 (260)
8 PRK01115 DNA polymerase slidin 99.5 1.2E-13 2.5E-18 91.3 7.8 57 2-58 191-247 (247)
9 cd00577 PCNA Proliferating Cel 99.3 1.4E-11 3E-16 80.0 7.5 57 2-58 192-248 (248)
10 COG0592 DnaN DNA polymerase sl 98.1 2.4E-07 5.1E-12 65.4 -1.8 57 3-59 263-325 (364)
11 cd00140 beta_clamp Beta clamp 97.8 9.2E-05 2E-09 50.6 6.1 51 3-56 313-364 (365)
12 PRK05643 DNA polymerase III su 97.5 0.00059 1.3E-08 47.3 6.6 50 3-55 314-364 (367)
13 PF02768 DNA_pol3_beta_3: DNA 96.2 0.036 7.8E-07 33.0 6.6 50 3-55 69-119 (121)
14 PRK14947 DNA polymerase III su 95.1 0.12 2.6E-06 36.8 6.7 55 3-60 320-376 (384)
15 PRK14940 DNA polymerase III su 94.0 0.35 7.5E-06 34.1 6.8 50 3-55 313-363 (367)
16 KOG3194|consensus 93.8 0.22 4.8E-06 34.9 5.5 54 3-56 214-271 (279)
17 PRK14945 DNA polymerase III su 93.5 0.42 9.2E-06 33.4 6.5 49 3-55 310-359 (362)
18 smart00480 POL3Bc DNA polymera 93.0 0.29 6.4E-06 33.8 5.0 37 3-40 296-333 (345)
19 PF04005 Hus1: Hus1-like prote 92.8 1 2.2E-05 31.0 7.4 51 4-54 238-289 (292)
20 cd00577 PCNA Proliferating Cel 92.1 2.1 4.7E-05 27.4 8.1 46 3-48 61-106 (248)
21 PRK14941 DNA polymerase III su 91.8 0.85 1.8E-05 32.2 6.2 52 3-55 316-369 (374)
22 PRK14942 DNA polymerase III su 90.7 1.5 3.2E-05 31.2 6.6 50 3-55 320-370 (373)
23 PRK14943 DNA polymerase III su 90.6 1.4 3E-05 30.8 6.3 48 3-55 322-370 (374)
24 PRK06673 DNA polymerase III su 90.5 1.5 3.3E-05 31.1 6.5 49 4-55 323-372 (376)
25 TIGR00663 dnan DNA polymerase 90.0 1.9 4.1E-05 29.9 6.5 50 3-55 314-364 (367)
26 PRK14944 DNA polymerase III su 89.6 2.1 4.5E-05 30.5 6.6 50 3-55 322-372 (375)
27 PRK07761 DNA polymerase III su 88.6 2.4 5.1E-05 29.8 6.3 52 3-55 315-371 (376)
28 PRK14946 DNA polymerase III su 88.4 2.2 4.7E-05 30.4 6.0 48 3-54 314-362 (366)
29 PF04139 Rad9: Rad9; InterPro 86.3 4.1 9E-05 27.1 6.2 54 2-55 196-251 (252)
30 PF00705 PCNA_N: Proliferating 85.6 6.2 0.00014 24.1 7.8 49 2-50 63-112 (127)
31 PF02144 Rad1: Repair protein 84.7 2.8 6.1E-05 28.7 4.9 39 3-41 235-273 (275)
32 COG0592 DnaN DNA polymerase sl 83.6 6.1 0.00013 28.0 6.3 50 3-55 311-361 (364)
33 PHA03383 PCNA-like protein; Pr 75.4 23 0.00051 24.2 7.2 53 2-54 69-124 (262)
34 TIGR00590 pcna proliferating c 71.9 28 0.00061 23.6 8.0 52 2-53 63-116 (259)
35 PLN00057 proliferating cell nu 62.2 47 0.001 22.6 8.0 52 2-53 63-116 (263)
36 PF13351 DUF4099: Protein of u 52.2 43 0.00092 19.2 4.1 44 14-57 27-75 (85)
37 COG3110 Uncharacterized protei 49.1 28 0.0006 23.8 3.3 38 21-62 67-104 (216)
38 PF00181 Ribosomal_L2: Ribosom 46.3 53 0.0011 18.4 4.1 33 24-56 35-67 (77)
39 cd02414 jag_KH jag_K homology 43.2 57 0.0012 17.9 4.4 36 12-48 2-37 (77)
40 PF03230 Antirestrict: Antires 42.5 26 0.00056 20.9 2.1 15 41-58 13-27 (94)
41 cd00140 beta_clamp Beta clamp 41.0 1.1E+02 0.0025 20.7 6.7 38 3-43 189-227 (365)
42 PF06366 FlhE: Flagellar prote 38.1 31 0.00067 21.0 2.0 19 31-49 72-90 (106)
43 PF02563 Poly_export: Polysacc 35.7 14 0.00031 20.6 0.3 34 22-55 14-47 (82)
44 PF12132 DUF3587: Protein of u 35.3 61 0.0013 21.8 3.3 22 24-45 59-80 (199)
45 PF06988 NifT: NifT/FixU prote 34.6 53 0.0012 18.4 2.5 19 38-56 2-20 (64)
46 COG5406 Nucleosome binding fac 34.6 40 0.00087 27.2 2.6 33 20-54 398-430 (1001)
47 PRK01115 DNA polymerase slidin 34.3 1.3E+02 0.0029 19.5 7.2 53 4-59 65-118 (247)
48 COG1951 TtdA Tartrate dehydrat 32.8 64 0.0014 23.1 3.2 29 29-57 119-147 (297)
49 PF11306 DUF3108: Protein of u 28.3 1.5E+02 0.0033 18.4 5.3 29 25-53 202-234 (238)
50 PF00262 Calreticulin: Calreti 28.2 51 0.0011 24.1 2.1 21 34-54 75-102 (367)
51 PF14451 Ub-Mut7C: Mut7-C ubiq 28.0 48 0.001 18.9 1.7 32 24-55 46-77 (81)
52 COG3294 HD supefamily hydrolas 26.9 66 0.0014 22.7 2.4 35 24-58 204-241 (269)
53 PTZ00113 proliferating cell nu 26.8 2.2E+02 0.0048 19.7 8.1 43 2-45 63-105 (275)
54 PF03723 Hemocyanin_C: Hemocya 26.5 82 0.0018 21.5 2.8 29 31-59 55-87 (250)
55 PF05681 Fumerase: Fumarate hy 25.7 1.2E+02 0.0026 21.2 3.5 29 29-57 109-137 (271)
56 PF05340 DUF740: Protein of un 25.3 45 0.00097 26.1 1.5 12 45-56 583-594 (603)
57 PF03633 Glyco_hydro_65C: Glyc 25.2 49 0.0011 16.9 1.3 35 7-41 10-45 (54)
58 COG5138 Uncharacterized conser 23.3 53 0.0011 21.5 1.3 19 32-50 13-31 (168)
59 PRK08312 putative indolepyruva 23.2 40 0.00087 25.6 0.9 14 46-59 341-354 (510)
60 cd05172 PIKKc_DNA-PK DNA-depen 22.6 2.5E+02 0.0054 18.8 4.7 33 22-54 3-35 (235)
61 cd02847 Chitobiase_C_term Chit 22.5 1.2E+02 0.0026 17.2 2.6 31 25-55 20-51 (78)
62 PF02792 Mago_nashi: Mago nash 22.0 75 0.0016 20.5 1.8 17 38-54 18-34 (143)
63 PF11359 gpUL132: Glycoprotein 21.0 94 0.002 21.5 2.2 38 17-54 159-197 (235)
64 cd01242 PH_ROK Rok (Rho- assoc 21.0 1.6E+02 0.0034 18.2 3.1 28 31-58 70-97 (112)
65 PF02767 DNA_pol3_beta_2: DNA 20.9 1.9E+02 0.004 16.7 5.0 38 5-45 64-102 (116)
66 COG0588 GpmA Phosphoglycerate 20.1 67 0.0014 22.2 1.4 23 20-42 195-217 (230)
67 TIGR00249 sixA phosphohistidin 20.1 1.4E+02 0.0031 18.3 2.8 26 30-55 127-152 (152)
No 1
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=99.90 E-value=1.2e-23 Score=144.23 Aligned_cols=62 Identities=35% Similarity=0.744 Sum_probs=57.8
Q ss_pred CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC----------CeEEEEEEeecCCCCCC
Q psy5572 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD----------IGHIRYYLAPKIESDDN 62 (62)
Q Consensus 1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~----------~g~l~~~lAPrie~e~~ 62 (62)
++++++++||++||++|+||+++|++|+|+|++|+||+++|++++ +|+|+||||||+++|++
T Consensus 201 v~~~~~~~ysl~YL~~f~Ka~~ls~~V~l~l~~d~Pl~ley~i~~~~~~~~~~~~~G~l~fyLAPkie~~~~ 272 (275)
T PTZ00113 201 VRKPIKQSYATKYLNMFAKSGCLSDVVTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKFFLAPKMDDDMD 272 (275)
T ss_pred ecCceeeEEhHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeccccccccccCCccEEEEEEcCccCcccc
Confidence 368999999999999999999999999999999999999999962 59999999999998874
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=99.90 E-value=2.6e-23 Score=128.31 Aligned_cols=55 Identities=51% Similarity=0.910 Sum_probs=52.5
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeec
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPr 56 (62)
+++++++|+++||++|+||+++|++|+|+|++|+||+++|+++++|+++||||||
T Consensus 74 ~~~~~~~fsl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~f~~~~~g~l~f~LAPK 128 (128)
T PF02747_consen 74 KEPVSSSFSLDYLNDFSKAAPLSDEVTLELGEDMPLKLEFELADGGSLKFYLAPK 128 (128)
T ss_dssp SSEEEEEEEHHHHHHHGGGGGTTSEEEEEEETTSEEEEEEEETTTEEEEEEE-BB
T ss_pred ccceeeEEeHHHHHhhhccccCCceEEEEEcCCCCEEEEEEeCCCeEEEEEEcCC
Confidence 5788999999999999999999999999999999999999999999999999997
No 3
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=99.89 E-value=2.4e-23 Score=141.18 Aligned_cols=61 Identities=64% Similarity=1.053 Sum_probs=58.3
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCCC
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN 62 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~~ 62 (62)
++++++.|+++||+.|+||+++|++|+|+|++++||+|+|+++++|+|+||||||+++|++
T Consensus 200 ~e~~~~~y~l~YL~~~~Ka~~ls~~V~i~~~~~~Pl~l~y~l~~~g~l~f~LAPri~~~~~ 260 (263)
T PLN00057 200 QEPVSLTFALRYLNSFTKATPLSDTVTLSLSKELPVVVEYKIAEMGYIRYYLAPKIEEDED 260 (263)
T ss_pred cCceEEEEhHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeCCCeEEEEEEcCCCCCccc
Confidence 5789999999999999999999999999999999999999999899999999999998763
No 4
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=99.89 E-value=3.1e-23 Score=141.51 Aligned_cols=59 Identities=42% Similarity=0.765 Sum_probs=55.8
Q ss_pred CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeC-------CCeEEEEEEeecCCC
Q psy5572 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKID-------DIGHIRYYLAPKIES 59 (62)
Q Consensus 1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~-------~~g~l~~~lAPrie~ 59 (62)
+++|++++|+++||++|+||+++|++|+|+|++++||+++|+++ ++|+|+||||||+|+
T Consensus 199 ~~~~v~~~fsl~YL~~f~Ka~~lsd~V~i~l~~~~Pl~ley~i~~~~~~~~~~G~l~fyLAPrie~ 264 (264)
T PTZ00483 199 STESLSQEFATRYLVLFSKATSLADEVSINLSAGIPLSVKFNFKDPLTDLQDSSFINFYLAPNIEE 264 (264)
T ss_pred ecCcchheehHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEecccccCCCCceEEEEEEccccCC
Confidence 46899999999999999999999999999999999999999995 589999999999985
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=99.89 E-value=5.8e-23 Score=138.94 Aligned_cols=60 Identities=62% Similarity=1.042 Sum_probs=57.9
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 61 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~ 61 (62)
++|++++|+++||+.|+||+++|++|+|+|++++||+++|++.++|+|+||||||+++|+
T Consensus 200 ~~~~~~~y~l~YL~~~~Ka~~ls~~V~l~~~~~~Pl~l~y~i~~~g~l~f~lAPrie~~~ 259 (259)
T TIGR00590 200 KEPVTLTFAIKYLNLFTKATPLSDRVTLSMSNDVPLVVEYKIKDMGFLRFFLAPKIEDEE 259 (259)
T ss_pred cCceeeeeeHHHHHHhhhhccCCCeEEEEEcCCCCEEEEEEeCCCeEEEEEEcCccCCCC
Confidence 578999999999999999999999999999999999999999989999999999999885
No 6
>PHA03383 PCNA-like protein; Provisional
Probab=99.87 E-value=3.4e-22 Score=136.14 Aligned_cols=57 Identities=25% Similarity=0.595 Sum_probs=54.4
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie 58 (62)
++|++++|+++||++|+||+++|++|+|+|++|+||+++|+++++|+++||||||+.
T Consensus 206 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~i~l~~d~Pl~ley~i~~~G~l~fyLAPri~ 262 (262)
T PHA03383 206 SPDYTGKFSLKYLTSFTKASGMSSSVEIYLKESNPLILKYNVGSLGNLKFVIAPKVS 262 (262)
T ss_pred CCceEEEEeHHHHHHhhccccCCCeEEEEEcCCCCEEEEEEeCCCcEEEEEEccccC
Confidence 367899999999999999999999999999999999999999999999999999984
No 7
>KOG1636|consensus
Probab=99.87 E-value=1.7e-22 Score=136.98 Aligned_cols=61 Identities=62% Similarity=1.111 Sum_probs=59.0
Q ss_pred CCCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCC
Q psy5572 1 MQEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDD 61 (62)
Q Consensus 1 ~~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~ 61 (62)
|++|++.+|+++|||.|+||++||++|+|+++++.|+.++|.+.+.|+++||||||++++|
T Consensus 199 ~~~pVtltfa~kYln~ftKatpLs~rV~lsls~~~P~~vey~i~~~g~lr~YLAPKieD~e 259 (260)
T KOG1636|consen 199 MNEPVTLTFALKYLNQFTKATPLSDRVTLSLSSEVPVVVEYKIEDMGHLRYYLAPKIEDEE 259 (260)
T ss_pred ecCcchhhhHHHHHHHhhccccccceEEEEecCCCcEEEEEecccCceEEEEEccccCCCC
Confidence 5799999999999999999999999999999999999999999999999999999999776
No 8
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=99.50 E-value=1.2e-13 Score=91.31 Aligned_cols=57 Identities=37% Similarity=0.693 Sum_probs=54.2
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie 58 (62)
+++++..|+.+||.++.|+.+.+++|+|+|+++.|++++|.+.++|++.||||||++
T Consensus 191 ~e~~~i~fn~~YL~d~lk~~~~~~~V~l~~~~~~P~~l~~~~~~~~~~~~~i~P~~~ 247 (247)
T PRK01115 191 EEPAKSSYSLDYLKDMVKATSASDEVTIEFGSDMPLKLEFEIAGGGKVTYLLAPRIE 247 (247)
T ss_pred cCceeEEEhHHHHHHhhccccCCCeEEEEECCCCCEEEEEEeCCCeEEEEEEecccC
Confidence 367899999999999999999999999999999999999999999999999999986
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=99.30 E-value=1.4e-11 Score=80.02 Aligned_cols=57 Identities=58% Similarity=0.942 Sum_probs=54.3
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIE 58 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie 58 (62)
.++++..|+.+||.++.|+..++++|+|++..+.|+.++|.+.+.|.+.|||||+++
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 478899999999999999999999999999999999999999889999999999975
No 10
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]
Probab=98.12 E-value=2.4e-07 Score=65.37 Aligned_cols=57 Identities=28% Similarity=0.284 Sum_probs=51.7
Q ss_pred CceeeEEehHHHHhhhcccCCCc-eEEEEeeCCCcEEEEEEeCCC-----eEEEEEEeecCCC
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSN-QVCLSMSLDVPLVVEFKIDDI-----GHIRYYLAPKIES 59 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~-~V~l~l~~~~Pl~l~~~l~~~-----g~l~~~lAPrie~ 59 (62)
++++..|++.|++.+.+...+++ +|+|+++++.|.++++++..+ |++.|++||++|.
T Consensus 263 ~al~r~~~l~~~~~~~~~~~~~~~~v~i~~~~~~~g~~~eei~~~~~g~~~~I~fn~~ylld~ 325 (364)
T COG0592 263 EALKRVYSLSYLKDRGKKLSLADGEVKLSLGNDEPGKAEEEIDVGYTGEELKIGFNLAYLLDV 325 (364)
T ss_pred HHHHHHHHHHhcccCceEEEeeCCeEEEEecCCCccceEEEEEeccCCceEEEEECHHHHHHH
Confidence 45567899999999999999999 999999999999999999864 8999999999974
No 11
>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=97.77 E-value=9.2e-05 Score=50.59 Aligned_cols=51 Identities=27% Similarity=0.419 Sum_probs=44.8
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEeec
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAPK 56 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAPr 56 (62)
++.+..|+.+||.++.|+.+ +++|+|.++.+ .|+.+++.- ++...|+|+|.
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 46788999999999999987 68999999998 899998864 57899999993
No 12
>PRK05643 DNA polymerase III subunit beta; Validated
Probab=97.46 E-value=0.00059 Score=47.28 Aligned_cols=50 Identities=30% Similarity=0.495 Sum_probs=44.1
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+..|..+||.++.|+.. +++|+|.|++. .|+.++. .+++...|+|+|
T Consensus 314 ~~~~i~~n~~yL~d~l~~~~-~~~v~i~~~~~~~p~~i~~--~~~~~~~~limP 364 (367)
T PRK05643 314 EELEIGFNVKYLLDVLKALD-SEEVRLSFNDANSPFLIRP--PDDDSFLYVIMP 364 (367)
T ss_pred CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc--CCCCceEEEEEe
Confidence 46788999999999999988 88999999996 7999988 456779999999
No 13
>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=96.24 E-value=0.036 Score=33.04 Aligned_cols=50 Identities=28% Similarity=0.546 Sum_probs=37.8
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.+..|+.. +++|+|+|.... |+.++= .++....|+|-|
T Consensus 69 ~~~~i~fN~~yL~d~L~~~~-~~~V~l~~~~~~~p~~i~~--~~d~~~~~liMP 119 (121)
T PF02768_consen 69 EPLEIAFNPKYLLDALKAID-GEEVTLEFSDPSSPILITP--EEDPDFKYLIMP 119 (121)
T ss_dssp S-EEEEEEHHHHHHHHHCC--SSEEEEEESSTTS-EEEEE--TTSSCEEEEE--
T ss_pred CceEEEECHHHHHHHHhhcC-CCEEEEEEcCCCCCEEEEe--CCCCceEEEEEe
Confidence 57788999999999999987 789999999888 987654 345667888877
No 14
>PRK14947 DNA polymerase III subunit beta; Provisional
Probab=95.11 E-value=0.12 Score=36.84 Aligned_cols=55 Identities=16% Similarity=0.222 Sum_probs=42.8
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee-cCCCC
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP-KIESD 60 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP-rie~e 60 (62)
++.+-.|..+||.++.++.. +++|.|+|.+. .|+.++ ..+ +....|.|-| |+.++
T Consensus 320 e~~~I~fN~~YL~d~L~~i~-~~~i~l~~~~~~~p~~i~-~~~-~~~~~~lIMPvr~~~~ 376 (384)
T PRK14947 320 DIKKIAFPTKNLIEILGHFQ-SDKITLTLTGAEGPCGIT-GED-DPDYLVIVMPMKIVEE 376 (384)
T ss_pred CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEE-cCC-CCceEEEEeceEECCC
Confidence 46788999999999999986 68999999886 599886 332 3345688988 66544
No 15
>PRK14940 DNA polymerase III subunit beta; Provisional
Probab=93.99 E-value=0.35 Score=34.09 Aligned_cols=50 Identities=14% Similarity=0.094 Sum_probs=40.1
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.+..|+.. +++|+|+|.+.. |+.++=. ++....|.|-|
T Consensus 313 e~~~I~fN~~yl~d~L~~i~-~~~v~l~~~~~~~p~~i~~~--~~~~~~~liMP 363 (367)
T PRK14940 313 EEEVIALNYLYLEEPLKVFT-SKEVQVEFTEAAKAITLRPV--PETDCFHIIMP 363 (367)
T ss_pred CcEEEEECHHHHHHHHhCCC-CCEEEEEECCCCCCEEEEeC--CCCcEEEEEEe
Confidence 56788999999999999986 689999998865 9987542 33456688887
No 16
>KOG3194|consensus
Probab=93.82 E-value=0.22 Score=34.93 Aligned_cols=54 Identities=24% Similarity=0.320 Sum_probs=47.5
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC-Ce---EEEEEEeec
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD-IG---HIRYYLAPK 56 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~-~g---~l~~~lAPr 56 (62)
+++..+|-+.-+..++||..++..|.|++.+.=-|-+.|-+.+ .| .+.|+.-|-
T Consensus 214 ~ev~~sy~fSli~~~tkAl~lasKv~lR~DerGvLS~qimi~~~dg~itfiefc~vp~ 271 (279)
T KOG3194|consen 214 DEVIGSYDFSLIDKITKALKLASKVLLRMDERGVLSVQIMIQTDDGIITFIEFCMVPI 271 (279)
T ss_pred hhhhceEeehhhHHHHHHHhhhheEEEEEcCCcEEEEEEEEecCCceEEEEEEEEeec
Confidence 4567789999999999999999999999999999999999863 45 678999993
No 17
>PRK14945 DNA polymerase III subunit beta; Provisional
Probab=93.46 E-value=0.42 Score=33.38 Aligned_cols=49 Identities=22% Similarity=0.255 Sum_probs=38.2
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|+.+||.++.|+.. ++|+|+|... .|+.++= .++....|.|-|
T Consensus 310 ~~~~i~fN~~yl~d~L~~~~--~~v~l~~~~~~~p~~i~~--~~~~~~~~limP 359 (362)
T PRK14945 310 PAMALAYNARYLLDALAPIE--GDARLGFSGPTSPSVLRS--VDDPGYLAVVVP 359 (362)
T ss_pred CCEEEEECHHHHHHHHHhCC--CcEEEEECCCCCCEEEEe--CCCCcEEEEEEe
Confidence 47899999999999999887 4699999875 4988743 223446777777
No 18
>smart00480 POL3Bc DNA polymerase III beta subunit.
Probab=92.97 E-value=0.29 Score=33.79 Aligned_cols=37 Identities=27% Similarity=0.490 Sum_probs=32.9
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEE
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVE 40 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~ 40 (62)
++.+-.|..+||.++.|+.. ++.|+|.|.+.. |+.++
T Consensus 296 ~~~~i~fN~~yL~d~l~~~~-~~~v~l~~~~~~~p~~i~ 333 (345)
T smart00480 296 EDLEIAFNPKYLLDALKALK-SEEIELKFTDSSSPFLIS 333 (345)
T ss_pred CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEE
Confidence 56788999999999999986 689999999977 99885
No 19
>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=92.76 E-value=1 Score=30.98 Aligned_cols=51 Identities=24% Similarity=0.359 Sum_probs=42.4
Q ss_pred ceeeEEehHHHHhhhcccCCC-ceEEEEeeCCCcEEEEEEeCCCeEEEEEEe
Q psy5572 4 PVSLNFACRYLLNFAKAAPLS-NQVCLSMSLDVPLVVEFKIDDIGHIRYYLA 54 (62)
Q Consensus 4 ~~~~~ysl~YL~~~~Ka~~ls-~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lA 54 (62)
.++....++-+..+.+...++ +.|.+.+..+.-+.+-.-+++.|.|.|||-
T Consensus 238 ~~sV~Vd~K~~~~~l~~~~~~p~~vi~~I~~~~~~vl~~~~~~~~~l~yyip 289 (292)
T PF04005_consen 238 FASVRVDIKDLAKFLKSHQLSPSRVICCICHNKALVLHVYLDEDVSLTYYIP 289 (292)
T ss_dssp -EEEEEEHHHHHHHHHH--S--SEEEEEEETTTEEEEEEEE-TTEEEEEEEE
T ss_pred EEEEEEEHHHHHHhhCccccCCCEEEEEEccCCeEEEEEEEcCCEEEEEEEe
Confidence 467788899999999988887 999999999999999999988999999984
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=92.05 E-value=2.1 Score=27.45 Aligned_cols=46 Identities=26% Similarity=0.259 Sum_probs=37.9
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeE
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGH 48 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~ 48 (62)
++.+...+++.|..+.|...-.+.|+|+++.+.|+.+.+.....|.
T Consensus 61 ~~~~~~i~~k~l~~~lk~~~~~~~v~i~~~~~~~l~i~~~~~~~~~ 106 (248)
T cd00577 61 EEISLGVNLKSLLKILKCAGNEDCVTLRADDEDPLKILFESSKGDV 106 (248)
T ss_pred CceEEEEEHHHHHHHHhhCCCCCEEEEEecCCCeEEEEEEcCCCce
Confidence 3457788899999999998888999999998888988888654333
No 21
>PRK14941 DNA polymerase III subunit beta; Provisional
Probab=91.78 E-value=0.85 Score=32.21 Aligned_cols=52 Identities=10% Similarity=0.278 Sum_probs=40.6
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEE-eCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFK-IDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~-l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.++.|+.. +++|.|+|.+.. |+.++=. -.++....|.|-|
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 56788999999999999986 689999998865 9888621 1134457888888
No 22
>PRK14942 DNA polymerase III subunit beta; Provisional
Probab=90.66 E-value=1.5 Score=31.16 Aligned_cols=50 Identities=18% Similarity=0.377 Sum_probs=39.5
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.+..++.. +++|.|+|.+.. |+.++ . .++....|.|-|
T Consensus 320 ~~~~I~fN~~ylld~L~~i~-~~~v~l~~~~~~~P~~i~-~-~~~~~~~~liMP 370 (373)
T PRK14942 320 EEITIAFKGEYLMDIFRSID-DNEVKIEFSDSSSPVIFK-D-PSDPEFISVIMP 370 (373)
T ss_pred CcEEEEECHHHHHHHHhcCC-CCeEEEEECCCCCCEEEE-e-CCCCceEEEEee
Confidence 56788999999999999986 789999998855 98774 2 234556788877
No 23
>PRK14943 DNA polymerase III subunit beta; Provisional
Probab=90.60 E-value=1.4 Score=30.85 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=38.4
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.+..|+.. +++|+|+|... .|+.+.= +. ...|.|-|
T Consensus 322 ~~~~i~fN~~yl~d~l~~~~-~~~v~l~~~~~~~p~~i~~---~~-~~~~limP 370 (374)
T PRK14943 322 PELQVAFNPDFFMAPLKALT-KDEVFFELKDEMSPGVFKT---LD-EFLCVIMP 370 (374)
T ss_pred CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEec---CC-CeEEEEEe
Confidence 56788999999999999986 68999999884 5998872 22 34677777
No 24
>PRK06673 DNA polymerase III subunit beta; Validated
Probab=90.55 E-value=1.5 Score=31.07 Aligned_cols=49 Identities=22% Similarity=0.399 Sum_probs=39.1
Q ss_pred ceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEEEEEEee
Q psy5572 4 PVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 4 ~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l~~~lAP 55 (62)
+.+-.|..+||.++.|+.. +++|+|+|.+. .|+.++= .++....|.+-|
T Consensus 323 ~~~I~fN~~YLld~L~~i~-~e~v~l~~~~~~~p~li~~--~~~~~~~~limP 372 (376)
T PRK06673 323 QLNISFDGRFMLDALRAIK-EETVTLSFSGSMRPILIEA--GTQSAAIHLISP 372 (376)
T ss_pred cEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc--CCCCceEEEEEe
Confidence 6788999999999999986 78999999876 5987753 233446788887
No 25
>TIGR00663 dnan DNA polymerase III, beta subunit. University).
Probab=90.02 E-value=1.9 Score=29.93 Aligned_cols=50 Identities=28% Similarity=0.511 Sum_probs=38.4
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.++.|+.. +++|+|.+.+.. |+.+.= .++....|.|-|
T Consensus 314 ~~~~i~fN~~yL~d~l~~~~-~~~v~l~~~~~~~p~~i~~--~~~~~~~~limP 364 (367)
T TIGR00663 314 EDLVIAFNIKYLLDALKALK-SKEIQIQFNDPSKPLLIEP--ENDEKITYLIMP 364 (367)
T ss_pred CcEEEEECHHHHHHHHhcCC-CCEEEEEECCCCCCEEEec--CCCCcEEEEEEe
Confidence 46677899999999999975 589999998755 987632 233446788888
No 26
>PRK14944 DNA polymerase III subunit beta; Provisional
Probab=89.59 E-value=2.1 Score=30.47 Aligned_cols=50 Identities=14% Similarity=0.356 Sum_probs=38.5
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|..+||.++.|+.. +++|+|.|.+.. |+.++= . ++....|.|-|
T Consensus 322 e~~~I~fN~~YL~d~L~~i~-~~~v~i~~~~~~~p~~i~~-~-~~~~~~~lImP 372 (375)
T PRK14944 322 NSFEIAFNAKYLEDILKVLS-VKEIVFYFDSPLKPFIVTT-L-EKDSSIHLILP 372 (375)
T ss_pred CcEEEEEcHHHHHHHHhcCC-CCEEEEEECCCCCCEEEEc-C-CCCceEEEEEe
Confidence 57888999999999999986 689999998765 987742 2 22345677776
No 27
>PRK07761 DNA polymerase III subunit beta; Validated
Probab=88.58 E-value=2.4 Score=29.79 Aligned_cols=52 Identities=25% Similarity=0.402 Sum_probs=40.2
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCC----CeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDD----IGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~----~g~l~~~lAP 55 (62)
++.+-.|..+||.+..|+.. +++|+|.|.+.. |+.++=.-.+ +....|.|-|
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 56788999999999999987 689999999864 9977522111 1357888888
No 28
>PRK14946 DNA polymerase III subunit beta; Provisional
Probab=88.43 E-value=2.2 Score=30.36 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=36.3
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEe
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLA 54 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lA 54 (62)
++.+-.|..+||.++.|+.. ++|.|.|.+.. |+.++ =.++....|.+|
T Consensus 314 e~~~IafN~~YL~D~L~~i~--~~v~l~~~~~~~p~~i~--~~~~~~~~~li~ 362 (366)
T PRK14946 314 ELAQVNVNYKYLKDAISVFD--KVINIFINEKKTKMLIV--SPEKKEICQLVG 362 (366)
T ss_pred CcEEEEEcHHHHHHHHHhCC--CeEEEEECCCCCCEEEE--CCCCCCeEEEEE
Confidence 57788999999999999998 56999998764 98763 123344566665
No 29
>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=86.33 E-value=4.1 Score=27.07 Aligned_cols=54 Identities=20% Similarity=0.316 Sum_probs=38.2
Q ss_pred CCceeeEEehHHHHhhhc-ccCCCceEEEEe-eCCCcEEEEEEeCCCeEEEEEEee
Q psy5572 2 QEPVSLNFACRYLLNFAK-AAPLSNQVCLSM-SLDVPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~K-a~~ls~~V~l~l-~~~~Pl~l~~~l~~~g~l~~~lAP 55 (62)
.+++.-.|+++=++.|.. |-.++..|.+.| ..+.|+.+++.=.++=...|.||-
T Consensus 196 ~~~~~itF~lKefka~l~~ae~~~~~i~~~f~~pG~Pi~~~~~~~~~~~~~~vlaT 251 (252)
T PF04139_consen 196 QEDTDITFSLKEFKAILSFAESLSLPISIYFDNPGRPILFELEQNDHFEAEFVLAT 251 (252)
T ss_dssp -TT-EEEEEHHHHHHHHHHHHHTTEEEEEEESSTTS-EEEEEE--SSEEEEEEE--
T ss_pred CCCCEEEEEeHHHHHHHHHHHhcCCcEEEEECCCCCcEEEEECCCCcEEEEEEEEc
Confidence 345778999999998886 445678999999 678899999994355578888873
No 30
>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=85.62 E-value=6.2 Score=24.15 Aligned_cols=49 Identities=18% Similarity=0.246 Sum_probs=39.0
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEE
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIR 50 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~ 50 (62)
+++.+-..+++.|..+.|.+.-.+.++|+..++. =+.+.|+-...+.++
T Consensus 63 d~~~~igvnl~~l~kiLk~~~~~D~l~l~~~~~~~~l~i~~~~~~~~~~~ 112 (127)
T PF00705_consen 63 DKELSIGVNLSDLKKILKRAKKDDSLELESDEEPDKLNIVFENEKKGRVR 112 (127)
T ss_dssp SSSEEEEEEHHHHHHHHTTSSTTSEEEEEEESSSSEEEEEEEETTSSEEE
T ss_pred CCCEEEEEEHHHHHHHHhhccCCCEEEEEEeCCCCEEEEEEEcCCCCeEE
Confidence 4577888999999999999999999999987664 244677777667654
No 31
>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=84.71 E-value=2.8 Score=28.66 Aligned_cols=39 Identities=23% Similarity=0.350 Sum_probs=32.2
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEE
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEF 41 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~ 41 (62)
+++.+.|....|....||.++|..|.|++..+==|.+.|
T Consensus 235 ~~~~~~Y~f~~i~~~~kAl~~ssKv~ir~d~~GlLs~Q~ 273 (275)
T PF02144_consen 235 EPVISRYKFSLIKKAMKALKISSKVSIRIDENGLLSLQF 273 (275)
T ss_dssp S-EEEEEEHHHHCCHHHHHTTSSEEEEEEESSS-EEEEE
T ss_pred ceEEEEEeHHHHHHHHHHhhhccEEEEEeCCCcEEEEEE
Confidence 566777999999999999999999999998776666555
No 32
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair]
Probab=83.58 E-value=6.1 Score=28.01 Aligned_cols=50 Identities=24% Similarity=0.501 Sum_probs=40.6
Q ss_pred CceeeEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEEEeCCCeEEEEEEee
Q psy5572 3 EPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~~l~~~g~l~~~lAP 55 (62)
++.+-.|.+.|+-+..|+.+ ++.|.+.|.+.. |+.++- .++....|.|.|
T Consensus 311 ~~~~I~fn~~ylld~l~~~~-~~~v~~~~~~~~~p~~i~~--~~~~~~~~~imP 361 (364)
T COG0592 311 EELKIGFNLAYLLDVLKALD-SEEVQFGFNDSSSPFLIRP--EENDDFKYLIMP 361 (364)
T ss_pred ceEEEEECHHHHHHHHhcCC-CCeEEEEEcCCCCcEEEEe--CCCCCceEEEEE
Confidence 46788999999999999988 899999998766 677665 344558888888
No 33
>PHA03383 PCNA-like protein; Provisional
Probab=75.41 E-value=23 Score=24.24 Aligned_cols=53 Identities=8% Similarity=0.187 Sum_probs=36.6
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCc--EEEEEEeCC-CeEEEEEEe
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVP--LVVEFKIDD-IGHIRYYLA 54 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~P--l~l~~~l~~-~g~l~~~lA 54 (62)
+++.+.-..++.|.++.|.+.-.+.++++...+-| |.+.|.=.. ++.-+|.|.
T Consensus 69 d~~~~iGv~~~~l~KILk~a~~~D~l~l~~~~~~~~~l~i~~~~~~~~~~~~f~l~ 124 (262)
T PHA03383 69 DQTYEIGVNVSNMFKLLRTAGSHDSILFRYLKNSPHFLEITIQNFEKNSLTKFQLK 124 (262)
T ss_pred CCceEEEEEHHHHHHHHhccCCCCEEEEEecCCCCCEEEEEEEeCCCCcEEEEEEE
Confidence 45666778999999999999999999998644444 444444322 334556654
No 34
>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=71.86 E-value=28 Score=23.56 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=38.9
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeC-CCcEEEEEEeCCCeEE-EEEE
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSL-DVPLVVEFKIDDIGHI-RYYL 53 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~-~~Pl~l~~~l~~~g~l-~~~l 53 (62)
+++++--.+++-|.++.|.++-.+.++|+..+ +-+|.+.|.-..+|.+ .|.|
T Consensus 63 d~~~~~gv~l~~l~kiLk~~~~~d~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l 116 (259)
T TIGR00590 63 DRNLALGVNLTSLSKILKCANNEDIVTLKAEDNADTLILVFESPKQDKISDYEL 116 (259)
T ss_pred CCceEEEEEHHHHHHHHhccCCCCEEEEEecCCCCEEEEEEEcCCCCeEEEEEE
Confidence 45666778999999999999999999998654 3578887775445554 3444
No 35
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=62.18 E-value=47 Score=22.56 Aligned_cols=52 Identities=12% Similarity=0.143 Sum_probs=37.3
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCC-CcEEEEEEeCCCeEE-EEEE
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLD-VPLVVEFKIDDIGHI-RYYL 53 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~-~Pl~l~~~l~~~g~l-~~~l 53 (62)
+++.+--.+++-|..+.|.++-.+.++|++.++ -++.+.+.-...|.. +|.|
T Consensus 63 d~~~~~gv~l~~l~kiLk~~~~~d~l~l~~~~~~~~l~i~~~~~~~~~~~~f~l 116 (263)
T PLN00057 63 DRNLSMGINLANMSKILKCAGNDDIITIKADDGGDTVTFMFESPKQDRISDFEL 116 (263)
T ss_pred CCceEEEEEHHHHHHHHhccCCCCEEEEEecCCCCEEEEEEEcCCCceEEEEEE
Confidence 355667788999999999999999999987654 366666554444554 3444
No 36
>PF13351 DUF4099: Protein of unknown function (DUF4099)
Probab=52.19 E-value=43 Score=19.19 Aligned_cols=44 Identities=9% Similarity=0.095 Sum_probs=29.9
Q ss_pred HHhhhcccCC-CceEEEEeeCC----CcEEEEEEeCCCeEEEEEEeecC
Q psy5572 14 LLNFAKAAPL-SNQVCLSMSLD----VPLVVEFKIDDIGHIRYYLAPKI 57 (62)
Q Consensus 14 L~~~~Ka~~l-s~~V~l~l~~~----~Pl~l~~~l~~~g~l~~~lAPri 57 (62)
|..+.+.-.. -=.|++.++.. +|.|+.+.-..+|.+..-+-|.-
T Consensus 27 Le~ll~G~kT~l~~i~~~~~~~~~~~~~arlsl~~~~dG~v~l~i~~ir 75 (85)
T PF13351_consen 27 LEALLNGYKTPLLPISVNFGGGKTIETDARLSLVRDEDGNVDLMIHPIR 75 (85)
T ss_pred HHHHhCCCccCCEEEEEecCCceEEecceEEEEEECCCCCEEEEEeeee
Confidence 5556643322 33455566666 78899998888999998888754
No 37
>COG3110 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.14 E-value=28 Score=23.84 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=25.0
Q ss_pred cCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEeecCCCCCC
Q psy5572 21 APLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPKIESDDN 62 (62)
Q Consensus 21 ~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPrie~e~~ 62 (62)
.+..+...|..+ -|+.+.|+= ..-.+.|. +||++++++
T Consensus 67 ~~~g~d~~ly~S--~plIvtF~~-~n~~lv~~-~P~~rn~re 104 (216)
T COG3110 67 IRLGSDRRLYIS--PPLIVTFNA-QNIDLVFF-LPRLRNERE 104 (216)
T ss_pred cCCCCceeEeec--CCEEEEEcc-cchhheee-ccccccchh
Confidence 344444555444 588888884 34667777 999998754
No 38
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=46.32 E-value=53 Score=18.37 Aligned_cols=33 Identities=15% Similarity=0.231 Sum_probs=20.0
Q ss_pred CceEEEEeeCCCcEEEEEEeCCCeEEEEEEeec
Q psy5572 24 SNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAPK 56 (62)
Q Consensus 24 s~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAPr 56 (62)
+-.+.|+...+.-..+-.-.-.+|...|.|||.
T Consensus 35 g~V~~i~~DP~Rsa~iAlV~~~~g~~~yiiA~e 67 (77)
T PF00181_consen 35 GIVIDIEYDPNRSAPIALVKYEDGEKRYIIAPE 67 (77)
T ss_dssp EEEEEEEEETTTSSEEEEEEETTSEEEEEEEBT
T ss_pred EEEEEEEecCCcCccEEEEEecCCcEEEEEeEC
Confidence 444566666666333333222449999999993
No 39
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=43.24 E-value=57 Score=17.92 Aligned_cols=36 Identities=22% Similarity=0.256 Sum_probs=24.7
Q ss_pred HHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCCCeE
Q psy5572 12 RYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDDIGH 48 (62)
Q Consensus 12 ~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~~g~ 48 (62)
+||..+.+.+.....|++....+ .+.+...=++.|.
T Consensus 2 ~~L~~il~~mg~~~~v~~~~~~~-~i~i~i~~~~~g~ 37 (77)
T cd02414 2 EFLEEVLELMGIEADVDVEEEGD-TVEVNISGDDIGL 37 (77)
T ss_pred hHHHHHHHHcCCCcEEEEEecCC-EEEEEEecCCCCe
Confidence 68999999999988888887443 4555444333343
No 40
>PF03230 Antirestrict: Antirestriction protein; InterPro: IPR004914 This family includes various protein that are involved in antirestriction. The ArdB protein efficiently inhibits restriction by members of the three known families of type I systems of Escherichia coli [].; PDB: 2WJ9_B 2KMG_A.
Probab=42.51 E-value=26 Score=20.86 Aligned_cols=15 Identities=27% Similarity=0.886 Sum_probs=8.4
Q ss_pred EEeCCCeEEEEEEeecCC
Q psy5572 41 FKIDDIGHIRYYLAPKIE 58 (62)
Q Consensus 41 ~~l~~~g~l~~~lAPrie 58 (62)
|++.++| +|+||..+
T Consensus 13 ~~lsnGg---~ymaP~~~ 27 (94)
T PF03230_consen 13 YTLSNGG---FYMAPDSD 27 (94)
T ss_dssp EEETTS----EEEEE---
T ss_pred EEeCCCe---EEeccCCC
Confidence 4666665 89999874
No 41
>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=40.99 E-value=1.1e+02 Score=20.68 Aligned_cols=38 Identities=21% Similarity=0.224 Sum_probs=29.0
Q ss_pred CceeeEEehHHHHhhhcccC-CCceEEEEeeCCCcEEEEEEe
Q psy5572 3 EPVSLNFACRYLLNFAKAAP-LSNQVCLSMSLDVPLVVEFKI 43 (62)
Q Consensus 3 ~~~~~~ysl~YL~~~~Ka~~-ls~~V~l~l~~~~Pl~l~~~l 43 (62)
++.+..+..+||.++.|..+ -.+.|+|.+..+ ++.+..
T Consensus 189 ~~~~~~i~~~~l~~l~k~l~~~~~~v~i~~~~~---~l~i~~ 227 (365)
T cd00140 189 EDFNVIVPRKTLNELLKLLEDDDEEVEISISEN---QILFKL 227 (365)
T ss_pred cCceEEEechHHHHHHHhccCCCCcEEEEEeCC---EEEEEE
Confidence 34566788899999999887 477899999876 455554
No 42
>PF06366 FlhE: Flagellar protein FlhE; InterPro: IPR009420 This family consists of several Enterobacterial FlhE flagellar proteins. The exact function of this family is unknown [].; GO: 0019861 flagellum
Probab=38.14 E-value=31 Score=20.97 Aligned_cols=19 Identities=16% Similarity=0.454 Sum_probs=16.1
Q ss_pred eeCCCcEEEEEEeCCCeEE
Q psy5572 31 MSLDVPLVVEFKIDDIGHI 49 (62)
Q Consensus 31 l~~~~Pl~l~~~l~~~g~l 49 (62)
+..+.|++|.|.+.+.|.|
T Consensus 72 ~~A~~pf~F~~~v~g~G~l 90 (106)
T PF06366_consen 72 LPANEPFRFVFRVPGGGRL 90 (106)
T ss_pred cCCCCCEEEEEEecCCCcc
Confidence 4567899999999998875
No 43
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=35.70 E-value=14 Score=20.58 Aligned_cols=34 Identities=21% Similarity=0.091 Sum_probs=23.4
Q ss_pred CCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEee
Q psy5572 22 PLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 22 ~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAP 55 (62)
.-.|.+.|.+-...++.-+|.+..+|.+.+=+..
T Consensus 14 ~pGD~l~i~v~~~~~l~~~~~V~~dG~I~lP~iG 47 (82)
T PF02563_consen 14 GPGDVLRISVFGWPELSGEYTVDPDGTISLPLIG 47 (82)
T ss_dssp -TT-EEEEEETT-HHHCCSEE--TTSEEEETTTE
T ss_pred CCCCEEEEEEecCCCcccceEECCCCcEeecccc
Confidence 3478999999999998779999999999874433
No 44
>PF12132 DUF3587: Protein of unknown function (DUF3587); InterPro: IPR021982 This entry is represented by Hyposoter fugitivus ichnovirus, Gp7; it is a family of uncharacterised viral proteins.
Probab=35.27 E-value=61 Score=21.79 Aligned_cols=22 Identities=18% Similarity=0.443 Sum_probs=19.4
Q ss_pred CceEEEEeeCCCcEEEEEEeCC
Q psy5572 24 SNQVCLSMSLDVPLVVEFKIDD 45 (62)
Q Consensus 24 s~~V~l~l~~~~Pl~l~~~l~~ 45 (62)
.-+++..|=++++|.++|+++.
T Consensus 59 t~~~~ttF~NGK~L~IeYnfDp 80 (199)
T PF12132_consen 59 THKITTTFLNGKPLEIEYNFDP 80 (199)
T ss_pred cceEEEEEECCcEEEEEEecCC
Confidence 3578899999999999999985
No 45
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=34.60 E-value=53 Score=18.38 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=10.8
Q ss_pred EEEEEeCCCeEEEEEEeec
Q psy5572 38 VVEFKIDDIGHIRYYLAPK 56 (62)
Q Consensus 38 ~l~~~l~~~g~l~~~lAPr 56 (62)
++-++-.+.|.+.+|+|=|
T Consensus 2 kVmiR~~~~G~ls~YVpKK 20 (64)
T PF06988_consen 2 KVMIRKNGAGGLSAYVPKK 20 (64)
T ss_dssp -EEEEE-SS--EEEEETTT
T ss_pred eEEEEeCCCcCEEEEEeCC
Confidence 4556666788999999743
No 46
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=34.57 E-value=40 Score=27.19 Aligned_cols=33 Identities=24% Similarity=0.299 Sum_probs=26.2
Q ss_pred ccCCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEe
Q psy5572 20 AAPLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLA 54 (62)
Q Consensus 20 a~~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lA 54 (62)
|..|.++++|.+++ |+.++=.-...|.+.||+-
T Consensus 398 al~l~dt~qi~ls~--p~~~t~~~kaq~~isf~fg 430 (1001)
T COG5406 398 ALLLIDTEQISLSN--PIVFTDSPKAQGDISFLFG 430 (1001)
T ss_pred hhhhccceEeecCC--ceecccCcccccceeEEec
Confidence 56788999999998 8666555556799999987
No 47
>PRK01115 DNA polymerase sliding clamp; Validated
Probab=34.25 E-value=1.3e+02 Score=19.50 Aligned_cols=53 Identities=15% Similarity=0.212 Sum_probs=33.5
Q ss_pred ceeeEEehHHHHhhhcccCCCceEEEEee-CCCcEEEEEEeCCCeEEEEEEeecCCC
Q psy5572 4 PVSLNFACRYLLNFAKAAPLSNQVCLSMS-LDVPLVVEFKIDDIGHIRYYLAPKIES 59 (62)
Q Consensus 4 ~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~-~~~Pl~l~~~l~~~g~l~~~lAPrie~ 59 (62)
|.+..-+++-|..+.|...-.+.|+|.+. ++..+.+++. + |....+..+-+|.
T Consensus 65 ~~~~~v~l~~l~~il~~~~~~~~v~i~~~~~~~~l~~~~~--~-~~~~~~~~~Lieg 118 (247)
T PRK01115 65 EEKIGVDLEDLKKILKRAKKGDKLELELDEEENKLKITFG--G-EKTREFSLPLLDV 118 (247)
T ss_pred CeEEEEEHHHHHHHHhhCCCCCEEEEEEcCCCCEEEEEEe--c-CcEEEEEEEeecc
Confidence 33445688889999988766788999983 2345665553 3 4444444444543
No 48
>COG1951 TtdA Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion]
Probab=32.76 E-value=64 Score=23.07 Aligned_cols=29 Identities=14% Similarity=0.149 Sum_probs=24.6
Q ss_pred EEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572 29 LSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57 (62)
Q Consensus 29 l~l~~~~Pl~l~~~l~~~g~l~~~lAPri 57 (62)
..-+++.|-.+.+++.++..++++++|+=
T Consensus 119 ~NtgdNtpa~i~~~~v~gd~v~i~~~~KG 147 (297)
T COG1951 119 VNTGDNTPAQIHVEIVPGDEVEILVAAKG 147 (297)
T ss_pred ccCCCCCCCeEEEEEcCCCcEEEEEEecC
Confidence 45578889999999988888999999974
No 49
>PF11306 DUF3108: Protein of unknown function (DUF3108); InterPro: IPR021457 This bacterial family of proteins has no known function. ; PDB: 3FZX_A.
Probab=28.27 E-value=1.5e+02 Score=18.39 Aligned_cols=29 Identities=17% Similarity=0.115 Sum_probs=16.3
Q ss_pred ceEEEEeeCC----CcEEEEEEeCCCeEEEEEE
Q psy5572 25 NQVCLSMSLD----VPLVVEFKIDDIGHIRYYL 53 (62)
Q Consensus 25 ~~V~l~l~~~----~Pl~l~~~l~~~g~l~~~l 53 (62)
..+++=|+.+ .|+|++.....++.+..-|
T Consensus 202 ~~~~~W~a~~d~~~vPVri~~~~~~g~~~~~~L 234 (238)
T PF11306_consen 202 RRTTIWFAPPDLNYVPVRIEAKEPIGKTVTMEL 234 (238)
T ss_dssp EEEEEEEETT----TEEEEEEEETS-EEEEEEE
T ss_pred cEEEEEEECCCcceEEEEEEEEeCCCcEEEEEE
Confidence 4556666644 6777776665433555443
No 50
>PF00262 Calreticulin: Calreticulin family; InterPro: IPR001580 Synonym(s): Calregulin, CRP55, HACBP Calreticulin [] is a high-capacity calcium-binding protein which is present in most tissues and located at the periphery of the endoplasmic (ER) and the sarcoplamic reticulum (SR) membranes. It probably plays a role in the storage of calcium in the lumen of the ER and SR and it may well have other important functions. Structurally, calreticulin is a protein of about 400 amino acid residues consisting of three domains: An N-terminal, probably globular, domain of about 180 amino acid residues (N-domain). A central domain of about 70 residues (P-domain) which contains three repeats of an acidic 17 amino acid motif. This region binds calcium with a low-capacity, but a high-affinity. A C-terminal domain rich in acidic residues and in lysine (C-domain). This region binds calcium with a high-capacity but a low-affinity. Calreticulin is evolutionarily related to several other calcium-binding proteins, including Onchocerca volvulus antigen RAL-1, calnexin [] and calmegin [].; GO: 0005509 calcium ion binding; PDB: 3POS_C 3DOW_B 3POW_A 1HHN_A 1K9C_A 1K91_A 3O0X_B 3O0W_A 3RG0_A 3O0V_A ....
Probab=28.23 E-value=51 Score=24.10 Aligned_cols=21 Identities=29% Similarity=0.404 Sum_probs=15.0
Q ss_pred CCcEEEEEEeC-------CCeEEEEEEe
Q psy5572 34 DVPLVVEFKID-------DIGHIRYYLA 54 (62)
Q Consensus 34 ~~Pl~l~~~l~-------~~g~l~~~lA 54 (62)
+.+|.|+|++. +||+|+++=+
T Consensus 75 ~k~LVvQYeVK~q~~idCGGaYIKLL~~ 102 (367)
T PF00262_consen 75 DKDLVVQYEVKFQQGIDCGGAYIKLLPA 102 (367)
T ss_dssp TS-EEEEEEEEETT--SEEE--EEEEBT
T ss_pred CCcEEEEEEEEeecceeccceEEEEecC
Confidence 79999999886 5789998765
No 51
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=28.02 E-value=48 Score=18.95 Aligned_cols=32 Identities=16% Similarity=0.283 Sum_probs=26.7
Q ss_pred CceEEEEeeCCCcEEEEEEeCCCeEEEEEEee
Q psy5572 24 SNQVCLSMSLDVPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 24 s~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lAP 55 (62)
-.+|.+-+-++.|.-++|.+.++..+..|=+.
T Consensus 46 ~tEV~~i~vNG~~v~~~~~~~~Gd~v~V~P~~ 77 (81)
T PF14451_consen 46 HTEVGLILVNGRPVDFDYRLKDGDRVAVYPVF 77 (81)
T ss_pred hHHeEEEEECCEECCCcccCCCCCEEEEEecc
Confidence 35789999999999999999988888877443
No 52
>COG3294 HD supefamily hydrolase [General function prediction only]
Probab=26.94 E-value=66 Score=22.65 Aligned_cols=35 Identities=20% Similarity=0.367 Sum_probs=26.9
Q ss_pred CceEEEEeeCCCcEEEEEEeCC-Ce--EEEEEEeecCC
Q psy5572 24 SNQVCLSMSLDVPLVVEFKIDD-IG--HIRYYLAPKIE 58 (62)
Q Consensus 24 s~~V~l~l~~~~Pl~l~~~l~~-~g--~l~~~lAPrie 58 (62)
=++|.|.=|.+.|++++..+.+ .| ++.=.|+||+.
T Consensus 204 I~rV~i~~g~~rPv~IeV~M~n~aGvfQVe~vL~~Ki~ 241 (269)
T COG3294 204 IERVEIQEGDERPVRIEVEMQNEAGVFQVEEVLGEKIH 241 (269)
T ss_pred hhheeeccCCcCcEEEEEEEcccCceeeHHHHHhhHhh
Confidence 4789999999999999999976 34 34455666653
No 53
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=26.79 E-value=2.2e+02 Score=19.70 Aligned_cols=43 Identities=9% Similarity=0.123 Sum_probs=32.7
Q ss_pred CCceeeEEehHHHHhhhcccCCCceEEEEeeCCCcEEEEEEeCC
Q psy5572 2 QEPVSLNFACRYLLNFAKAAPLSNQVCLSMSLDVPLVVEFKIDD 45 (62)
Q Consensus 2 ~~~~~~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~Pl~l~~~l~~ 45 (62)
+++.+.-.+++.|.++.|.+.-.+.|+|+.. +-|=++.+.+.+
T Consensus 63 d~~~~lGvn~~~l~KILk~~~~~D~l~l~~~-~~~~~l~i~~~~ 105 (275)
T PTZ00113 63 DRERALGINIASVTKVFKLCSNNDSVLIQSE-EDKDNINFVFEN 105 (275)
T ss_pred CCCcEEEEEHHHHHHHHHhCCCCCEEEEEEc-CCCCEEEEEEEc
Confidence 4566777899999999999999999999863 445445555544
No 54
>PF03723 Hemocyanin_C: Hemocyanin, ig-like domain; InterPro: IPR005203 Haemocyanins are copper-containing oxygen transport proteins found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases [], but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit []. Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases []. Larval storage proteins (LSP) [] are proteins from the hemolymph of insects, which may serve as a store of amino acids for synthesis of adult proteins. There are two classes of LSP's, arylphorins, which are rich in aromatic amino acids, and methionine-rich LSP's. LSP's forms hexameric complexes. LSP's are structurally related to arthropods hemocyanins.; PDB: 3HHS_A 1HCY_A 1HC1_C 1LL1_A 1NOL_A 1LLA_A 1OXY_A 3IXV_E 3IXW_L 3GWJ_F ....
Probab=26.55 E-value=82 Score=21.51 Aligned_cols=29 Identities=17% Similarity=0.387 Sum_probs=18.6
Q ss_pred eeCCCcEEEEEEeCC----CeEEEEEEeecCCC
Q psy5572 31 MSLDVPLVVEFKIDD----IGHIRYYLAPKIES 59 (62)
Q Consensus 31 l~~~~Pl~l~~~l~~----~g~l~~~lAPrie~ 59 (62)
-=+..|-....++.+ .+.++.||||+.++
T Consensus 55 rLnHkpF~y~i~V~s~~~~~~~VRiFL~Pk~D~ 87 (250)
T PF03723_consen 55 RLNHKPFTYKINVNSDKAQDAVVRIFLGPKYDE 87 (250)
T ss_dssp EEEE--EEEEEEEEESSSSEEEEEEEEEESB-T
T ss_pred ecCCCcEEEEEEEEcCCCCeEEEEEEeCccccc
Confidence 335567777776653 35899999999875
No 55
>PF05681 Fumerase: Fumarate hydratase (Fumerase); InterPro: IPR004646 This entry represents various Fe-S type hydro-lyases, including the alpha subunit from both L-tartrate dehydratase (TtdA; 4.2.1.32 from EC) and class 1 fumarate hydratases (4.2.1.2 from EC), which includes both aerobic (FumA) and anaerobic (FumB) types []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this group is unknown. Fumarate hydratase (also known as fumarase) is a component of the citric acid cycle. In facultative anaerobes such as E. coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre [].; GO: 0016829 lyase activity
Probab=25.71 E-value=1.2e+02 Score=21.21 Aligned_cols=29 Identities=14% Similarity=0.187 Sum_probs=23.8
Q ss_pred EEeeCCCcEEEEEEeCCCeEEEEEEeecC
Q psy5572 29 LSMSLDVPLVVEFKIDDIGHIRYYLAPKI 57 (62)
Q Consensus 29 l~l~~~~Pl~l~~~l~~~g~l~~~lAPri 57 (62)
..-+++.|..+.|.+-++-+++..+.|+=
T Consensus 109 ~Ntgdn~P~ii~~~~v~gd~l~i~~~~KG 137 (271)
T PF05681_consen 109 KNTGDNTPAIIHIEIVPGDKLEITVLPKG 137 (271)
T ss_pred ccCCCCCCceEEEEEcCCCEEEEEEEecC
Confidence 44566899999999988788999998874
No 56
>PF05340 DUF740: Protein of unknown function (DUF740); InterPro: IPR008004 This family consists of several uncharacterised plant chloroplastic proteins of unknown function.
Probab=25.31 E-value=45 Score=26.06 Aligned_cols=12 Identities=50% Similarity=1.065 Sum_probs=10.5
Q ss_pred CCeEEEEEEeec
Q psy5572 45 DIGHIRYYLAPK 56 (62)
Q Consensus 45 ~~g~l~~~lAPr 56 (62)
++|-|+|||.|-
T Consensus 583 DNGmLRFYLTPm 594 (603)
T PF05340_consen 583 DNGMLRFYLTPM 594 (603)
T ss_pred cCceEEEEeccc
Confidence 679999999993
No 57
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=25.25 E-value=49 Score=16.87 Aligned_cols=35 Identities=20% Similarity=0.353 Sum_probs=21.6
Q ss_pred eEEehHHHHhhhcccCCCceEEEEeeCCC-cEEEEE
Q psy5572 7 LNFACRYLLNFAKAAPLSNQVCLSMSLDV-PLVVEF 41 (62)
Q Consensus 7 ~~ysl~YL~~~~Ka~~ls~~V~l~l~~~~-Pl~l~~ 41 (62)
.+|.+.|=..-.+..=-.++|++.+.++- |+.+..
T Consensus 10 l~F~~~~rg~~l~v~i~~~~v~v~~~~g~~~l~i~v 45 (54)
T PF03633_consen 10 LSFRLRYRGHWLEVEITHEKVTVTLLSGDAPLTIKV 45 (54)
T ss_dssp EEEEEEETTEEEEEEEETTEEEEEEEESS--EEEEE
T ss_pred eEEEEEECCEEEEEEEECCEEEEEEccCCccEEEEE
Confidence 45666666665554444677888888775 766543
No 58
>COG5138 Uncharacterized conserved protein [Function unknown]
Probab=23.33 E-value=53 Score=21.55 Aligned_cols=19 Identities=21% Similarity=0.455 Sum_probs=15.5
Q ss_pred eCCCcEEEEEEeCCCeEEE
Q psy5572 32 SLDVPLVVEFKIDDIGHIR 50 (62)
Q Consensus 32 ~~~~Pl~l~~~l~~~g~l~ 50 (62)
++..|+++++.|.+-|++.
T Consensus 13 ~s~ipctf~~~IpglG~l~ 31 (168)
T COG5138 13 ESRIPCTFKHKIPGLGFLG 31 (168)
T ss_pred CCccceeeEeecCCcccCC
Confidence 4567999999999988654
No 59
>PRK08312 putative indolepyruvate oxidoreductase subunit B; Reviewed
Probab=23.19 E-value=40 Score=25.60 Aligned_cols=14 Identities=21% Similarity=0.622 Sum_probs=11.3
Q ss_pred CeEEEEEEeecCCC
Q psy5572 46 IGHIRYYLAPKIES 59 (62)
Q Consensus 46 ~g~l~~~lAPrie~ 59 (62)
..+++|+|||++.+
T Consensus 341 ~~~~~~~laPp~~~ 354 (510)
T PRK08312 341 IVQVTEFMHPRLEE 354 (510)
T ss_pred cceEEEeeCCcHHh
Confidence 45899999998763
No 60
>cd05172 PIKKc_DNA-PK DNA-dependent protein kinase (DNA-PK), catalytic domain; The DNA-PK catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. DNA-PK is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). DNA-PK is comprised of a regulatory subunit, containing the Ku70/80 subunit, and a catalytic subunit, which contains a NUC194 domain of unknown function, a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. It is part of a multi-component system involved in non-homologous end joining (NHEJ), a process of repairing double st
Probab=22.58 E-value=2.5e+02 Score=18.80 Aligned_cols=33 Identities=15% Similarity=0.205 Sum_probs=26.6
Q ss_pred CCCceEEEEeeCCCcEEEEEEeCCCeEEEEEEe
Q psy5572 22 PLSNQVCLSMSLDVPLVVEFKIDDIGHIRYYLA 54 (62)
Q Consensus 22 ~ls~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lA 54 (62)
...++|+|-=+...|.++.+.-.++....|.+-
T Consensus 3 ~~~~~v~v~~S~~~Pkri~~~~~dG~~~~fl~K 35 (235)
T cd05172 3 GFDERVLVLSSLRKPKRITIRGSDEKEYPFLVK 35 (235)
T ss_pred CcCCceEEeccCCCCEEEEEECCCCCEEEEEEE
Confidence 567889999899999999999766556777774
No 61
>cd02847 Chitobiase_C_term Chitobiase C-terminus domain. Chitobiase (AKA N-acetylglucosaminidase) digests the beta, 1-4 glycosidic bonds of the N-acetylglucosamine (NAG) oligomers found in chitin, an important structural element of fungal cell wall and arthropod exoskeletons. It is thought to proceed through an acid-base reaction mechanism, in which one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction with retention of the anomeric configuration. The C-terminus of chitobiase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chit
Probab=22.46 E-value=1.2e+02 Score=17.24 Aligned_cols=31 Identities=23% Similarity=0.360 Sum_probs=21.8
Q ss_pred ceEEEEeeCCCc-EEEEEEeCCCeEEEEEEee
Q psy5572 25 NQVCLSMSLDVP-LVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 25 ~~V~l~l~~~~P-l~l~~~l~~~g~l~~~lAP 55 (62)
+.-+|.+...+| +.++|.+++++.=.-|=+|
T Consensus 20 ~~g~l~~n~~~pg~~i~Yt~dgg~~w~~Y~~p 51 (78)
T cd02847 20 ENGKLEMNVSLPGLTLQYSTDGGKNWNIYDAA 51 (78)
T ss_pred EcCEEEEeccCCCcEEEEEecCCccCeecccc
Confidence 345677788899 9999999865544445444
No 62
>PF02792 Mago_nashi: Mago nashi protein; InterPro: IPR004023 This family was originally identified in drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene []. The human homologue has been shown to interact with an RNA binding protein, ribonucleoprotein rbm8 (Q9Y5S9 from SWISSPROT) []. An RNAi knockout of the Caenorhabditis elegans homologue causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination [] but the protein is also found in hermaphrodites and other organisms without a sexual differentiation.; GO: 0005634 nucleus; PDB: 2XB2_Y 2J0S_C 3EX7_A 2J0Q_F 1P27_C 2HYI_A 2X1G_B 1HL6_B 1RK8_B 1OO0_A ....
Probab=21.98 E-value=75 Score=20.48 Aligned_cols=17 Identities=29% Similarity=0.528 Sum_probs=12.6
Q ss_pred EEEEEeCCCeEEEEEEe
Q psy5572 38 VVEFKIDDIGHIRYYLA 54 (62)
Q Consensus 38 ~l~~~l~~~g~l~~~lA 54 (62)
.++|++..+|.++|.=-
T Consensus 18 fLEfEfr~dG~lRYaNn 34 (143)
T PF02792_consen 18 FLEFEFRPDGKLRYANN 34 (143)
T ss_dssp EEEEEEETTSEEEEEEE
T ss_pred EEEEEeccCCeEEEccc
Confidence 36788888899988543
No 63
>PF11359 gpUL132: Glycoprotein UL132; InterPro: IPR021023 Glycoprotein UL132 is a low-abundance structural component of Human herpesvirus 5 []. The function of this protein is not fully understood.
Probab=21.01 E-value=94 Score=21.51 Aligned_cols=38 Identities=32% Similarity=0.515 Sum_probs=29.9
Q ss_pred hhcccCC-CceEEEEeeCCCcEEEEEEeCCCeEEEEEEe
Q psy5572 17 FAKAAPL-SNQVCLSMSLDVPLVVEFKIDDIGHIRYYLA 54 (62)
Q Consensus 17 ~~Ka~~l-s~~V~l~l~~~~Pl~l~~~l~~~g~l~~~lA 54 (62)
|-|--.| -..|.=..|.+.||.|+=...++-.|+||+.
T Consensus 159 f~k~gnldtsfvnpnyg~~spm~ies~~~d~e~i~yy~s 197 (235)
T PF11359_consen 159 FDKDGNLDTSFVNPNYGRGSPMTIESHADDDENIRYYMS 197 (235)
T ss_pred EccCCCccceeeCCCCCCCCCceeecccCCccceeEEee
Confidence 4444455 5566677889999999999999899999985
No 64
>cd01242 PH_ROK Rok (Rho- associated kinase) pleckstrin homology (PH) domain. Rok (Rho- associated kinase) pleckstrin homology (PH) domain. Rok is a serine/threonine kinase that binds GTP-rho. It consists of a kinase domain, a coiled coil region and a PH domain. The Rok PH domain is interrupted by a C1 domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=20.96 E-value=1.6e+02 Score=18.21 Aligned_cols=28 Identities=14% Similarity=0.267 Sum_probs=22.5
Q ss_pred eeCCCcEEEEEEeCCCeEEEEEEeecCC
Q psy5572 31 MSLDVPLVVEFKIDDIGHIRYYLAPKIE 58 (62)
Q Consensus 31 l~~~~Pl~l~~~l~~~g~l~~~lAPrie 58 (62)
=.+|.|-.|....++.+.-.++|||..+
T Consensus 70 ~~kDiP~IF~I~~~~~~~~lllLA~s~~ 97 (112)
T cd01242 70 DAKEIPKIFQILYANEARDLLLLAPQTD 97 (112)
T ss_pred CcccCCeEEEEEeCCccceEEEEeCCch
Confidence 4578899888888777888999998654
No 65
>PF02767 DNA_pol3_beta_2: DNA polymerase III beta subunit, central domain; InterPro: IPR022637 This entry describes the central 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: 3T0P_B 3P16_A 3RB9_B 2AWA_C 1VPK_A 2AVT_B 2XUR_B 3Q4K_A 3BEP_A 3D1G_A ....
Probab=20.92 E-value=1.9e+02 Score=16.73 Aligned_cols=38 Identities=24% Similarity=0.298 Sum_probs=29.0
Q ss_pred eeeEEehHHHHhhhcccCC-CceEEEEeeCCCcEEEEEEeCC
Q psy5572 5 VSLNFACRYLLNFAKAAPL-SNQVCLSMSLDVPLVVEFKIDD 45 (62)
Q Consensus 5 ~~~~ysl~YL~~~~Ka~~l-s~~V~l~l~~~~Pl~l~~~l~~ 45 (62)
.+...+.+.|+.+.|...- .+.|+|.++.++ +.|..++
T Consensus 64 ~~~iIp~k~l~~l~k~l~~~~~~v~i~~~~~~---i~f~~~~ 102 (116)
T PF02767_consen 64 FSFIIPAKALKELKKLLSDEDEEVEISISDNQ---IIFKFDN 102 (116)
T ss_dssp EEEEEEHHHHHHHHHHSSTTSSEEEEEEESSE---EEEEESS
T ss_pred eEEEEechHHHHHhhhcccCCceEEEEEcCCE---EEEEECC
Confidence 5567778999999998887 889999999654 4455543
No 66
>COG0588 GpmA Phosphoglycerate mutase 1 [Carbohydrate transport and metabolism]
Probab=20.11 E-value=67 Score=22.23 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=18.0
Q ss_pred ccCCCceEEEEeeCCCcEEEEEE
Q psy5572 20 AAPLSNQVCLSMSLDVPLVVEFK 42 (62)
Q Consensus 20 a~~ls~~V~l~l~~~~Pl~l~~~ 42 (62)
-.+-.+-+.+.+.++.||.++++
T Consensus 195 ~iSd~dI~~l~IPtg~Plvyeld 217 (230)
T COG0588 195 GISDEDILDLNIPTGIPLVYELD 217 (230)
T ss_pred CCCHHHhhhcccCCCCcEEEEEC
Confidence 33446778899999999987775
No 67
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=20.09 E-value=1.4e+02 Score=18.27 Aligned_cols=26 Identities=8% Similarity=0.229 Sum_probs=18.5
Q ss_pred EeeCCCcEEEEEEeCCCeEEEEEEee
Q psy5572 30 SMSLDVPLVVEFKIDDIGHIRYYLAP 55 (62)
Q Consensus 30 ~l~~~~Pl~l~~~l~~~g~l~~~lAP 55 (62)
.|.+.-=+.++++..+.|.+.+++.|
T Consensus 127 ~~~~~~~~~l~~~~~~~~~l~w~~~p 152 (152)
T TIGR00249 127 MFTTGAIASLLWDESKNGTLNWQMSP 152 (152)
T ss_pred cCcceeEEEEEEecCCCeEEEEecCC
Confidence 45555556677766667899999876
Done!