Query 015213
Match_columns 411
No_of_seqs 134 out of 201
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:10:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015213hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3056 Protein required for S 100.0 7.3E-57 1.6E-61 465.7 16.8 318 1-339 63-398 (578)
2 PF09329 zf-primase: Primase z 99.7 3.4E-18 7.4E-23 126.5 1.3 46 217-262 1-46 (46)
3 cd04474 RPA1_DBD_A RPA1_DBD_A: 97.4 0.0022 4.7E-08 54.4 10.8 83 128-210 8-99 (104)
4 cd04497 hPOT1_OB1_like hPOT1_O 96.6 0.036 7.7E-07 49.4 11.9 82 112-198 2-86 (138)
5 cd04490 PolII_SU_OBF PolII_SU_ 95.7 0.035 7.6E-07 45.2 6.4 53 132-190 2-57 (79)
6 TIGR00617 rpa1 replication fac 95.7 0.073 1.6E-06 58.3 10.7 80 111-198 178-262 (608)
7 cd03524 RPA2_OBF_family RPA2_O 95.2 0.1 2.3E-06 38.3 7.1 60 134-197 2-62 (75)
8 PF01336 tRNA_anti-codon: OB-f 95.2 0.089 1.9E-06 40.2 6.8 70 132-209 1-71 (75)
9 PRK07211 replication factor A; 95.0 0.15 3.3E-06 54.7 10.3 86 128-216 170-259 (485)
10 cd04485 DnaE_OBF DnaE_OBF: A s 94.7 0.1 2.2E-06 40.1 6.0 71 134-209 2-73 (84)
11 PRK12366 replication factor A; 94.6 0.16 3.5E-06 55.9 9.5 81 131-213 293-380 (637)
12 cd04491 SoSSB_OBF SoSSB_OBF: A 94.2 0.56 1.2E-05 37.6 9.4 75 134-213 2-79 (82)
13 PRK15491 replication factor A; 93.8 0.46 9.9E-06 49.3 10.3 87 129-216 176-266 (374)
14 PRK12366 replication factor A; 93.5 0.67 1.5E-05 51.2 11.5 68 129-197 73-144 (637)
15 PRK08402 replication factor A; 93.4 0.6 1.3E-05 48.3 10.4 78 130-209 73-155 (355)
16 cd04492 YhaM_OBF_like YhaM_OBF 93.3 0.23 4.9E-06 38.7 5.5 58 136-196 4-61 (83)
17 cd04475 RPA1_DBD_B RPA1_DBD_B: 92.9 1.1 2.4E-05 37.2 9.5 64 134-198 4-72 (101)
18 cd04489 ExoVII_LU_OBF ExoVII_L 92.6 0.57 1.2E-05 36.6 7.0 52 133-190 3-55 (78)
19 PRK06461 single-stranded DNA-b 92.0 1.1 2.5E-05 39.6 8.9 83 130-218 15-100 (129)
20 KOG3416 Predicted nucleic acid 91.5 1.3 2.9E-05 40.0 8.6 83 129-217 14-96 (134)
21 PF02765 POT1: Telomeric singl 91.2 0.53 1.1E-05 42.2 6.0 71 128-198 11-91 (146)
22 PRK07373 DNA polymerase III su 91.0 0.81 1.7E-05 48.7 8.1 109 89-209 246-356 (449)
23 cd04481 RPA1_DBD_B_like RPA1_D 90.0 2.5 5.4E-05 35.7 8.7 65 134-198 2-75 (106)
24 PRK15491 replication factor A; 89.9 2.6 5.5E-05 43.9 10.5 62 129-191 67-134 (374)
25 PRK05673 dnaE DNA polymerase I 89.7 0.96 2.1E-05 53.2 8.0 110 89-210 943-1054(1135)
26 TIGR00617 rpa1 replication fac 89.7 2.5 5.5E-05 46.6 10.8 95 111-213 296-395 (608)
27 PRK14699 replication factor A; 89.4 2.1 4.5E-05 46.1 9.5 81 129-209 286-369 (484)
28 PRK02801 primosomal replicatio 86.2 3.2 6.9E-05 35.3 7.1 60 131-190 4-75 (101)
29 PRK07211 replication factor A; 83.5 6.6 0.00014 42.5 9.5 89 131-223 280-372 (485)
30 PRK07374 dnaE DNA polymerase I 83.5 3.6 7.8E-05 48.8 8.1 110 89-210 966-1077(1170)
31 cd04496 SSB_OBF SSB_OBF: A sub 83.1 5.1 0.00011 32.3 6.7 59 133-191 2-72 (100)
32 PRK06920 dnaE DNA polymerase I 82.8 3.9 8.4E-05 48.3 8.0 76 130-210 943-1020(1107)
33 PRK06826 dnaE DNA polymerase I 82.2 4.3 9.4E-05 48.0 8.1 116 89-209 948-1068(1151)
34 PRK14699 replication factor A; 79.7 8.3 0.00018 41.6 8.7 82 130-213 396-481 (484)
35 PRK05672 dnaE2 error-prone DNA 77.7 6.6 0.00014 46.1 7.7 106 90-209 920-1027(1046)
36 PF00436 SSB: Single-strand bi 74.6 6.3 0.00014 32.2 4.8 60 132-191 4-76 (104)
37 PRK07279 dnaE DNA polymerase I 70.9 11 0.00023 44.4 7.1 72 133-209 888-961 (1034)
38 PF13891 zf-C3Hc3H: Potential 69.5 2.2 4.8E-05 33.7 0.9 30 222-251 33-64 (65)
39 PF07750 GcrA: GcrA cell cycle 67.3 2 4.4E-05 39.8 0.4 47 205-262 111-159 (162)
40 PRK07135 dnaE DNA polymerase I 67.1 12 0.00025 43.9 6.4 55 132-189 900-954 (973)
41 PRK06752 single-stranded DNA-b 62.1 32 0.0007 29.5 6.8 61 132-192 5-76 (112)
42 COG0587 DnaE DNA polymerase II 61.1 23 0.00049 42.2 7.3 65 131-196 978-1042(1139)
43 PRK07274 single-stranded DNA-b 59.8 36 0.00079 30.1 6.9 60 132-191 5-75 (131)
44 PRK06386 replication factor A; 59.2 84 0.0018 32.9 10.4 72 129-209 116-190 (358)
45 TIGR00621 ssb single stranded 56.8 45 0.00098 30.7 7.2 61 131-191 6-79 (164)
46 PRK07772 single-stranded DNA-b 55.8 85 0.0018 29.9 9.0 96 130-229 5-119 (186)
47 PF13742 tRNA_anti_2: OB-fold 54.7 48 0.001 27.9 6.5 72 130-209 22-96 (99)
48 PRK07459 single-stranded DNA-b 54.7 50 0.0011 29.0 6.8 60 132-191 6-72 (121)
49 PRK13480 3'-5' exoribonuclease 53.5 40 0.00086 34.5 6.8 64 132-198 14-77 (314)
50 PF09104 BRCA-2_OB3: BRCA2, ol 52.1 32 0.00069 31.7 5.3 95 128-240 17-114 (143)
51 PRK08486 single-stranded DNA-b 51.3 57 0.0012 30.9 7.0 88 132-220 5-109 (182)
52 PRK06642 single-stranded DNA-b 48.7 70 0.0015 29.3 7.0 61 131-191 7-82 (152)
53 PRK05813 single-stranded DNA-b 48.6 71 0.0015 31.2 7.4 63 130-192 110-176 (219)
54 PRK06293 single-stranded DNA-b 48.5 67 0.0014 30.0 6.9 61 132-192 4-72 (161)
55 PRK06751 single-stranded DNA-b 46.6 79 0.0017 29.7 7.2 61 131-191 4-75 (173)
56 PRK07218 replication factor A; 45.8 2.1E+02 0.0046 30.7 11.0 77 129-213 171-251 (423)
57 PRK05733 single-stranded DNA-b 44.2 85 0.0018 29.5 7.0 87 131-217 7-112 (172)
58 PRK08763 single-stranded DNA-b 42.5 1.1E+02 0.0023 28.6 7.3 62 131-192 7-81 (164)
59 PRK13732 single-stranded DNA-b 41.9 1.1E+02 0.0024 28.8 7.4 62 130-191 7-82 (175)
60 PRK07275 single-stranded DNA-b 40.8 1.2E+02 0.0025 28.3 7.2 63 131-193 4-77 (162)
61 PRK06341 single-stranded DNA-b 40.7 1.1E+02 0.0023 28.7 7.0 80 131-210 7-107 (166)
62 cd04488 RecG_wedge_OBF RecG_we 38.1 1.5E+02 0.0032 21.9 6.4 53 134-190 2-55 (75)
63 PRK08182 single-stranded DNA-b 35.9 1.4E+02 0.0031 27.1 6.9 64 131-194 4-85 (148)
64 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 32.3 1.6E+02 0.0035 25.7 6.3 59 134-197 2-63 (100)
65 cd04484 polC_OBF polC_OBF: A s 31.3 1.9E+02 0.0041 23.5 6.3 73 132-207 2-76 (82)
66 PRK06958 single-stranded DNA-b 31.2 1.8E+02 0.0038 27.8 6.9 61 131-191 6-80 (182)
67 PF07708 Tash_PEST: Tash prote 30.6 37 0.0008 21.4 1.5 13 398-410 6-18 (19)
68 COG5352 Uncharacterized protei 28.8 21 0.00046 33.1 0.4 16 244-259 148-163 (169)
69 PRK09010 single-stranded DNA-b 27.0 2.6E+02 0.0057 26.4 7.3 62 130-191 7-82 (177)
70 KOG4757 Predicted telomere bin 25.9 1.6E+02 0.0034 32.1 6.1 83 109-196 5-90 (522)
71 cd04482 RPA2_OBF_like RPA2_OBF 24.6 3E+02 0.0065 22.8 6.5 52 134-190 3-57 (91)
72 PF10983 DUF2793: Protein of u 24.5 33 0.00071 29.0 0.7 30 8-41 8-39 (87)
73 PRK06863 single-stranded DNA-b 24.1 2.7E+02 0.0059 26.1 6.8 61 131-191 6-80 (168)
74 PF08879 WRC: WRC; InterPro: 23.0 50 0.0011 24.9 1.4 33 221-254 3-35 (46)
75 PRK07218 replication factor A; 22.9 3.9E+02 0.0085 28.7 8.5 80 130-217 68-150 (423)
76 cd04487 RecJ_OBF2_like RecJ_OB 22.3 4.1E+02 0.0089 21.2 7.7 65 134-209 3-69 (73)
77 PRK00036 primosomal replicatio 21.2 4.5E+02 0.0097 23.2 7.1 77 130-209 2-92 (107)
No 1
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7.3e-57 Score=465.68 Aligned_cols=318 Identities=30% Similarity=0.409 Sum_probs=247.0
Q ss_pred CCCcccccccccccccccccCCCCCCCCCCC----------CCCCCCCCCCCCCCCCCCchhHhHhhhhhccCCCCCcCC
Q 015213 1 MSNHQEDLSLLLSLQDKFLETPPGSPSNPGS----------SSPGYLSDDGSPRQRGQVDMSAFRNIVQDCLDYEPKPVD 70 (411)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~p~~~~~~d~s~fr~~v~d~l~~~p~~~~ 70 (411)
|...++|.++|+.+.|++++|+++++.+... .+.+|.+++.++......+.+-+|.+++| +..|.
T Consensus 63 ~~~~~~~~~~~~l~~~~~~~t~~~s~~~~p~~~~~k~~~~~~~~a~~~~~ks~~k~~~~~~~r~~~v~~d--ee~~~--- 137 (578)
T KOG3056|consen 63 NRTQQGDKFELELIVDKRLETKQGSLQKKPPGPTPSYFMEKFTNAKKTEDKSIKKNESSMNTRVRTVGTD--EEKPI--- 137 (578)
T ss_pred ccccccchhhhhhhhhhhhccccccccCCCCCCCcchhhhhhcccccCcchhhhhcCccCCCCceeeccc--cccce---
Confidence 4567899999999999999999999855331 22355667777777777777777777777 22122
Q ss_pred CCCCcccCCCCCCCcccCCcCceeccCccCHHHHHhHhcCCceeehhh-HHhhhcCCCCCCCeEEEEEEecCCCccccCC
Q 015213 71 KIKKPKLSKKSNDPEVENFSGLRIRNPVVAPSELSERFSEIRFVRLST-IKNLLLGDTLSGCWATVAVLTEKGHPKTSSI 149 (411)
Q Consensus 71 ~~pk~k~~~~~~~~~~Ep~SGLrL~~R~IS~~~L~e~l~~~k~vrls~-Lk~~v~~~~~~~dWVtvGVIv~Ks~pK~ss~ 149 (411)
....++.++++++++.+|++++..+|.+++-|+|+. ++++++++++.+||||||||++|+++|.+++
T Consensus 138 ------------~i~~~~~f~~~~~~pr~ss~~~~k~~~g~k~i~ls~~~~~l~r~~kf~~~Wvt~GvI~~K~~~K~t~~ 205 (578)
T KOG3056|consen 138 ------------IIDELDKFSNLWIKPRYSSTSDLKRMTGRKLIRLSGKLFNLIRGPKFEENWVTMGVIVEKSDPKFTSN 205 (578)
T ss_pred ------------eeeeccchhhhhhccccCchhhHHHhhcCcceeehhhhhhcccCcccccCeEEEEEEeecCCcccccC
Confidence 124456677888888888999999999999999984 6789999999999999999999999999999
Q ss_pred CccEEEEEEeeCCC-CeEEEEEechHHHhhcCcccccEEEEECceeccCCCCC--cceEEecCCccEEEeeeeccCccce
Q 015213 150 GQNYCIWKLGCLEE-NTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGP--GFSLSVSSASQIIKMGTSVDYGVCK 226 (411)
Q Consensus 150 Gk~Y~iwkLsDL~~-~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~--~fsLsV~s~d~ILeIG~S~DlG~CK 226 (411)
|++|+||+|+||++ .+|+|||||+||++|||++.|+|||||||+|++++.|. .|+|+|+++++||+||.|+|||+|+
T Consensus 206 G~~y~iwkL~dLk~~q~vslfLFG~a~k~~wk~k~GtVialLNp~v~k~~~gs~~~f~LsIds~~~ileiG~S~dlGtC~ 285 (578)
T KOG3056|consen 206 GNPYSIWKLTDLKDHQTVSLFLFGKAHKRYWKIKLGTVIALLNPEVLKDRPGSRKSFSLSIDSSKKILEIGQSADLGTCK 285 (578)
T ss_pred CCceEEEEeeecCccceeEEEEecHHHHHHhhhccCcEEEEeCccccCCCCCCcceEEEEecCccceEEeeccccccccc
Confidence 99999999999997 49999999999999999999999999999999988765 8999999999999999999999999
Q ss_pred eeecCCcccccccccccccccccchHHHhhhhccCCceecCCCcc----cccCCCCCCCCeeeeCCccccccCCCCCCcc
Q 015213 227 GKRKDGMACNTVINKRKGIYCGYHRLKASDRFITTRSELKGGNLR----TAFRSPLNSEGIYLFDPLTDRTNLQKPKQPV 302 (411)
Q Consensus 227 a~kKdG~~Ct~~VNk~~~eyC~yHv~~a~rK~~s~R~EL~ggn~~----~~~~~p~~~~G~y~~~p~a~~~n~k~~~~~~ 302 (411)
+++|||++|++|||++.|+||+||++.++++.+++|.||+++... ...+..|+..+.||-.-.-..-|-- ...
T Consensus 286 a~rK~G~~Cts~VN~~l~~~C~yHv~~~~~k~sakR~el~s~~ag~~v~~l~~e~l~k~~~~yg~~s~~~~~a~---~~a 362 (578)
T KOG3056|consen 286 AKRKDGEKCTSVVNKSLCDYCDYHVEQAYRKLSAKRIELNSGTAGGAVPKLSSEGLRKGLSLYGGKSFNGFNAI---KGA 362 (578)
T ss_pred ccccCCCcccccccchHHHHHHHHHHHHHhhcccchhhhccccccCCCcccchhhccCCccccccccccccccc---ccc
Confidence 999999999999999999999999999999999999999976321 1111223333333221111000000 000
Q ss_pred eEEeechhhhhhccCCccccccccccchhhhhhcCCC
Q 015213 303 KVLSVEGLKKALSNAGKVTTNTHSQGIRFLNEMAGPK 339 (411)
Q Consensus 303 ~~lsv~g~~~~l~~~~~~~~~~~s~g~~f~~~vag~~ 339 (411)
.+-.-+-.+..+. +..+++.+++++-+|-.....++
T Consensus 363 ~~~~s~~~~~~~~-~~~~~~~s~s~~~~~~~k~e~pt 398 (578)
T KOG3056|consen 363 RKSLSEAERDTMK-SSHNFTKSNSAKAFFKEKFEEPT 398 (578)
T ss_pred cccccHHHHHHHh-hccCcccccchhhhhhhhhhcch
Confidence 0000011111111 45678888999988888877766
No 2
>PF09329 zf-primase: Primase zinc finger; InterPro: IPR015408 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger domain is found in Mcm10 proteins and DnaG-type primases []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 3H15_A 3EBE_C.
Probab=99.70 E-value=3.4e-18 Score=126.54 Aligned_cols=46 Identities=43% Similarity=0.785 Sum_probs=37.0
Q ss_pred eeeccCccceeeecCCcccccccccccccccccchHHHhhhhccCC
Q 015213 217 GTSVDYGVCKGKRKDGMACNTVINKRKGIYCGYHRLKASDRFITTR 262 (411)
Q Consensus 217 G~S~DlG~CKa~kKdG~~Ct~~VNk~~~eyC~yHv~~a~rK~~s~R 262 (411)
|.|+|||+|+++++||++|++|||+++++||+||++.+++|.+++|
T Consensus 1 G~s~DlG~Ck~~kkdG~~C~~~Vn~~~~~~C~yH~~~~~~k~~s~R 46 (46)
T PF09329_consen 1 GSSRDLGYCKAVKKDGKPCTNPVNKSKGEYCDYHVESAYRKSRSKR 46 (46)
T ss_dssp EEETTEEE-SSB-TTSSB---EEETTT-SS-TTTHHHHHCHHHHH-
T ss_pred CCCCcCccccCCCCCCCcccCceeCCCCcccHHHHHHHHHHHhcCC
Confidence 8999999999999999999999999999999999999999998877
No 3
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=97.39 E-value=0.0022 Score=54.41 Aligned_cols=83 Identities=20% Similarity=0.256 Sum_probs=67.2
Q ss_pred CCCCeEEEEEEecCCCccccCCC---ccEEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEECceeccCCC----
Q 015213 128 LSGCWATVAVLTEKGHPKTSSIG---QNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAK---- 199 (411)
Q Consensus 128 ~~~dWVtvGVIv~Ks~pK~ss~G---k~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~---- 199 (411)
...+|.+.|-|+.|++++.-.++ ..+.-+.|.|=.+.++.+-+|+++.++|+ .+++|.|+.|-|..|.+.+.
T Consensus 8 ~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~a~~~y~~ 87 (104)
T cd04474 8 YQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVANKKFNT 87 (104)
T ss_pred CCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEEeeccccCCC
Confidence 45689999999999999986553 45667889999778999999999999988 58999999999999987532
Q ss_pred -CCcceEEecCC
Q 015213 200 -GPGFSLSVSSA 210 (411)
Q Consensus 200 -g~~fsLsV~s~ 210 (411)
++.+.+.++..
T Consensus 88 ~~~~yeI~f~~~ 99 (104)
T cd04474 88 LKNDYEITFNRD 99 (104)
T ss_pred CCCcEEEEECCC
Confidence 24566666543
No 4
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=96.63 E-value=0.036 Score=49.36 Aligned_cols=82 Identities=16% Similarity=0.209 Sum_probs=64.8
Q ss_pred ceeehhhHHhhhcCCCCCCCeEEEEEEecCCCccccCCCccEEEEEEeeCCC---CeEEEEEechHHHhhcCcccccEEE
Q 015213 112 RFVRLSTIKNLLLGDTLSGCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLEE---NTISVFLFGDAYQKNWKEHAGTVFA 188 (411)
Q Consensus 112 k~vrls~Lk~~v~~~~~~~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~---~~VsLfLFG~A~ek~wKl~~GtVIA 188 (411)
.|+.|.+|.. ...+---++|||++.++|+.+....-.+.++|.|-.. ..|.+-||+.-.+.+=.+.+|+||+
T Consensus 2 ~f~~i~~~~~-----~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v~~GDVIl 76 (138)
T cd04497 2 KYTPLSSALK-----ESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDIIL 76 (138)
T ss_pred ceEeHHHHHh-----ccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCEEE
Confidence 4677776665 2345566999999999998876544567889999864 6799999999877777789999999
Q ss_pred EECceeccCC
Q 015213 189 LFNCSVRKDA 198 (411)
Q Consensus 189 ILNP~Im~~~ 198 (411)
|=|-.|...+
T Consensus 77 l~~~kv~~~~ 86 (138)
T cd04497 77 LRRVKIQSYN 86 (138)
T ss_pred EEEEEEEEEC
Confidence 9998886543
No 5
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=95.71 E-value=0.035 Score=45.24 Aligned_cols=53 Identities=15% Similarity=0.182 Sum_probs=43.7
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHH--hhc-CcccccEEEEE
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQ--KNW-KEHAGTVFALF 190 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~e--k~w-Kl~~GtVIAIL 190 (411)
..++|+|.+.. .|++|++ +.+|.|+. ..+.+.+|.+.|+ +|- .+.+|.+|.|-
T Consensus 2 v~i~GiI~~v~---~TK~g~~--~~~leD~~-G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~ 57 (79)
T cd04490 2 VSIIGMVNDVR---STKNGHR--IVELEDTT-GRITVLLTKDKEELFEEAEDILPDEVIGVS 57 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEECCC-CEEEEEEeCchhhhhhhhhhccCCCEEEEE
Confidence 46789999886 7788888 99999997 6799999999999 765 46777777654
No 6
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.67 E-value=0.073 Score=58.31 Aligned_cols=80 Identities=20% Similarity=0.256 Sum_probs=64.7
Q ss_pred CceeehhhHHhhhcCCCCCCCeEEEEEEecCCCccccC--C--CccEEEEEEeeCCCCeEEEEEechHHHhhc-Cccccc
Q 015213 111 IRFVRLSTIKNLLLGDTLSGCWATVAVLTEKGHPKTSS--I--GQNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGT 185 (411)
Q Consensus 111 ~k~vrls~Lk~~v~~~~~~~dWVtvGVIv~Ks~pK~ss--~--Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~Gt 185 (411)
+++++|+.|. +..++|.+-|-|+.|++.|.-. + |+ ..-+.|.| .+.+|..-+|+++.++|+ .+++|.
T Consensus 178 ~~~~pI~~L~------py~~~wtIkaRV~~Ks~ir~~~~~~gegk-vfsv~L~D-egg~Irat~f~~~~dkf~~~l~eG~ 249 (608)
T TIGR00617 178 RRVMPIASLS------PYQNKWTIKARVTNKSEIRTWSNARGEGK-LFNVELLD-ESGEIRATAFNEQADKFYDIIQEGK 249 (608)
T ss_pred cceEEHHHCC------CCCCceEEEEEEEeccccceecCCCCCce-eeEEEEec-CCCeEEEEECchHHHHHhhhcccCC
Confidence 4677777654 3567899999999999998732 2 44 45567899 788999999999999988 589999
Q ss_pred EEEEECceeccCC
Q 015213 186 VFALFNCSVRKDA 198 (411)
Q Consensus 186 VIAILNP~Im~~~ 198 (411)
|+.|-|..|.+.+
T Consensus 250 VY~Is~~~Vk~an 262 (608)
T TIGR00617 250 VYYISKGSLKPAN 262 (608)
T ss_pred EEEECceEEEEcc
Confidence 9999999997643
No 7
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=95.20 E-value=0.1 Score=38.35 Aligned_cols=60 Identities=23% Similarity=0.189 Sum_probs=48.8
Q ss_pred EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEECceeccC
Q 015213 134 TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKD 197 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~ 197 (411)
++|+|++.....+ |+.|..++|.|..+..+.+.+|.+.++.+. .+.+|.+|.|- ..+...
T Consensus 2 v~g~v~~~~~~~~---~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~ 62 (75)
T cd03524 2 IVGIVVAVEEIRT---EGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKF 62 (75)
T ss_pred eEEEEEeeccccc---CCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEec
Confidence 6788988876544 888999999998657899999999888864 67999998887 777543
No 8
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=95.16 E-value=0.089 Score=40.20 Aligned_cols=70 Identities=17% Similarity=0.176 Sum_probs=54.2
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEech-HHHhhcCcccccEEEEECceeccCCCCCcceEEecC
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGD-AYQKNWKEHAGTVFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~-A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsLsV~s 209 (411)
+.+.|.|.+.. .++++|..++|.|-. ..+.+.+|++ ....+..+.+|++|.|. ..+...+.+ .+.|.+.+
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D~t-g~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~-~~~l~~~~ 71 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLEDGT-GSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGG-ELELIVPK 71 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEETT-EEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTS-SEEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEECC-ccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCc-cEEEEECE
Confidence 45789998886 678889999999996 7999999994 45566789999999999 777665432 36666654
No 9
>PRK07211 replication factor A; Reviewed
Probab=95.03 E-value=0.15 Score=54.68 Aligned_cols=86 Identities=16% Similarity=0.160 Sum_probs=64.3
Q ss_pred CCCCeEEEEEEecCCCccc--cCCCccEEE--EEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcc
Q 015213 128 LSGCWATVAVLTEKGHPKT--SSIGQNYCI--WKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGF 203 (411)
Q Consensus 128 ~~~dWVtvGVIv~Ks~pK~--ss~Gk~Y~i--wkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~f 203 (411)
....|.++|+|.+++++|. .++|+.-.+ ..|.|=. ..|++-||++..+.+-.+.+|+||.|.|..+...+ +..
T Consensus 170 ~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeT-G~IR~TlW~d~Ad~~~~le~G~Vv~I~~a~Vre~~--g~~ 246 (485)
T PRK07211 170 GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDET-GRVRVTLWDDRADLAEELDAGESVEIVDGYVRERD--GSL 246 (485)
T ss_pred CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCC-CeEEEEEechhhhhhccCCCCCEEEEEeeEEEecC--CcE
Confidence 3578999999999999886 345644444 4555543 47999999998888877999999999999997653 356
Q ss_pred eEEecCCccEEEe
Q 015213 204 SLSVSSASQIIKM 216 (411)
Q Consensus 204 sLsV~s~d~ILeI 216 (411)
.|++.+...|.++
T Consensus 247 ELsl~~~s~I~~~ 259 (485)
T PRK07211 247 ELHVGDRGAVEEV 259 (485)
T ss_pred EEEECCCceEEEC
Confidence 7777665555554
No 10
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=94.68 E-value=0.1 Score=40.14 Aligned_cols=71 Identities=17% Similarity=0.266 Sum_probs=51.3
Q ss_pred EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEecC
Q 015213 134 TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV~s 209 (411)
++|+|.+.. .+.+++|+.|...+|.|-. ..+.+.+|.+.|+++- .+.+|.++.|. -.+.... +...|.+.+
T Consensus 2 i~g~v~~~~-~~~~k~g~~~~~~~l~D~t-g~~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~--~~~~l~~~~ 73 (84)
T cd04485 2 VAGLVTSVR-RRRTKKGKRMAFVTLEDLT-GSIEVVVFPETYEKYRDLLKEDALLLVE-GKVERRD--GGLRLIAER 73 (84)
T ss_pred EEEEEEEeE-EEEcCCCCEEEEEEEEeCC-CeEEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecC--CceEEEeec
Confidence 578887753 4677889999999999986 5799999998886553 57889888664 3443332 346666654
No 11
>PRK12366 replication factor A; Reviewed
Probab=94.62 E-value=0.16 Score=55.93 Aligned_cols=81 Identities=15% Similarity=0.140 Sum_probs=60.3
Q ss_pred CeEEEEEEecCCCccccC----CCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCC--CC-Ccc
Q 015213 131 CWATVAVLTEKGHPKTSS----IGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDA--KG-PGF 203 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss----~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~--~g-~~f 203 (411)
.|.+.|-|+.|+++|.=. .|+-|. ..|.|=. .+|++-+|+++.++++.+.+|+|+.|-|..+..++ .+ ..+
T Consensus 293 ~~~I~grV~~~~~~R~f~~~~g~gkv~s-~~l~D~t-G~IR~t~w~~~~d~~~~l~~G~vy~is~~~vk~y~~~~~~~~~ 370 (637)
T PRK12366 293 EVDVKGRIIAISDKREVERDDRTAEVQD-IELADGT-GRVRVSFWGEKAKILENLKEGDAVKIENCKVRTYYDNEGEKRV 370 (637)
T ss_pred EEEEEEEEEecCCceEEEcCCCcEEEEE-EEEEcCC-CeEEEEEeCchhhhhcccCCCCEEEEecCEEeeccccCCCcCE
Confidence 799999999999988832 244343 4777743 58999999999999999999999999999998543 22 245
Q ss_pred eEEecCCccE
Q 015213 204 SLSVSSASQI 213 (411)
Q Consensus 204 sLsV~s~d~I 213 (411)
.|++++...|
T Consensus 371 El~~~~~s~I 380 (637)
T PRK12366 371 DLNAGYSSEI 380 (637)
T ss_pred EEEcCCceEE
Confidence 5555443333
No 12
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=94.16 E-value=0.56 Score=37.57 Aligned_cols=75 Identities=20% Similarity=0.141 Sum_probs=58.1
Q ss_pred EEEEEecCCCccccC---CCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceEEecCC
Q 015213 134 TVAVLTEKGHPKTSS---IGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSLSVSSA 210 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss---~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsLsV~s~ 210 (411)
+.|+|.+.++++.-. ....|..+.|.|=. ..+.+-+|++.. .-.+.+|+||.|-|..+...+ ....|++...
T Consensus 2 v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~T-G~i~~~~W~~~~--~~~~~~G~vv~i~~~~v~~~~--g~~ql~i~~~ 76 (82)
T cd04491 2 VEGKVLSISEPREFTRDGSEGKVQSGLVGDET-GTIRFTLWDEKA--ADDLEPGDVVRIENAYVREFN--GRLELSVGKN 76 (82)
T ss_pred EEEEEEEccCCeEeccCCCeeEEEEEEEECCC-CEEEEEEECchh--cccCCCCCEEEEEeEEEEecC--CcEEEEeCCc
Confidence 689999999988743 44568888888854 489999999865 567899999999999997654 3477777765
Q ss_pred ccE
Q 015213 211 SQI 213 (411)
Q Consensus 211 d~I 213 (411)
..|
T Consensus 77 ~~i 79 (82)
T cd04491 77 SEI 79 (82)
T ss_pred eEE
Confidence 444
No 13
>PRK15491 replication factor A; Provisional
Probab=93.78 E-value=0.46 Score=49.34 Aligned_cols=87 Identities=14% Similarity=0.120 Sum_probs=65.9
Q ss_pred CCCeEEEEEEecCCCcccc--CCCccEEE--EEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcce
Q 015213 129 SGCWATVAVLTEKGHPKTS--SIGQNYCI--WKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFS 204 (411)
Q Consensus 129 ~~dWVtvGVIv~Ks~pK~s--s~Gk~Y~i--wkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fs 204 (411)
..+|-+.|+|+.++++|.= +.|+...+ ..|.|=. ..|++-||++..+.+..+.+|++|-|.|..++-..-.+...
T Consensus 176 ~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~Det-G~Ir~t~W~~~a~~~~~l~~Gd~V~i~~~~~r~~~~~g~~E 254 (374)
T PRK15491 176 DSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDET-GKIRVTLWDGKTDLADKLENGDSVEIINGYARTNNYSQEVE 254 (374)
T ss_pred CccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCC-CeEEEEEecchhcccccCCCCCEEEEEeceEEEeccCCCEE
Confidence 4579999999999988773 46764333 5556643 47999999998888888999999999999886433234678
Q ss_pred EEecCCccEEEe
Q 015213 205 LSVSSASQIIKM 216 (411)
Q Consensus 205 LsV~s~d~ILeI 216 (411)
|++.+...|.+.
T Consensus 255 l~~~~~s~I~~~ 266 (374)
T PRK15491 255 IQIGNHGSLRKT 266 (374)
T ss_pred EEeCCCceEEEC
Confidence 888776666654
No 14
>PRK12366 replication factor A; Reviewed
Probab=93.47 E-value=0.67 Score=51.20 Aligned_cols=68 Identities=19% Similarity=0.061 Sum_probs=56.3
Q ss_pred CCCeEEEEEEecCCCcccc--CCC--ccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccC
Q 015213 129 SGCWATVAVLTEKGHPKTS--SIG--QNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKD 197 (411)
Q Consensus 129 ~~dWVtvGVIv~Ks~pK~s--s~G--k~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~ 197 (411)
..+|.+.|-|++++++|.- .+| .++....|.|=. .++++-+|+++.+.|-.+.+|+|+-|-|..+...
T Consensus 73 ~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~Det-G~Ir~t~W~~~~~~~~~le~G~v~~i~~~~v~~~ 144 (637)
T PRK12366 73 QINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNT-GTIRLTLWNDNAKLLKGLKEGDVIKIENARSRKW 144 (637)
T ss_pred CcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCC-CEEEEEEEchhhhhhccCCCCCEEEEeccEeccc
Confidence 4689999999999999963 445 357778888854 5899999999877666899999999999988654
No 15
>PRK08402 replication factor A; Reviewed
Probab=93.42 E-value=0.6 Score=48.30 Aligned_cols=78 Identities=18% Similarity=0.170 Sum_probs=57.1
Q ss_pred CCeEEEEEEecCCCccc--cCCCcc--EEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEECceeccCCCCCcce
Q 015213 130 GCWATVAVLTEKGHPKT--SSIGQN--YCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFS 204 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~--ss~Gk~--Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fs 204 (411)
.+|-+.|-|++++++|. ..+|.. ..-..|.|= ...+.+-||++....++ .+.+|+||+|.|..+.....| .++
T Consensus 73 ~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~De-TG~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G-~~e 150 (355)
T PRK08402 73 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDD-TGRARVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSG-LPE 150 (355)
T ss_pred ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcC-CCeEEEEEechhhhhhcccCCCCCEEEEECCEEeecCCC-cEE
Confidence 46788999999998885 345654 444577774 35889999999877766 499999999999999764333 234
Q ss_pred EEecC
Q 015213 205 LSVSS 209 (411)
Q Consensus 205 LsV~s 209 (411)
|+|..
T Consensus 151 Lsvg~ 155 (355)
T PRK08402 151 LHINF 155 (355)
T ss_pred EEECC
Confidence 55443
No 16
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=93.26 E-value=0.23 Score=38.68 Aligned_cols=58 Identities=17% Similarity=0.188 Sum_probs=43.9
Q ss_pred EEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceecc
Q 015213 136 AVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRK 196 (411)
Q Consensus 136 GVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~ 196 (411)
.+|.+.. .+.+++|++|..+.|.|.. ..+.+.+|++.+...-.+.+|.+|.|- -.+..
T Consensus 4 ~~v~~~~-~~~tk~g~~~~~~~l~D~t-g~i~~~~f~~~~~~~~~l~~g~~v~v~-G~v~~ 61 (83)
T cd04492 4 FLIKSKE-LRTAKNGKPYLALTLQDKT-GEIEAKLWDASEEDEEKFKPGDIVHVK-GRVEE 61 (83)
T ss_pred EEEEEee-eecccCCCcEEEEEEEcCC-CeEEEEEcCCChhhHhhCCCCCEEEEE-EEEEE
Confidence 3566664 5778899999999999996 579999999776444468899888766 55533
No 17
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=92.91 E-value=1.1 Score=37.16 Aligned_cols=64 Identities=16% Similarity=0.119 Sum_probs=47.7
Q ss_pred EEEEEecCCCcccc--CC-Ccc--EEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCC
Q 015213 134 TVAVLTEKGHPKTS--SI-GQN--YCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDA 198 (411)
Q Consensus 134 tvGVIv~Ks~pK~s--s~-Gk~--Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~ 198 (411)
++|+|.+.++++.- ++ |+. -.-+.|.|-.+..+.|-|+|+-.+.+.... |+||+|-|+.|...+
T Consensus 4 vig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~-~~vv~~~~~~i~~~~ 72 (101)
T cd04475 4 VIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE-NPVIAIKGVKVSEFN 72 (101)
T ss_pred EEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCC-CCEEEEEeeEEEecC
Confidence 68999999988763 33 654 445566777667999999999655544333 999999999996654
No 18
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=92.61 E-value=0.57 Score=36.60 Aligned_cols=52 Identities=10% Similarity=0.038 Sum_probs=40.5
Q ss_pred EEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEE
Q 015213 133 ATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALF 190 (411)
Q Consensus 133 VtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAIL 190 (411)
.+.|+|++-. .+++| +.+++|.|.. ..+.+.+|.+.++++- .+.+|++|.|.
T Consensus 3 ~v~g~v~~i~---~tk~g--~~~~~L~D~~-~~i~~~~f~~~~~~~~~~l~~g~~v~v~ 55 (78)
T cd04489 3 WVEGEISNLK---RPSSG--HLYFTLKDED-ASIRCVMWRSNARRLGFPLEEGMEVLVR 55 (78)
T ss_pred EEEEEEecCE---ECCCc--EEEEEEEeCC-eEEEEEEEcchhhhCCCCCCCCCEEEEE
Confidence 3667777543 36666 9999999986 7899999999988865 67899876554
No 19
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=92.02 E-value=1.1 Score=39.57 Aligned_cols=83 Identities=17% Similarity=0.152 Sum_probs=61.9
Q ss_pred CCeEEEEEEecCCCccc--cCCC-ccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceEE
Q 015213 130 GCWATVAVLTEKGHPKT--SSIG-QNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSLS 206 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~--ss~G-k~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsLs 206 (411)
.+.-++|+|.++++++. +++| ..|..+.|.|=. ..|.+-||++..+ .+.+|+||.|-|..+...+ ....|+
T Consensus 15 ~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~T-G~I~~tlW~~~a~---~l~~GdvV~I~na~v~~f~--G~lqL~ 88 (129)
T PRK06461 15 ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDET-GRVKLTLWGEQAG---SLKEGEVVEIENAWTTLYR--GKVQLN 88 (129)
T ss_pred CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCC-CEEEEEEeCCccc---cCCCCCEEEEECcEEeeeC--CEEEEE
Confidence 35667899998877554 4444 348888888875 4799999997443 5789999999999986543 347888
Q ss_pred ecCCccEEEeee
Q 015213 207 VSSASQIIKMGT 218 (411)
Q Consensus 207 V~s~d~ILeIG~ 218 (411)
|.....|..++.
T Consensus 89 i~~~~~i~~~~~ 100 (129)
T PRK06461 89 VGKYGSISESDD 100 (129)
T ss_pred ECCCEEEEECCc
Confidence 887777777764
No 20
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=91.49 E-value=1.3 Score=39.98 Aligned_cols=83 Identities=13% Similarity=0.160 Sum_probs=60.4
Q ss_pred CCCeEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceEEec
Q 015213 129 SGCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSLSVS 208 (411)
Q Consensus 129 ~~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsLsV~ 208 (411)
-.|..++-+|.+-.....+++|+.|.+|++.|=. .+|.+-++++ ...-+++||||-|-+-----.+ ++..|.+.
T Consensus 14 ~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~T-gsI~isvW~e---~~~~~~PGDIirLt~Gy~Si~q--g~LtL~~G 87 (134)
T KOG3416|consen 14 LKNINVTFIVLEYGRATKTKDGHEVRSCKVADET-GSINISVWDE---EGCLIQPGDIIRLTGGYASIFQ--GCLTLYVG 87 (134)
T ss_pred hhcceEEEEEEeeceeeeccCCCEEEEEEEeccc-ceEEEEEecC---cCcccCCccEEEecccchhhhc--CceEEEec
Confidence 3466777788888888889999999999999985 6899999883 3445799999988774321111 24666666
Q ss_pred CCccEEEee
Q 015213 209 SASQIIKMG 217 (411)
Q Consensus 209 s~d~ILeIG 217 (411)
....+-+||
T Consensus 88 K~Ge~~KiG 96 (134)
T KOG3416|consen 88 KGGEVQKIG 96 (134)
T ss_pred CCceEeEee
Confidence 666666665
No 21
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=91.23 E-value=0.53 Score=42.18 Aligned_cols=71 Identities=13% Similarity=0.153 Sum_probs=57.7
Q ss_pred CCCCeEEEEEEecCCCc--cccCCCccEEEEEEeeCCC-------CeEEEEEechHHHhhcCccc-ccEEEEECceeccC
Q 015213 128 LSGCWATVAVLTEKGHP--KTSSIGQNYCIWKLGCLEE-------NTISVFLFGDAYQKNWKEHA-GTVFALFNCSVRKD 197 (411)
Q Consensus 128 ~~~dWVtvGVIv~Ks~p--K~ss~Gk~Y~iwkLsDL~~-------~~VsLfLFG~A~ek~wKl~~-GtVIAILNP~Im~~ 197 (411)
...---++|||+.-+.| +.+..+.-.+.++|.|-.- ..|.|.+|..-.+.+=.+.. |+||.|-+-+|...
T Consensus 11 ~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii~l~r~kv~~~ 90 (146)
T PF02765_consen 11 FGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDIIRLRRVKVQSY 90 (146)
T ss_dssp SSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEEEEEEEEEEEE
T ss_pred CCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEEEEEEEEEEEE
Confidence 34466799999999999 7776666678889999862 47999999887888888877 99999998888655
Q ss_pred C
Q 015213 198 A 198 (411)
Q Consensus 198 ~ 198 (411)
+
T Consensus 91 ~ 91 (146)
T PF02765_consen 91 N 91 (146)
T ss_dssp T
T ss_pred C
Confidence 4
No 22
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=91.02 E-value=0.81 Score=48.70 Aligned_cols=109 Identities=13% Similarity=0.197 Sum_probs=68.6
Q ss_pred CcCceeccCccCHHHHHhHhcCCceeehhhHHhhhcCCCCCCCeE-EEEEEecCCCccccCCCccEEEEEEeeCCCCeEE
Q 015213 89 FSGLRIRNPVVAPSELSERFSEIRFVRLSTIKNLLLGDTLSGCWA-TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTIS 167 (411)
Q Consensus 89 ~SGLrL~~R~IS~~~L~e~l~~~k~vrls~Lk~~v~~~~~~~dWV-tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~Vs 167 (411)
+-|+.|+.--+ +...+.+.......+.+|.. ...+.+| ++|+|... -.+.|++|+.+.+.+|.|+. ..+.
T Consensus 246 ~LGfylS~HPl--~~~~~~l~~~~~~~~~~l~~-----~~~~~~v~vaG~I~~i-k~~~TKkG~~maf~~leD~t-G~ie 316 (449)
T PRK07373 246 LLGFYVSEHPL--KSIRRPARLLSPINLSELEE-----QKEKTKVSAVVMLNEV-KKIVTKKGDPMAFLQLEDLS-GQSE 316 (449)
T ss_pred HhccccCcCch--HHHHHHHHHcCCcCHHHHhc-----ccCCCEEEEEEEEEEe-EecccCCCCEEEEEEEEECC-CCEE
Confidence 34666654432 34445554444455555521 1234444 56666665 46778899999999999997 6799
Q ss_pred EEEechHHHhhcC-cccccEEEEECceeccCCCCCcceEEecC
Q 015213 168 VFLFGDAYQKNWK-EHAGTVFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 168 LfLFG~A~ek~wK-l~~GtVIAILNP~Im~~~~g~~fsLsV~s 209 (411)
+.+|.+.|+++-. +.+|.+|.|- -.+-.. .....|.++.
T Consensus 317 ~vvFp~~y~~~~~~l~~~~~v~v~-G~v~~~--~~~~~liv~~ 356 (449)
T PRK07373 317 AVVFPKSYERISELLQVDARLIIW-GKVDRR--DDQVQLIVED 356 (449)
T ss_pred EEECHHHHHHHHHHhccCCEEEEE-EEEEec--CCeEEEEEeE
Confidence 9999999999874 6777777663 344222 1234555544
No 23
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=89.96 E-value=2.5 Score=35.66 Aligned_cols=65 Identities=11% Similarity=0.289 Sum_probs=50.6
Q ss_pred EEEEEecCCCccccC---CCccEEEEEEeeCCCCeEEEEEech---HHHhhcC--cccccEEEEEC-ceeccCC
Q 015213 134 TVAVLTEKGHPKTSS---IGQNYCIWKLGCLEENTISVFLFGD---AYQKNWK--EHAGTVFALFN-CSVRKDA 198 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss---~Gk~Y~iwkLsDL~~~~VsLfLFG~---A~ek~wK--l~~GtVIAILN-P~Im~~~ 198 (411)
++|+|++-++..... .-..+..+.|-|..+..+.+-|+|+ .|..+|. -..+-||||+. -.|...+
T Consensus 2 viG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~ 75 (106)
T cd04481 2 VIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYK 75 (106)
T ss_pred eeEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEc
Confidence 589999888766533 2345888999999888999999998 3666664 68888999998 7776654
No 24
>PRK15491 replication factor A; Provisional
Probab=89.92 E-value=2.6 Score=43.91 Aligned_cols=62 Identities=15% Similarity=0.045 Sum_probs=50.0
Q ss_pred CCCeEEEEEEecCCCccc--cCCCccEEE--EEEeeCCCCeEEEEEechHHHhhcC--cccccEEEEEC
Q 015213 129 SGCWATVAVLTEKGHPKT--SSIGQNYCI--WKLGCLEENTISVFLFGDAYQKNWK--EHAGTVFALFN 191 (411)
Q Consensus 129 ~~dWVtvGVIv~Ks~pK~--ss~Gk~Y~i--wkLsDL~~~~VsLfLFG~A~ek~wK--l~~GtVIAILN 191 (411)
..+|.+.|-|++++++|. ...|....+ ..|.|= ...+++-||.+..+.++. +.+|+|+-|-+
T Consensus 67 ~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~De-TG~ir~tlW~~~a~~~~~~~le~G~v~~I~~ 134 (374)
T PRK15491 67 SSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADE-TGSIRLTLWDDLADLIKTGDIEVGKSLNISG 134 (374)
T ss_pred CCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcC-CCeEEEEEECchhhhhccCCcCCCCEEEEee
Confidence 478999999999999998 445644444 477773 468999999998888874 99999999865
No 25
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=89.75 E-value=0.96 Score=53.22 Aligned_cols=110 Identities=20% Similarity=0.291 Sum_probs=70.7
Q ss_pred CcCceeccCccCHHHHHhHhcCCceeehhhHHhhhcCCCCCCCeEE-EEEEecCCCccccCCCccEEEEEEeeCCCCeEE
Q 015213 89 FSGLRIRNPVVAPSELSERFSEIRFVRLSTIKNLLLGDTLSGCWAT-VAVLTEKGHPKTSSIGQNYCIWKLGCLEENTIS 167 (411)
Q Consensus 89 ~SGLrL~~R~IS~~~L~e~l~~~k~vrls~Lk~~v~~~~~~~dWVt-vGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~Vs 167 (411)
+-|+.|+.--+ +...+.+.......+.+|.. ...+.+|. +|+|.+. ..+.|++|++|.+.+|.|.. .++.
T Consensus 943 ~lG~yls~HPl--~~~~~~~~~~~~~~~~~l~~-----~~~g~~V~v~G~I~~v-k~~~TKkG~~mafltLeD~T-G~iE 1013 (1135)
T PRK05673 943 TLGLYLSGHPL--DGYEDELRRLRDTRLADLEP-----TEGGSVVTVAGLVVSV-RRRVTKRGNKMAIVTLEDLS-GRIE 1013 (1135)
T ss_pred HhCcccCcCch--HHHHHHHHHhCCcCHHHHhc-----cccCceEEEEEEEEEE-EecccCCCCeEEEEEEEeCC-CcEE
Confidence 34666654433 34444554444455555531 12355555 5555555 56788899999999999997 5899
Q ss_pred EEEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEecCC
Q 015213 168 VFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSVSSA 210 (411)
Q Consensus 168 LfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV~s~ 210 (411)
+.+|.+.|+++- .+.+|.+|.|-- .|... +....|.+++.
T Consensus 1014 vviFp~~ye~~~~~L~~g~iV~V~G-kVe~~--~~~~qlii~~I 1054 (1135)
T PRK05673 1014 VMLFSEALEKYRDLLEEDRIVVVKG-QVSFD--DGGLRLTAREV 1054 (1135)
T ss_pred EEECHHHHHHHHHHhccCCEEEEEE-EEEec--CCeEEEEEeec
Confidence 999999999876 578899887733 44222 23456666543
No 26
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.73 E-value=2.5 Score=46.56 Aligned_cols=95 Identities=20% Similarity=0.222 Sum_probs=65.8
Q ss_pred CceeehhhHHhhhcCCCCCCCeEEEEEEecCCCccc---cCCCccE--EEEEEeeCCCCeEEEEEechHHHhhcCccccc
Q 015213 111 IRFVRLSTIKNLLLGDTLSGCWATVAVLTEKGHPKT---SSIGQNY--CIWKLGCLEENTISVFLFGDAYQKNWKEHAGT 185 (411)
Q Consensus 111 ~k~vrls~Lk~~v~~~~~~~dWVtvGVIv~Ks~pK~---ss~Gk~Y--~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~Gt 185 (411)
..|+.|.+|..... ...-=++|||.+.++... .++|+.+ --+.|.|..+..|.|-|||+-... +...+|.
T Consensus 296 ~~f~~i~dI~~~~~----~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~-~~~~~~~ 370 (608)
T TIGR00617 296 FNFVKIDDIGGYEG----NSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATK-FDVSVQP 370 (608)
T ss_pred ccceEHHHhhhhcC----CCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhh-cCCCCCC
Confidence 45666666654321 124458999999988777 3456654 567788887778999999995444 3488999
Q ss_pred EEEEECceeccCCCCCcceEEecCCccE
Q 015213 186 VFALFNCSVRKDAKGPGFSLSVSSASQI 213 (411)
Q Consensus 186 VIAILNP~Im~~~~g~~fsLsV~s~d~I 213 (411)
||||-+..|... . +.+|+..+..+|
T Consensus 371 Vva~kg~~V~~f-~--g~sLs~~~~S~i 395 (608)
T TIGR00617 371 VIAIKGVRVSDF-G--GKSLSTGGSSTI 395 (608)
T ss_pred EEEEEeEEEEec-C--CceEeccCCceE
Confidence 999999988655 2 356666554444
No 27
>PRK14699 replication factor A; Provisional
Probab=89.39 E-value=2.1 Score=46.15 Aligned_cols=81 Identities=10% Similarity=0.016 Sum_probs=59.5
Q ss_pred CCCeEEEEEEecCCCcccc--CCCccEEEEEEeeCCC-CeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceE
Q 015213 129 SGCWATVAVLTEKGHPKTS--SIGQNYCIWKLGCLEE-NTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSL 205 (411)
Q Consensus 129 ~~dWVtvGVIv~Ks~pK~s--s~Gk~Y~iwkLsDL~~-~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsL 205 (411)
..+|.+.|.|++++++|+= .+|+...+..+.-.++ ..|.+-+|++..+.|..+.+|++|-|.|..+....-.+.+.|
T Consensus 286 ~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~Ir~T~W~~~a~~~~~i~~Gd~v~i~~~y~~~~~~~~~~eL 365 (484)
T PRK14699 286 MNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGKIRLTLWDEKTNFLDEIDFDETVEVLNAYSRENTFSQQVEL 365 (484)
T ss_pred CceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCeEEEEEeCcccccccccCCCceEEEEeEEEEeccCCccEEE
Confidence 4789999999999998873 4676666664444442 479999999977667788999999999999864432234444
Q ss_pred EecC
Q 015213 206 SVSS 209 (411)
Q Consensus 206 sV~s 209 (411)
++..
T Consensus 366 ~~~~ 369 (484)
T PRK14699 366 NLGA 369 (484)
T ss_pred EecC
Confidence 4443
No 28
>PRK02801 primosomal replication protein N; Provisional
Probab=86.19 E-value=3.2 Score=35.32 Aligned_cols=60 Identities=15% Similarity=0.168 Sum_probs=49.0
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC-----C------CeEEEEEechHHHhhc-CcccccEEEEE
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE-----E------NTISVFLFGDAYQKNW-KEHAGTVFALF 190 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~-----~------~~VsLfLFG~A~ek~w-Kl~~GtVIAIL 190 (411)
.-+.+|-|++..+.|.+.+|.+++-++|.==. + ..+.+.+||+..+... .+..|+.|+|-
T Consensus 4 ~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~ 75 (101)
T PRK02801 4 RLVLSGTVCRTPKRKVSPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQ 75 (101)
T ss_pred EEEEEEEECcCcceEECCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEE
Confidence 35789999999999999999999988884311 1 1388999999988888 59999999873
No 29
>PRK07211 replication factor A; Reviewed
Probab=83.53 E-value=6.6 Score=42.49 Aligned_cols=89 Identities=12% Similarity=0.098 Sum_probs=68.2
Q ss_pred CeEEEEEEecCCCcccc--CCCccEE--EEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceEE
Q 015213 131 CWATVAVLTEKGHPKTS--SIGQNYC--IWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSLS 206 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~s--s~Gk~Y~--iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsLs 206 (411)
..-++|+|.+-++++.- .+|+.+. -..|.|=.+ .|.|-|||+..+. .+.+|++|+|-|+.|..... .+.+|+
T Consensus 280 ~vdV~GvV~~v~~~rtf~r~dG~~~~vr~l~l~D~TG-~IrvTLWg~~A~~--~i~~GdvV~Ikg~~V~dg~~-ggleLS 355 (485)
T PRK07211 280 TVDIAGVVRSADPKRTFDRDDGSEGQVRNVRIQDDTG-DIRVALWGEKADL--DIGPGDEVVAADVEIQDGWQ-DDLEAS 355 (485)
T ss_pred ceeEEEEEEEccCcEEEEcCCCCEeEEEEEEEEcCCC-cEEEEEeCccccC--CCCCCCEEEEEccEEEecCC-CCEEEE
Confidence 45689999999988773 3577544 455666654 8999999996533 68999999999999966432 468999
Q ss_pred ecCCccEEEeeeeccCc
Q 015213 207 VSSASQIIKMGTSVDYG 223 (411)
Q Consensus 207 V~s~d~ILeIG~S~DlG 223 (411)
+.....|..|....|..
T Consensus 356 ~g~~s~i~~~~~~~~~~ 372 (485)
T PRK07211 356 AGWQSTVVVLDDGADAA 372 (485)
T ss_pred ecCCceEEEcccccccc
Confidence 99989999888766643
No 30
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=83.48 E-value=3.6 Score=48.79 Aligned_cols=110 Identities=15% Similarity=0.259 Sum_probs=68.4
Q ss_pred CcCceeccCccCHHHHHhHhcCCceeehhhHHhhhcCCCCCCCeE-EEEEEecCCCccccCCCccEEEEEEeeCCCCeEE
Q 015213 89 FSGLRIRNPVVAPSELSERFSEIRFVRLSTIKNLLLGDTLSGCWA-TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTIS 167 (411)
Q Consensus 89 ~SGLrL~~R~IS~~~L~e~l~~~k~vrls~Lk~~v~~~~~~~dWV-tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~Vs 167 (411)
+-|+.|+.--+ +...+.+.......+.+|.. ...+.+| ++|+|... ..+.|++|+++.+.+|.|.. ..++
T Consensus 966 ~lG~yls~HPl--~~~~~~~~~~~~~~~~~l~~-----~~~~~~v~v~g~i~~~-k~~~Tk~G~~maf~~leD~t-g~~e 1036 (1170)
T PRK07374 966 LLGFYLSDHPL--KQLTEPAKLLAPISLSSLEE-----QPDKAKVSAIAMIPEM-KQVTTRKGDRMAILQLEDLT-GSCE 1036 (1170)
T ss_pred HhCcccCcCch--HHHHHHHHHhCCcCHHHHhc-----ccCCCEEEEEEEEEEe-EecccCCCCEEEEEEEEECC-CCEE
Confidence 44555554333 23444444444445555521 1235555 45555555 46778899999999999997 6799
Q ss_pred EEEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEecCC
Q 015213 168 VFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSVSSA 210 (411)
Q Consensus 168 LfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV~s~ 210 (411)
+.+|-+.|+++- .+.+|.++.|- -.|-.. +....|.++..
T Consensus 1037 ~vvFp~~y~~~~~~l~~~~~~~v~-g~v~~~--~~~~~~~~~~i 1077 (1170)
T PRK07374 1037 AVVFPKSYERLSDHLMTDTRLLVW-AKVDRR--DDRVQLIIDDC 1077 (1170)
T ss_pred EEECHHHHHHHHHHhccCCEEEEE-EEEEec--CCeEEEEEeee
Confidence 999999999986 47888877763 344221 22356666543
No 31
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=83.13 E-value=5.1 Score=32.30 Aligned_cols=59 Identities=14% Similarity=0.136 Sum_probs=45.7
Q ss_pred EEEEEEecCCCccccCCCccEEEEEEeeCC-----------CCeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 133 ATVAVLTEKGHPKTSSIGQNYCIWKLGCLE-----------ENTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 133 VtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~-----------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
.++|-|+.....+.+.+|+.|+.++|.--. ...+.+.+||+..+..- .++.|+.|.|--
T Consensus 2 ~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G 72 (100)
T cd04496 2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEG 72 (100)
T ss_pred EEEEEecCCCEEEECCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEE
Confidence 478999999989999999999998884221 24699999999544444 489999987754
No 32
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=82.79 E-value=3.9 Score=48.26 Aligned_cols=76 Identities=11% Similarity=0.129 Sum_probs=53.1
Q ss_pred CCeEE-EEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEe
Q 015213 130 GCWAT-VAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSV 207 (411)
Q Consensus 130 ~dWVt-vGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV 207 (411)
+.+|+ +|+|+.. ..+.|++|+.+.+.+|.|.. ..+++.+|.+.|+++- .+.+|.+|.|-- .+-.. +....|.+
T Consensus 943 ~~~v~v~g~i~~~-~~~~tk~g~~maf~~leD~t-g~~e~~vFp~~y~~~~~~l~~~~~~~v~G-~v~~~--~~~~~~~~ 1017 (1107)
T PRK06920 943 KKVQRAIVYITSV-KVIRTKKGQKMAFITFCDQN-DEMEAVVFPETYIHFSDKLQEGAIVLVDG-TIELR--NHKLQWIV 1017 (1107)
T ss_pred CCEEEEEEEEEEe-EeecCCCCCeEEEEEEeeCC-CcEEEEECHHHHHHHHHHhccCCEEEEEE-EEEec--CCcEEEEE
Confidence 44554 5555554 46778899999999999996 6799999999999986 578888877643 33221 22345655
Q ss_pred cCC
Q 015213 208 SSA 210 (411)
Q Consensus 208 ~s~ 210 (411)
+..
T Consensus 1018 ~~i 1020 (1107)
T PRK06920 1018 NGL 1020 (1107)
T ss_pred eec
Confidence 543
No 33
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=82.16 E-value=4.3 Score=48.04 Aligned_cols=116 Identities=16% Similarity=0.122 Sum_probs=70.1
Q ss_pred CcCceeccCccCHHHHHhHhcCCceeehhhHHhhhc----CCCCCCCeEEEEEEecCCCccccCCCccEEEEEEeeCCCC
Q 015213 89 FSGLRIRNPVVAPSELSERFSEIRFVRLSTIKNLLL----GDTLSGCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLEEN 164 (411)
Q Consensus 89 ~SGLrL~~R~IS~~~L~e~l~~~k~vrls~Lk~~v~----~~~~~~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~ 164 (411)
+-|+.|+.--+ +.....+.......+.+|..... .....+.+|+|+.++..-..+.|++|+++.+.+|.|.. .
T Consensus 948 ~lG~yls~HPl--~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~v~v~g~i~~~~~~~tk~G~~maf~~leD~~-g 1024 (1151)
T PRK06826 948 MLGLYISGHPL--EEYEETLKKQTSATISDIISDEEEDGESKLKDGDKVIIGGIITEVKRKTTRNNEMMAFLTLEDLY-G 1024 (1151)
T ss_pred HhCCccCCCch--HHHHHHHHHcCCcCHHHHhhhccccccccccCCcEEEEEEEEEEeEeeccCCCCeEEEEEEEECC-C
Confidence 45666654433 23444454444455555531110 01124566655544444456778899999999999997 6
Q ss_pred eEEEEEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEecC
Q 015213 165 TISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 165 ~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV~s 209 (411)
.+.+.+|.+.|+++- .+.+|.+|.|- -.+-... +....|.++.
T Consensus 1025 ~~e~~vfp~~~~~~~~~l~~~~~~~v~-g~v~~~~-~~~~~~~~~~ 1068 (1151)
T PRK06826 1025 TVEVIVFPKVYEKYRSLLNEDNIVLIK-GRVSLRE-DEEPKLICEE 1068 (1151)
T ss_pred cEEEEECHHHHHHHHHHhccCCEEEEE-EEEEecC-CCceEEEEee
Confidence 799999999999986 57888887763 3442211 2235565544
No 34
>PRK14699 replication factor A; Provisional
Probab=79.72 E-value=8.3 Score=41.62 Aligned_cols=82 Identities=15% Similarity=0.178 Sum_probs=62.5
Q ss_pred CCeEEEEEEecCCCccc--cCCCccEEEEEE--eeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceE
Q 015213 130 GCWATVAVLTEKGHPKT--SSIGQNYCIWKL--GCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSL 205 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~--ss~Gk~Y~iwkL--sDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsL 205 (411)
...-++|+|.+-.+++. +.+|+.|.+=.| .|=.+ .|.|-|||+..+++..+.+|+-|.|.|+.++..-. ...-|
T Consensus 396 ~~vdV~G~V~~v~~~~~~~~~~g~~~~vr~i~l~D~TG-~Ir~tlWg~~A~~~~~~~~~~~v~~~~~~~~~g~~-~~~e~ 473 (484)
T PRK14699 396 ESYSVQGKVSEIGELREFEREDGTENVVANLQLKDETG-SIRLTLWGEQAYVIEDLDIDSEIQIIDAYARYGLN-EEIEL 473 (484)
T ss_pred CeeEEEEEEEEcCCcceEEecCCCEEEEEEEEEEcCCC-eEEEEEcchhhhhccccCCCCeEEEechhhhhccc-ccEEE
Confidence 36689999999988666 357888776555 45444 99999999999999999999999999999965321 24666
Q ss_pred EecCCccE
Q 015213 206 SVSSASQI 213 (411)
Q Consensus 206 sV~s~d~I 213 (411)
++.....|
T Consensus 474 s~g~~s~~ 481 (484)
T PRK14699 474 SVGNRSRV 481 (484)
T ss_pred EecCceEE
Confidence 66654444
No 35
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=77.69 E-value=6.6 Score=46.09 Aligned_cols=106 Identities=12% Similarity=0.177 Sum_probs=64.7
Q ss_pred cCceeccCccCHHHHHhHhcCCceeehhhHHhhhcCCCCCCCeE-EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEE
Q 015213 90 SGLRIRNPVVAPSELSERFSEIRFVRLSTIKNLLLGDTLSGCWA-TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISV 168 (411)
Q Consensus 90 SGLrL~~R~IS~~~L~e~l~~~k~vrls~Lk~~v~~~~~~~dWV-tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsL 168 (411)
-|+.|+.--+ +...+.+....+.++.+|... ..+.+| ++|+|..+. .+.|++| +.+.+|.|.. ..+++
T Consensus 920 lG~~ls~HPl--~~~~~~l~~~~~~~~~~l~~~-----~~~~~v~v~g~i~~~~-~~~TkkG--maf~~leD~~-g~~e~ 988 (1046)
T PRK05672 920 TGLSLDSHPL--ALLRPRLDARGVVSAAELLDV-----EDGRRVRVAGVVTHRQ-RPGTASG--VTFLTLEDET-GMVNV 988 (1046)
T ss_pred HCCcCCcCcH--HHHHHHHHhhcCcCHHHHhhc-----cCCCEEEEEEEEEEEE-EecCCCc--eEEEEEecCC-CCEEE
Confidence 3555533222 334444444455555555431 134444 555666554 4556778 8999999997 67999
Q ss_pred EEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEecC
Q 015213 169 FLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 169 fLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV~s 209 (411)
.+|.+.|+++- .+.+|.++.|- -.+... +....|.++.
T Consensus 989 ~ifp~~~~~~~~~l~~~~~~~v~-g~v~~~--~~~~~~~~~~ 1027 (1046)
T PRK05672 989 VVWPGLWERQRREALGARLLLVR-GRVQNA--EGVRHLVADR 1027 (1046)
T ss_pred EECHHHHHHHHHHhccCCEEEEE-EEEEec--CCeEEEEEee
Confidence 99999999986 57888887763 344322 2235666654
No 36
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=74.56 E-value=6.3 Score=32.16 Aligned_cols=60 Identities=12% Similarity=0.090 Sum_probs=45.0
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCC------C------CeEEEEEechHHHhhcC-cccccEEEEEC
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------E------NTISVFLFGDAYQKNWK-EHAGTVFALFN 191 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------~------~~VsLfLFG~A~ek~wK-l~~GtVIAILN 191 (411)
-.++|-|+..-..+.+.+|+.|+.+.|.--. + ..+.+.+||+..+..-+ +..|+.|.|--
T Consensus 4 v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 76 (104)
T PF00436_consen 4 VTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEG 76 (104)
T ss_dssp EEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEE
T ss_pred EEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEE
Confidence 4678999999889999999999988885433 1 36899999996666555 89999988865
No 37
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=70.93 E-value=11 Score=44.44 Aligned_cols=72 Identities=11% Similarity=0.208 Sum_probs=49.8
Q ss_pred EEEEEEecCCCccccC-CCccEEEEEEeeCCCCeEEEEEechHHHhhc-CcccccEEEEECceeccCCCCCcceEEecC
Q 015213 133 ATVAVLTEKGHPKTSS-IGQNYCIWKLGCLEENTISVFLFGDAYQKNW-KEHAGTVFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 133 VtvGVIv~Ks~pK~ss-~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im~~~~g~~fsLsV~s 209 (411)
.++|+|+.-. .+.++ +|+.+.+.+|.|.. ..+++.+|.+.|+++- .+.+|.++.|- -.|-.. +....|.++.
T Consensus 888 ~~~~~i~~~~-~~~tk~~g~~maf~~leD~~-g~ie~~vFp~~y~~~~~~l~~~~~~~v~-G~v~~~--~~~~~l~~~~ 961 (1034)
T PRK07279 888 TILVQIQSIR-VIRTKTKGQQMAFLSVTDTK-KKLDVTLFPETYRQYKDELKEGKFYYLK-GKIQER--DGRLQMVLQQ 961 (1034)
T ss_pred eEEEEEEEEE-EEEEcCCCCeEEEEEEeeCC-CcEEEEECHHHHHHHHHHhccCCEEEEE-EEEEec--CCeeEEEEee
Confidence 4556665543 45556 89999999999996 6899999999999986 56778777663 344222 2234555543
No 38
>PF13891 zf-C3Hc3H: Potential DNA-binding domain
Probab=69.49 E-value=2.2 Score=33.68 Aligned_cols=30 Identities=20% Similarity=0.398 Sum_probs=26.3
Q ss_pred CccceeeecCCccccccccccc--ccccccch
Q 015213 222 YGVCKGKRKDGMACNTVINKRK--GIYCGYHR 251 (411)
Q Consensus 222 lG~CKa~kKdG~~Ct~~VNk~~--~eyC~yHv 251 (411)
|-.|.++..+|..|..+|=+.. ..+|.+|.
T Consensus 33 f~~C~~~~~~~~~C~~Pv~~~~~~~~~C~~H~ 64 (65)
T PF13891_consen 33 FKQCSYVFSNGKRCQNPVLKSENEPPLCPEHA 64 (65)
T ss_pred cccCcCccCCCCcCCCcccccCCCCCcChhhc
Confidence 7889999999999999998764 47999995
No 39
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=67.27 E-value=2 Score=39.77 Aligned_cols=47 Identities=21% Similarity=0.379 Sum_probs=33.4
Q ss_pred EEecCCccEEEeee--eccCccceeeecCCcccccccccccccccccchHHHhhhhccCC
Q 015213 205 LSVSSASQIIKMGT--SVDYGVCKGKRKDGMACNTVINKRKGIYCGYHRLKASDRFITTR 262 (411)
Q Consensus 205 LsV~s~d~ILeIG~--S~DlG~CKa~kKdG~~Ct~~VNk~~~eyC~yHv~~a~rK~~s~R 262 (411)
|.+....|-.-||. ..||.+|-.....| ..||.+|...+|+..+..|
T Consensus 111 ~~L~~~~CrwPiGdp~~~~f~FCG~~~~~g-----------~~YC~~H~~~ay~p~~~~r 159 (162)
T PF07750_consen 111 LELTEGTCRWPIGDPGEPDFHFCGAPTQPG-----------SPYCAAHARIAYQPASERR 159 (162)
T ss_pred hhCCcCCccCcCCCCCCCCccccCCcCCCC-----------CchhHHHHHHhcCCccccc
Confidence 34444567777775 36788887765555 4799999999998776554
No 40
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=67.05 E-value=12 Score=43.88 Aligned_cols=55 Identities=11% Similarity=0.127 Sum_probs=44.8
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEE
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFAL 189 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAI 189 (411)
..++|+|.+.-. +. ++|+++.+.+|.|+. ..+++++|.+.|+++-.+.+|.++-|
T Consensus 900 ~~v~g~i~~~~~-~~-K~g~~maf~~~eD~~-~~~e~~~F~~~~~~~~~l~~~~~~~~ 954 (973)
T PRK07135 900 YRLAIEVKNVKR-LR-KANKEYKKVILSDDS-VEITIFVNDNDYLLFETLKKGDIYEF 954 (973)
T ss_pred EEEEEEEEEEEE-Ee-eCCCeEEEEEEEECC-CcEEEEEcHHHHHHHHHhhcCCEEEE
Confidence 346666666543 44 889999999999997 67999999999999988889997665
No 41
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=62.11 E-value=32 Score=29.47 Aligned_cols=61 Identities=10% Similarity=0.069 Sum_probs=45.9
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCCC----------CeEEEEEechHHHhhc-CcccccEEEEECc
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLEE----------NTISVFLFGDAYQKNW-KEHAGTVFALFNC 192 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~----------~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP 192 (411)
-+++|-|+...+.+.+.+|+.|+.+.|.--.. ..+.+.+||...+..- .+..|+.|+|---
T Consensus 5 v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~ 76 (112)
T PRK06752 5 VVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITGR 76 (112)
T ss_pred EEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEEE
Confidence 46889999998889999999999998864321 3588899997433322 3789999988653
No 42
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=61.10 E-value=23 Score=42.25 Aligned_cols=65 Identities=11% Similarity=0.124 Sum_probs=48.0
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceecc
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRK 196 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~ 196 (411)
.|+++|+|+..-..+++.+|+.+.+.+|.|-.+ .+.+.+|-+-|++|...-.+.=+.+++-.|-.
T Consensus 978 ~~~~~~~i~~vr~~~tk~~G~~~~f~tl~D~~g-~~e~v~f~~~~~~~~~~l~~~~~~~v~g~v~~ 1042 (1139)
T COG0587 978 RVVLAGGIVAVRQRPTKAKGNKMAFLTLEDETG-ILEVVVFPSEYERYRRLLLEGRLLIVKGKVQR 1042 (1139)
T ss_pred eeEEEEEEEEEEEeeccCCCCEEEEEEEecCCC-cEEEEEcHHHHHHHHHHhccCcEEEEEEEEEe
Confidence 499999999986444444899999999999986 89999998778777754333344445544533
No 43
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=59.81 E-value=36 Score=30.13 Aligned_cols=60 Identities=13% Similarity=0.121 Sum_probs=44.9
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCC------C----CeEEEEEechHHHhhcC-cccccEEEEEC
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------E----NTISVFLFGDAYQKNWK-EHAGTVFALFN 191 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------~----~~VsLfLFG~A~ek~wK-l~~GtVIAILN 191 (411)
..++|-|+..-+.+.+.+|+.|+.+.|.--. + ..+.+.+||...+..-+ +..|+.|+|--
T Consensus 5 v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~G 75 (131)
T PRK07274 5 VILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISIDG 75 (131)
T ss_pred EEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 5688999998888888899999888886332 1 25888999985544443 78999988754
No 44
>PRK06386 replication factor A; Reviewed
Probab=59.16 E-value=84 Score=32.94 Aligned_cols=72 Identities=13% Similarity=0.053 Sum_probs=48.7
Q ss_pred CCCeE-EEEEEecCCCccccCCCc--cEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceE
Q 015213 129 SGCWA-TVAVLTEKGHPKTSSIGQ--NYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSL 205 (411)
Q Consensus 129 ~~dWV-tvGVIv~Ks~pK~ss~Gk--~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsL 205 (411)
...|+ +.|-|++-.++-....|. .....-|+|=- ..|.+-||++ .+.+|++|-|.|+.+...+. .+.|
T Consensus 116 g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeT-GrIr~TlW~~------~l~eGd~v~i~na~v~e~~G--~~el 186 (358)
T PRK06386 116 VTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDT-ARVRISSFGK------PLEDNRFVRIENARVSQYNG--YIEI 186 (358)
T ss_pred CCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCC-CeEEEEEccc------cccCCCEEEEeeeEEEccCC--eEEE
Confidence 45787 778888776644444443 34455566653 5899999997 47899999999999876642 3444
Q ss_pred EecC
Q 015213 206 SVSS 209 (411)
Q Consensus 206 sV~s 209 (411)
+++.
T Consensus 187 ~v~~ 190 (358)
T PRK06386 187 SVGN 190 (358)
T ss_pred EeCC
Confidence 4443
No 45
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.77 E-value=45 Score=30.67 Aligned_cols=61 Identities=13% Similarity=0.095 Sum_probs=46.8
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC------------CCeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------------ENTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
..+++|-|+..-+.|.+.+|+.|+.+.|.--. ...+.+.+||+..+... .+..|+.|.|--
T Consensus 6 ~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G 79 (164)
T TIGR00621 6 KVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEG 79 (164)
T ss_pred EEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhCCCCCEEEEEE
Confidence 45789999999888899999999888885432 13688999999555444 589999988754
No 46
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=55.77 E-value=85 Score=29.93 Aligned_cols=96 Identities=13% Similarity=0.132 Sum_probs=62.0
Q ss_pred CCeEEEEEEecCCCccccCCCccEEEEEEeeCC--------------CCeEEEEEechHHHhhc-CcccccEEEEE---C
Q 015213 130 GCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE--------------ENTISVFLFGDAYQKNW-KEHAGTVFALF---N 191 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~--------------~~~VsLfLFG~A~ek~w-Kl~~GtVIAIL---N 191 (411)
....++|=|+..-+.|.+.+|+.|+.++|---. ...+.+.+|++..+..- .+..|+.|.|- .
T Consensus 5 ~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL~ 84 (186)
T PRK07772 5 TTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRLK 84 (186)
T ss_pred CEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEEEEEE
Confidence 456789999999999999999999999986431 12578999998544433 38999999884 4
Q ss_pred ceeccCCCCC-cceEEecCCccEEEeeeeccCccceeee
Q 015213 192 CSVRKDAKGP-GFSLSVSSASQIIKMGTSVDYGVCKGKR 229 (411)
Q Consensus 192 P~Im~~~~g~-~fsLsV~s~d~ILeIG~S~DlG~CKa~k 229 (411)
.....++++. ...+.|. +-+||.+-.|+.-+..+
T Consensus 85 ~r~wedkdG~~rt~~eV~----a~~Vg~~L~~~~a~~~r 119 (186)
T PRK07772 85 QRSYETREGEKRTVVELE----VDEIGPSLRYATAKVTR 119 (186)
T ss_pred cCceECCCCCEEEEEEEE----EEEcccceeeeeceeee
Confidence 4444444443 2222221 22456655665544443
No 47
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=54.67 E-value=48 Score=27.90 Aligned_cols=72 Identities=19% Similarity=0.139 Sum_probs=47.1
Q ss_pred CCeEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhc--CcccccEEEE-ECceeccCCCCCcceEE
Q 015213 130 GCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNW--KEHAGTVFAL-FNCSVRKDAKGPGFSLS 206 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~w--Kl~~GtVIAI-LNP~Im~~~~g~~fsLs 206 (411)
++..+.|=|. ..+.+.+| .++++|-| .+..++..+|...+.+.- .++.|+-|.+ -.+++.+. ...++|.
T Consensus 22 ~~vwV~GEIs---~~~~~~~g--h~YftLkD-~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~--~G~~sl~ 93 (99)
T PF13742_consen 22 PNVWVEGEIS---NLKRHSSG--HVYFTLKD-EEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEP--RGSLSLI 93 (99)
T ss_pred CCEEEEEEEe---ecEECCCc--eEEEEEEc-CCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECC--CcEEEEE
Confidence 3333445544 44444444 57788888 458999999999887754 7899986544 44666554 2358887
Q ss_pred ecC
Q 015213 207 VSS 209 (411)
Q Consensus 207 V~s 209 (411)
|.+
T Consensus 94 v~~ 96 (99)
T PF13742_consen 94 VED 96 (99)
T ss_pred EEE
Confidence 764
No 48
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=54.65 E-value=50 Score=29.00 Aligned_cols=60 Identities=12% Similarity=0.112 Sum_probs=46.2
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCC------CCeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------ENTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
-.++|-|+...+.+.+.+|+.|+.+.|.--. ...+.+-+||...+... .+.-|+.|+|--
T Consensus 6 v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G 72 (121)
T PRK07459 6 VTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITG 72 (121)
T ss_pred EEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 4689999999888999999999999996432 13588999997433322 389999998865
No 49
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=53.45 E-value=40 Score=34.50 Aligned_cols=64 Identities=9% Similarity=0.037 Sum_probs=48.4
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCC
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDA 198 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~ 198 (411)
.-.+.+|.++ ..+++++|++|..++|.|=. .+|+--+|...-+..-...+|+||-| +-.|...+
T Consensus 14 v~~~~lv~~~-~~~~~knG~~yl~l~l~D~t-G~I~ak~W~~~~~~~~~~~~g~vv~v-~G~v~~y~ 77 (314)
T PRK13480 14 VDHFLLIKSA-TKGVASNGKPFLTLILQDKS-GDIEAKLWDVSPEDEATYVPETIVHV-KGDIINYR 77 (314)
T ss_pred eeEEEEEEEc-eeeecCCCCeEEEEEEEcCC-cEEEEEeCCCChhhHhhcCCCCEEEE-EEEEEEEC
Confidence 4446667776 57889999999999999964 68999999877666667899998854 44554443
No 50
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=52.13 E-value=32 Score=31.73 Aligned_cols=95 Identities=16% Similarity=0.085 Sum_probs=50.8
Q ss_pred CCCCeEEEEEEecCCCccccCCCccEEE-EEEeeCCCCeEEEEEechHHHhhc--CcccccEEEEECceeccCCCCCcce
Q 015213 128 LSGCWATVAVLTEKGHPKTSSIGQNYCI-WKLGCLEENTISVFLFGDAYQKNW--KEHAGTVFALFNCSVRKDAKGPGFS 204 (411)
Q Consensus 128 ~~~dWVtvGVIv~Ks~pK~ss~Gk~Y~i-wkLsDL~~~~VsLfLFG~A~ek~w--Kl~~GtVIAILNP~Im~~~~g~~fs 204 (411)
..+..=+||+|+.-. ++..|.. .-|+|-..+-|.|-.|++--+=-| -+.+|.+||+-|=+.+.....
T Consensus 17 p~~EvD~VG~VvsV~------~~~~f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR~~s~s---- 86 (143)
T PF09104_consen 17 PYGEVDTVGFVVSVS------KKQGFQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLIAASNLQWRPESTS---- 86 (143)
T ss_dssp CCCEEEEEEEEEEEE--------TTS--EEEEE-TTS-EEEEEESS-------SS---TT-EEEEEEEEE-S-TTS----
T ss_pred CccccceEEEEEEEE------ecCCCceeEEeecCCccEEEEEeccCccccchhhhcCcceEEEEeeeEeeccccc----
Confidence 467788999999882 2234544 667899877788888877332233 469999999999999854211
Q ss_pred EEecCCccEEEeeeeccCccceeeecCCcccccccc
Q 015213 205 LSVSSASQIIKMGTSVDYGVCKGKRKDGMACNTVIN 240 (411)
Q Consensus 205 LsV~s~d~ILeIG~S~DlG~CKa~kKdG~~Ct~~VN 240 (411)
-+-.-.|.||..=...-|-+..+..+-+
T Consensus 87 --------~iP~~~A~d~S~FS~nPK~~hLqe~~~~ 114 (143)
T PF09104_consen 87 --------GIPTLFATDLSVFSANPKESHLQEAFNK 114 (143)
T ss_dssp --------SS-EEEEECCEEEESS-SSCCCHHHHHH
T ss_pred --------CCCeeEeccceeeecCccHHHHHHHHHH
Confidence 1133345566665555566655555444
No 51
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=51.26 E-value=57 Score=30.92 Aligned_cols=88 Identities=15% Similarity=0.087 Sum_probs=56.8
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCC------------CCeEEEEEechHHHhhc-CcccccEEEEECc---eec
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------------ENTISVFLFGDAYQKNW-KEHAGTVFALFNC---SVR 195 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP---~Im 195 (411)
.+++|-|+..-+.|.+.+|..++.+.|.--. ...+.|.+||...+..- .+.-|+.|+|--- ..+
T Consensus 5 V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeGrL~~~~y 84 (182)
T PRK08486 5 VILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESW 84 (182)
T ss_pred EEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEeCcE
Confidence 4789999999888999999999988883211 13588999998544433 4899999988543 223
Q ss_pred cCCCCC-cceEEecCCccEEEeeeec
Q 015213 196 KDAKGP-GFSLSVSSASQIIKMGTSV 220 (411)
Q Consensus 196 ~~~~g~-~fsLsV~s~d~ILeIG~S~ 220 (411)
.+++|. ...+.|. .+.|-.|+...
T Consensus 85 ~dkdG~~r~~~eI~-a~~v~~L~~~~ 109 (182)
T PRK08486 85 MDQNGQKRSKHTIT-AESMQMLDSKS 109 (182)
T ss_pred ECCCCcEEEEEEEE-EeEEEECCCCC
Confidence 444443 2333332 33455555443
No 52
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=48.68 E-value=70 Score=29.28 Aligned_cols=61 Identities=11% Similarity=0.046 Sum_probs=46.5
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC-------------CCeEEEEEech-HHHhhc-CcccccEEEEEC
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE-------------ENTISVFLFGD-AYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~-------------~~~VsLfLFG~-A~ek~w-Kl~~GtVIAILN 191 (411)
...++|-|+...+.|.+.+|+.|+.+.|.--. ..-+.|.+||+ ..+... .+..|+.|+|--
T Consensus 7 ~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~V~V~G 82 (152)
T PRK06642 7 KVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKLYIEG 82 (152)
T ss_pred EEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCEEEEEE
Confidence 45789999999888999999999999986221 12588999996 344333 389999998865
No 53
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=48.64 E-value=71 Score=31.18 Aligned_cols=63 Identities=10% Similarity=0.055 Sum_probs=50.3
Q ss_pred CCeEEEEEEecCCCccccCCCccEEEEEEeeCC----CCeEEEEEechHHHhhcCcccccEEEEECc
Q 015213 130 GCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE----ENTISVFLFGDAYQKNWKEHAGTVFALFNC 192 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~----~~~VsLfLFG~A~ek~wKl~~GtVIAILNP 192 (411)
....++|=|+...+.|.+.+|+.++-+.|---. ...+.+.+||...+..-.+..|+-|+|---
T Consensus 110 N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~~l~KG~~V~V~Gr 176 (219)
T PRK05813 110 NEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNARFCKTLEVGDNIRVWGR 176 (219)
T ss_pred cEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHhhCCCCCEEEEEEE
Confidence 457799999999999999999999999996322 246999999985444445999999998753
No 54
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=48.47 E-value=67 Score=30.01 Aligned_cols=61 Identities=16% Similarity=0.173 Sum_probs=47.2
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCC-------CCeEEEEEechHHHhhc-CcccccEEEEECc
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLE-------ENTISVFLFGDAYQKNW-KEHAGTVFALFNC 192 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~-------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP 192 (411)
..++|=|+..-+.|.+.+|+.|+.++|.--. ..-+.+.+||...+..- -+.-|+.|+|---
T Consensus 4 V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGr 72 (161)
T PRK06293 4 GYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGE 72 (161)
T ss_pred EEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEE
Confidence 5689999999899999999999999996332 13588999998544433 3899999988653
No 55
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=46.64 E-value=79 Score=29.74 Aligned_cols=61 Identities=11% Similarity=0.080 Sum_probs=45.7
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC------C----CeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------E----NTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------~----~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
..+++|-|+...+.|.+.+|..++.+.|.--. + ..+.+-+||...+..- .+..|+.|+|--
T Consensus 4 ~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeG 75 (173)
T PRK06751 4 RVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDG 75 (173)
T ss_pred EEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEE
Confidence 46789999999888889999989888884221 1 2588889998544433 378999998864
No 56
>PRK07218 replication factor A; Provisional
Probab=45.81 E-value=2.1e+02 Score=30.66 Aligned_cols=77 Identities=13% Similarity=-0.007 Sum_probs=49.3
Q ss_pred CCCeE-EEEEEecCCCccc-c-CCCcc-EEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcce
Q 015213 129 SGCWA-TVAVLTEKGHPKT-S-SIGQN-YCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFS 204 (411)
Q Consensus 129 ~~dWV-tvGVIv~Ks~pK~-s-s~Gk~-Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fs 204 (411)
...|| +.|.|++. .+|. . ..|.. +...-|+|=. ..+.+-||++. -.+.+|++|-|.|+.+...+ ..+.
T Consensus 171 g~~~V~v~g~Vl~~-~~r~f~~~dg~~~v~~giigDeT-G~Ir~tlW~~~----~~l~~Gd~v~I~na~v~e~~--G~~e 242 (423)
T PRK07218 171 GDRGVNVEARVLEL-EHREIDGRDGETTILSGVLADET-GRLPFTDWDPL----PEIEIGASIRIEDAYVREFR--GVPS 242 (423)
T ss_pred CCCceEEEEEEEEe-cceeEEcCCCCeEEEEEEEECCC-ceEEEEEeccc----ccCCCCCEEEEeeeEEeccC--CeEE
Confidence 35675 56777777 4554 2 33422 3333456653 58999999973 25899999999999997754 2355
Q ss_pred EEecCCccE
Q 015213 205 LSVSSASQI 213 (411)
Q Consensus 205 LsV~s~d~I 213 (411)
|.|+....|
T Consensus 243 lnv~~~t~I 251 (423)
T PRK07218 243 VNVSEFTTV 251 (423)
T ss_pred EEECCceEE
Confidence 555543333
No 57
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=44.18 E-value=85 Score=29.54 Aligned_cols=87 Identities=14% Similarity=0.034 Sum_probs=55.9
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC---C----------CeEEEEEechHHHhhc-CcccccEEEEECceec-
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE---E----------NTISVFLFGDAYQKNW-KEHAGTVFALFNCSVR- 195 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~---~----------~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP~Im- 195 (411)
..+++|-|+.--+.+.+.+|+.|+.+.|.--. + .-+.|-+||...+..- .++.|+.|+|-----.
T Consensus 7 kV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~VeGrLr~~ 86 (172)
T PRK05733 7 KVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKLQTR 86 (172)
T ss_pred EEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEEEEEeC
Confidence 45789999998888889999999888885321 1 1388999997444333 3899999988543221
Q ss_pred cC-CCCC---cceEEecCCccEEEee
Q 015213 196 KD-AKGP---GFSLSVSSASQIIKMG 217 (411)
Q Consensus 196 ~~-~~g~---~fsLsV~s~d~ILeIG 217 (411)
.. ++|. ...|.+++...|-.||
T Consensus 87 ~y~kdG~~r~~~eVvvd~~g~v~~L~ 112 (172)
T PRK05733 87 EWEKDGIKRYTTEIVVDMQGTMQLLG 112 (172)
T ss_pred cEecCCEEEEEEEEEEeecCeEEECc
Confidence 11 2332 2345555545555555
No 58
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=42.53 E-value=1.1e+02 Score=28.65 Aligned_cols=62 Identities=15% Similarity=-0.006 Sum_probs=46.2
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC------C------CeEEEEEechHHHhhc-CcccccEEEEECc
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE------E------NTISVFLFGDAYQKNW-KEHAGTVFALFNC 192 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~------~------~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP 192 (411)
...++|-|+.--+.+.+.+|..|+.+.|.--. + .-+.|.+||...+..- .+..|+.|+|---
T Consensus 7 kv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeGr 81 (164)
T PRK08763 7 KVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEGS 81 (164)
T ss_pred EEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEEE
Confidence 46789999998888899999999999885321 1 2488999997433222 3899999998654
No 59
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=41.88 E-value=1.1e+02 Score=28.83 Aligned_cols=62 Identities=15% Similarity=0.031 Sum_probs=46.6
Q ss_pred CCeEEEEEEecCCCccccCCCccEEEEEEeeCC-------C------CeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 130 GCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE-------E------NTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~-------~------~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
....++|-|+..-+.|.+.+|..|+.+.|.--. + ..+.|.+||.-.+..- .+..|+.|+|--
T Consensus 7 N~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~VeG 82 (175)
T PRK13732 7 NKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEG 82 (175)
T ss_pred eEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEEE
Confidence 356789999998888999999999999885321 1 2478999997433333 389999998865
No 60
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=40.82 E-value=1.2e+02 Score=28.30 Aligned_cols=63 Identities=8% Similarity=0.084 Sum_probs=46.3
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeC------CC----CeEEEEEechHHHh-hcCcccccEEEEECce
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCL------EE----NTISVFLFGDAYQK-NWKEHAGTVFALFNCS 193 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL------~~----~~VsLfLFG~A~ek-~wKl~~GtVIAILNP~ 193 (411)
..+++|=|+..-+.|.+.+|..++.++|.-- .+ ..+.+.+||...+. ...++-|+.|+|----
T Consensus 4 ~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeGrl 77 (162)
T PRK07275 4 NVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTGRI 77 (162)
T ss_pred EEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEEEE
Confidence 3567888998888888999998888888421 11 35889999985444 2358999999986543
No 61
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=40.67 E-value=1.1e+02 Score=28.75 Aligned_cols=80 Identities=11% Similarity=0.053 Sum_probs=53.8
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC--------C-----CeEEEEEech-HHHhhc-CcccccEEEEECcee-
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE--------E-----NTISVFLFGD-AYQKNW-KEHAGTVFALFNCSV- 194 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~--------~-----~~VsLfLFG~-A~ek~w-Kl~~GtVIAILNP~I- 194 (411)
.-.++|-|+...+.|.+.+|++|+-+.|.--. + ..+.+.+||+ ..+... .++.|+.|+|-----
T Consensus 7 ~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~VeGrL~~ 86 (166)
T PRK06341 7 KVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAKVYIEGQLQT 86 (166)
T ss_pred EEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhcCCCCEEEEEEEEEe
Confidence 35678999998888889999999988885431 0 2478999997 445554 579999998754322
Q ss_pred --ccCCCCC---cceEEecCC
Q 015213 195 --RKDAKGP---GFSLSVSSA 210 (411)
Q Consensus 195 --m~~~~g~---~fsLsV~s~ 210 (411)
+.+++|. .+.|.+++.
T Consensus 87 r~w~dkdG~~r~~~eIiv~~~ 107 (166)
T PRK06341 87 RKWTDQSGVERYSTEVVLQGF 107 (166)
T ss_pred CcEECCCCCEEEEEEEEEEec
Confidence 3334442 344555553
No 62
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=38.12 E-value=1.5e+02 Score=21.87 Aligned_cols=53 Identities=13% Similarity=0.110 Sum_probs=34.4
Q ss_pred EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEec-hHHHhhcCcccccEEEEE
Q 015213 134 TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFG-DAYQKNWKEHAGTVFALF 190 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG-~A~ek~wKl~~GtVIAIL 190 (411)
+.|.|.+..... .. |+.|....+.|= ...+.+..|+ ..+. .-.+.+|+.+.+.
T Consensus 2 i~~~V~~~~~~~-~~-~~~~~~~~~~D~-~g~i~~~~F~~~~~~-~~~~~~G~~~~v~ 55 (75)
T cd04488 2 VEGTVVSVEVVP-RR-GRRRLKVTLSDG-TGTLTLVFFNFQPYL-KKQLPPGTRVRVS 55 (75)
T ss_pred EEEEEEEEEecc-CC-CccEEEEEEEcC-CCEEEEEEECCCHHH-HhcCCCCCEEEEE
Confidence 567666653222 22 667888888886 3689999998 4442 1246788877665
No 63
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=35.95 E-value=1.4e+02 Score=27.14 Aligned_cols=64 Identities=6% Similarity=-0.139 Sum_probs=44.9
Q ss_pred CeEEEEEEecCCCccccCCCcc----EEEEEEe-eC----C--------CCeEEEEEechHHHhhc-CcccccEEEEECc
Q 015213 131 CWATVAVLTEKGHPKTSSIGQN----YCIWKLG-CL----E--------ENTISVFLFGDAYQKNW-KEHAGTVFALFNC 192 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~----Y~iwkLs-DL----~--------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILNP 192 (411)
.+.++|=|+.-.+.|.+.+|.. ++.+.|. |- . ...+.+-+||...+... .+.-|+.|+|---
T Consensus 4 ~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~Gr 83 (148)
T PRK08182 4 HFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEGR 83 (148)
T ss_pred EEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEEEE
Confidence 4678899998888888888875 7777772 20 1 12588999997544333 3899999998764
Q ss_pred ee
Q 015213 193 SV 194 (411)
Q Consensus 193 ~I 194 (411)
--
T Consensus 84 L~ 85 (148)
T PRK08182 84 ME 85 (148)
T ss_pred EE
Confidence 33
No 64
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=32.29 E-value=1.6e+02 Score=25.74 Aligned_cols=59 Identities=19% Similarity=0.144 Sum_probs=40.4
Q ss_pred EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHHHhhcC---cccccEEEEECceeccC
Q 015213 134 TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAYQKNWK---EHAGTVFALFNCSVRKD 197 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~ek~wK---l~~GtVIAILNP~Im~~ 197 (411)
++|||+.-+.+- -+.|=..-|+|=+-+-+-|..+.+ ++++.. ++++++||+-|-+.++.
T Consensus 2 ~VGvVvsV~~~~----~g~~~~vYLaDe~~nll~vkfw~~-l~~~~~EDvvk~~~lia~SNLQwR~~ 63 (100)
T cd04495 2 TVGVVISVGKPI----EGKFPAVYLADECLNLLCVKFWSS-LEQYAYEDVVKRRVLLAASNLQWRTE 63 (100)
T ss_pred ceEEEEEEcccc----cCccceEEEecCCcCEEEEEEecc-hHHhhhhhhcccceEEEEecceEecc
Confidence 689999887543 234666678887655566666653 333332 47899999999999875
No 65
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=31.32 E-value=1.9e+02 Score=23.51 Aligned_cols=73 Identities=12% Similarity=0.084 Sum_probs=44.6
Q ss_pred eEEEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEech-HHHhhcCcc-cccEEEEECceeccCCCCCcceEEe
Q 015213 132 WATVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGD-AYQKNWKEH-AGTVFALFNCSVRKDAKGPGFSLSV 207 (411)
Q Consensus 132 WVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~-A~ek~wKl~-~GtVIAILNP~Im~~~~g~~fsLsV 207 (411)
-++-|-|... +.|.+++|+.-..+.|+|.. ..+.+=+|.. -.+.+-.++ .|+-|-+ .-.+.-++-.+...|.+
T Consensus 2 v~i~G~Vf~~-e~re~k~g~~i~~~~itD~t-~Si~~K~F~~~~~~~~~~ik~~G~~v~v-~G~v~~D~f~~e~~~~i 76 (82)
T cd04484 2 VVVEGEVFDL-EIRELKSGRKILTFKVTDYT-SSITVKKFLRKDEKDKEELKSKGDWVRV-RGKVQYDTFSKELVLMI 76 (82)
T ss_pred EEEEEEEEEE-EEEEecCCCEEEEEEEEcCC-CCEEEEEeccCChhHHhhcccCCCEEEE-EEEEEEccCCCceEEEe
Confidence 3566777776 67888999888889999986 4555555653 233334577 8876654 33343333223344444
No 66
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=31.24 E-value=1.8e+02 Score=27.83 Aligned_cols=61 Identities=13% Similarity=0.018 Sum_probs=46.0
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeCC-------------CCeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE-------------ENTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~-------------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
..+++|=|+..-+.+.+.+|+.++.+.|.--. ..-+.|.+||.-.+... .++.|+.|.|--
T Consensus 6 ~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeG 80 (182)
T PRK06958 6 KVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred EEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEE
Confidence 45789999999888889999999888884211 13588899998544433 379999998865
No 67
>PF07708 Tash_PEST: Tash protein PEST motif; InterPro: IPR011695 The PEST motif is found in one or more copies in Tash AT-hook proteins from Theileria annulata. Tash proteins are transported to the host nucleus and are thought to be involved in pathogenesis []. The PEST motif is often found in conjunction with the (IPR007480 from INTERPRO), whose function is unknown. These repeats may be part of the PEST motif (a signal for rapid proteolytic degradation) [], though this is not proven. This motif is also found in other T. annulata proteins, which have no other known domains.
Probab=30.64 E-value=37 Score=21.36 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=11.2
Q ss_pred ceEEEeccCCCCC
Q 015213 398 KMIELDMVSSDED 410 (411)
Q Consensus 398 ~~~~~~~~~~~~~ 410 (411)
.+|.+++.|||||
T Consensus 6 Eti~vEi~SDeee 18 (19)
T PF07708_consen 6 ETIPVEIGSDEEE 18 (19)
T ss_pred ceEEEEecccccC
Confidence 5899999999886
No 68
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.79 E-value=21 Score=33.08 Aligned_cols=16 Identities=38% Similarity=0.590 Sum_probs=13.1
Q ss_pred ccccccchHHHhhhhc
Q 015213 244 GIYCGYHRLKASDRFI 259 (411)
Q Consensus 244 ~eyC~yHv~~a~rK~~ 259 (411)
+.||.||...+|+-..
T Consensus 148 gpYC~~Har~Afqp~a 163 (169)
T COG5352 148 GPYCEYHARVAFQPAA 163 (169)
T ss_pred CcchhHhhhhhcchHH
Confidence 7899999988887543
No 69
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=26.96 E-value=2.6e+02 Score=26.40 Aligned_cols=62 Identities=18% Similarity=0.062 Sum_probs=46.3
Q ss_pred CCeEEEEEEecCCCccccCCCccEEEEEEeeCC--------C-----CeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 130 GCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE--------E-----NTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~--------~-----~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
...+++|=|+..-+.|.+.+|..++.++|.--. + .-+.+-+||...+..- .|+.|+-|+|--
T Consensus 7 N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 7 NKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEG 82 (177)
T ss_pred eEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEEEEEE
Confidence 356789999999888999999998888884221 1 2478999997544433 489999998865
No 70
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=25.93 E-value=1.6e+02 Score=32.07 Aligned_cols=83 Identities=13% Similarity=0.165 Sum_probs=57.0
Q ss_pred cCCceeehhhHHhhhcCCCCCCCeEEEEEEecCCCccccCCCccEEEEEEeeCC--CCeEEEEEechHHHhhcCc-cccc
Q 015213 109 SEIRFVRLSTIKNLLLGDTLSGCWATVAVLTEKGHPKTSSIGQNYCIWKLGCLE--ENTISVFLFGDAYQKNWKE-HAGT 185 (411)
Q Consensus 109 ~~~k~vrls~Lk~~v~~~~~~~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~--~~~VsLfLFG~A~ek~wKl-~~Gt 185 (411)
.+.+++|+++-... ...---++|||.+-.+|+.+.+.---+..+|+|=. +--+.+.||..-++.+=.+ +.|+
T Consensus 5 ds~k~Iri~da~kk-----~~tiVNl~GiVkef~pp~qs~g~D~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GD 79 (522)
T KOG4757|consen 5 DSLKLIRISDALKK-----KNTIVNLIGIVKEFTPPRQSLGKDWVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGD 79 (522)
T ss_pred cchheeechHHHHh-----cCcEEEEEEEEEeccChhhccCCceEEEEEEeCCCCCCCCcEEEEecCchhhCccccccCc
Confidence 34566777642211 12233489999999999998844445788999943 3468888998777776543 7899
Q ss_pred EEEEECceecc
Q 015213 186 VFALFNCSVRK 196 (411)
Q Consensus 186 VIAILNP~Im~ 196 (411)
+|.+--=+|.-
T Consensus 80 iillhRiKiq~ 90 (522)
T KOG4757|consen 80 IILLHRIKIQS 90 (522)
T ss_pred EEEEEEEEEEE
Confidence 99887777743
No 71
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=24.58 E-value=3e+02 Score=22.83 Aligned_cols=52 Identities=12% Similarity=0.169 Sum_probs=34.8
Q ss_pred EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechH--HH-hhcCcccccEEEEE
Q 015213 134 TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDA--YQ-KNWKEHAGTVFALF 190 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A--~e-k~wKl~~GtVIAIL 190 (411)
+-|.|++.. +.-+.|. .+++|.|= +..++..+|... +. -...+++|+-|.+.
T Consensus 3 v~GeVs~~~--~~~~sGH--~yFtlkD~-~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~ 57 (91)
T cd04482 3 VTGKVVEEP--RTIEGGH--VFFKISDG-TGEIDCAAYEPTKEFRDVVRLLIPGDEVTVY 57 (91)
T ss_pred EEEEEeCCe--ecCCCCC--EEEEEECC-CcEEEEEEECcccccccccCCCCCCCEEEEE
Confidence 567777653 2225666 66777784 468999999776 43 35689999955543
No 72
>PF10983 DUF2793: Protein of unknown function (DUF2793); InterPro: IPR021251 This entry is represented by Bacteriophage D3112, Orf54. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.50 E-value=33 Score=28.98 Aligned_cols=30 Identities=30% Similarity=0.612 Sum_probs=20.4
Q ss_pred ccccc--ccccccccCCCCCCCCCCCCCCCCCCCCC
Q 015213 8 LSLLL--SLQDKFLETPPGSPSNPGSSSPGYLSDDG 41 (411)
Q Consensus 8 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (411)
||.|. ++.++.+-|||++|.. -..|+-+..
T Consensus 8 LD~lvql~V~s~~~t~PP~~P~~----Gd~yiv~~~ 39 (87)
T PF10983_consen 8 LDALVQLAVLSRDLTAPPASPAE----GDRYIVPAG 39 (87)
T ss_pred HHhhhhhheecccccCCCCCCCC----CCEEEECCC
Confidence 45554 4589999999999966 346654444
No 73
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=24.06 E-value=2.7e+02 Score=26.09 Aligned_cols=61 Identities=8% Similarity=-0.020 Sum_probs=44.8
Q ss_pred CeEEEEEEecCCCccccCCCccEEEEEEeeC------C-------CCeEEEEEechHHHhhc-CcccccEEEEEC
Q 015213 131 CWATVAVLTEKGHPKTSSIGQNYCIWKLGCL------E-------ENTISVFLFGDAYQKNW-KEHAGTVFALFN 191 (411)
Q Consensus 131 dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL------~-------~~~VsLfLFG~A~ek~w-Kl~~GtVIAILN 191 (411)
.-.++|=|+..-+.|.+.+|+.+..+.|.-- . ..-+.+.+||...+..- .+..|+.|.|--
T Consensus 6 ~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 6 KVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred EEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE
Confidence 3567899999888889999998888887421 1 12588899997544433 379999998865
No 74
>PF08879 WRC: WRC; InterPro: IPR014977 WRC is named after the conserved Trp-Arg-Cys motif, it contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that WRC functions in DNA binding []. ; GO: 0005515 protein binding
Probab=23.02 E-value=50 Score=24.92 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=20.5
Q ss_pred cCccceeeecCCcccccccccccccccccchHHH
Q 015213 221 DYGVCKGKRKDGMACNTVINKRKGIYCGYHRLKA 254 (411)
Q Consensus 221 DlG~CKa~kKdG~~Ct~~VNk~~~eyC~yHv~~a 254 (411)
+.+.|+-+--.|=.|...+.. --.||+||....
T Consensus 3 e~~RC~R~DGK~WrC~~~a~~-g~~~Ce~H~~~~ 35 (46)
T PF08879_consen 3 EPWRCRRNDGKGWRCSRRALP-GYSLCEHHLDRG 35 (46)
T ss_pred ccceeeCCCCCccccCCccCC-CccHHHHHHHHH
Confidence 456675432333358877654 346999998764
No 75
>PRK07218 replication factor A; Provisional
Probab=22.90 E-value=3.9e+02 Score=28.66 Aligned_cols=80 Identities=15% Similarity=0.053 Sum_probs=55.7
Q ss_pred CCeE-EEEEEecCCCccccCCCc--cEEEEEEeeCCCCeEEEEEechHHHhhcCcccccEEEEECceeccCCCCCcceEE
Q 015213 130 GCWA-TVAVLTEKGHPKTSSIGQ--NYCIWKLGCLEENTISVFLFGDAYQKNWKEHAGTVFALFNCSVRKDAKGPGFSLS 206 (411)
Q Consensus 130 ~dWV-tvGVIv~Ks~pK~ss~Gk--~Y~iwkLsDL~~~~VsLfLFG~A~ek~wKl~~GtVIAILNP~Im~~~~g~~fsLs 206 (411)
..|| +.|-|++.++.-....|. .+....|.|=. ..|++-||++. -+.+|++|-|-|+.+...+ +.+.|+
T Consensus 68 ~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeT-G~Ir~tlW~~~-----~l~~Gdvv~I~na~vre~~--g~~el~ 139 (423)
T PRK07218 68 DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADET-GTISYTAWKDF-----GLSPGDTVTIGNAGVREWD--GRPELN 139 (423)
T ss_pred CceeEEEEEEEEecceeEecCCCceEEEEEEEECCC-CeEEEEEECCC-----CCCCCCEEEEeccEeeccC--CceEEe
Confidence 3566 578888887632234453 56777778774 68999999954 3999999999999997764 236666
Q ss_pred ecCCccEEEee
Q 015213 207 VSSASQIIKMG 217 (411)
Q Consensus 207 V~s~d~ILeIG 217 (411)
+.....|.++-
T Consensus 140 ig~~t~I~~~d 150 (423)
T PRK07218 140 IGESTTVSLLD 150 (423)
T ss_pred ccCcceEEEcC
Confidence 66555554443
No 76
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=22.31 E-value=4.1e+02 Score=21.22 Aligned_cols=65 Identities=17% Similarity=0.138 Sum_probs=43.3
Q ss_pred EEEEEecCCCccccCCCccEEEEEEeeCCCCeEEEEEechHH-HhhcCccccc-EEEEECceeccCCCCCcceEEecC
Q 015213 134 TVAVLTEKGHPKTSSIGQNYCIWKLGCLEENTISVFLFGDAY-QKNWKEHAGT-VFALFNCSVRKDAKGPGFSLSVSS 209 (411)
Q Consensus 134 tvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL~~~~VsLfLFG~A~-ek~wKl~~Gt-VIAILNP~Im~~~~g~~fsLsV~s 209 (411)
+-|.|++.. + ++|. .+++|.| .+..+++.+|.... ...-++.+|+ |++.=++++ + ...+.|.+++
T Consensus 3 v~GeVs~~~--~--~~GH--vyfsLkD-~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~-~---~G~~ql~v~~ 69 (73)
T cd04487 3 IEGEVVQIK--Q--TSGP--TIFTLRD-ETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP-R---DGQLQIEVES 69 (73)
T ss_pred EEEEEeccc--c--CCCC--EEEEEEc-CCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEec-C---CeEEEEEEee
Confidence 457777664 2 5565 6778888 44689999997654 3345789999 777666665 2 2346666654
No 77
>PRK00036 primosomal replication protein N; Reviewed
Probab=21.24 E-value=4.5e+02 Score=23.16 Aligned_cols=77 Identities=18% Similarity=0.060 Sum_probs=52.8
Q ss_pred CCeEEEEEEecCCCccccCCCccEEEEEEeeC---CC--------CeEEEEEechHHHhhcCcccccEEE---EECceec
Q 015213 130 GCWATVAVLTEKGHPKTSSIGQNYCIWKLGCL---EE--------NTISVFLFGDAYQKNWKEHAGTVFA---LFNCSVR 195 (411)
Q Consensus 130 ~dWVtvGVIv~Ks~pK~ss~Gk~Y~iwkLsDL---~~--------~~VsLfLFG~A~ek~wKl~~GtVIA---ILNP~Im 195 (411)
..++..|+|++....|+|-.|=+-+-|.|-=- .+ ..+.+.++|+..++.-.+.+|+.|- .|+.
T Consensus 2 N~l~Ltg~v~~~~~lryTPAGIp~~~~~LeH~S~q~EAG~~Rqv~~~i~ava~G~~a~~~~~l~~Gs~v~v~GFLa~--- 78 (107)
T PRK00036 2 NTLELSARVLECGAMRHTPAGLPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLADTPLGTEMQVQGFLAP--- 78 (107)
T ss_pred CEEEEEEEEeccCccccCCCCCceEEEEEEEeEEeEeCCCcceEEEEEEEEEEhhHHHHhcccCCCCEEEEEEEEEE---
Confidence 35788999999999999999988777777322 11 4789999996555555799998764 4554
Q ss_pred cCCCCCcceEEecC
Q 015213 196 KDAKGPGFSLSVSS 209 (411)
Q Consensus 196 ~~~~g~~fsLsV~s 209 (411)
..+..+..-|.+..
T Consensus 79 ~~~~~~~LVLHi~~ 92 (107)
T PRK00036 79 ARKDSVKVKLHLQQ 92 (107)
T ss_pred CCCCCCcEEEEhHH
Confidence 33333344554443
Done!