Query 001266
Match_columns 1112
No_of_seqs 213 out of 235
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 20:16:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001266.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001266hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4751 DNA recombinational re 100.0 5E-103 1E-107 890.2 21.2 696 1-724 1-755 (756)
2 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 100.0 3.7E-52 7.9E-57 445.2 23.5 228 720-955 1-251 (251)
3 PF09103 BRCA-2_OB1: BRCA2, ol 100.0 9.3E-40 2E-44 317.3 9.6 117 587-716 1-117 (118)
4 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 100.0 9E-35 2E-39 273.1 11.5 100 599-711 1-100 (100)
5 PF09169 BRCA-2_helical: BRCA2 99.9 3E-28 6.6E-33 250.8 8.8 101 484-584 70-195 (195)
6 PF09104 BRCA-2_OB3: BRCA2, ol 99.8 2E-19 4.3E-24 179.2 10.8 116 953-1090 1-120 (143)
7 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 99.6 6.5E-15 1.4E-19 138.3 9.1 98 971-1088 1-98 (100)
8 KOG4751 DNA recombinational re 99.6 3.3E-16 7.2E-21 181.6 -0.6 308 775-1106 25-370 (756)
9 PF00634 BRCA2: BRCA2 repeat; 98.6 6.4E-09 1.4E-13 81.7 0.7 33 220-252 2-34 (35)
10 PF00634 BRCA2: BRCA2 repeat; 98.5 1.8E-08 4E-13 79.1 0.4 32 117-148 4-35 (35)
11 TIGR00617 rpa1 replication fac 98.2 0.00055 1.2E-08 84.2 27.9 171 886-1088 227-410 (608)
12 PF09121 Tower: Tower; InterP 98.0 2E-06 4.3E-11 69.3 2.0 38 747-784 1-42 (42)
13 PRK12366 replication factor A; 95.8 0.29 6.3E-06 61.2 17.7 159 886-1074 328-499 (637)
14 PRK07218 replication factor A; 95.6 1.6 3.4E-05 52.3 22.2 169 867-1072 73-257 (423)
15 PRK07211 replication factor A; 95.5 0.27 5.9E-06 59.4 15.5 251 632-1049 91-347 (485)
16 PRK12366 replication factor A; 94.8 0.42 9.1E-06 59.8 14.8 139 885-1049 110-253 (637)
17 PF04057 Rep-A_N: Replication 94.1 0.13 2.8E-06 49.8 6.6 75 588-673 5-79 (101)
18 PRK15491 replication factor A; 94.0 2.2 4.8E-05 50.3 17.7 135 885-1047 104-245 (374)
19 cd04475 RPA1_DBD_B RPA1_DBD_B: 93.7 0.44 9.5E-06 45.3 9.3 93 970-1089 2-100 (101)
20 cd04477 RPA1N RPA1N: A subfami 93.6 0.14 3E-06 49.4 5.8 73 588-671 2-75 (97)
21 PRK06386 replication factor A; 92.4 9.1 0.0002 45.2 19.2 175 859-1072 11-200 (358)
22 PRK07211 replication factor A; 91.3 3.1 6.7E-05 50.6 14.3 155 885-1071 101-261 (485)
23 cd04497 hPOT1_OB1_like hPOT1_O 90.6 2.4 5.1E-05 43.1 10.7 74 966-1051 13-87 (138)
24 PRK15491 replication factor A; 90.5 4.9 0.00011 47.5 14.7 135 886-1047 214-354 (374)
25 PRK14699 replication factor A; 87.6 6.3 0.00014 48.2 13.1 136 886-1048 324-465 (484)
26 PRK14699 replication factor A; 87.1 9.1 0.0002 46.8 14.1 277 632-1069 94-376 (484)
27 PF02765 POT1: Telomeric singl 74.1 47 0.001 34.0 12.0 113 967-1090 12-146 (146)
28 cd04491 SoSSB_OBF SoSSB_OBF: A 63.9 24 0.00051 32.3 6.7 53 864-929 22-74 (82)
29 cd04481 RPA1_DBD_B_like RPA1_D 62.6 16 0.00035 35.2 5.6 96 971-1080 1-103 (106)
30 cd04491 SoSSB_OBF SoSSB_OBF: A 58.8 46 0.00099 30.5 7.6 67 972-1056 2-72 (82)
31 PRK07217 replication factor A; 50.6 2.8E+02 0.0061 32.5 13.6 50 885-938 112-161 (311)
32 PRK08402 replication factor A; 49.7 87 0.0019 37.2 9.7 91 886-981 110-208 (355)
33 PRK06461 single-stranded DNA-b 40.6 96 0.0021 31.4 7.2 61 864-939 39-99 (129)
34 PF01336 tRNA_anti-codon: OB-f 38.4 72 0.0016 27.7 5.3 53 865-928 16-69 (75)
35 cd04488 RecG_wedge_OBF RecG_we 36.1 88 0.0019 26.9 5.5 41 865-915 18-58 (75)
36 PRK06461 single-stranded DNA-b 35.8 1.4E+02 0.0031 30.2 7.5 70 968-1056 15-88 (129)
37 cd04474 RPA1_DBD_A RPA1_DBD_A: 32.0 65 0.0014 31.2 4.3 31 885-915 46-77 (104)
38 cd04497 hPOT1_OB1_like hPOT1_O 29.5 1.7E+02 0.0037 29.8 7.0 70 865-941 37-106 (138)
39 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 27.7 3.2E+02 0.0069 31.3 9.2 38 933-975 185-222 (251)
40 cd04498 hPOT1_OB2 hPOT1_OB2: A 25.3 75 0.0016 32.4 3.5 34 885-918 59-92 (123)
41 PRK08402 replication factor A; 24.7 4.6E+02 0.01 31.3 10.3 93 967-1076 72-169 (355)
42 PRK06386 replication factor A; 23.5 2.9E+02 0.0064 33.0 8.4 80 885-981 152-231 (358)
43 cd04492 YhaM_OBF_like YhaM_OBF 20.9 2.2E+02 0.0048 25.2 5.4 42 864-915 18-59 (83)
No 1
>KOG4751 consensus DNA recombinational repair protein BRCA2 [Replication, recombination and repair]
Probab=100.00 E-value=4.9e-103 Score=890.22 Aligned_cols=696 Identities=38% Similarity=0.499 Sum_probs=603.4
Q ss_pred CcceeeeccC-CCCceEEeecceeccCCCCCCCCCCCCCCCCchHHHHHhhccccccccCCCCCCCCCCCceecCCCcee
Q 001266 1 MSTWQIFSDA-DNNFKWQVSGRILQPEPNGSPIQPHSSSFRLPSMSDLLLEGHSKLRENGNEGADNVSTPMFKTGSGKAV 79 (1112)
Q Consensus 1 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~TgsGK~V 79 (1112)
|+||+.|.++ +.+|+||+.+||++...|+++..+..+++++|||+|+|+|+|.|++..-|..|+. -|||+||+||.|
T Consensus 1 ~~t~~~~~s~s~s~f~fesafr~~S~veDst~~~~s~~~~~~~S~~D~L~~e~~k~Ir~~E~~~~~--~~~f~Talgkev 78 (756)
T KOG4751|consen 1 MSTWALFYSSSGSGFRFESAFRILSSVEDSTPTKASESTAPLPSMADLLLQECSKLIRREELMPGE--IPMFRTALGKEV 78 (756)
T ss_pred CccceeeccccCCchhHHHHHHHHhhhhccchhhhhhcccCCcchhhhhhhhhhhhhcchhhcccc--chhhhhccccce
Confidence 8999999876 9999999999999999999999999999999999999999999999988777765 899999999999
Q ss_pred ecchhhHHHHHHHhCCC--------------------------------------------------CCCCCCCCCCCCC
Q 001266 80 PLKQSSIEKALSVLGTD--------------------------------------------------NDCGISFAGEEHP 109 (1112)
Q Consensus 80 ~vsesSiqkAr~~l~~~--------------------------------------------------~~~~~~~~~~~~~ 109 (1112)
++.|+|+.|||.||++- ++..+...++++|
T Consensus 79 ~l~EsS~~k~ksVLee~~k~e~~r~~~~s~~~r~~vs~aetm~d~r~ge~~v~P~ke~S~~k~l~l~g~~~is~~d~enP 158 (756)
T KOG4751|consen 79 VLKESSIAKAKSVLEEKVKYEDLRNTNCSIPQRRQVSTAETMPDFRTGEGKVVPLKESSIAKELSLLGSDCISDSDNENP 158 (756)
T ss_pred eehhcCHHHHHHHHHHHHHHHHHhhccCCchhhhhhhhccccccCCCCCCCcCcccccccccceeecCCcccccCcccCc
Confidence 99999999999999882 1112223677778
Q ss_pred CCCCCCccCCccccCCCceEEechhHHHHHHHHhccccCCCCcccccccCCC-CcCCCcceeecCCcccccccccccccC
Q 001266 110 RENGFGFSNSLFQTGSGKTVNISSAGLVRAKSLLGLEEGRNDWSFEGLQHTR-MTSTPRFEVKEGVKGNVFESDTSVLRP 188 (1112)
Q Consensus 110 ~~~~~~~~~~iFsTaSGKsV~VS~asLqkAkqvf~~~e~~~~~s~q~f~~~~-~~~~~~~~~~eg~~~~v~ee~~~~~~~ 188 (1112)
+..+++..+++|+|+|-|+|+|+++||.+|+.||+.+|++ .-+|.|+. .+.+.|...|.+.+.+- |-+....+.
T Consensus 159 ~e~~~~~~~S~Fqt~srkkV~vtk~sL~~ak~llg~Eeds----~~~~~h~~gsss~~qd~p~K~~~th~-eFd~~e~~~ 233 (756)
T KOG4751|consen 159 RESGFGVVNSLFQTASRKKVNVTKASLARAKALLGLEEDS----LNGFNHVNGSSSSPQDHPWKGLKTHE-EFDATEVKH 233 (756)
T ss_pred cccCcccceeccccccceeeeechhHHHHHhhhhCccccc----ccccccccCCCCCcccCCccccCchh-hccchhhhc
Confidence 8899999999999999999999999999999999999985 66788886 44555656666654432 222222221
Q ss_pred CCccccccccccccccccccccccccCCCCCCCCCcceecCCCceEEeCHHHHHHHHHhcCCCCCCcccccccc--cccc
Q 001266 189 SSISKAGFAESRFKNKISSNMMQTEGLNSAPKPPQIKFQTAGGRSLSVSSDALQYARNLLGDPELGTFFHEVDV--DQLD 266 (1112)
Q Consensus 189 ~~~s~~g~~~~~~~~~~~~~~~~p~~~n~~~~~~~~gFsTAsGK~VsVSe~aL~rAk~lL~e~dl~~~~~~~~~--~~~~ 266 (1112)
+..+ .|.+..++.+.. .-+++|. -+.+++.|+++.|++++||=.|+..|+.+|+|+++.-++++.++ |+..
T Consensus 234 ~~~t-~~ry~~yvg~~~-i~Vl~ps-----~kv~~td~~dri~e~~svSLeA~ks~~~~l~D~~l~~~~~~L~gv~gd~~ 306 (756)
T KOG4751|consen 234 HSGT-PGRYEAYVGGKR-IEVLNPS-----LKVPPTDFQDRIGESLSVSLEALKSARNLLGDPELGSFFDDLAGVGGDQF 306 (756)
T ss_pred ccCC-cchheeeeccee-EEeeccc-----cccCcccHHhhhhhhhhHHHHHhhhhhhhcCCCccceeeeeeecccccce
Confidence 1111 122222221111 2234443 37889999999999999999999999999999999999999998 9999
Q ss_pred ccccccCCCCCCCCCCCCCcccceeeeccCCCccccccccCcccccCccccccCCccccccCCccceeeecccCCCccCC
Q 001266 267 LTSFKHRRFDDSSSNKENDVFTSFFRLGTAGTKTASKNFTSPLRLFSNPVRSRINSENINTSANLIEKFDAVDHDGVSGL 346 (1112)
Q Consensus 267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~f~~~l~~~~~~~~~~~~~~~~~~g~~~~~~~~a~~~~~~~~~ 346 (1112)
++.-+++++++.+.++.......+.|...+..||.+.+|.+|++++.+.+. +.|.++...|+|+|++|+..++.-.|.+
T Consensus 307 ~tke~de~~s~iaia~g~en~~y~~neE~~~~kh~s~s~a~~g~~~~k~fs-S~Nv~~R~l~~~ii~~Fkt~~l~yr~~~ 385 (756)
T KOG4751|consen 307 FTKEKDERLSDIAIANGSENRGYIANEEKTSNKHTSNSFASPGHSSSKQFS-SVNVENRALGGNIIKKFKTAVLEYRCAL 385 (756)
T ss_pred echhhhcccccceeccchhhhhhhhhHHHhhhcccccccccCCCChHHhhc-chhHHHHhcCCceeeeehhhhhhhhhhh
Confidence 999999999999999999999999999999999999999999999999987 8899999999999999999998877766
Q ss_pred CCCCCCCCCCcc-ccCCCceeecCCCcccccccccccCCCCCCCcccccccccccccccccc-ccccccc-CCCCCCCCC
Q 001266 347 NGKIPSIKKPIR-STHGHKAIMDNSVEDDIGSKINSLGRSSGKPLADITNSTSTACANIKQT-CEKKRLL-RSSISPFKR 423 (1112)
Q Consensus 347 ~~~~~~~~kp~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pl~~isn~~~~~~~~~~~~-~~krr~g-~~~~sp~k~ 423 (1112)
|=. +.+--.+- ..++-++.++++++|++..+.....+|...|++|++|..++++.+++|. +.++|++ ...++||+|
T Consensus 386 ~~r-~~~~~~~n~~g~~Sd~~~n~~kvne~~~~~k~~~~~a~~~~~~~~~~r~~dla~~~Q~~~~~~dlrit~~~~~~~r 464 (756)
T KOG4751|consen 386 NFR-LATHGLSNNRGLASDMAVNNSKVNEFIPRVKQEGRPADQPLVDITNRRDTDLARNKQDSTQKKDLRITVSVSPFKR 464 (756)
T ss_pred hcc-HhhhcccCCCCccchhhcccccccceeehhccCCCccccccccccccchHHHHHhhhhhhhhhhcceeeeeccccc
Confidence 611 11111111 1222389999999999999999999999999999999999999999998 9999999 999999999
Q ss_pred CCcCCcccccccCC-CCCCCCCccCCCCCCceeeeeecCCCCCcccchhhccCCCCCccccccccccchhcccccCccce
Q 001266 424 PRISKFSTPLRTNL-SSPNGLSTLSSEQSGCEKKVFSRYPYQIPRMCVKEYFGMPPSAQGMLDHLQDQVRQMKSHNADKY 502 (1112)
Q Consensus 424 p~~~~~~~p~~~~~-~~p~~~~~~s~~~~~~~~~~~~~~p~~~~R~~i~~~f~~~~~~~~~~~~v~~~v~~i~~~nA~~y 502 (1112)
|+..+|++|+..+. ...+++++.+..+..|+++...|||-..||.+|+++|||+|++.+.+-+.++.|..|.-.+|..|
T Consensus 465 p~~gs~~~~~~~~~p~is~g~~V~~~~~~~s~~k~l~~y~~~~~~vki~~~~~~~~~~~t~~~~~~~~~~~~~~~~ad~~ 544 (756)
T KOG4751|consen 465 PRIGSFKTPWKKPAPQISSGLSVVSCDTLTSKKKLLTRYPEKSPRVKIKVFFGMHPTATTRMFGKESLVTGIGIQLADGG 544 (756)
T ss_pred CCCCceeccccCcccccccCceeEEEecccccccceeeccccCcceEeeeccccCcceeeeeccchhhhcccceeeccCc
Confidence 99999999999988 78899999999999999999999999999999999999999999888899999999999999999
Q ss_pred eeecCCCCcccCHHHHHHHHHhCCCCccccCHhHHHHHHHHHHHHHhhhhhcccccccCCCCCHHHHHHHHHHHHHHHHh
Q 001266 503 MFHDASGLNCIGAEALFNMLAQSGASTQYASKLWVSNHYKWIVWKLACYERCYLAKSAGKFLTVFNVLEELKYRYEREVN 582 (1112)
Q Consensus 503 ~F~~~~~~~~~G~eef~~~L~~~G~~~~l~~~~WV~NHyrwIVWKLA~~er~~P~~~~~~~lTp~~VL~QLkyRYerEi~ 582 (1112)
-|.. ++..|.+|||.+||+. -+....|+.|||+|||||||||+.+||.+|+++|||+++||+|||||||+|+|
T Consensus 545 ~~~~---~~~~~~~e~~~~l~~~----~~~~~~~~~~~~~wivwkla~~~~~~p~~~~~~~lt~~~vl~~lkyry~~ev~ 617 (756)
T KOG4751|consen 545 WLIP---DGKKGKEEFYLALCDT----PLKVCDWSFEACMWIVWKLACYDIYYPAKCRGNFLTITNVLEELKYRYEREVN 617 (756)
T ss_pred eecc---cccchHHHHHHHHhcc----hhhhhhhhhHHHHHHHHHHhHhhhcChHHHhcCcCCHHHHHHHHHHHHhhhcc
Confidence 9987 4567899999999974 37889999999999999999999999999999999999999999999999999
Q ss_pred cCCCchhhhhHhCCCCCCCeEEEEEEeeeecCCCCcCCCccccCCCCCCcccEEEEeeceeEEeccccHHHHHHHHcCCc
Q 001266 583 NGHRSAIKRILEGDALPSSMMVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLELTDGWYSVDAFLDVLLSKHLAAGKL 662 (1112)
Q Consensus 583 ~~~RSaLRrIlE~D~~~s~~MVLcVs~I~~~~~~~~e~~~~~~~g~~~~~~~~LELTDGWY~IkA~lD~~L~~~l~~GkI 662 (1112)
+++||||||||+||++|+++||||||+|.+..+ +.+++...++++..++||||||||+++|+||++|++.|.+|||
T Consensus 618 ~~~~saik~i~~~d~~a~~~~vlcis~i~~~t~----n~s~~~~~~d~~~~~~veltdgwy~~~a~ld~~l~~~l~~g~l 693 (756)
T KOG4751|consen 618 HGHCSAIKRILSGDAPASSMMVLCISAINPLTD----NISQEAHCSDTCSNVKVELTDGWYSMNAALDVVLTKQLNAGKL 693 (756)
T ss_pred cchHHHHHHHHcCCCcchheEeeehhhcccccc----CcccccccccccceeEEEeecchhhhhhccchHHHHHhccCce
Confidence 999999999999999999999999999976443 3344456667888999999999999999999999999999999
Q ss_pred ccCceEEEEcceeccCCCCCCccccCCccEEEEEeeceeeccccCccccccCCC-Ccccceee
Q 001266 663 FVGQKLRIWGAILCGWVGPVSPLEASGSISLQLNINGTYRAHWADRLGFCKGFG-APLAFRCI 724 (1112)
Q Consensus 663 ~vG~KL~I~GA~L~~~~~~~sPLEa~~~~~L~L~~NstrrA~W~akLGf~~~~~-~p~~L~sl 724 (1112)
+|||||+.+|+.+.+....|.||+++++.++.|.+ +||+++|..++|+.+.+. ++.+|.++
T Consensus 694 ~vgqk~~~~~~~~~~~~~~~~~l~~~~t~~~~~~a-~~~~~~~~~~~~~~~~~~~~~~~l~~~ 755 (756)
T KOG4751|consen 694 FVGQKLRHAYVLISYLKILGAGLSGWATPTSPLEA-VISSTICLLLNINGTYRAHWADRLGFC 755 (756)
T ss_pred ehhhhhhhhheeeecccccCCCcCcccccCcchhh-hccchhhheeccCCCCccccccccccc
Confidence 99999999999999999999999999988888888 888888888888877654 35566543
No 2
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) 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=100.00 E-value=3.7e-52 Score=445.23 Aligned_cols=228 Identities=33% Similarity=0.577 Sum_probs=197.2
Q ss_pred cceeeccCCCeEeeEEEEEEEEccceEEEEccCCcccccCHHHHHHHHHHHHHHHHHHHHhhHHHH----hhcCCcc---
Q 001266 720 AFRCIKSNGGPVPRTLVGVTRIYPVLYKERLSDGRSIVRSERMECKVMQLYQHRQSMVVEGIVSEF----QRGNKDS--- 792 (1112)
Q Consensus 720 ~L~sl~~~GG~V~~idVvV~RvyP~~y~Ek~~~G~~i~Rner~E~k~~~~~~~r~e~l~e~i~~E~----ere~~~~--- 792 (1112)
||+||+++||+|+|+||+|+|+||++||||+++|.+||||||+|++++++|.+++++++|+|..++ +++..+.
T Consensus 1 pl~sl~~~GG~V~cv~viV~RvYP~~~~Ek~~~g~~I~RseR~E~r~a~~~~~~~~~~~e~l~~~iq~e~e~~~~~~~~~ 80 (251)
T cd04494 1 PLSSLYDSGGLVGCVDVIILRVYPLQWVEKTSEGGSVFRSERAEEREARLHAQRQQKKLEALFSKIQEEFEKEEEDNNQR 80 (251)
T ss_pred CCccccCCCCeEeEEEEEEEEecchhheeecCCCceEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccc
Confidence 689999999999999999999999999999999999999999999999999999887777665554 4443221
Q ss_pred ----ccccc----CchhHHHHHHHHhccCChHHHHhcCCHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH----HhcCCCC
Q 001266 793 ----HILND----SNSEGAKLFKMLETVAEPEVIMAEMSPEQLTSFATYQAKLEATRQSNMERSIEKAL----ENAGLRE 860 (1112)
Q Consensus 793 ----~~~~~----~~s~Ga~l~~~le~~~dp~~l~~~ls~~Ql~~l~~~r~~~~~~~Q~~~~~~i~~aL----~~~g~~~ 860 (1112)
+..+. ..+||++||++|+++.||+++|++||++|+++|++||+++++++|+++|.++++++ ++.|+++
T Consensus 81 ~~~~~~~~~~~v~~l~dGaeLyeale~a~Dps~le~~lS~~Q~~~L~~y~~~~~~~kq~~lQ~~~~ka~~~a~~~~~~~~ 160 (251)
T cd04494 81 RPRSRTRTRQNVTDLQDGAELYEALEAAADPSFLEAELSEEQLEALSNYQQLQNEKKQARLQEEFRKAVEEALKEEGLSK 160 (251)
T ss_pred ccccCcccceehhccccHHHHHHHHHcCCChHHHHhhCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 12111 12499999999999999999999999999999999999998888887776666555 4568889
Q ss_pred CCceeeEEEEEeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCC----CceeEeeeecceeee
Q 001266 861 RDVTPFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDS----NTLYLQARGSTTKWQ 936 (1112)
Q Consensus 861 R~Vtp~~klRV~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s----~~l~L~~r~~~Trw~ 936 (1112)
|+|||||||||+|+++ + ..++++||||||++++.++|+||++|+||||.|+.+++ +++||++|+ +|+|+
T Consensus 161 RdVtp~~klRV~d~~~-----~-~~~~~~LTIWrPtedl~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk-~Tr~~ 233 (251)
T cd04494 161 RDVTPVWKLRVTDYRS-----K-PEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATK-KTRYQ 233 (251)
T ss_pred CcceeEEEEEEeeccc-----C-CCceEEEEEeCCCHHHHhhhcCCcEEEEEeccccCCCCCCCcceEEEEecC-cccce
Confidence 9999999999999873 1 36899999999999999999999999999999999887 899999975 89999
Q ss_pred eCCccccccCCCCcCCcce
Q 001266 937 PLSPLATEHFKPFFSPRRS 955 (1112)
Q Consensus 937 ~L~~~~~~~~~~~y~PR~~ 955 (1112)
+|++.+..+|. .|+||++
T Consensus 234 ~l~~~~~~~~~-~~~pR~~ 251 (251)
T cd04494 234 PLPVSQRELFQ-PFQPRKA 251 (251)
T ss_pred ECCHHHhcccc-ccccCCC
Confidence 99987777665 4999974
No 3
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 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. OB1 has a shallow 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 weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=100.00 E-value=9.3e-40 Score=317.25 Aligned_cols=117 Identities=50% Similarity=0.738 Sum_probs=78.2
Q ss_pred chhhhhHhCCCCCCCeEEEEEEeeeecCCCCcCCCccccCCCCCCcccEEEEeeceeEEeccccHHHHHHHHcCCcccCc
Q 001266 587 SAIKRILEGDALPSSMMVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQ 666 (1112)
Q Consensus 587 SaLRrIlE~D~~~s~~MVLcVs~I~~~~~~~~e~~~~~~~g~~~~~~~~LELTDGWY~IkA~lD~~L~~~l~~GkI~vG~ 666 (1112)
|+||||+|+|++|++||||||++|.... ....+..+||||||||+|+|++|.+|+++|++|||+|||
T Consensus 1 saLrrI~E~D~~~~~~mVL~Vs~i~~~~-------------~~~~~~~~lelTDGWY~Ika~lD~~L~~~l~~gki~vG~ 67 (118)
T PF09103_consen 1 SALRRILEGDDSASKPMVLCVSSISSSD-------------NDSPESAILELTDGWYSIKAQLDPPLTRLLRKGKIRVGQ 67 (118)
T ss_dssp -HHHHHHTTSSTTB-SEEEEEEE--------------------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-
T ss_pred CHhHHHhhCCCCcCCcEEEEEEEEccCC-------------CCCCccCEEEEecCCEEEEEEeCHHHHHHHHhCCccCCc
Confidence 7999999999999999999999993211 123457899999999999999999999999999999999
Q ss_pred eEEEEcceeccCCCCCCccccCCccEEEEEeeceeeccccCccccccCCC
Q 001266 667 KLRIWGAILCGWVGPVSPLEASGSISLQLNINGTYRAHWADRLGFCKGFG 716 (1112)
Q Consensus 667 KL~I~GA~L~~~~~~~sPLEa~~~~~L~L~~NstrrA~W~akLGf~~~~~ 716 (1112)
||+|+||+|+++.+||+|||++++++|+||+||||||+|++||||+++++
T Consensus 68 KL~v~GA~L~~~~~~~~pLE~~~~~~L~l~~Nstr~a~w~~kLG~~~~~~ 117 (118)
T PF09103_consen 68 KLRVCGAELLGSKEPCSPLEAPDSVMLKLHANSTRPARWDAKLGFQKDPR 117 (118)
T ss_dssp EEEESSBEEES--S---CCC--SS-EEE--CCCEEEB-SSS-SEE-S--S
T ss_pred cEEEECceecCCCCCcCCCcCCCceEEEEEeeeEEeccccccCCCCCCCC
Confidence 99999999999999999999999999999999999999999999999875
No 4
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) 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). BRCA2DBD OB1 binds DNA weakly.
Probab=100.00 E-value=9e-35 Score=273.06 Aligned_cols=100 Identities=51% Similarity=0.773 Sum_probs=93.5
Q ss_pred CCCeEEEEEEeeeecCCCCcCCCccccCCCCCCcccEEEEeeceeEEeccccHHHHHHHHcCCcccCceEEEEcceeccC
Q 001266 599 PSSMMVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQKLRIWGAILCGW 678 (1112)
Q Consensus 599 ~s~~MVLcVs~I~~~~~~~~e~~~~~~~g~~~~~~~~LELTDGWY~IkA~lD~~L~~~l~~GkI~vG~KL~I~GA~L~~~ 678 (1112)
|+++||||||+|.+.+. ..++..+||||||||+|+|+||++|+++|++|||+|||||+|+||+|+++
T Consensus 1 ~~~~mVL~Vs~I~~~~~-------------~~~~~~~lEltDGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i~GA~l~~~ 67 (100)
T cd04493 1 ASRLMVLCVSGINSEER-------------LSPHMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRICGAELLGS 67 (100)
T ss_pred CCceEEEEEEEEeeccC-------------CCCcccEEEEecCeEEEEEEeCHHHHHHHHcCCeecccEEEEECceeecC
Confidence 68999999999986542 13456899999999999999999999999999999999999999999998
Q ss_pred CCCCCccccCCccEEEEEeeceeeccccCcccc
Q 001266 679 VGPVSPLEASGSISLQLNINGTYRAHWADRLGF 711 (1112)
Q Consensus 679 ~~~~sPLEa~~~~~L~L~~NstrrA~W~akLGf 711 (1112)
.+||+|||++++++|+||+||||||+|++||||
T Consensus 68 ~~~~sple~~~~~~L~l~~Nstr~a~w~~~LGf 100 (100)
T cd04493 68 ANPCSPLEAPDSVRLKINANSTRRARWDARLGF 100 (100)
T ss_pred CCCcCcccCCCcEEEEEEccceeccccccccCC
Confidence 899999999999999999999999999999998
No 5
>PF09169 BRCA-2_helical: BRCA2, helical; InterPro: IPR015252 The mechanism of double-strand break repair (DSBR) is evolutionarily conserved and can be divided into two main pathways: homologous recombination (HR) and non-homologous end joining (NHEJ). NHEJ involves the ligation of broken DNA ends, requires little or no sequence homology and may be mutagenic. HR can occur conservatively by gene conversion using a homologous strand of DNA as a template or non-conservatively by single-strand annealing, which takes place between repeat sequences and can lead to the loss of intervening genomic DNA or translocations. Brca2 cancer susceptibility protein functions in double-strand DNA break repair by homologous recombination []. Double-strand breaks in DNA elicit a coordinated response that results in either repair of the damage or elimination of the cell. Mutations in Brca2 lead to various types of cancer, and also give rise to the multi-faceted Fanconi anaemia syndrome []. Brca2 is an essential component of the homologous recombination repair pathway and the Fanconi Anaemia complex []. This entry represents a domain found in Brca2 proteins. This domain adopts a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approximately 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 (IPR015187 from INTERPRO) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. This domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0003697 single-stranded DNA binding, 0000724 double-strand break repair via homologous recombination, 0006310 DNA recombination, 0007090 regulation of S phase of mitotic cell cycle, 0005634 nucleus; PDB: 1MIU_A 1IYJ_D.
Probab=99.95 E-value=3e-28 Score=250.79 Aligned_cols=101 Identities=39% Similarity=0.710 Sum_probs=80.0
Q ss_pred ccccccchhcccccCccceeeecC------------------------CCCcccCHHHHHHHHHh-CCCCccccCHhHHH
Q 001266 484 LDHLQDQVRQMKSHNADKYMFHDA------------------------SGLNCIGAEALFNMLAQ-SGASTQYASKLWVS 538 (1112)
Q Consensus 484 ~~~v~~~v~~i~~~nA~~y~F~~~------------------------~~~~~~G~eef~~~L~~-~G~~~~l~~~~WV~ 538 (1112)
..+|+..++.|+++||+.|.|+.. ++++.+|.+||+++|++ +|++|+|++.+||.
T Consensus 70 ~~gV~~~~~~its~nA~~f~F~~~d~~~~e~l~~~~GI~l~Dgg~li~~~~g~~G~~Ef~~all~~~gv~~~Lis~~WV~ 149 (195)
T PF09169_consen 70 GCGVSKKCLAITSENAESFKFNCEDFYGKEALENGDGIQLGDGGWLIPDEDGCVGKEEFYRALLASPGVDPKLISKEWVE 149 (195)
T ss_dssp CCT--TTCCC--TTTTTT--B-CHHHHTTTTTTSTT-EEECCCEEE---TTS-B-HHHHHHHHHCSTT--CCC--HHHHH
T ss_pred hCCccHHHhhhcccccccEEEechhhcCHHHhhcCCCeEccCCCEEEeCCCCcchHHHHHHHHHhCCCCCcccCChHHHH
Confidence 358899999999999999999631 24577999999999887 79999999999999
Q ss_pred HHHHHHHHHHhhhhhcccccccCCCCCHHHHHHHHHHHHHHHHhcC
Q 001266 539 NHYKWIVWKLACYERCYLAKSAGKFLTVFNVLEELKYRYEREVNNG 584 (1112)
Q Consensus 539 NHyrwIVWKLA~~er~~P~~~~~~~lTp~~VL~QLkyRYerEi~~~ 584 (1112)
|||||||||||+|+++||+.+++++|||++||.||+||||||||++
T Consensus 150 NHyrWIVWKLA~mer~fP~~~~~~~lt~~~Vl~QLkYRYdrEi~~a 195 (195)
T PF09169_consen 150 NHYRWIVWKLASMERAFPDHFAGRCLTPENVLLQLKYRYDREIDRA 195 (195)
T ss_dssp HHHHHHHHHHHHCCCCSTTTTTTTSSSHHHHHHHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHHHHHHhChhhccCCcCCHHHHHHHHHHHHHhhhccC
Confidence 9999999999999999999999999999999999999999999874
No 6
>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=99.80 E-value=2e-19 Score=179.21 Aligned_cols=116 Identities=27% Similarity=0.200 Sum_probs=78.0
Q ss_pred cceeccccc---CCCCCCCccceEEEEEEeCCcccccccceeE-EEEecCcccccccccccCceEEEEeecCCcCCCCCC
Q 001266 953 RRSVLISNL---GEVPLSSEFDIAAFVVHVGDVYEDSQQKKQW-VFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFS 1028 (1112)
Q Consensus 953 R~~v~~s~l---~~~P~~~EfD~vG~Vv~Vg~~~~~~~qk~Qw-vflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~ 1028 (1112)
|+++.|++| .++|+|+|||+||+||+|. .++.+|. |||+|+++ +||+|.||+++..+ +
T Consensus 1 R~~~~f~~l~~p~f~pp~~EvD~VG~VvsV~-----~~~~f~~~vYLsD~~~----------Nll~Ikfw~~l~~~---~ 62 (143)
T PF09104_consen 1 RECTHFSDLQDPDFQPPYGEVDTVGFVVSVS-----KKQGFQPLVYLSDECH----------NLLAIKFWTGLNQY---G 62 (143)
T ss_dssp --B--CGGGGSTT--TCCCEEEEEEEEEEEE-------TTS--EEEEE-TTS-----------EEEEEESS---------
T ss_pred CceechhhhcCcccCCCccccceEEEEEEEE-----ecCCCceeEEeecCCc----------cEEEEEeccCcccc---c
Confidence 667766655 4599999999999999993 2455666 99999996 69999999999954 4
Q ss_pred cccccccCceEEeeceEEeccCCCCCeeEEEeccceeeEecCCCCCChhHHHHHHHHHHHHh
Q 001266 1029 PINYNLVGSTVGFCNLIKRPKDHLNHIWVAEATENSSYFLSFDFPTCSHLRSAAASAQSWAK 1090 (1112)
Q Consensus 1029 ~~~~~~~G~vV~f~NL~~r~~D~~n~i~va~AtE~s~~sl~~~~~~~~~l~~a~~~l~~wa~ 1090 (1112)
..|.+++|++|+++||+|| .+.+..|++++|||.|+||.||.. .||.+++..++.--+
T Consensus 63 ~eDilk~~~liA~SNLqwR-~~s~s~iP~~~A~d~S~FS~nPK~---~hLqe~~~~Lk~~i~ 120 (143)
T PF09104_consen 63 YEDILKPGSLIAASNLQWR-PESTSGIPTLFATDLSVFSANPKE---SHLQEAFNKLKNTIE 120 (143)
T ss_dssp -SS---TT-EEEEEEEEE--S-TTSSS-EEEEECCEEEESS-SS---CCCHHHHHHHCHHHH
T ss_pred hhhhcCcceEEEEeeeEee-cccccCCCeeEeccceeeecCccH---HHHHHHHHHHHHHhh
Confidence 5568999999999999999 666899999999999999999988 888888887776543
No 7
>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=99.57 E-value=6.5e-15 Score=138.27 Aligned_cols=98 Identities=20% Similarity=0.148 Sum_probs=86.6
Q ss_pred ceEEEEEEeCCcccccccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEeeceEEeccC
Q 001266 971 DIAAFVVHVGDVYEDSQQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCNLIKRPKD 1050 (1112)
Q Consensus 971 D~vG~Vv~Vg~~~~~~~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~NL~~r~~D 1050 (1112)
|+||+||+|+...+ +++|.|||+|+++ +||+|.||++..++. ..+..+++..||.|||+||...
T Consensus 1 D~VGvVvsV~~~~~---g~~~~vYLaDe~~----------nll~vkfw~~l~~~~---~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 1 DTVGVVISVGKPIE---GKFPAVYLADECL----------NLLCVKFWSSLEQYA---YEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred CceEEEEEEccccc---CccceEEEecCCc----------CEEEEEEecchHHhh---hhhhcccceEEEEecceEeccc
Confidence 89999999998663 6899999999996 699999999988762 3447889999999999999766
Q ss_pred CCCCeeEEEeccceeeEecCCCCCChhHHHHHHHHHHH
Q 001266 1051 HLNHIWVAEATENSSYFLSFDFPTCSHLRSAAASAQSW 1088 (1112)
Q Consensus 1051 ~~n~i~va~AtE~s~~sl~~~~~~~~~l~~a~~~l~~w 1088 (1112)
+..||++.|+|+|+||.||.. .|+.++..+|+..
T Consensus 65 -~~~iPtl~Age~t~FS~nPKe---~hlQe~~~~Lk~~ 98 (100)
T cd04495 65 -TSGVPTLFAGEYSTFSANPKE---SHLQEEFNNLKHL 98 (100)
T ss_pred -cCCCceeeeecceeecCCccH---HHHHHHHHHHHhh
Confidence 559999999999999999998 9999998888754
No 8
>KOG4751 consensus DNA recombinational repair protein BRCA2 [Replication, recombination and repair]
Probab=99.56 E-value=3.3e-16 Score=181.62 Aligned_cols=308 Identities=20% Similarity=0.170 Sum_probs=245.7
Q ss_pred HHHHHhhHHHHhhcCCcccccccCc-hhHHHHHH----------HHhccCChHHHHhcCCHHHHhhHHHHHHHHHHHH--
Q 001266 775 SMVVEGIVSEFQRGNKDSHILNDSN-SEGAKLFK----------MLETVAEPEVIMAEMSPEQLTSFATYQAKLEATR-- 841 (1112)
Q Consensus 775 e~l~e~i~~E~ere~~~~~~~~~~~-s~Ga~l~~----------~le~~~dp~~l~~~ls~~Ql~~l~~~r~~~~~~~-- 841 (1112)
+.+.+..-.+|++-....+...|.. .+++++++ +++.+.+++.++.|.|.+|++.+-.+..+.++.+
T Consensus 25 S~veDst~~~~s~~~~~~~S~~D~L~~e~~k~Ir~~E~~~~~~~~f~Talgkev~l~EsS~~k~ksVLee~~k~e~~r~~ 104 (756)
T KOG4751|consen 25 SSVEDSTPTKASESTAPLPSMADLLLQECSKLIRREELMPGEIPMFRTALGKEVVLKESSIAKAKSVLEEKVKYEDLRNT 104 (756)
T ss_pred hhhhccchhhhhhcccCCcchhhhhhhhhhhhhcchhhccccchhhhhccccceeehhcCHHHHHHHHHHHHHHHHHhhc
Confidence 4444445556665544444444433 36777776 7889999999999999999999999999999888
Q ss_pred ----HHHHHHHHHHHHHhcCCCCCCceeeEE------EEEeeccccccCCCC----CCceEEEEEeCCChhhhccccccc
Q 001266 842 ----QSNMERSIEKALENAGLRERDVTPFMR------VRVVGLTGKNYQGKG----SSREGIITIWNPAEKQQCELVEGQ 907 (1112)
Q Consensus 842 ----Q~~~~~~i~~aL~~~g~~~R~Vtp~~k------lRV~d~~~k~~~~k~----~~~~aiLTIWrPsedl~~~L~EG~ 907 (1112)
+.+.+.-....|...+.+.+.|+|+++ |++....+..+.... ..-...+|+|.+.+-..-.++++.
T Consensus 105 ~~s~~~r~~vs~aetm~d~r~ge~~v~P~ke~S~~k~l~l~g~~~is~~d~enP~e~~~~~~~S~Fqt~srkkV~vtk~s 184 (756)
T KOG4751|consen 105 NCSIPQRRQVSTAETMPDFRTGEGKVVPLKESSIAKELSLLGSDCISDSDNENPRESGFGVVNSLFQTASRKKVNVTKAS 184 (756)
T ss_pred cCCchhhhhhhhccccccCCCCCCCcCcccccccccceeecCCcccccCcccCccccCcccceeccccccceeeeechhH
Confidence 766666667777778899999999999 888876543332211 112469999999998888999999
Q ss_pred EEEEEeeecCCCCCCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccCCCCCCCccce------E----EEEE
Q 001266 908 AYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGEVPLSSEFDI------A----AFVV 977 (1112)
Q Consensus 908 ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~P~~~EfD~------v----G~Vv 977 (1112)
.|+.++|.+-..++...+.+++++..+|++++.... -+..|||+ + .|+.
T Consensus 185 L~~ak~llg~Eeds~~~~~h~~gsss~~qd~p~K~~---------------------~th~eFd~~e~~~~~~t~~ry~~ 243 (756)
T KOG4751|consen 185 LARAKALLGLEEDSLNGFNHVNGSSSSPQDHPWKGL---------------------KTHEEFDATEVKHHSGTPGRYEA 243 (756)
T ss_pred HHHHhhhhCcccccccccccccCCCCCcccCCcccc---------------------CchhhccchhhhcccCCcchhee
Confidence 999999999998888899999988999999986332 22335555 3 7899
Q ss_pred EeCCcccccccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEeeceEEeccCCCCCeeE
Q 001266 978 HVGDVYEDSQQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCNLIKRPKDHLNHIWV 1057 (1112)
Q Consensus 978 ~Vg~~~~~~~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~NL~~r~~D~~n~i~v 1057 (1112)
+||..++..-+.+||++++|.. ....|+++.+|.|+.+...+++|+.-.-+-..++|.+ ++.+++++..+-.|++|+
T Consensus 244 yvg~~~i~Vl~ps~kv~~td~~--dri~e~~svSLeA~ks~~~~l~D~~l~~~~~~L~gv~-gd~~~tke~de~~s~iai 320 (756)
T KOG4751|consen 244 YVGGKRIEVLNPSLKVPPTDFQ--DRIGESLSVSLEALKSARNLLGDPELGSFFDDLAGVG-GDQFFTKEKDERLSDIAI 320 (756)
T ss_pred eecceeEEeeccccccCcccHH--hhhhhhhhHHHHHhhhhhhhcCCCccceeeeeeeccc-ccceechhhhccccccee
Confidence 9999999888999999999998 3567889999999999988888865333445677777 999999999999999999
Q ss_pred EEeccceeeEecCCCCCChhHHHHHHH-HHHHHhhhhHHHHHHHHhHhhh
Q 001266 1058 AEATENSSYFLSFDFPTCSHLRSAAAS-AQSWAKISSLIIDKLKENVLFI 1106 (1112)
Q Consensus 1058 a~AtE~s~~sl~~~~~~~~~l~~a~~~-l~~wa~~s~~~i~~lk~~v~~~ 1106 (1112)
|.+.|++.|.-+-+....+|.++++.+ +..|+|-+++.-.+++.-...|
T Consensus 321 a~g~en~~y~~neE~~~~kh~s~s~a~~g~~~~k~fsS~Nv~~R~l~~~i 370 (756)
T KOG4751|consen 321 ANGSENRGYIANEEKTSNKHTSNSFASPGHSSSKQFSSVNVENRALGGNI 370 (756)
T ss_pred ccchhhhhhhhhHHHhhhcccccccccCCCChHHhhcchhHHHHhcCCce
Confidence 999999999999999999999888777 9999999998886665544444
No 9
>PF00634 BRCA2: BRCA2 repeat; InterPro: IPR002093 The breast cancer type 2 susceptibility protein has a number of 39 amino acid repeats [] that are critical for binding to RAD51 (a key protein in DNA recombinational repair) and resistance to methyl methanesulphonate treatment [, , ]. BRCA2 is a breast tumour suppressor with a potential function in the cellular response to DNA damage. At the cellular level, expression is regulated in a cell-cycle dependent manner and peak expression of BRCA2 mRNA is found in S phase, suggesting BRCA2 may participate in regulating cell proliferation. There are eight repeats in BRCA2 designated as BRC1 to BRC8. BRC1, BRC2, BRC3, BRC4, BRC7, and BRC8 are highly conserved and bind to Rad51, whereas BRC5 and BRC6 are less well conserved and do not bind to Rad51 []. It has been suggested that BRCA2 plays a role in positioning Rad51 at the site of DNA repair or in removing Rad51 from DNA once repair has been completed. ; GO: 0005515 protein binding, 0006302 double-strand break repair; PDB: 1N0W_B.
Probab=98.64 E-value=6.4e-09 Score=81.66 Aligned_cols=33 Identities=42% Similarity=0.611 Sum_probs=20.4
Q ss_pred CCCCcceecCCCceEEeCHHHHHHHHHhcCCCC
Q 001266 220 KPPQIKFQTAGGRSLSVSSDALQYARNLLGDPE 252 (1112)
Q Consensus 220 ~~~~~gFsTAsGK~VsVSe~aL~rAk~lL~e~d 252 (1112)
.+.++||+||+||+|+||++||+|||.||.|.|
T Consensus 2 ~~~~~~F~TasGk~v~VS~~sl~Kak~lf~d~e 34 (35)
T PF00634_consen 2 ENSFLGFQTASGKKVSVSEESLQKAKKLFSDIE 34 (35)
T ss_dssp --GGGS-EETTS-B----HHHHHHTTTTT----
T ss_pred CCCCCceEcCCCCEEEEcHHHHHHHHHHhcccC
Confidence 356899999999999999999999999999864
No 10
>PF00634 BRCA2: BRCA2 repeat; InterPro: IPR002093 The breast cancer type 2 susceptibility protein has a number of 39 amino acid repeats [] that are critical for binding to RAD51 (a key protein in DNA recombinational repair) and resistance to methyl methanesulphonate treatment [, , ]. BRCA2 is a breast tumour suppressor with a potential function in the cellular response to DNA damage. At the cellular level, expression is regulated in a cell-cycle dependent manner and peak expression of BRCA2 mRNA is found in S phase, suggesting BRCA2 may participate in regulating cell proliferation. There are eight repeats in BRCA2 designated as BRC1 to BRC8. BRC1, BRC2, BRC3, BRC4, BRC7, and BRC8 are highly conserved and bind to Rad51, whereas BRC5 and BRC6 are less well conserved and do not bind to Rad51 []. It has been suggested that BRCA2 plays a role in positioning Rad51 at the site of DNA repair or in removing Rad51 from DNA once repair has been completed. ; GO: 0005515 protein binding, 0006302 double-strand break repair; PDB: 1N0W_B.
Probab=98.53 E-value=1.8e-08 Score=79.15 Aligned_cols=32 Identities=44% Similarity=0.428 Sum_probs=19.7
Q ss_pred cCCccccCCCceEEechhHHHHHHHHhccccC
Q 001266 117 SNSLFQTGSGKTVNISSAGLVRAKSLLGLEEG 148 (1112)
Q Consensus 117 ~~~iFsTaSGKsV~VS~asLqkAkqvf~~~e~ 148 (1112)
++..|+|||||+|.||++||+|||++|.++|+
T Consensus 4 ~~~~F~TasGk~v~VS~~sl~Kak~lf~d~e~ 35 (35)
T PF00634_consen 4 SFLGFQTASGKKVSVSEESLQKAKKLFSDIEE 35 (35)
T ss_dssp GGGS-EETTS-B----HHHHHHTTTTT-----
T ss_pred CCCceEcCCCCEEEEcHHHHHHHHHHhcccCC
Confidence 46789999999999999999999999998874
No 11
>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=98.19 E-value=0.00055 Score=84.17 Aligned_cols=171 Identities=18% Similarity=0.152 Sum_probs=111.5
Q ss_pred ceEEEEEeCCCh-hhhcccccccEEEEEee--ecCCCC----CCceeEeeeecceeeeeCCccccccCCCCcCCcceecc
Q 001266 886 REGIITIWNPAE-KQQCELVEGQAYAILGL--IPMNSD----SNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLI 958 (1112)
Q Consensus 886 ~~aiLTIWrPse-dl~~~L~EG~ry~V~~L--~ps~~~----s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~ 958 (1112)
..+..|+|+..- ...+.|+||+.|.|.+. .|.+.+ .....|+.. ..|.-++....+ .+ |.+ .-..+.+
T Consensus 227 g~Irat~f~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f~-~~T~I~~~~d~~--~i-P~~-~~~f~~i 301 (608)
T TIGR00617 227 GEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLD-RDTVIEECEDET--AI-PKI-QFNFVKI 301 (608)
T ss_pred CeEEEEECchHHHHHhhhcccCCEEEECceEEEEccccccCCCCCEEEEEC-CCeEEEECCCcc--cC-Ccc-cccceEH
Confidence 578899999754 34678999999999864 444322 234455553 245555543211 11 221 1133445
Q ss_pred cccCCCCCCCccceEEEEEEeCCccccc------ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccc
Q 001266 959 SNLGEVPLSSEFDIAAFVVHVGDVYEDS------QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINY 1032 (1112)
Q Consensus 959 s~l~~~P~~~EfD~vG~Vv~Vg~~~~~~------~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~ 1032 (1112)
++|.......-+|++|+|+.|++..... ...+-.|.|.|.+ ..-+-|.+|+..... | +
T Consensus 302 ~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~s----------g~sI~vTLWG~~A~~--~---~- 365 (608)
T TIGR00617 302 DDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDS----------GKSVRVTLWGDDATK--F---D- 365 (608)
T ss_pred HHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCC----------CCEEEEEEEhhhhhh--c---C-
Confidence 6665555556899999999999966521 2234579999998 246899999876532 2 2
Q ss_pred cccCceEEeeceEEeccCCCCCeeEEEeccceeeEecCCCCCChhHHHHHHHHHHH
Q 001266 1033 NLVGSTVGFCNLIKRPKDHLNHIWVAEATENSSYFLSFDFPTCSHLRSAAASAQSW 1088 (1112)
Q Consensus 1033 ~~~G~vV~f~NL~~r~~D~~n~i~va~AtE~s~~sl~~~~~~~~~l~~a~~~l~~w 1088 (1112)
...|.||+|.++.+..++ .. .+-.+=.|++..+|+.|- +..|+.|
T Consensus 366 ~~~~~Vva~kg~~V~~f~-g~---sLs~~~~S~i~iNPdipE-------a~~L~~w 410 (608)
T TIGR00617 366 VSVQPVIAIKGVRVSDFG-GK---SLSTGGSSTIIVNPDIPE-------AEKLKGW 410 (608)
T ss_pred CCCCCEEEEEeEEEEecC-Cc---eEeccCCceEEECCCcHH-------HHHHHHH
Confidence 357899999999998883 32 233455789999998743 4566667
No 12
>PF09121 Tower: Tower; InterPro: IPR015205 This domain adopts a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA []. ; PDB: 1IYJ_D 1MIU_A.
Probab=98.05 E-value=2e-06 Score=69.33 Aligned_cols=38 Identities=24% Similarity=0.272 Sum_probs=30.4
Q ss_pred EEEccCCcccccCHHHHHHHHHHHHH----HHHHHHHhhHHH
Q 001266 747 KERLSDGRSIVRSERMECKVMQLYQH----RQSMVVEGIVSE 784 (1112)
Q Consensus 747 ~Ek~~~G~~i~Rner~E~k~~~~~~~----r~e~l~e~i~~E 784 (1112)
||++++|.+||||+|+|+|++.+|.. ++++|+.+||.|
T Consensus 1 mEK~~~G~~vFRn~RaEekEA~k~a~~qqkklE~Lf~kIQ~e 42 (42)
T PF09121_consen 1 MEKTPSGSYVFRNERAEEKEAAKHAEAQQKKLEALFTKIQAE 42 (42)
T ss_dssp EEE-SSSSEEEE-CCHHHHHHHHHHHHTTSHHHHHHHHHHTT
T ss_pred CCccCCCceEeecchHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 79999999999999999999999954 467777777654
No 13
>PRK12366 replication factor A; Reviewed
Probab=95.75 E-value=0.29 Score=61.15 Aligned_cols=159 Identities=13% Similarity=0.040 Sum_probs=107.4
Q ss_pred ceEEEEEeCCChhhhcccccccEEEEEeeecCCCC----CCceeEeeeecceeeeeCCccccccCCCCcCCcc---eecc
Q 001266 886 REGIITIWNPAEKQQCELVEGQAYAILGLIPMNSD----SNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRR---SVLI 958 (1112)
Q Consensus 886 ~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~----s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~---~v~~ 958 (1112)
..+-+|.|+..-+....|.||+.|.|.+-...... ...+.|++.. .|.-.. .. +.. .|.. .+.+
T Consensus 328 G~IR~t~w~~~~d~~~~l~~G~vy~is~~~vk~y~~~~~~~~~El~~~~-~s~I~~-d~-~~~------~p~~~~~~~~i 398 (637)
T PRK12366 328 GRVRVSFWGEKAKILENLKEGDAVKIENCKVRTYYDNEGEKRVDLNAGY-SSEIIK-DE-SIS------FEEIEEKIYKI 398 (637)
T ss_pred CeEEEEEeCchhhhhcccCCCCEEEEecCEEeeccccCCCcCEEEEcCC-ceEEEe-cc-CCc------ccceeeccccH
Confidence 57899999998777777899999999987655322 1355565542 344433 21 111 1332 2345
Q ss_pred cccCCC-CCCCccceEEEEEEeCCcccc-----cccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccc
Q 001266 959 SNLGEV-PLSSEFDIAAFVVHVGDVYED-----SQQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINY 1032 (1112)
Q Consensus 959 s~l~~~-P~~~EfD~vG~Vv~Vg~~~~~-----~~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~ 1032 (1112)
.++... +...-+|++|+|+.++++... .....+.++|.|.+- -+-+.+|+.-.+ | .
T Consensus 399 ~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k~G~~~~~r~i~l~D~TG-----------~I~vtlWg~~a~---~----~ 460 (637)
T PRK12366 399 KDILNLEEDDNDITVIARVVEDYPVNEFERSDGSKGKVRNIELADGTG-----------SIRLTLWDDDAE---I----E 460 (637)
T ss_pred HHhhcccCCCcEEEEEEEEEEccCceEEEecCCCEeEEEEEEEEeCCC-----------EEEEEEeccccc---c----C
Confidence 555444 356789999999999996441 133578899999982 367789976442 1 2
Q ss_pred cccCceEEeeceEEeccCCCCCeeEEEeccceeeEecCCCCC
Q 001266 1033 NLVGSTVGFCNLIKRPKDHLNHIWVAEATENSSYFLSFDFPT 1074 (1112)
Q Consensus 1033 ~~~G~vV~f~NL~~r~~D~~n~i~va~AtE~s~~sl~~~~~~ 1074 (1112)
+.+|.+|.+.|...+.+. +..-.-.+-+|++..+|+.+-
T Consensus 461 ~~~G~vi~i~~~~V~~~~---g~~~Ls~~~~s~i~~~p~~~e 499 (637)
T PRK12366 461 IKEGDAIKILHPYVKENG---DYLDLSIGRYGRIEINPEGEI 499 (637)
T ss_pred CCCCCEEEEEeeEEEeCC---CeeEEEecCcceEEECCCCcc
Confidence 457999999999998664 444445566889999998865
No 14
>PRK07218 replication factor A; Provisional
Probab=95.62 E-value=1.6 Score=52.34 Aligned_cols=169 Identities=15% Similarity=0.048 Sum_probs=108.4
Q ss_pred EEEEEeeccccccCCCC------------CCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeeccee
Q 001266 867 MRVRVVGLTGKNYQGKG------------SSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTK 934 (1112)
Q Consensus 867 ~klRV~d~~~k~~~~k~------------~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Tr 934 (1112)
++.||.++..+..+..+ ....+-+|+|+.. .|++|+.|.|.|......+ +.+.|++. +.|.
T Consensus 73 v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~-----~l~~Gdvv~I~na~vre~~-g~~el~ig-~~t~ 145 (423)
T PRK07218 73 VTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDF-----GLSPGDTVTIGNAGVREWD-GRPELNIG-ESTT 145 (423)
T ss_pred EEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCC-----CCCCCCEEEEeccEeeccC-CceEEecc-Ccce
Confidence 55677776543322211 2468889999932 3999999999998776654 44555553 3454
Q ss_pred eeeCCccccccCCCCcCCcceecccccCC-CCCCCccceEEEEEEeCCccc---ccccceeEEEEecCcccccccccccC
Q 001266 935 WQPLSPLATEHFKPFFSPRRSVLISNLGE-VPLSSEFDIAAFVVHVGDVYE---DSQQKKQWVFVTDGSMLELQLEDLSK 1010 (1112)
Q Consensus 935 w~~L~~~~~~~~~~~y~PR~~v~~s~l~~-~P~~~EfD~vG~Vv~Vg~~~~---~~~qk~QwvflaD~s~~~~~~~~~~~ 1010 (1112)
-..++.. . .+.+. .....++.+ .|....+++.|.|+.+.+... .+...-|...|.|.+-
T Consensus 146 I~~~de~-~---~~~~~---~~~~~kI~DL~~g~~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG---------- 208 (423)
T PRK07218 146 VSLLDDS-S---LPPYS---IGGDKKLIDLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETG---------- 208 (423)
T ss_pred EEEcCcc-c---ccCcc---ccCccchhhccCCCCceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCc----------
Confidence 4444421 1 12121 122223334 344556999999999965321 2334467788999983
Q ss_pred ceEEEEeecCCcCCCCCCcccccccCceEEeeceEEeccCCCCCeeEEEeccceeeEecCCC
Q 001266 1011 SLLAISISSPYIDDDSFSPINYNLVGSTVGFCNLIKRPKDHLNHIWVAEATENSSYFLSFDF 1072 (1112)
Q Consensus 1011 ~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~NL~~r~~D~~n~i~va~AtE~s~~sl~~~~ 1072 (1112)
-+-+..|.+. ..+.+|.+|-+.|...+.+. .-+-.-..++|++...++.
T Consensus 209 -~Ir~tlW~~~---------~~l~~Gd~v~I~na~v~e~~---G~~elnv~~~t~I~~~d~~ 257 (423)
T PRK07218 209 -RLPFTDWDPL---------PEIEIGASIRIEDAYVREFR---GVPSVNVSEFTTVEALDRE 257 (423)
T ss_pred -eEEEEEeccc---------ccCCCCCEEEEeeeEEeccC---CeEEEEECCceEEEECCCC
Confidence 3555667542 13578999999999999876 5667777899999998765
No 15
>PRK07211 replication factor A; Reviewed
Probab=95.49 E-value=0.27 Score=59.38 Aligned_cols=251 Identities=16% Similarity=0.133 Sum_probs=161.4
Q ss_pred cccEEEEeeceeEEeccc-cHHHHHHHHcCCcccCceEEEEcceeccCCCCCCccccCCccEEEEEeeceeeccccCccc
Q 001266 632 YAAKLELTDGWYSVDAFL-DVLLSKHLAAGKLFVGQKLRIWGAILCGWVGPVSPLEASGSISLQLNINGTYRAHWADRLG 710 (1112)
Q Consensus 632 ~~~~LELTDGWY~IkA~l-D~~L~~~l~~GkI~vG~KL~I~GA~L~~~~~~~sPLEa~~~~~L~L~~NstrrA~W~akLG 710 (1112)
.-..++|-|--=.|++.+ |....+ ..+.|.+|+-+.|.|+- .. .+..+ .|+.+.+.++. +..+-
T Consensus 91 kv~~v~l~DeTG~Ir~TlW~d~ad~--~~~~Le~GdV~~I~~~~-~~---------~ys~~--El~i~~ve~~~-d~~i~ 155 (485)
T PRK07211 91 RVINVEVADETGSVRVAFWDEQAVA--AEEELEVGQVLRIKGRP-KD---------GYNGL--EVSVDKVEPDP-DAEID 155 (485)
T ss_pred EEEEEEEEcCCCeEEEEEechHhHh--hhcccCCCCEEEEeceE-ec---------cccce--EEEEeeEEEcc-ccccc
Confidence 457889999888999987 544444 33579999999998753 21 22332 55555555554 22222
Q ss_pred cccCCCCcccceeeccCCCeEeeEEEEEEEEccceEEEEccCCcccccCHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCC
Q 001266 711 FCKGFGAPLAFRCIKSNGGPVPRTLVGVTRIYPVLYKERLSDGRSIVRSERMECKVMQLYQHRQSMVVEGIVSEFQRGNK 790 (1112)
Q Consensus 711 f~~~~~~p~~L~sl~~~GG~V~~idVvV~RvyP~~y~Ek~~~G~~i~Rner~E~k~~~~~~~r~e~l~e~i~~E~ere~~ 790 (1112)
.+.. ...+|..|.++... -.+.++|+.+.|+.=.++. +
T Consensus 156 ~~~~--~~~~I~dL~~~~~~-v~I~grV~~v~~iRtf~r~-d-------------------------------------- 193 (485)
T PRK07211 156 VQIG--DTYTVEDLSLGLSD-VTLVGVVLDTDSVRTFDRD-D-------------------------------------- 193 (485)
T ss_pred cccc--CCccHHHcCCCCCc-eEEEEEEEEcCCCeEEECC-C--------------------------------------
Confidence 2211 12477888875444 4578888888877211110 0
Q ss_pred cccccccCchhHHHHHHHHhccCChHHHHhcCCHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCceeeEEEE
Q 001266 791 DSHILNDSNSEGAKLFKMLETVAEPEVIMAEMSPEQLTSFATYQAKLEATRQSNMERSIEKALENAGLRERDVTPFMRVR 870 (1112)
Q Consensus 791 ~~~~~~~~~s~Ga~l~~~le~~~dp~~l~~~ls~~Ql~~l~~~r~~~~~~~Q~~~~~~i~~aL~~~g~~~R~Vtp~~klR 870 (1112)
| .+.. ++.+-
T Consensus 194 ------------------------------------------------------------------G-seGk---v~sv~ 203 (485)
T PRK07211 194 ------------------------------------------------------------------G-SEGR---VSNLT 203 (485)
T ss_pred ------------------------------------------------------------------C-CeeE---EEEEE
Confidence 1 0112 33445
Q ss_pred EeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCccccccCCCCc
Q 001266 871 VVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLATEHFKPFF 950 (1112)
Q Consensus 871 V~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y 950 (1112)
|.|- ...+-+|+|+...+....|.+|..|.|.+-.+... .+.+.|++.. .|.-.++.. +.+ |
T Consensus 204 L~De----------TG~IR~TlW~d~Ad~~~~le~G~Vv~I~~a~Vre~-~g~~ELsl~~-~s~I~~~~d-ev~-----~ 265 (485)
T PRK07211 204 VGDE----------TGRVRVTLWDDRADLAEELDAGESVEIVDGYVRER-DGSLELHVGD-RGAVEEVDE-DVE-----Y 265 (485)
T ss_pred EEcC----------CCeEEEEEechhhhhhccCCCCCEEEEEeeEEEec-CCcEEEEECC-CceEEECCc-ccc-----c
Confidence 6662 24699999998777777899999999998765443 3666776643 566666543 111 3
Q ss_pred CCcceecccccCCCCCCCccceEEEEEEeCCccccc-----ccceeEEEEecCcccccccccccCceEEEEeecCCcCCC
Q 001266 951 SPRRSVLISNLGEVPLSSEFDIAAFVVHVGDVYEDS-----QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDD 1025 (1112)
Q Consensus 951 ~PR~~v~~s~l~~~P~~~EfD~vG~Vv~Vg~~~~~~-----~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~ 1025 (1112)
.|. +.++.+..++.-+|++|+|+.++++.... ....+.+.|.|.+- -+-+.+|.+-.+
T Consensus 266 vp~----~~~I~dl~~g~~vdV~GvV~~v~~~rtf~r~dG~~~~vr~l~l~D~TG-----------~IrvTLWg~~A~-- 328 (485)
T PRK07211 266 VPD----TTPIESLEIDETVDIAGVVRSADPKRTFDRDDGSEGQVRNVRIQDDTG-----------DIRVALWGEKAD-- 328 (485)
T ss_pred ccc----cccHhhcCCCCceeEEEEEEEccCcEEEEcCCCCEeEEEEEEEEcCCC-----------cEEEEEeCcccc--
Confidence 232 24454555666799999999999966632 13567899999982 478899987553
Q ss_pred CCCcccccccCceEEeeceEEecc
Q 001266 1026 SFSPINYNLVGSTVGFCNLIKRPK 1049 (1112)
Q Consensus 1026 sf~~~~~~~~G~vV~f~NL~~r~~ 1049 (1112)
+ .+.+|++|.|.|...+..
T Consensus 329 ----~-~i~~GdvV~Ikg~~V~dg 347 (485)
T PRK07211 329 ----L-DIGPGDEVVAADVEIQDG 347 (485)
T ss_pred ----C-CCCCCCEEEEEccEEEec
Confidence 2 256899999999999866
No 16
>PRK12366 replication factor A; Reviewed
Probab=94.78 E-value=0.42 Score=59.77 Aligned_cols=139 Identities=18% Similarity=0.186 Sum_probs=91.8
Q ss_pred CceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccCCC
Q 001266 885 SREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGEV 964 (1112)
Q Consensus 885 ~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~ 964 (1112)
...+-+|+|+...+++..|.||+.|.|.+...... .+...|... +.|.-..+...+.... |.... .. ++.+.
T Consensus 110 tG~Ir~t~W~~~~~~~~~le~G~v~~i~~~~v~~~-~~~~el~~~-~~t~I~~~~~~d~~~i-~~~~~--~~---~I~el 181 (637)
T PRK12366 110 TGTIRLTLWNDNAKLLKGLKEGDVIKIENARSRKW-NNDVELNSG-SETRIDKLEKYDESRY-PIIKE--NY---DIPEL 181 (637)
T ss_pred CCEEEEEEEchhhhhhccCCCCCEEEEeccEeccc-CCceEEEcC-CcceEEEccccccccC-Ccccc--cc---ccccc
Confidence 35889999998877788899999999999754433 344555553 3466666652111111 11101 11 33444
Q ss_pred CCCCccceEEEEEEeCCcccc----c-ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceE
Q 001266 965 PLSSEFDIAAFVVHVGDVYED----S-QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTV 1039 (1112)
Q Consensus 965 P~~~EfD~vG~Vv~Vg~~~~~----~-~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV 1039 (1112)
.++..+|+.|.|+.+.++... + ..+.+.+.|.|.+. -+-+.+|+.-.+ + .+.+|++|
T Consensus 182 ~~g~~v~v~G~V~~~~~~~~f~rkdg~~~~~r~~~l~D~TG-----------~irvTlW~~~a~------~-~~~~g~vv 243 (637)
T PRK12366 182 EPNLSATIEGEVTKAYPIKEFTRKDGSEGKLKSFILKDDTG-----------SIRVTLWNDLTD------I-EVNKGDIV 243 (637)
T ss_pred CCCCeEEEEEEEEEccCcEEEEEcCCCeeEEEEEEEEcCCC-----------cEEEEEEChhhc------c-cCCCCCEE
Confidence 566799999999999996652 1 25678899999982 478889976442 1 25689999
Q ss_pred EeeceEEecc
Q 001266 1040 GFCNLIKRPK 1049 (1112)
Q Consensus 1040 ~f~NL~~r~~ 1049 (1112)
.+-+..+..|
T Consensus 244 ~i~g~~~~~~ 253 (637)
T PRK12366 244 RVKGYVKQGY 253 (637)
T ss_pred EEEeEEecCc
Confidence 9988655555
No 17
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=94.15 E-value=0.13 Score=49.85 Aligned_cols=75 Identities=25% Similarity=0.268 Sum_probs=54.0
Q ss_pred hhhhhHhCCCCCCCeEEEEEEeeeecCCCCcCCCccccCCCCCCcccEEEEeeceeEEeccccHHHHHHHHcCCcccCce
Q 001266 588 AIKRILEGDALPSSMMVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQK 667 (1112)
Q Consensus 588 aLRrIlE~D~~~s~~MVLcVs~I~~~~~~~~e~~~~~~~g~~~~~~~~LELTDGWY~IkA~lD~~L~~~l~~GkI~vG~K 667 (1112)
||.+|++.++... ..||=|.++..-+.. +........+.|+||=|.++|-|-..|..++.+|.|+.|.-
T Consensus 5 ai~~I~~~~~~~~-~pvlQVl~~k~i~~~----------~~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~si 73 (101)
T PF04057_consen 5 AIEAIFSSGDVND-NPVLQVLNIKKINSK----------QGGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSI 73 (101)
T ss_dssp HHHHHHHHTSSS---TEEEEEEEEEE--------------TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-E
T ss_pred HHHHHHhCCCCCC-CcEEEEEeeEEccCC----------CCCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCE
Confidence 7889999433333 777778787653210 11234579999999999999999999999999999999999
Q ss_pred EEEEcc
Q 001266 668 LRIWGA 673 (1112)
Q Consensus 668 L~I~GA 673 (1112)
+++.--
T Consensus 74 irl~~y 79 (101)
T PF04057_consen 74 IRLKQY 79 (101)
T ss_dssp EEEEEE
T ss_pred EEEeEE
Confidence 988743
No 18
>PRK15491 replication factor A; Provisional
Probab=94.00 E-value=2.2 Score=50.30 Aligned_cols=135 Identities=16% Similarity=0.141 Sum_probs=85.1
Q ss_pred CceEEEEEeCCChhhh--cccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccC
Q 001266 885 SREGIITIWNPAEKQQ--CELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLG 962 (1112)
Q Consensus 885 ~~~aiLTIWrPsedl~--~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~ 962 (1112)
...+.+|+|+...+.. ..|.+|+.|.|.+.......+ +.+++.. .|.-.+... + ....| + .+.+++|.
T Consensus 104 TG~ir~tlW~~~a~~~~~~~le~G~v~~I~~~~~~~y~g--~Ei~i~~-~~~i~~~~~---~-~~~~~-~--~~~I~dl~ 173 (374)
T PRK15491 104 TGSIRLTLWDDLADLIKTGDIEVGKSLNISGYAKEGYSG--IEVNIGR-YGGISESDE---N-VKASI-N--SQKISDIK 173 (374)
T ss_pred CCeEEEEEECchhhhhccCCcCCCCEEEEeeeeccCccc--EEEEeCC-Cceeeeccc---c-ccccc-C--cccHHHcC
Confidence 3578899999776665 359999999998864444433 5555532 343333321 1 11112 1 13344442
Q ss_pred CCCCCCccceEEEEEEeCCcccc----c-ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCc
Q 001266 963 EVPLSSEFDIAAFVVHVGDVYED----S-QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGS 1037 (1112)
Q Consensus 963 ~~P~~~EfD~vG~Vv~Vg~~~~~----~-~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~ 1037 (1112)
+.-.++|+.|.|+.+++...- + ..+.+.+.|.|.+- -+-+.+|.+-.+. ++.+.+|.
T Consensus 174 --~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG-----------~Ir~t~W~~~a~~-----~~~l~~Gd 235 (374)
T PRK15491 174 --DGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG-----------KIRVTLWDGKTDL-----ADKLENGD 235 (374)
T ss_pred --CCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC-----------eEEEEEecchhcc-----cccCCCCC
Confidence 223579999999999985332 1 23566799999872 3778899765432 23577899
Q ss_pred eEEeeceEEe
Q 001266 1038 TVGFCNLIKR 1047 (1112)
Q Consensus 1038 vV~f~NL~~r 1047 (1112)
+|-+.|-..|
T Consensus 236 ~V~i~~~~~r 245 (374)
T PRK15491 236 SVEIINGYAR 245 (374)
T ss_pred EEEEEeceEE
Confidence 9999996554
No 19
>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=93.69 E-value=0.44 Score=45.28 Aligned_cols=93 Identities=15% Similarity=0.182 Sum_probs=64.8
Q ss_pred cceEEEEEEeCCcccc------cccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEeec
Q 001266 970 FDIAAFVVHVGDVYED------SQQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCN 1043 (1112)
Q Consensus 970 fD~vG~Vv~Vg~~~~~------~~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~N 1043 (1112)
+|++|+|..|++.... .....-.|.|.|.+- .-+.+.+|+.-.+. |.. ..|.+|+|.|
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~----------~~i~vtLWg~~a~~--~~~----~~~~vv~~~~ 65 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESG----------HSVELTLWGEQAEL--FDG----SENPVIAIKG 65 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCC----------CEEEEEEEHHHhhh--ccc----CCCCEEEEEe
Confidence 7999999999996542 234466799999982 47889999765432 222 1289999999
Q ss_pred eEEeccCCCCCeeEEEeccceeeEecCCCCCChhHHHHHHHHHHHH
Q 001266 1044 LIKRPKDHLNHIWVAEATENSSYFLSFDFPTCSHLRSAAASAQSWA 1089 (1112)
Q Consensus 1044 L~~r~~D~~n~i~va~AtE~s~~sl~~~~~~~~~l~~a~~~l~~wa 1089 (1112)
+....+. ... .-+.-.|.+..+|+.| -+..|+.|.
T Consensus 66 ~~i~~~~-~~~---l~~~~~s~i~~np~~~-------e~~~l~~w~ 100 (101)
T cd04475 66 VKVSEFN-GKS---LSTGSSSTIIINPDIP-------EAHKLRGWY 100 (101)
T ss_pred eEEEecC-CeE---EeecCceeEEECCCcH-------HHHHHHHhh
Confidence 9988665 332 2334589999999853 345566663
No 20
>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain 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). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.
Probab=93.61 E-value=0.14 Score=49.36 Aligned_cols=73 Identities=26% Similarity=0.303 Sum_probs=56.1
Q ss_pred hhhhhHhCCCC-CCCeEEEEEEeeeecCCCCcCCCccccCCCCCCcccEEEEeeceeEEeccccHHHHHHHHcCCcccCc
Q 001266 588 AIKRILEGDAL-PSSMMVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQ 666 (1112)
Q Consensus 588 aLRrIlE~D~~-~s~~MVLcVs~I~~~~~~~~e~~~~~~~g~~~~~~~~LELTDGWY~IkA~lD~~L~~~l~~GkI~vG~ 666 (1112)
+|..|+++++. ....-||=|.+|...+. . ........+.|+||=|.++|-|...|..++++|.|+.|.
T Consensus 2 ai~~i~~~~~~~~~~~PvlQv~~ik~i~~-----~------~~~~~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~s 70 (97)
T cd04477 2 ALAAIFNGEDRSNVIKPVLQVLNIKKIDS-----S------NGSSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGS 70 (97)
T ss_pred hHHHhhcCCCcCCCCCCEEEEEEEEEccC-----C------CCCcceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCc
Confidence 67889988874 22346677777754221 0 012357899999999999999999999999999999999
Q ss_pred eEEEE
Q 001266 667 KLRIW 671 (1112)
Q Consensus 667 KL~I~ 671 (1112)
-+++.
T Consensus 71 Iirl~ 75 (97)
T cd04477 71 IIRLK 75 (97)
T ss_pred EEEEC
Confidence 99884
No 21
>PRK06386 replication factor A; Reviewed
Probab=92.44 E-value=9.1 Score=45.15 Aligned_cols=175 Identities=12% Similarity=0.047 Sum_probs=109.1
Q ss_pred CCCCceeeEEEEEeeccccccCCCC------------CCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeE
Q 001266 859 RERDVTPFMRVRVVGLTGKNYQGKG------------SSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYL 926 (1112)
Q Consensus 859 ~~R~Vtp~~klRV~d~~~k~~~~k~------------~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L 926 (1112)
+.+.|+ ++.||+++..+....+. ....+.+|+|++. ..|+||+.|+|.|......++ ...|
T Consensus 11 ~~~~V~--v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~~----~~l~~Gd~v~i~na~v~~~~G-~~~L 83 (358)
T PRK06386 11 ARQNVD--LKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEFP----DAVKSGDVIEIKYCYSKEYNG-KIRI 83 (358)
T ss_pred CCCcEE--EEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCCc----ccCCCCCEEEEEeEEEeeECC-EEEE
Confidence 345566 56688876533222221 2467889999953 468999999999987665543 4445
Q ss_pred eeeecceeeeeCCccccccCCCCcCCcceecccccCCCCCCCccceEEEEEEeCCcccc---cccceeEEEEecCccccc
Q 001266 927 QARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGEVPLSSEFDIAAFVVHVGDVYED---SQQKKQWVFVTDGSMLEL 1003 (1112)
Q Consensus 927 ~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~P~~~EfD~vG~Vv~Vg~~~~~---~~qk~QwvflaD~s~~~~ 1003 (1112)
.+.. .|.-......+.+ ..+.| ..+.+.+| .|....+++.|-|+.+.+.... ....-|.++|.|.+-
T Consensus 84 nv~~-~t~v~~~~d~~ie-v~~~~---~~~KI~DL--~~g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTG--- 153 (358)
T PRK06386 84 YFDS-RSEVMLKPDENIE-VKRTY---KLVKIRDL--SLVTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTA--- 153 (358)
T ss_pred EEcC-ceEEEecCccccc-ccccc---CccEeEec--cCCCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCC---
Confidence 5432 3434333322221 11112 22344455 4555678999999998774332 235577899999983
Q ss_pred ccccccCceEEEEeecCCcCCCCCCcccccccCceEEeeceEEeccCCCCCeeEEEeccceeeEecCCC
Q 001266 1004 QLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCNLIKRPKDHLNHIWVAEATENSSYFLSFDF 1072 (1112)
Q Consensus 1004 ~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~NL~~r~~D~~n~i~va~AtE~s~~sl~~~~ 1072 (1112)
-+-+..|.. .+.+|.+|-+.|...+.| +.-+-.-++.+|++.-.++.
T Consensus 154 --------rIr~TlW~~-----------~l~eGd~v~i~na~v~e~---~G~~el~v~~~t~I~~~~~~ 200 (358)
T PRK06386 154 --------RVRISSFGK-----------PLEDNRFVRIENARVSQY---NGYIEISVGNKSVIKEVESD 200 (358)
T ss_pred --------eEEEEEccc-----------cccCCCEEEEeeeEEEcc---CCeEEEEeCCeEEEEECCCC
Confidence 344455632 356799999999998877 36667777888888776554
No 22
>PRK07211 replication factor A; Reviewed
Probab=91.32 E-value=3.1 Score=50.64 Aligned_cols=155 Identities=15% Similarity=0.107 Sum_probs=92.4
Q ss_pred CceEEEEEeCCChh-hhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccCC
Q 001266 885 SREGIITIWNPAEK-QQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGE 963 (1112)
Q Consensus 885 ~~~aiLTIWrPsed-l~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~ 963 (1112)
...+.+|+|+-.-+ .+..|+||+.|.|.+-....+ +.+.|+.. ...+-. +.+ .. +.......+.+|
T Consensus 101 TG~Ir~TlW~d~ad~~~~~Le~GdV~~I~~~~~~~y--s~~El~i~----~ve~~~--d~~-i~--~~~~~~~~I~dL-- 167 (485)
T PRK07211 101 TGSVRVAFWDEQAVAAEEELEVGQVLRIKGRPKDGY--NGLEVSVD----KVEPDP--DAE-ID--VQIGDTYTVEDL-- 167 (485)
T ss_pred CCeEEEEEechHhHhhhcccCCCCEEEEeceEeccc--cceEEEEe----eEEEcc--ccc-cc--ccccCCccHHHc--
Confidence 36788999996533 356899999999987433222 23444442 122111 111 10 111122233444
Q ss_pred CCCCCccceEEEEEEeCCcccc-c----ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCce
Q 001266 964 VPLSSEFDIAAFVVHVGDVYED-S----QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGST 1038 (1112)
Q Consensus 964 ~P~~~EfD~vG~Vv~Vg~~~~~-~----~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~v 1038 (1112)
.|-.+.+|+.|.|+.++++.+- + ..+...+-|.|.+- -+-+.+|....+. | +.+.+|.+
T Consensus 168 ~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG-----------~IR~TlW~d~Ad~--~---~~le~G~V 231 (485)
T PRK07211 168 SLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-----------RVRVTLWDDRADL--A---EELDAGES 231 (485)
T ss_pred CCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC-----------eEEEEEechhhhh--h---ccCCCCCE
Confidence 3445679999999999996542 1 23445688999872 3777888654432 3 35778999
Q ss_pred EEeeceEEeccCCCCCeeEEEeccceeeEecCC
Q 001266 1039 VGFCNLIKRPKDHLNHIWVAEATENSSYFLSFD 1071 (1112)
Q Consensus 1039 V~f~NL~~r~~D~~n~i~va~AtE~s~~sl~~~ 1071 (1112)
|.+.|-..+.++....| -.+..|++..-++
T Consensus 232 v~I~~a~Vre~~g~~EL---sl~~~s~I~~~~d 261 (485)
T PRK07211 232 VEIVDGYVRERDGSLEL---HVGDRGAVEEVDE 261 (485)
T ss_pred EEEEeeEEEecCCcEEE---EECCCceEEECCc
Confidence 99999988876543333 2455555555444
No 23
>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=90.62 E-value=2.4 Score=43.10 Aligned_cols=74 Identities=15% Similarity=0.166 Sum_probs=54.8
Q ss_pred CCCccceEEEEEEeCCccccc-ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEeece
Q 001266 966 LSSEFDIAAFVVHVGDVYEDS-QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCNL 1044 (1112)
Q Consensus 966 ~~~EfD~vG~Vv~Vg~~~~~~-~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~NL 1044 (1112)
...-+|++|+|+.++++.... ....-.+-|+|.++.. ..-+.|.++.+.++. -| ...+|+||.|.|+
T Consensus 13 ~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~-------~~~l~v~~F~~~~~~---LP--~v~~GDVIll~~~ 80 (138)
T cd04497 13 SGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLAN-------SDGLTVKLFRPNEES---LP--IVKVGDIILLRRV 80 (138)
T ss_pred cCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCC-------CCcEEEEEECCChhh---CC--CCCCCCEEEEEEE
Confidence 456799999999999977642 2223458999999620 256788888887654 23 3478999999999
Q ss_pred EEeccCC
Q 001266 1045 IKRPKDH 1051 (1112)
Q Consensus 1045 ~~r~~D~ 1051 (1112)
.++.++-
T Consensus 81 kv~~~~g 87 (138)
T cd04497 81 KIQSYNG 87 (138)
T ss_pred EEEEECC
Confidence 9998873
No 24
>PRK15491 replication factor A; Provisional
Probab=90.48 E-value=4.9 Score=47.49 Aligned_cols=135 Identities=13% Similarity=0.205 Sum_probs=83.7
Q ss_pred ceEEEEEeCCChhhhcccccccEEEEEeeecCC-CCCCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccCCC
Q 001266 886 REGIITIWNPAEKQQCELVEGQAYAILGLIPMN-SDSNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGEV 964 (1112)
Q Consensus 886 ~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~-~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~ 964 (1112)
..+-+|+|++.-++...|.+|..|.|.|-..-- .-.+.+.|+... .|.-.+... +. .+...| +.+.+|.
T Consensus 214 G~Ir~t~W~~~a~~~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~-~s~I~~~~~-~~-e~~~~f-----~~I~dl~-- 283 (374)
T PRK15491 214 GKIRVTLWDGKTDLADKLENGDSVEIINGYARTNNYSQEVEIQIGN-HGSLRKTDR-NV-EYEEDF-----TPIADII-- 283 (374)
T ss_pred CeEEEEEecchhcccccCCCCCEEEEEeceEEEeccCCCEEEEeCC-CceEEECCc-cc-ccCCCc-----cCHHHcC--
Confidence 469999999987777889999999998843211 113566676543 455555432 11 111112 2344443
Q ss_pred CCCCccceEEEEEEeCCcccc---c--ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceE
Q 001266 965 PLSSEFDIAAFVVHVGDVYED---S--QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTV 1039 (1112)
Q Consensus 965 P~~~EfD~vG~Vv~Vg~~~~~---~--~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV 1039 (1112)
+..-+|++|+|..+++.... . ..+.-.++|.|.+- . +.+.+|++-.+- ++..-.|+.|
T Consensus 284 -~~~~~dv~G~V~~v~~~~~~~~~~G~~~~~r~i~l~D~Tg----------~-Ir~tlWg~~a~~-----~~~~~~g~~i 346 (374)
T PRK15491 284 -PGQPYSIKGAVSGLGDLKEFTKSDGSENKVSNIYVSDDTG----------R-IRIALWGEKAEL-----VDKLDIDTPI 346 (374)
T ss_pred -CCCceeEEEEEEEcCCcEEEEccCCCEeEEEeEEEEeCCC----------c-EEEEEccccccc-----ccccCCCCeE
Confidence 34558999999999884432 1 22345689999982 3 888999765531 2234456777
Q ss_pred EeeceEEe
Q 001266 1040 GFCNLIKR 1047 (1112)
Q Consensus 1040 ~f~NL~~r 1047 (1112)
-+.+-..+
T Consensus 347 ~i~~~~~k 354 (374)
T PRK15491 347 KIIDAFSK 354 (374)
T ss_pred EEEEEEEe
Confidence 77766554
No 25
>PRK14699 replication factor A; Provisional
Probab=87.60 E-value=6.3 Score=48.16 Aligned_cols=136 Identities=11% Similarity=0.116 Sum_probs=89.0
Q ss_pred ceEEEEEeCCChhhhcccccccEEEEEeeecCCCC-CCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccCCC
Q 001266 886 REGIITIWNPAEKQQCELVEGQAYAILGLIPMNSD-SNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGEV 964 (1112)
Q Consensus 886 ~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~-s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~ 964 (1112)
..+-+|+|++..+.+..+.+|..+.|.+.-..... ++.+.|++.+ .|.-.+... ..+ |.+ .|..+.+.
T Consensus 324 G~Ir~T~W~~~a~~~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~-~t~I~~~~~-~~e-----~~~----~~~~I~di 392 (484)
T PRK14699 324 GKIRLTLWDEKTNFLDEIDFDETVEVLNAYSRENTFSQQVELNLGA-RGIIQKSEK-KVE-----YRE----KFTDIADI 392 (484)
T ss_pred CeEEEEEeCcccccccccCCCceEEEEeEEEEeccCCccEEEEecC-ceeEeecCC-cce-----eee----ccccHHHc
Confidence 47889999998888888889998888877554322 3567777754 454433321 111 211 23333344
Q ss_pred CCCCccceEEEEEEeCCcccc---ccc--ceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceE
Q 001266 965 PLSSEFDIAAFVVHVGDVYED---SQQ--KKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTV 1039 (1112)
Q Consensus 965 P~~~EfD~vG~Vv~Vg~~~~~---~~q--k~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV 1039 (1112)
.....+|++|+|+.|++.... .+. ..=.++|.|++- -+.+.+|+.-.+. ++.+.+|.-|
T Consensus 393 e~~~~vdV~G~V~~v~~~~~~~~~~g~~~~vr~i~l~D~TG-----------~Ir~tlWg~~A~~-----~~~~~~~~~v 456 (484)
T PRK14699 393 IPGESYSVQGKVSEIGELREFEREDGTENVVANLQLKDETG-----------SIRLTLWGEQAYV-----IEDLDIDSEI 456 (484)
T ss_pred cCCCeeEEEEEEEEcCCcceEEecCCCEEEEEEEEEEcCCC-----------eEEEEEcchhhhh-----ccccCCCCeE
Confidence 567799999999999985442 111 233689999982 5677889654431 2346678999
Q ss_pred EeeceEEec
Q 001266 1040 GFCNLIKRP 1048 (1112)
Q Consensus 1040 ~f~NL~~r~ 1048 (1112)
.+.|...+.
T Consensus 457 ~~~~~~~~~ 465 (484)
T PRK14699 457 QIIDAYARY 465 (484)
T ss_pred EEechhhhh
Confidence 999988763
No 26
>PRK14699 replication factor A; Provisional
Probab=87.09 E-value=9.1 Score=46.82 Aligned_cols=277 Identities=14% Similarity=0.123 Sum_probs=160.3
Q ss_pred cccEEEEeeceeEEeccccHHHHHHHHcCCcccCceEEEEcceeccCCCCCCccccCCccEEEEEeeceeeccccCcccc
Q 001266 632 YAAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQKLRIWGAILCGWVGPVSPLEASGSISLQLNINGTYRAHWADRLGF 711 (1112)
Q Consensus 632 ~~~~LELTDGWY~IkA~lD~~L~~~l~~GkI~vG~KL~I~GA~L~~~~~~~sPLEa~~~~~L~L~~NstrrA~W~akLGf 711 (1112)
.-..++|-|--=.|+..|=.-+..++..|.|.+|+-|.|-|+ ...+. ....|.++-+++=. .-+...-.
T Consensus 94 ~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~GDvv~I~~~-~r~~~---------~g~el~~~~~~~i~-~~~~~i~v 162 (484)
T PRK14699 94 RVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTLQISGY-AKQGY---------SGVEVNIGNNGVLT-ESEEEIDV 162 (484)
T ss_pred EEEEEEEecCCCeEEEEEecCccchhhhcCCCCCCEEEEcce-eccCC---------CCceEEeCCCceee-ccCccccc
Confidence 345788999877888888335588899999999999999886 22211 22223332222222 21233322
Q ss_pred ccCCCCcccceeeccCCCeEeeEEEEEEEEccceEEEEccCCcccccCHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCCc
Q 001266 712 CKGFGAPLAFRCIKSNGGPVPRTLVGVTRIYPVLYKERLSDGRSIVRSERMECKVMQLYQHRQSMVVEGIVSEFQRGNKD 791 (1112)
Q Consensus 712 ~~~~~~p~~L~sl~~~GG~V~~idVvV~RvyP~~y~Ek~~~G~~i~Rner~E~k~~~~~~~r~e~l~e~i~~E~ere~~~ 791 (1112)
.. +...+..|.++.+. -.+.+.|+.++|+-=.++ .+|.
T Consensus 163 ~~---~~~~I~dL~~~~~~-V~i~gkVl~~~~~R~f~~-~dG~------------------------------------- 200 (484)
T PRK14699 163 AA---NSQKIKDIKDGMGD-LNLTGKVLEISEIRTFQR-KDGT------------------------------------- 200 (484)
T ss_pred CC---CCcchhhcCCCCCc-eEEEEEEEeccCceEEec-CCCC-------------------------------------
Confidence 11 23467888876665 467788888887432211 0110
Q ss_pred ccccccCchhHHHHHHHHhccCChHHHHhcCCHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCceeeEEEEE
Q 001266 792 SHILNDSNSEGAKLFKMLETVAEPEVIMAEMSPEQLTSFATYQAKLEATRQSNMERSIEKALENAGLRERDVTPFMRVRV 871 (1112)
Q Consensus 792 ~~~~~~~~s~Ga~l~~~le~~~dp~~l~~~ls~~Ql~~l~~~r~~~~~~~Q~~~~~~i~~aL~~~g~~~R~Vtp~~klRV 871 (1112)
+..|. .+=|
T Consensus 201 --------------------------------------------------------------------~g~v~---~~~i 209 (484)
T PRK14699 201 --------------------------------------------------------------------SGKVG---NLLL 209 (484)
T ss_pred --------------------------------------------------------------------ceEEE---EEEE
Confidence 11122 2234
Q ss_pred eeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeeecCCCC-CCceeEeeeecceeeeeCCccccccCCCCc
Q 001266 872 VGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSD-SNTLYLQARGSTTKWQPLSPLATEHFKPFF 950 (1112)
Q Consensus 872 ~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~-s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y 950 (1112)
.|- ...+-+|+|++.-++...|.+|+.|+|.|--+-... .+.+.|++.. .| .+...+.+ ..|
T Consensus 210 gDe----------TG~ir~tlW~~~a~~~~~l~~Gd~v~I~~a~vr~~~~~~~~el~~~~-~s---~i~~~~~~---~e~ 272 (484)
T PRK14699 210 GDE----------TGTLRVTLWDDKTDFLNQIEYGDTVELINAYARENAFTQKVELQVGN-RS---IIRKSEKK---VEY 272 (484)
T ss_pred EcC----------CceEEEEEECcccccccccCCCCEEEEecceEeecccCCceEEEecC-ce---Eeeccccc---ccc
Confidence 442 468999999997777788999999999876442211 2567777642 23 22211111 112
Q ss_pred CCcceecccccCCCCCCCccceEEEEEEeCCcccc----c-ccceeEEEEecCcccccccccccCceEEEEeecCCcCCC
Q 001266 951 SPRRSVLISNLGEVPLSSEFDIAAFVVHVGDVYED----S-QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDD 1025 (1112)
Q Consensus 951 ~PR~~v~~s~l~~~P~~~EfD~vG~Vv~Vg~~~~~----~-~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~ 1025 (1112)
.+ ..+.+.+| .|-.+.+|+.|.|+.+++..+- + ..+.+.+.|.|++- -+-+.+|.+-.+
T Consensus 273 ~~-~~~~I~~L--~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG-----------~Ir~T~W~~~a~-- 336 (484)
T PRK14699 273 EE-EFTPIEDI--KADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTG-----------KIRLTLWDEKTN-- 336 (484)
T ss_pred cc-cccCHHHc--CCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCC-----------eEEEEEeCcccc--
Confidence 22 12334555 3556899999999999985442 1 34567789999982 467788866432
Q ss_pred CCCcccccccCceEEeeceEEeccCCCCCeeEEEeccceeeEec
Q 001266 1026 SFSPINYNLVGSTVGFCNLIKRPKDHLNHIWVAEATENSSYFLS 1069 (1112)
Q Consensus 1026 sf~~~~~~~~G~vV~f~NL~~r~~D~~n~i~va~AtE~s~~sl~ 1069 (1112)
|. +.+..|.+|-+-|--++..+- +.-+-.-....|.+...
T Consensus 337 -~~--~~i~~Gd~v~i~~~y~~~~~~-~~~~eL~~~~~t~I~~~ 376 (484)
T PRK14699 337 -FL--DEIDFDETVEVLNAYSRENTF-SQQVELNLGARGIIQKS 376 (484)
T ss_pred -cc--cccCCCceEEEEeEEEEeccC-CccEEEEecCceeEeec
Confidence 11 245568887777777663332 22233333444444433
No 27
>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=74.15 E-value=47 Score=34.05 Aligned_cols=113 Identities=15% Similarity=0.147 Sum_probs=65.0
Q ss_pred CCccceEEEEEEeCCc--ccc-cccceeEEEEecCccccccccccc-CceEEEEeecCCcCCCCCCcccccccCceEEee
Q 001266 967 SSEFDIAAFVVHVGDV--YED-SQQKKQWVFVTDGSMLELQLEDLS-KSLLAISISSPYIDDDSFSPINYNLVGSTVGFC 1042 (1112)
Q Consensus 967 ~~EfD~vG~Vv~Vg~~--~~~-~~qk~QwvflaD~s~~~~~~~~~~-~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~ 1042 (1112)
+.=+|++|+|+....+ ... +..-.-.+-|+|.++.+ +... ..|....|. +.++. -| +.-..|.||-+.
T Consensus 12 ~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~---~~~~~~~l~v~iF~-~~~~~---LP-~v~~~GDii~l~ 83 (146)
T PF02765_consen 12 GKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLND---SNQKLSGLTVNIFR-PHKES---LP-NVKSVGDIIRLR 83 (146)
T ss_dssp SEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSC---SSCCCCEEEEEEEE-SSHHH---SC-TTCSTTHEEEEE
T ss_pred CCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCc---cccccCCEEEEEEC-CCHHH---CC-CCCCCCCEEEEE
Confidence 4569999999999887 443 32234458899999641 1111 345555554 33322 23 123349999999
Q ss_pred ceEEeccCCCCCeeEEEecc--ceeeEec----------CCC--CCChhHHH----HHHHHHHHHh
Q 001266 1043 NLIKRPKDHLNHIWVAEATE--NSSYFLS----------FDF--PTCSHLRS----AAASAQSWAK 1090 (1112)
Q Consensus 1043 NL~~r~~D~~n~i~va~AtE--~s~~sl~----------~~~--~~~~~l~~----a~~~l~~wa~ 1090 (1112)
++.++.|+...+ +.+++ +++|-+= |-. ++.-.+.+ =++.|+.|++
T Consensus 84 r~kv~~~~~~~~---~~~~~~~~ss~~vf~~~~~~~~~~p~~~s~~~~~~~~~e~~~~~~Lr~w~~ 146 (146)
T PF02765_consen 84 RVKVQSYNGKPQ---GLSNSTSNSSWAVFSSGGSGAPFEPYQKSSNPFEFSDEEKKYVESLRKWAQ 146 (146)
T ss_dssp EEEEEEETTEEE---EEEECECTEEEEEECTSSTTTCCCSSCESTSSTT-HHHHHHHHHHHHHHH-
T ss_pred EEEEEEECCEEE---EEecCCCcEEEEEEecCCCCCCccccccCCCccCCCHHHHHHHHHHHHhhC
Confidence 999999886433 33322 3555444 211 22233322 3888999985
No 28
>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=63.93 E-value=24 Score=32.33 Aligned_cols=53 Identities=15% Similarity=0.081 Sum_probs=39.3
Q ss_pred eeeEEEEEeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeee
Q 001266 864 TPFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQAR 929 (1112)
Q Consensus 864 tp~~klRV~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r 929 (1112)
..++.+.|.|- ..++.+++|++.. ...++||..|.|.|......+ +.++|++.
T Consensus 22 ~~~~~~~l~D~----------TG~i~~~~W~~~~--~~~~~~G~vv~i~~~~v~~~~-g~~ql~i~ 74 (82)
T cd04491 22 GKVQSGLVGDE----------TGTIRFTLWDEKA--ADDLEPGDVVRIENAYVREFN-GRLELSVG 74 (82)
T ss_pred eEEEEEEEECC----------CCEEEEEEECchh--cccCCCCCEEEEEeEEEEecC-CcEEEEeC
Confidence 45666677662 3589999999886 577999999999987665553 55666654
No 29
>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=62.56 E-value=16 Score=35.18 Aligned_cols=96 Identities=16% Similarity=0.159 Sum_probs=61.1
Q ss_pred ceEEEEEEeCCccccc----ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCccc--ccccCceEEeec-
Q 001266 971 DIAAFVVHVGDVYEDS----QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPIN--YNLVGSTVGFCN- 1043 (1112)
Q Consensus 971 D~vG~Vv~Vg~~~~~~----~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~--~~~~G~vV~f~N- 1043 (1112)
|++|+|+.|++..... ...+--+.|.|.+ +..|-+.+|+...++ |.... ....++|||+-.
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~----------~~~l~~tlwG~~A~~--f~~~~~~~~~~~~VVav~~~ 68 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLS----------DERLKCTLWGEYAEE--FDAKFQSAGNGEPVVAVLRF 68 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCC----------CCEEEEEEEHHHHHH--HHHHHHHhCCCCcEEEEEEe
Confidence 8999999999966531 2335568888887 368889999765533 22110 235678898866
Q ss_pred eEEeccCCCCCeeEEEeccceeeEecCCCCCChhHHH
Q 001266 1044 LIKRPKDHLNHIWVAEATENSSYFLSFDFPTCSHLRS 1080 (1112)
Q Consensus 1044 L~~r~~D~~n~i~va~AtE~s~~sl~~~~~~~~~l~~ 1080 (1112)
.....|--...+..+. =.|+++.||+.|....++.
T Consensus 69 ~rV~~~~g~~~ls~~~--~~s~v~inp~ipe~~~~~~ 103 (106)
T cd04481 69 WKIKEYKGPKSLSNSF--GASKVYINPDIPEVPEIKM 103 (106)
T ss_pred EEEEEEcCCcEEEcCC--CceEEEECCCcHHHHHHHh
Confidence 5555453222333221 5789999999876665543
No 30
>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=58.77 E-value=46 Score=30.46 Aligned_cols=67 Identities=16% Similarity=0.046 Sum_probs=48.8
Q ss_pred eEEEEEEeCCcccc----cccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEeeceEEe
Q 001266 972 IAAFVVHVGDVYED----SQQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCNLIKR 1047 (1112)
Q Consensus 972 ~vG~Vv~Vg~~~~~----~~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~NL~~r 1047 (1112)
+.|.|+.++++... ...+.+.+.|.|.+. -+-+.+|..-. ...+.+|.+|.+.|...+
T Consensus 2 v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG-----------~i~~~~W~~~~-------~~~~~~G~vv~i~~~~v~ 63 (82)
T cd04491 2 VEGKVLSISEPREFTRDGSEGKVQSGLVGDETG-----------TIRFTLWDEKA-------ADDLEPGDVVRIENAYVR 63 (82)
T ss_pred EEEEEEEccCCeEeccCCCeeEEEEEEEECCCC-----------EEEEEEECchh-------cccCCCCCEEEEEeEEEE
Confidence 67999999987742 456788899999982 35666775421 235678999999999998
Q ss_pred ccCCCCCee
Q 001266 1048 PKDHLNHIW 1056 (1112)
Q Consensus 1048 ~~D~~n~i~ 1056 (1112)
.|....+|-
T Consensus 64 ~~~g~~ql~ 72 (82)
T cd04491 64 EFNGRLELS 72 (82)
T ss_pred ecCCcEEEE
Confidence 887544443
No 31
>PRK07217 replication factor A; Reviewed
Probab=50.56 E-value=2.8e+02 Score=32.54 Aligned_cols=50 Identities=20% Similarity=0.313 Sum_probs=34.2
Q ss_pred CceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeC
Q 001266 885 SREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPL 938 (1112)
Q Consensus 885 ~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L 938 (1112)
...+-+|+|.-++ ...|+||+.|+|.|......+ +...|.+. +.|.-..+
T Consensus 112 TG~IkfT~W~~s~--~~~leeGd~~rI~na~v~ey~-G~~~lnlg-~~t~I~~~ 161 (311)
T PRK07217 112 TGTIKFTKWAKSD--LPELEEGKSYLLKNVVTDEYQ-GRFSVKLN-RTTSIEEL 161 (311)
T ss_pred CceEEEEEccCCC--CCcccCCCEEEEEeEEEeeEC-CEEEEEeC-CceEEEeC
Confidence 3678899999753 356999999999998776654 44555543 23444443
No 32
>PRK08402 replication factor A; Reviewed
Probab=49.69 E-value=87 Score=37.18 Aligned_cols=91 Identities=11% Similarity=0.093 Sum_probs=53.1
Q ss_pred ceEEEEEeCCChh-hhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCcccc-ccCCCC------cCCcceec
Q 001266 886 REGIITIWNPAEK-QQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLAT-EHFKPF------FSPRRSVL 957 (1112)
Q Consensus 886 ~~aiLTIWrPsed-l~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~-~~~~~~------y~PR~~v~ 957 (1112)
..+-+|+|+..-+ ....|.+|..|+|.|..+.....+...|++.. .|.-...+.... +.+... ...|+.+
T Consensus 110 G~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~-~s~i~~~pd~~ea~~i~~~~~~~~~~~~~k~I- 187 (355)
T PRK08402 110 GRARVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINF-RARIILNPDDPRVEEIPPLEEVRSYNYTRKKI- 187 (355)
T ss_pred CeEEEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECC-CceEEeCCCcccccccccccccccccccccCH-
Confidence 4678999998743 34679999999999998887655665666643 444444442111 112111 1122222
Q ss_pred ccccCCCCCCCccceEEEEEEeCC
Q 001266 958 ISNLGEVPLSSEFDIAAFVVHVGD 981 (1112)
Q Consensus 958 ~s~l~~~P~~~EfD~vG~Vv~Vg~ 981 (1112)
.++.... .-|.+.|.|+++-.
T Consensus 188 -~ei~~gd--~~v~v~g~Iv~i~~ 208 (355)
T PRK08402 188 -GELEGGE--RFVEVRGTIAKVYR 208 (355)
T ss_pred -HHcccCC--cEEEEEEEEEEEec
Confidence 2332211 12788999999764
No 33
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=40.65 E-value=96 Score=31.41 Aligned_cols=61 Identities=13% Similarity=0.085 Sum_probs=41.9
Q ss_pred eeeEEEEEeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCC
Q 001266 864 TPFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLS 939 (1112)
Q Consensus 864 tp~~klRV~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~ 939 (1112)
..++.+.|.|- ...+.+++|+... ..|++|..+.|.|......+ +.++|.+. +.++-..+.
T Consensus 39 ~~v~~~~l~D~----------TG~I~~tlW~~~a---~~l~~GdvV~I~na~v~~f~-G~lqL~i~-~~~~i~~~~ 99 (129)
T PRK06461 39 RTISEAVVGDE----------TGRVKLTLWGEQA---GSLKEGEVVEIENAWTTLYR-GKVQLNVG-KYGSISESD 99 (129)
T ss_pred eEEEEEEEECC----------CCEEEEEEeCCcc---ccCCCCCEEEEECcEEeeeC-CEEEEEEC-CCEEEEECC
Confidence 34677777763 3479999999743 46899999999987655543 55777664 345555554
No 34
>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=38.37 E-value=72 Score=27.73 Aligned_cols=53 Identities=15% Similarity=0.146 Sum_probs=35.9
Q ss_pred eeEEEEEeeccccccCCCCCCceEEEEEeC-CChhhhcccccccEEEEEeeecCCCCCCceeEee
Q 001266 865 PFMRVRVVGLTGKNYQGKGSSREGIITIWN-PAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQA 928 (1112)
Q Consensus 865 p~~klRV~d~~~k~~~~k~~~~~aiLTIWr-Psedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~ 928 (1112)
.++.+.+.|. .....+.+|+ ........|++|+.+.|++-.-.. ++++++|.+
T Consensus 16 ~~~~~~l~D~----------tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~-~~~~~~l~~ 69 (75)
T PF01336_consen 16 KIVFFTLEDG----------TGSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRY-NGGELELIV 69 (75)
T ss_dssp TEEEEEEEET----------TEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEE-TTSSEEEEE
T ss_pred CEEEEEEEEC----------CccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEE-CCccEEEEE
Confidence 3455566652 3689999999 566667889999999999764433 223466654
No 35
>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=36.13 E-value=88 Score=26.88 Aligned_cols=41 Identities=12% Similarity=0.120 Sum_probs=31.6
Q ss_pred eeEEEEEeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeee
Q 001266 865 PFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLI 915 (1112)
Q Consensus 865 p~~klRV~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ 915 (1112)
+++++.+.|- ...+.+++|++...+...|++|..|.|++-.
T Consensus 18 ~~~~~~~~D~----------~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv 58 (75)
T cd04488 18 RRLKVTLSDG----------TGTLTLVFFNFQPYLKKQLPPGTRVRVSGKV 58 (75)
T ss_pred cEEEEEEEcC----------CCEEEEEEECCCHHHHhcCCCCCEEEEEEEE
Confidence 4677777662 3578899999766667889999999999853
No 36
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=35.80 E-value=1.4e+02 Score=30.22 Aligned_cols=70 Identities=11% Similarity=0.030 Sum_probs=47.9
Q ss_pred CccceEEEEEEeCCccc---ccc-cceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEeec
Q 001266 968 SEFDIAAFVVHVGDVYE---DSQ-QKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGFCN 1043 (1112)
Q Consensus 968 ~EfD~vG~Vv~Vg~~~~---~~~-qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f~N 1043 (1112)
..||++|.|+.+++... .+. .+...+.|.|.+- -+.+.+|... .+.+.+|.+|.+.|
T Consensus 15 ~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG-----------~I~~tlW~~~--------a~~l~~GdvV~I~n 75 (129)
T PRK06461 15 ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETG-----------RVKLTLWGEQ--------AGSLKEGEVVEIEN 75 (129)
T ss_pred CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCC-----------EEEEEEeCCc--------cccCCCCCEEEEEC
Confidence 68999999999886322 222 3356689999982 2567778642 12457899999999
Q ss_pred eEEeccCCCCCee
Q 001266 1044 LIKRPKDHLNHIW 1056 (1112)
Q Consensus 1044 L~~r~~D~~n~i~ 1056 (1112)
-..+.+.-.-+|-
T Consensus 76 a~v~~f~G~lqL~ 88 (129)
T PRK06461 76 AWTTLYRGKVQLN 88 (129)
T ss_pred cEEeeeCCEEEEE
Confidence 8877665333343
No 37
>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=32.03 E-value=65 Score=31.19 Aligned_cols=31 Identities=29% Similarity=0.132 Sum_probs=25.0
Q ss_pred CceEEEEEeCCC-hhhhcccccccEEEEEeee
Q 001266 885 SREGIITIWNPA-EKQQCELVEGQAYAILGLI 915 (1112)
Q Consensus 885 ~~~aiLTIWrPs-edl~~~L~EG~ry~V~~L~ 915 (1112)
.....+++|+.. +.....|+||+.|.|.+..
T Consensus 46 ~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~ 77 (104)
T cd04474 46 GGEIRATFFNDAVDKFYDLLEVGKVYYISKGS 77 (104)
T ss_pred CCEEEEEEehHHHHHhhcccccccEEEEeccE
Confidence 358899999864 4456789999999999753
No 38
>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=29.46 E-value=1.7e+02 Score=29.80 Aligned_cols=70 Identities=7% Similarity=0.091 Sum_probs=48.5
Q ss_pred eeEEEEEeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCcc
Q 001266 865 PFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPL 941 (1112)
Q Consensus 865 p~~klRV~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~ 941 (1112)
-.+.|+|+|-. ... ...+.++||++..+.+-.+.+|..+++.++.-....+...-+ ...+.+.|--....
T Consensus 37 ~~~tl~i~D~S---~~~---~~~l~v~~F~~~~~~LP~v~~GDVIll~~~kv~~~~g~~~~~-~~~~~ss~avf~~~ 106 (138)
T cd04497 37 YCCTLTITDPS---LAN---SDGLTVKLFRPNEESLPIVKVGDIILLRRVKIQSYNGKPQGI-SNDRGSSWAVFRGD 106 (138)
T ss_pred EEEEEEEECCC---CCC---CCcEEEEEECCChhhCCCCCCCCEEEEEEEEEEEECCceEEE-ECCCceeEEEEcCC
Confidence 57788999843 110 368999999999777676799999999998776665443333 22235777776543
No 39
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) 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=27.67 E-value=3.2e+02 Score=31.25 Aligned_cols=38 Identities=11% Similarity=0.241 Sum_probs=18.5
Q ss_pred eeeeeCCccccccCCCCcCCcceecccccCCCCCCCccceEEE
Q 001266 933 TKWQPLSPLATEHFKPFFSPRRSVLISNLGEVPLSSEFDIAAF 975 (1112)
Q Consensus 933 Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~P~~~EfD~vG~ 975 (1112)
|-|.|... +...+.+-+++.+.+|.-.+..+.++...+
T Consensus 185 TIWrPted-----l~s~L~EG~ry~i~~L~~s~~k~~~~~~~v 222 (251)
T cd04494 185 SIWRPTED-----LRSLLTEGKRYRIYGLATSNSKKRSGNEEV 222 (251)
T ss_pred EEeCCCHH-----HHhhhcCCcEEEEEeccccCCCCCCCcceE
Confidence 56877542 112345566666666644333344443333
No 40
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=25.32 E-value=75 Score=32.42 Aligned_cols=34 Identities=12% Similarity=0.042 Sum_probs=28.8
Q ss_pred CceEEEEEeCCChhhhcccccccEEEEEeeecCC
Q 001266 885 SREGIITIWNPAEKQQCELVEGQAYAILGLIPMN 918 (1112)
Q Consensus 885 ~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~ 918 (1112)
...++|++|+|=.+..-.|++|.-++|+|+-...
T Consensus 59 ~~ti~It~yD~H~~~ar~lK~GdfV~L~NVhiK~ 92 (123)
T cd04498 59 QLTIDILVYDNHVELAKSLKPGDFVRIYNVHAKS 92 (123)
T ss_pred eEEEEEEEEcchHHHHhhCCCCCEEEEEEEEEEe
Confidence 4799999999988776679999999999986533
No 41
>PRK08402 replication factor A; Reviewed
Probab=24.71 E-value=4.6e+02 Score=31.31 Aligned_cols=93 Identities=13% Similarity=0.072 Sum_probs=65.1
Q ss_pred CCccceEEEEEEeCCcccc----c-ccceeEEEEecCcccccccccccCceEEEEeecCCcCCCCCCcccccccCceEEe
Q 001266 967 SSEFDIAAFVVHVGDVYED----S-QQKKQWVFVTDGSMLELQLEDLSKSLLAISISSPYIDDDSFSPINYNLVGSTVGF 1041 (1112)
Q Consensus 967 ~~EfD~vG~Vv~Vg~~~~~----~-~qk~QwvflaD~s~~~~~~~~~~~~lLaI~f~~~~~~~~sf~~~~~~~~G~vV~f 1041 (1112)
-..|.++|-|+.+.++... + .++--.+.|.|.+- -+-+.+|..-.+. | ++.+.+|++|.+
T Consensus 72 ~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG-----------~ir~TlW~~~a~~--~--~~~l~~Gdvi~I 136 (355)
T PRK08402 72 MRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTG-----------RARVVLWDAKVAK--Y--YNKINVGDVIKV 136 (355)
T ss_pred CceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCC-----------eEEEEEechhhhh--h--cccCCCCCEEEE
Confidence 3589999999999764321 1 11222478999882 3478889764431 1 234678999999
Q ss_pred eceEEeccCCCCCeeEEEeccceeeEecCCCCCCh
Q 001266 1042 CNLIKRPKDHLNHIWVAEATENSSYFLSFDFPTCS 1076 (1112)
Q Consensus 1042 ~NL~~r~~D~~n~i~va~AtE~s~~sl~~~~~~~~ 1076 (1112)
-|...+.. -+..+-.-..++|++.++|+.|-.+
T Consensus 137 ~~a~V~e~--~~G~~eLsvg~~s~i~~~pd~~ea~ 169 (355)
T PRK08402 137 IDAQVRES--LSGLPELHINFRARIILNPDDPRVE 169 (355)
T ss_pred ECCEEeec--CCCcEEEEECCCceEEeCCCccccc
Confidence 99999853 2366677789999999999997543
No 42
>PRK06386 replication factor A; Reviewed
Probab=23.47 E-value=2.9e+02 Score=33.00 Aligned_cols=80 Identities=13% Similarity=0.193 Sum_probs=51.7
Q ss_pred CceEEEEEeCCChhhhcccccccEEEEEeeecCCCCCCceeEeeeecceeeeeCCccccccCCCCcCCcceecccccCCC
Q 001266 885 SREGIITIWNPAEKQQCELVEGQAYAILGLIPMNSDSNTLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGEV 964 (1112)
Q Consensus 885 ~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ps~~~s~~l~L~~r~~~Trw~~L~~~~~~~~~~~y~PR~~v~~s~l~~~ 964 (1112)
...+-+|+|++ .|.||..|+|.|.....+ .+.+.|++.+ .|+-.+++. +.+ .. ++ ...+.++.
T Consensus 152 TGrIr~TlW~~------~l~eGd~v~i~na~v~e~-~G~~el~v~~-~t~I~~~~~-~ie-v~----~~-~~~I~di~-- 214 (358)
T PRK06386 152 TARVRISSFGK------PLEDNRFVRIENARVSQY-NGYIEISVGN-KSVIKEVES-DIN-LE----SR-NIFIFEIK-- 214 (358)
T ss_pred CCeEEEEEccc------cccCCCEEEEeeeEEEcc-CCeEEEEeCC-eEEEEECCC-Ccc-cC----cc-ccchhhhh--
Confidence 46899999986 389999999999876665 4777787754 577777653 232 11 11 11222221
Q ss_pred CCCCccceEEEEEEeCC
Q 001266 965 PLSSEFDIAAFVVHVGD 981 (1112)
Q Consensus 965 P~~~EfD~vG~Vv~Vg~ 981 (1112)
...+-+-++|-||.|..
T Consensus 215 ~~~g~v~i~G~iv~i~~ 231 (358)
T PRK06386 215 SPVGGITIMGFIVSVGQ 231 (358)
T ss_pred ccCCeEEEEEEEEEEcC
Confidence 11223778899999885
No 43
>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=20.92 E-value=2.2e+02 Score=25.19 Aligned_cols=42 Identities=17% Similarity=0.409 Sum_probs=33.2
Q ss_pred eeeEEEEEeeccccccCCCCCCceEEEEEeCCChhhhcccccccEEEEEeee
Q 001266 864 TPFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAYAILGLI 915 (1112)
Q Consensus 864 tp~~klRV~d~~~k~~~~k~~~~~aiLTIWrPsedl~~~L~EG~ry~V~~L~ 915 (1112)
.+++.+.|.|.. ..+.+.+|+........|++|..+.|++-.
T Consensus 18 ~~~~~~~l~D~t----------g~i~~~~f~~~~~~~~~l~~g~~v~v~G~v 59 (83)
T cd04492 18 KPYLALTLQDKT----------GEIEAKLWDASEEDEEKFKPGDIVHVKGRV 59 (83)
T ss_pred CcEEEEEEEcCC----------CeEEEEEcCCChhhHhhCCCCCEEEEEEEE
Confidence 468888888743 578899998665566789999999999765
Done!