RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15132
(786 letters)
>gnl|CDD|233055 TIGR00617, rpa1, replication factor-a protein 1 (rpa1). All
proteins in this family for which functions are known
are part of a multiprotein complex made up of homologs
of RPA1, RPA2 and RPA3 that bind ssDNA and function in
the recognition of DNA damage for nucleotide excision
repairThis family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford University)
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 608
Score = 442 bits (1138), Expect = e-146
Identities = 209/537 (38%), Positives = 289/537 (53%), Gaps = 82/537 (15%)
Query: 325 IPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGVSSGSATNRSVLIILELNI 384
I DG+ S AMLATQLN ++ +G L E TI+++ ++ V+ + R VLI+ EL +
Sbjct: 48 ISDGIY-YSKAMLATQLNPLVREGELQEGTIIRLTKFEVNTIGKDG---RKVLIVYELEV 103
Query: 385 IKPGTEIGFKIGNPQPLNTNTDNSSTQQ------------TPAATNTNGSNGVHNNVAIP 432
+KP ++ KIGNP D+ +Q P A +NN A P
Sbjct: 104 VKPELKVRDKIGNPVTYEKYLDSWHEEQVLASKPATNPANPPNAKAPKNEVASYNNAANP 163
Query: 433 RQASAPVVQT-------HPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL 485
+ +AP PI SLSPYQNKWTIKARVTNK+ IR W+NARG GKLF+++LL
Sbjct: 164 ERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELL 223
Query: 486 DESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVI 545
DESGEIRAT FN++ ++F+D+I++ KVYYIS +LKPANK+F+++ NDYEM+ T +
Sbjct: 224 DESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIE 283
Query: 546 PCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRD 605
C ++ +P +++ FV + I + +DV+G+ + ++T + N K + KRD
Sbjct: 284 ECEDET--AIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRD 341
Query: 606 ITLVDQSQASVTMTLWGKEAET-------------------------------------- 627
ITLVD S SV +TLWG +A
Sbjct: 342 ITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGVRVSDFGGKSLSTGGSSTIIVNPDI 401
Query: 628 ---------FDASNKPVIAV-----KAARVSEFQGNLLLMREIQDQQLGMGDKADYCSVR 673
+D K +A + RV + EIQ + LG DK DY SV+
Sbjct: 402 PEAEKLKGWYDNEGKGTMASSISDMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVK 461
Query: 674 GIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTN 733
I + N Y+ACPS+DCNKKV+DQ +G YRCEKCNK F F YR IL + I D T
Sbjct: 462 ATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETG 521
Query: 734 SVWVTLFQNEAESILGVTAQEVGESTEDHPA-----LKKALFTQYIFRLRAKLEHYN 785
+WVT F ++AE ILG +A E+GE E+ P ++A F YIFRLR K + YN
Sbjct: 522 QLWVTAFNDQAEQILGKSAAELGELKEEDPDEFEAIFQEAQFVPYIFRLRVKQDTYN 578
Score = 333 bits (855), Expect = e-104
Identities = 142/327 (43%), Positives = 196/327 (59%), Gaps = 9/327 (2%)
Query: 5 PANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLG 64
PANK+F+++ NDYEM+ T + C ++ +P +++ FV + I + +DV+G
Sbjct: 260 PANKQFTNLGNDYEMTLDRDTVIEECEDET--AIPKIQFNFVKIDDIGGYEGNSLVDVIG 317
Query: 65 VCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAA 124
+ + ++T + N K + KRDITLVD S SV +TLWG +A FD S +PVIA+K
Sbjct: 318 IVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGV 377
Query: 125 RVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQ-TNTRFEPVSQRTGGMGGGAAG 183
RVS+F GGK+LS SS + +NPDIPE KL+GW+ + T +S G GG+
Sbjct: 378 RVSDF-GGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRVGGSNA 436
Query: 184 NLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRC 243
+ EIQ + LG DK DY SV+ I + N Y+ACPS+DCNKKV+DQ +G YRC
Sbjct: 437 ERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRC 496
Query: 244 EKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHPA---- 299
EKCNK F F YR IL + I D T +WVT F ++AE ILG +A E+GE E+ P
Sbjct: 497 EKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEEDPDEFEA 556
Query: 300 -LKKALFTQYIFRLRAKLEHYNGTKKI 325
++A F YIFRLR K + YN +
Sbjct: 557 IFQEAQFVPYIFRLRVKQDTYNDESRQ 583
>gnl|CDD|239920 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 functionally. Antibodies to hRPA
do not cross-react with ScRPA, and null mutations in the
ScRPA subunits are not complemented by corresponding
human genes. Also, ScRPA cannot support Simian virus 40
(SV40) DNA replication in vitro, whereas human RPA can.
Length = 104
Score = 167 bits (425), Expect = 6e-49
Identities = 67/104 (64%), Positives = 84/104 (80%), Gaps = 1/104 (0%)
Query: 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDE-SGEIRATMFNDECNR 502
PI SL+PYQNKWTIKARVTNK+ IR W+NARG GKLFS DLLDE GEIRAT FND ++
Sbjct: 1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDK 60
Query: 503 FHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIP 546
F+D++E KVYYIS ++K ANKKF+++ NDYE++F T++I
Sbjct: 61 FYDLLEVGKVYYISKGSVKVANKKFNTLKNDYEITFNRDTSIIE 104
Score = 37.6 bits (88), Expect = 0.003
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 5 PANKKFSSINNDYEMSFTHSTTVIP 29
ANKKF+++ NDYE++F T++I
Sbjct: 80 VANKKFNTLKNDYEITFNRDTSIIE 104
>gnl|CDD|239922 cd04476, RPA1_DBD_C, RPA1_DBD_C: A subfamily of OB folds
corresponding to the C-terminal OB fold, the
ssDNA-binding domain (DBD)-C, 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-C,
RPA1 contains three other OB folds: DBD-A, DBD-B, and
RPA1N. The major DNA binding activity of RPA is
associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is
involved in DNA binding and trimerization. It contains
two structural insertions not found to date in other
OB-folds: a zinc ribbon and a three-helix bundle. RPA1
DBD-C also contains a Cys4-type zinc-binding motif,
which plays a role in the ssDNA binding function of this
domain. It appears that zinc itself may not be required
for ssDNA binding.
Length = 166
Score = 163 bits (415), Expect = 1e-46
Identities = 57/141 (40%), Positives = 81/141 (57%), Gaps = 7/141 (4%)
Query: 190 EIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKE 249
EI+++ LG G+K DY +V+ I + N Y ACP CNKKV+++ NG YRCEKCNK
Sbjct: 3 EIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP--GCNKKVVEEGNGTYRCEKCNKS 60
Query: 250 FNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP-----ALKKAL 304
YR IL + + D T W+TLF AE I G +A+E+ E E+ P A++ +
Sbjct: 61 VPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDLV 120
Query: 305 FTQYIFRLRAKLEHYNGTKKI 325
++FR+ K E YN +I
Sbjct: 121 GKTFLFRVSVKEETYNDEGRI 141
Score = 161 bits (409), Expect = 7e-46
Identities = 56/136 (41%), Positives = 79/136 (58%), Gaps = 7/136 (5%)
Query: 655 EIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKE 714
EI+++ LG G+K DY +V+ I + N Y ACP CNKKV+++ NG YRCEKCNK
Sbjct: 3 EIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP--GCNKKVVEEGNGTYRCEKCNKS 60
Query: 715 FNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP-----ALKKAL 769
YR IL + + D T W+TLF AE I G +A+E+ E E+ P A++ +
Sbjct: 61 VPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDLV 120
Query: 770 FTQYIFRLRAKLEHYN 785
++FR+ K E YN
Sbjct: 121 GKTFLFRVSVKEETYN 136
>gnl|CDD|149635 pfam08646, Rep_fac-A_C, Replication factor-A C terminal domain.
This domain is found at the C terminal of replication
factor A. Replication factor A (RPA) binds
single-stranded DNA and is involved in replication,
repair, and recombination of DNA.
Length = 146
Score = 158 bits (402), Expect = 3e-45
Identities = 60/127 (47%), Positives = 79/127 (62%), Gaps = 5/127 (3%)
Query: 204 YCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMI 263
Y SV+ I + N Y ACPS+DCNKKV +Q +G +RCEKC+KEF YR IL + I
Sbjct: 1 YFSVKATIVFIKQDNFWYPACPSEDCNKKVTEQGDGTWRCEKCDKEFPEPKYRYILSINI 60
Query: 264 GDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHPA-----LKKALFTQYIFRLRAKLEH 318
D T +WVTLF AE ILG++A+E+ E E+ +KALF +Y+FRLR K E
Sbjct: 61 SDHTGQIWVTLFNEAAEEILGMSAEELMELKEEDDNEFEKIFQKALFREYVFRLRVKEET 120
Query: 319 YNGTKKI 325
YN ++
Sbjct: 121 YNDESRV 127
Score = 155 bits (395), Expect = 3e-44
Identities = 60/122 (49%), Positives = 77/122 (63%), Gaps = 5/122 (4%)
Query: 669 YCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMI 728
Y SV+ I + N Y ACPS+DCNKKV +Q +G +RCEKC+KEF YR IL + I
Sbjct: 1 YFSVKATIVFIKQDNFWYPACPSEDCNKKVTEQGDGTWRCEKCDKEFPEPKYRYILSINI 60
Query: 729 GDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHPA-----LKKALFTQYIFRLRAKLEH 783
D T +WVTLF AE ILG++A+E+ E E+ +KALF +Y+FRLR K E
Sbjct: 61 SDHTGQIWVTLFNEAAEEILGMSAEELMELKEEDDNEFEKIFQKALFREYVFRLRVKEET 120
Query: 784 YN 785
YN
Sbjct: 121 YN 122
>gnl|CDD|239921 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 functionally. Antibodies to hRPA
do not cross-react with ScRPA, and null mutations in the
ScRPA subunits are not complemented by corresponding
human genes. Also, ScRPA cannot support Simian virus 40
(SV40) DNA replication in vitro, whereas human RPA can.
Length = 101
Score = 130 bits (328), Expect = 1e-35
Identities = 51/101 (50%), Positives = 71/101 (70%), Gaps = 1/101 (0%)
Query: 59 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPV 118
+DV+GV ++++T K+ + KR+ITLVD+S SV +TLWG++AE FD S PV
Sbjct: 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSENPV 60
Query: 119 IAVKAARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWF 159
IA+K +VSEF GK+LS SS + +NPDIPE HKL+GW+
Sbjct: 61 IAIKGVKVSEFN-GKSLSTGSSSTIIINPDIPEAHKLRGWY 100
Score = 95.3 bits (238), Expect = 1e-23
Identities = 35/73 (47%), Positives = 50/73 (68%)
Query: 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPV 635
+DV+GV ++++T K+ + KR+ITLVD+S SV +TLWG++AE FD S PV
Sbjct: 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSENPV 60
Query: 636 IAVKAARVSEFQG 648
IA+K +VSEF G
Sbjct: 61 IAIKGVKVSEFNG 73
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed.
Length = 637
Score = 87.8 bits (218), Expect = 6e-18
Identities = 64/323 (19%), Positives = 132/323 (40%), Gaps = 32/323 (9%)
Query: 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYI 515
+K R+ + RE + ++ I+L D +G +R + + ++ ++ E D I
Sbjct: 295 DVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILENLKEGD-AVKI 353
Query: 516 SNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDE 575
NC ++ +++ +S+ +I +DE + ++ +K I + D+
Sbjct: 354 ENCKVRTYYDNEG--EKRVDLNAGYSSEII---KDESISFEEIEEKIYKIKDILNLEEDD 408
Query: 576 -NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKP 634
+I V+ ++ ++ +++ R+I L D + S+ +TLW +AE +
Sbjct: 409 NDITVIARVVEDYPVNEFE-RSDGSKGKVRNIELADGT-GSIRLTLWDDDAEI-EIKEGD 465
Query: 635 VIAVKAARVSEFQGNLLLMR------EIQDQQLGMGDKADYCS---------VRGIIQVF 679
I + V E L L EI + + + + +RG +
Sbjct: 466 AIKILHPYVKENGDYLDLSIGRYGRIEINPEGEIIKSNRKFIADLEEDDTVEIRGTVVDI 525
Query: 680 RGSNTTYKACPSQDCNKKVIDQNNGMYRCEKC-NKEFNTFTYRLILPVMIGDWTNSVWVT 738
R CP+ C K+V ++ +G Y CE C E N L+L + D T ++
Sbjct: 526 RKQKIILYLCPN--CRKRV-EEVDGEYICEFCGEVEPN---ELLMLNFTLDDGTGTINCR 579
Query: 739 LFQNEAESILGVTAQEVGESTED 761
+ E +LG++ +E+ E +
Sbjct: 580 FYGKNVEKLLGMSKEELKELNLE 602
Score = 58.5 bits (142), Expect = 1e-08
Identities = 52/281 (18%), Positives = 111/281 (39%), Gaps = 51/281 (18%)
Query: 18 EMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDE-NIDVLGVCIDAAELSSVT 76
+++ +S+ +I +DE + ++ +K I + D+ +I V+ ++ ++
Sbjct: 371 DLNAGYSSEII---KDESISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFE 427
Query: 77 GKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLS 136
+++ R+I L D + S+ +TLW +AE + I + V E LS
Sbjct: 428 -RSDGSKGKVRNIELADGT-GSIRLTLWDDDAEI-EIKEGDAIKILHPYVKENGDYLDLS 484
Query: 137 LSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMREIQDQQL 196
+ + +NP+ ++N +F + ++++
Sbjct: 485 IGRYGRIEINPE---------GEIIKSNRKF--------------------IADLEEDDT 515
Query: 197 GMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKC-NKEFNTFTY 255
+RG + R CP+ C K+V ++ +G Y CE C E N
Sbjct: 516 VE--------IRGTVVDIRKQKIILYLCPN--CRKRV-EEVDGEYICEFCGEVEPN---E 561
Query: 256 RLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTED 296
L+L + D T ++ + E +LG++ +E+ E +
Sbjct: 562 LLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNLE 602
Score = 48.9 bits (117), Expect = 8e-06
Identities = 40/185 (21%), Positives = 73/185 (39%), Gaps = 15/185 (8%)
Query: 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDECNR 502
I + Q I R+ + I+ + GS GKL +I + D +G IR T++ND
Sbjct: 65 KISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWNDNAKL 124
Query: 503 FHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCF 562
+++ V I N + NND E++ T + + + P +K +
Sbjct: 125 LKG-LKEGDVIKIENARSR-------KWNNDVELNSGSETRIDKLEKYDESRYPIIKENY 176
Query: 563 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG 622
I E+ P+ + + G A + T + + + L D + S+ +TLW
Sbjct: 177 ----DIPELEPNLSATIEGEVTKAYPIKEFT-RKDGSEGKLKSFILKDDT-GSIRVTLWN 230
Query: 623 KEAET 627
+
Sbjct: 231 DLTDI 235
>gnl|CDD|224515 COG1599, RFA1, Single-stranded DNA-binding replication protein A
(RPA), large (70 kD) subunit and related ssDNA-binding
proteins [DNA replication, recombination, and repair].
Length = 407
Score = 69.4 bits (170), Expect = 2e-12
Identities = 44/194 (22%), Positives = 69/194 (35%), Gaps = 24/194 (12%)
Query: 458 KARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517
KARV + I+ ++N G K+FS +L DE E +F D D + VY I
Sbjct: 173 KARVVVGSEIKTFDNQGGESKVFSNELEDE--ERGVIVFTDW-----DPSQDGDVYRIEG 225
Query: 518 CTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENI 577
+K NK+ N E+ V + FV +
Sbjct: 226 ARVKTKNKQP-EENLAEELVLRVEVRV-------AIEKAEREE-FVD----EVKESVSLV 272
Query: 578 DVLGVCIDAAELSSVT--GKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPV 635
+ G +D + + +DI L D + +TLWG +A + + V
Sbjct: 273 EADGAVVDVTRVPECERVVRKGGCKGHGKDIGLDD-LTGKIRVTLWG-DATEVLINEESV 330
Query: 636 IAVKAARVSEFQGN 649
A+K V + G
Sbjct: 331 EALKGINVEDASGI 344
>gnl|CDD|239923 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.
Length = 97
Score = 61.8 bits (151), Expect = 8e-12
Identities = 22/62 (35%), Positives = 38/62 (61%), Gaps = 6/62 (9%)
Query: 325 IPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGVSSGSATNRSVLIILELNI 384
+ DGV AMLATQLN ++ G L +I+++KR+I + + + +LIIL+L +
Sbjct: 42 LSDGVYYV-QAMLATQLNPLVESGQLQRGSIIRLKRFICNVIK-----GKRILIILDLEV 95
Query: 385 IK 386
++
Sbjct: 96 VQ 97
>gnl|CDD|239926 cd04480, RPA1_DBD_A_like, RPA1_DBD_A_like: A subgroup of
uncharacterized plant OB folds with similarity 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 RPA 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.
Length = 86
Score = 58.0 bits (141), Expect = 1e-10
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 456 TIKARVTNKTPIREWNNARGSGKLFSID--LLDESGE-IRATMFNDECNRFHDMIEKDKV 512
I RV +R W+ + S++ L+DE G I AT+ +F ++++ K
Sbjct: 1 KICVRV-----LRLWD-VYNNASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKW 54
Query: 513 YYISNCTLKPANKKFSSINNDYEMSFTHSTTV 544
Y ISN + P + ++ Y++ F T V
Sbjct: 55 YTISNFEVAPNTGSYRPTDHPYKIKFMSDTVV 86
>gnl|CDD|202872 pfam04057, Rep-A_N, Replication factor-A protein 1, N-terminal
domain.
Length = 99
Score = 57.7 bits (140), Expect = 2e-10
Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 5/63 (7%)
Query: 325 IPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGVSSGSATNRSVLIILELNI 384
+ DG N +S AMLATQLN ++ G L +IVQ+ RY V+ + G R VLIILEL +
Sbjct: 42 LSDGKNKSS-AMLATQLNPLVISGKLQNGSIVQLTRYTVNDIKDG----RRVLIILELEV 96
Query: 385 IKP 387
+K
Sbjct: 97 LKS 99
>gnl|CDD|239927 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.
Length = 106
Score = 54.6 bits (132), Expect = 4e-09
Identities = 36/99 (36%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 61 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDAS------ 114
DV+GV +D L + K D + D S + TLWG+ AE FDA
Sbjct: 1 DVIGVIVDVGPLEELPPVNKPS--RKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGN 58
Query: 115 NKPVIAV-KAARVSEFQGGKTLSLSMS-SVLSLNPDIPE 151
+PV+AV + ++ E++G K+LS S S + +NPDIPE
Sbjct: 59 GEPVVAVLRFWKIKEYKGPKSLSNSFGASKVYINPDIPE 97
Score = 47.3 bits (113), Expect = 1e-06
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 578 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDAS------ 631
DV+GV +D L + K D + D S + TLWG+ AE FDA
Sbjct: 1 DVIGVIVDVGPLEELPPVNKPS--RKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGN 58
Query: 632 NKPVIAV-KAARVSEFQGNLLLMREI 656
+PV+AV + ++ E++G L
Sbjct: 59 GEPVVAVLRFWKIKEYKGPKSLSNSF 84
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding domain
of lysyl, aspartyl, and asparaginyl -tRNA synthetases
(See pfam00152). Aminoacyl-tRNA synthetases catalyze the
addition of an amino acid to the appropriate tRNA
molecule EC:6.1.1.-. This family also includes part of
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.
Length = 75
Score = 50.7 bits (122), Expect = 3e-08
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYY 514
T+ RVT+ R GK+ + L D +G I+ +F +E + +++ V
Sbjct: 1 VTVAGRVTSVR--------RSGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKKLKEGDVVL 52
Query: 515 IS 516
++
Sbjct: 53 VT 54
>gnl|CDD|239937 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 the DNA helicase activity
of MCM.
Length = 82
Score = 41.8 bits (99), Expect = 6e-05
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYI 515
+++ +V + + RE+ GK+ S + DE+G IR T+++++ D +E V I
Sbjct: 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEKAA---DDLEPGDVVRI 57
Query: 516 SNCTLK 521
N ++
Sbjct: 58 ENAYVR 63
Score = 31.8 bits (73), Expect = 0.20
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 87 RDITLVDQSQASVTMTLWGKEA-ETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSL 145
+ + D++ ++ TLW ++A + + + V+ ++ A V EF G LS+ +S +
Sbjct: 25 QSGLVGDET-GTIRFTLWDEKAADDLEPGD--VVRIENAYVREFNGRLELSVGKNSEIEK 81
Query: 146 N 146
Sbjct: 82 L 82
>gnl|CDD|145722 pfam02721, DUF223, Domain of unknown function DUF223.
Length = 95
Score = 38.8 bits (91), Expect = 8e-04
Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 484 LLDESG-EIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHST 542
L DE+G +I AT+ + D I + + I+ ++P + + +++Y + F T
Sbjct: 4 LADENGDKIEATIRRRLAAFYADRISEGEWKTITTFVVRPNSGSYRITSHEYGILFMDQT 63
Query: 543 TVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENI 577
V + E + P I E + D+N+
Sbjct: 64 VVTKSDTRE----TVLFNNLTPFDYIIEDTVDKNV 94
>gnl|CDD|169427 PRK08402, PRK08402, replication factor A; Reviewed.
Length = 355
Score = 42.1 bits (99), Expect = 0.001
Identities = 68/263 (25%), Positives = 105/263 (39%), Gaps = 58/263 (22%)
Query: 46 VPLKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRD---------ITLVDQS 95
PL I+++ P ++++G V K + Y K+D I D
Sbjct: 60 APLMHISDLVPGMRGVNIVG---------RVLRKYPPREYTKKDGSTGRVASLIIYDDTG 110
Query: 96 QASVTMTLW-GKEAETFDASN-KPVIAVKAARVSE-FQGGKTLSLSMSSVLSLNPDIPEC 152
+A V LW K A+ ++ N VI V A+V E G L ++ + + LNPD P
Sbjct: 111 RARVV--LWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPDDPRV 168
Query: 153 HKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDKADYCSVRGII- 211
++ E V + +L G++ + VRG I
Sbjct: 169 EEI---------PPLEEVRSYN-------------YTRKKIGELEGGER--FVEVRGTIA 204
Query: 212 QVFRGSNTTYKACPSQDCNKKV-IDQNNGMYRC-EKCNKEFNTFTYRLILPVMIGDWTNS 269
+V+R Y ACP +C +KV D + C E E T IL + D T
Sbjct: 205 KVYR--VLVYDACP--ECRRKVDYDPATDTWICPEHGEVEPIKIT---ILDFGLDDGTGY 257
Query: 270 VWVTLFQNEAESILGVTAQEVGE 292
+ VTLF ++A +LGV +E+ E
Sbjct: 258 IRVTLFGDDAAELLGVEPEEIAE 280
Score = 41.3 bits (97), Expect = 0.001
Identities = 34/107 (31%), Positives = 51/107 (47%), Gaps = 12/107 (11%)
Query: 654 REIQDQQLGMGDKADYCSVRGII-QVFRGSNTTYKACPSQDCNKKV-IDQNNGMYRC-EK 710
+ +L G++ + VRG I +V+R Y ACP +C +KV D + C E
Sbjct: 183 TRKKIGELEGGER--FVEVRGTIAKVYR--VLVYDACP--ECRRKVDYDPATDTWICPEH 236
Query: 711 CNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGE 757
E T IL + D T + VTLF ++A +LGV +E+ E
Sbjct: 237 GEVEPIKIT---ILDFGLDDGTGYIRVTLFGDDAAELLGVEPEEIAE 280
Score = 34.8 bits (80), Expect = 0.15
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 445 IVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDECNRF 503
I L P I RV K P RE+ GS G++ S+ + D++G R +++ + ++
Sbjct: 65 ISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAKY 124
Query: 504 HDMIEKDKVYYISNCTLK 521
++ I V + + ++
Sbjct: 125 YNKINVGDVIKVIDAQVR 142
>gnl|CDD|216524 pfam01485, IBR, IBR domain. The IBR (In Between Ring fingers)
domain is often found to occur between pairs of ring
fingers (pfam00097). This domain has also been called
the C6HC domain and DRIL (for double RING finger linked)
domain. Proteins that contain two Ring fingers and an
IBR domain (these proteins are also termed RBR family
proteins) are thought to exist in all eukaryotic
organisms. RBR family members play roles in protein
quality control and can indirectly regulate
transcription. Evidence suggests that RBR proteins are
often parts of cullin-containing ubiquitin ligase
complexes. The ubiquitin ligase Parkin is an RBR family
protein whose mutations are involved in forms of
familial Parkinson's disease.
Length = 63
Score = 36.4 bits (84), Expect = 0.003
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 210 IIQVFRGSNTTYKACPSQDCNKKVI--DQNNGMYRCEKCNKEF 250
++ + S K CP+ DC + D + C KC EF
Sbjct: 7 SLKKYVESPKNLKWCPTPDCGNIIEKTDGGSQNVTCSKCGTEF 49
Score = 36.4 bits (84), Expect = 0.003
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 675 IIQVFRGSNTTYKACPSQDCNKKVI--DQNNGMYRCEKCNKEF 715
++ + S K CP+ DC + D + C KC EF
Sbjct: 7 SLKKYVESPKNLKWCPTPDCGNIIEKTDGGSQNVTCSKCGTEF 49
>gnl|CDD|173162 PRK14699, PRK14699, replication factor A; Provisional.
Length = 484
Score = 38.4 bits (89), Expect = 0.015
Identities = 45/183 (24%), Positives = 85/183 (46%), Gaps = 17/183 (9%)
Query: 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDECNR 502
PI + N I RV + + +R + GS G++ ++ L D +G+IR T++ DE
Sbjct: 278 PIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGKIRLTLW-DEKTN 336
Query: 503 FHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCF 562
F D I+ D+ + N A + ++ + E++ + +I +E +V
Sbjct: 337 FLDEIDFDETVEVLN-----AYSRENTFSQQVELNLG-ARGIIQKSEKKVEYREK----- 385
Query: 563 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG 622
IA+I P E+ V G + EL + + + ++ L D++ S+ +TLWG
Sbjct: 386 --FTDIADIIPGESYSVQGKVSEIGELREFEREDGTENVVA-NLQLKDET-GSIRLTLWG 441
Query: 623 KEA 625
++A
Sbjct: 442 EQA 444
Score = 31.1 bits (70), Expect = 2.2
Identities = 45/193 (23%), Positives = 80/193 (41%), Gaps = 54/193 (27%)
Query: 457 IKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYI 515
+ +V + IR + G SGK+ ++ L DE+G +R T+++D+ + + + D V I
Sbjct: 181 LTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTDFLNQIEYGDTVELI 240
Query: 516 SNCTLKPANKKFSSINNDY--EMSFTHSTTVIPCNEDEVGNMPSVKYC---------FVP 564
N Y E +FT E +VGN ++ F P
Sbjct: 241 ----------------NAYARENAFTQKV------ELQVGNRSIIRKSEKKVEYEEEFTP 278
Query: 565 LKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDIT-------LVDQSQASV 616
I +I D NI++ G +D +E+ +T+ K+D + L+ S +
Sbjct: 279 ---IEDIKADMNNINISGRVLDISEV---------RTFEKKDGSPGRVGNLLLGDSTGKI 326
Query: 617 TMTLWGKEAETFD 629
+TLW ++ D
Sbjct: 327 RLTLWDEKTNFLD 339
>gnl|CDD|180574 PRK06461, PRK06461, single-stranded DNA-binding protein; Reviewed.
Length = 129
Score = 35.4 bits (82), Expect = 0.031
Identities = 25/114 (21%), Positives = 51/114 (44%), Gaps = 14/114 (12%)
Query: 47 PLKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG 105
+ I ++ P E ++V ++ E + K +T + + D++ V +TLWG
Sbjct: 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTI--SEAVVGDET-GRVKLTLWG 59
Query: 106 KEAETFDASNKPVIAVKAARVSEFQG------GKTLSLSMSSVLSLNP--DIPE 151
++A + V+ ++ A + ++G GK S+S S + +IPE
Sbjct: 60 EQAGSL--KEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDDEEVPEAEEIPE 111
Score = 33.5 bits (77), Expect = 0.12
Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 564 PLKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG 622
+ I ++ P E ++V ++ E + K +T + + D++ V +TLWG
Sbjct: 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTI--SEAVVGDET-GRVKLTLWG 59
Query: 623 KEAETFDASNKPVIAVKAARVSEFQGNLLL 652
++A + V+ ++ A + ++G + L
Sbjct: 60 EQAGSL--KEGEVVEIENAWTTLYRGKVQL 87
Score = 30.4 bits (69), Expect = 1.5
Identities = 13/73 (17%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 445 IVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFH 504
I L P + + RV + G + + DE+G ++ T++ ++
Sbjct: 7 IKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQA---- 62
Query: 505 DMIEKDKVYYISN 517
+++ +V I N
Sbjct: 63 GSLKEGEVVEIEN 75
>gnl|CDD|239931 cd04485, DnaE_OBF, DnaE_OBF: A subfamily of OB folds corresponding
to the C-terminal OB-fold nucleic acid binding domain of
Thermus aquaticus and Escherichia coli type C
replicative DNA polymerase III alpha subunit (DnaE). The
DNA polymerase holoenzyme of E. coli contains two copies
of this replicative polymerase, each of which copies a
different DNA strand. This group also contains Bacillus
subtilis DnaE. Replication in B. subtilis and
Staphylococcus aureus requires two different type C
polymerases, polC and DnaE, both of which are thought to
be included in the DNA polymerase holoenzyme. At the B.
subtilis replication fork, polC appears to be involved
in leading strand synthesis and DnaE in lagging strand
synthesis.
Length = 84
Score = 33.3 bits (77), Expect = 0.057
Identities = 7/34 (20%), Positives = 19/34 (55%)
Query: 482 IDLLDESGEIRATMFNDECNRFHDMIEKDKVYYI 515
+ L D +G I +F + ++ D++++D + +
Sbjct: 23 VTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLV 56
>gnl|CDD|223660 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
recombination, and repair].
Length = 1139
Score = 36.1 bits (84), Expect = 0.081
Identities = 11/73 (15%), Positives = 29/73 (39%), Gaps = 3/73 (4%)
Query: 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRF 503
++ L + + + A+G+ F + L DE+G + +F E R+
Sbjct: 968 RLLDLVEDGRRVVLAGGIVAVRQRP--TKAKGNKMAF-LTLEDETGILEVVVFPSEYERY 1024
Query: 504 HDMIEKDKVYYIS 516
++ + ++ +
Sbjct: 1025 RRLLLEGRLLIVK 1037
>gnl|CDD|239601 cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of
oligonucleotide binding (OB) folds with similarity to
the OB fold of the single strand (ss) DNA-binding domain
(DBD)-D of human RPA2 (also called RPA32). RPA2 is a
subunit of Replication protein A (RPA). RPA is a nuclear
ssDNA-binding protein (SSB) which appears to be involved
in all aspects of DNA metabolism including replication,
recombination, and repair. RPA also mediates specific
interactions of various nuclear proteins. In animals,
plants, and fungi, RPA is a heterotrimer with subunits
of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA
contains six OB folds, which are involved in ssDNA
binding and in trimerization. The ssDNA binding
mechanism is believed to be multistep and to involve
conformational change. This family also includes OB
folds similar to those found in Escherichia coli SSB,
the wedge domain of E. coli RecG (a
branched-DNA-specific helicase), E. coli ssDNA specific
exodeoxyribonuclease VII large subunit, Pyrococcus
abyssi DNA polymerase II (Pol II) small subunit,
Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM
(a 3'-to-5'exoribonuclease). It also includes the OB
folds of breast cancer susceptibility gene 2 protein
(BRCA2), Oxytricha nova telomere end binding protein
(TEBP), Saccharomyces cerevisiae telomere-binding
protein (Cdc13), and human protection of telomeres 1
protein (POT1).
Length = 75
Score = 31.2 bits (71), Expect = 0.25
Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGE-IRATMFNDECNRFHDMIEKDKVYY 514
TI V IR GK+ L D +G IR T+F + +++++ +V Y
Sbjct: 1 TIVGIVVAVEEIRTE------GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVY 54
Query: 515 ISNCTLKPANKKFSSINNDYEM 536
I +K + I E+
Sbjct: 55 IK-GKVKKFRGRLQLIVESIEL 75
Score = 28.9 bits (65), Expect = 1.9
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 75 VTGKTNQKTYMKR-DITLVDQSQASVTMTLWGKEAETFDASNKP--VIAVKAARVSEFQG 131
V +T K TL D + ++ +TL+G+ AE + K V+ +K +V +F+G
Sbjct: 6 VVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRG 64
Query: 132 GKTLSLS 138
L +
Sbjct: 65 RLQLIVE 71
Score = 27.3 bits (61), Expect = 6.6
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 592 VTGKTNQKTYMKR-DITLVDQSQASVTMTLWGKEAETFDASNKP--VIAVKAARVSEFQG 648
V +T K TL D + ++ +TL+G+ AE + K V+ +K +V +F+G
Sbjct: 6 VVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRG 64
Query: 649 NL-LLMREIQ 657
L L++ I+
Sbjct: 65 RLQLIVESIE 74
>gnl|CDD|184884 PRK14890, PRK14890, putative Zn-ribbon RNA-binding protein;
Provisional.
Length = 59
Score = 30.7 bits (70), Expect = 0.28
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 198 MGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFT 254
+ C+ GI R + CP +C + +I YRCEKC K+ N +T
Sbjct: 3 EMMEPPKCTSCGIEIAPREKAVKF-LCP--NCGEVII------YRCEKCRKQSNPYT 50
Score = 30.7 bits (70), Expect = 0.28
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 663 MGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFT 719
+ C+ GI R + CP +C + +I YRCEKC K+ N +T
Sbjct: 3 EMMEPPKCTSCGIEIAPREKAVKF-LCP--NCGEVII------YRCEKCRKQSNPYT 50
>gnl|CDD|185388 PRK15491, PRK15491, replication factor A; Provisional.
Length = 374
Score = 34.1 bits (78), Expect = 0.29
Identities = 45/209 (21%), Positives = 92/209 (44%), Gaps = 37/209 (17%)
Query: 435 ASAPVVQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRA 493
+ V T I ++ + A+V + +E+N G+ G++ +I + DE+G IR
Sbjct: 50 VTDTGVDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRL 109
Query: 494 TMFNDECNRFHD-MIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEV 552
T+++D + IE K IS A + +S I E++ + +E+
Sbjct: 110 TLWDDLADLIKTGDIEVGKSLNISGY----AKEGYSGI----EVNIGRYGGISESDENVK 161
Query: 553 GNMPSVKYCFVPLKTIAEISP-DENIDVLGVCIDAAELSSVTGKTNQKTYMKRD------ 605
++ S K I++I D +I+++G +D +++ +T+ K+D
Sbjct: 162 ASINSQK--------ISDIKDGDSDINIVGKVLDISDV---------RTFQKKDGSQGRV 204
Query: 606 --ITLVDQSQASVTMTLWGKEAETFDASN 632
IT+ D++ + +TLW + + D
Sbjct: 205 RNITIGDET-GKIRVTLWDGKTDLADKLE 232
Score = 29.5 bits (66), Expect = 7.1
Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 9/103 (8%)
Query: 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDECNR 502
PI + P Q ++IK V+ ++E+ + GS K+ +I + D++G IR ++ ++
Sbjct: 278 PIADIIPGQ-PYSIKGAVSGLGDLKEFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAE- 335
Query: 503 FHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVI 545
D ++ D I + K N D E+S + + V+
Sbjct: 336 LVDKLDIDTPIKIIDAFSKSG------YNEDVELSAGNRSRVV 372
>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers. the domains occurs
between pairs og RING fingers.
Length = 64
Score = 30.5 bits (69), Expect = 0.35
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 217 SNTTYKACPSQDCNKKVIDQNNG---MYRCEKCNKEF 250
SN K CP+ DC+ +I C KC F
Sbjct: 14 SNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50
Score = 30.5 bits (69), Expect = 0.35
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 682 SNTTYKACPSQDCNKKVIDQNNG---MYRCEKCNKEF 715
SN K CP+ DC+ +I C KC F
Sbjct: 14 SNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50
>gnl|CDD|239934 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 chain substrates.
Length = 75
Score = 31.0 bits (71), Expect = 0.35
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 5/42 (11%)
Query: 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFN 497
T++ V + + R + + L D +G + FN
Sbjct: 1 TVEGTVVSVEVVP-----RRGRRRLKVTLSDGTGTLTLVFFN 37
>gnl|CDD|180890 PRK07218, PRK07218, replication factor A; Provisional.
Length = 423
Score = 33.8 bits (78), Expect = 0.38
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 9/101 (8%)
Query: 49 KTIAEISPDE-NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKE 107
K I E+S D+ N+ V G + E S + Y L D++ +++ T W
Sbjct: 59 KDIKELSTDDKNVTVTGRVLTIGERSIRYQGDDHVIYEGI---LADET-GTISYTAW--- 111
Query: 108 AETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSLNPD 148
+ F S + + A V E+ G L++ S+ +SL D
Sbjct: 112 -KDFGLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDD 151
>gnl|CDD|180887 PRK07211, PRK07211, replication factor A; Reviewed.
Length = 485
Score = 34.0 bits (78), Expect = 0.38
Identities = 32/147 (21%), Positives = 65/147 (44%), Gaps = 19/147 (12%)
Query: 442 THPIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDEC 500
T+ + LS + T+ V + +R ++ GS G++ ++ + DE+G +R T+++D
Sbjct: 161 TYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRA 220
Query: 501 NRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKY 560
+ + ++ + I + ++ + E+ V +ED V+Y
Sbjct: 221 DLA-EELDAGESVEIVDGYVRER-------DGSLELHVGDRGAVEEVDED-------VEY 265
Query: 561 CFVPLKT-IAEISPDENIDVLGVCIDA 586
VP T I + DE +D+ GV A
Sbjct: 266 --VPDTTPIESLEIDETVDIAGVVRSA 290
>gnl|CDD|148664 pfam07191, DUF1407, Protein of unknown function (DUF1407). This
family consists of several short, hypothetical bacterial
proteins of around 70 residues in length. Members of
this family have 8 highly conserved cysteine residues,
which form two zinc ribbon domains.
Length = 70
Score = 28.8 bits (65), Expect = 1.8
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 224 CPSQDCNKKVIDQNNGMYRCEKCNKEF 250
CP C ++ ++ G Y C++C K+F
Sbjct: 4 CP--QC-QQELEWKGGHYHCDQCQKDF 27
Score = 28.8 bits (65), Expect = 1.8
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 689 CPSQDCNKKVIDQNNGMYRCEKCNKEF 715
CP C ++ ++ G Y C++C K+F
Sbjct: 4 CP--QC-QQELEWKGGHYHCDQCQKDF 27
>gnl|CDD|191179 pfam05053, Menin, Menin. MEN1, the gene responsible for multiple
endocrine neoplasia type 1, is a tumour suppressor gene
that encodes a protein called Menin which may be an
atypical GTPase stimulated by nm23.
Length = 618
Score = 31.1 bits (70), Expect = 2.4
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 397 NPQPLNTNTDNSSTQQTPAATNTN---GSNGVHNNVAIPRQASAPVVQTHPIVSL 448
N N N +N + ++ AAT N SNG +V +P + P + P+++
Sbjct: 508 NSNS-NNNNNNGADRKEAAATTGNATTTSNGSGTSVPLPVSSEPPQHKEGPVITF 561
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 31.2 bits (71), Expect = 2.5
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 224 CPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLI 258
CP DC +V +G C +C+ E + R I
Sbjct: 695 CP--DCGAEVPPDESGRVECPRCDVELTPYQRRTI 727
Score = 31.2 bits (71), Expect = 2.5
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 689 CPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLI 723
CP DC +V +G C +C+ E + R I
Sbjct: 695 CP--DCGAEVPPDESGRVECPRCDVELTPYQRRTI 727
>gnl|CDD|116585 pfam07975, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterized by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C (pfam00130).
Length = 48
Score = 27.7 bits (62), Expect = 2.9
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 229 CNKKVIDQNNGM---YRCEKCNKEF 250
C +K+ D N YRC KC F
Sbjct: 5 CQQKLPDGINKTSSVYRCPKCKNVF 29
Score = 27.7 bits (62), Expect = 2.9
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 694 CNKKVIDQNNGM---YRCEKCNKEF 715
C +K+ D N YRC KC F
Sbjct: 5 CQQKLPDGINKTSSVYRCPKCKNVF 29
>gnl|CDD|216103 pfam00757, Furin-like, Furin-like cysteine rich region.
Length = 143
Score = 29.3 bits (66), Expect = 3.6
Identities = 11/43 (25%), Positives = 12/43 (27%), Gaps = 14/43 (32%)
Query: 220 TYKACPSQDCNKKVIDQ--------------NNGMYRCEKCNK 248
T K CP N VI N +CE C
Sbjct: 94 TAKECPKPGYNPLVIHNGECVRECPSGYTEVENNSRKCEPCEG 136
Score = 29.3 bits (66), Expect = 3.6
Identities = 11/43 (25%), Positives = 12/43 (27%), Gaps = 14/43 (32%)
Query: 685 TYKACPSQDCNKKVIDQ--------------NNGMYRCEKCNK 713
T K CP N VI N +CE C
Sbjct: 94 TAKECPKPGYNPLVIHNGECVRECPSGYTEVENNSRKCEPCEG 136
>gnl|CDD|166698 PLN03059, PLN03059, beta-galactosidase; Provisional.
Length = 840
Score = 30.7 bits (69), Expect = 3.7
Identities = 26/93 (27%), Positives = 46/93 (49%), Gaps = 10/93 (10%)
Query: 631 SNKPVIAVKAARVSEFQGNLLLMREIQDQ------QLGMGDKADYCSVRGIIQVFRGSNT 684
+ K V +K+ ++ E QG +++ +I+++ ++G KA Y + V G+
Sbjct: 158 TEKIVDMMKSEKLFEPQGGPIILSQIENEYGPVEWEIGAPGKA-YTKWAADMAVKLGTGV 216
Query: 685 TYKACPSQDCNKKVIDQNNGMYRCE--KCNKEF 715
+ C +D VID NG Y CE K NK++
Sbjct: 217 PWVMCKQEDAPDPVIDTCNGFY-CENFKPNKDY 248
>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional.
Length = 331
Score = 30.4 bits (69), Expect = 3.7
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 396 GNPQPLNTNTDNSSTQQTPAATNTNGSNGVHNNVAIPRQASAPVVQTHPIVSLSPYQN 453
G PL+T+T + TPA + ++ A AP V ++P Q
Sbjct: 159 GQSVPLDTST-TTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQA 215
>gnl|CDD|117742 pfam09188, DUF1951, Domain of unknown function (DUF1951).
Members of this family of Mycoplasma hypothetical
proteins adopt a helical structure, with a buried
central helix. Their function has not, as yet, been
determined.
Length = 137
Score = 29.2 bits (65), Expect = 4.5
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 30 CNEDEVGNMPSVKYCFVPLKTIAEISPDEN--IDVLGVCIDAAELSSVTGKTNQ 81
C+ E +V P+K I EI+ DE I++L + I+ + S G + Q
Sbjct: 29 CSTRESDTFSNVDVPLAPIKNIIEIAKDEENQIEILKIAIENIKTLSSVGASGQ 82
Score = 29.2 bits (65), Expect = 4.5
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 547 CNEDEVGNMPSVKYCFVPLKTIAEISPDEN--IDVLGVCIDAAELSSVTGKTNQ 598
C+ E +V P+K I EI+ DE I++L + I+ + S G + Q
Sbjct: 29 CSTRESDTFSNVDVPLAPIKNIIEIAKDEENQIEILKIAIENIKTLSSVGASGQ 82
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 30.5 bits (70), Expect = 4.5
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 472 NARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYIS 516
RG+ K+ + L D SG I +F++ ++ D++E+D++ +
Sbjct: 994 TKRGN-KMAIVTLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVK 1037
>gnl|CDD|182315 PRK10220, PRK10220, hypothetical protein; Provisional.
Length = 111
Score = 28.8 bits (64), Expect = 4.5
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 224 CPSQDCNKKVIDQNNGMYRCEKCNKEFN 251
CP CN + ++NGMY C +C E+N
Sbjct: 6 CPK--CNSEYTYEDNGMYICPECAHEWN 31
Score = 28.8 bits (64), Expect = 4.5
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 689 CPSQDCNKKVIDQNNGMYRCEKCNKEFN 716
CP CN + ++NGMY C +C E+N
Sbjct: 6 CPK--CNSEYTYEDNGMYICPECAHEWN 31
>gnl|CDD|215390 PLN02733, PLN02733, phosphatidylcholine-sterol O-acyltransferase.
Length = 440
Score = 30.0 bits (68), Expect = 5.4
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 479 LFSIDLLDESGEIRATMFNDECNRFHDMIEK 509
L++ID+LD IR DE FHDMIE+
Sbjct: 90 LYAIDILDPDVIIRL----DEVYYFHDMIEQ 116
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 29.7 bits (68), Expect = 6.7
Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 8/95 (8%)
Query: 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDEC 500
+ PI L P K T++ V + + G + ++ + D +G + FN
Sbjct: 49 RLKPIAELRP-GEKVTVEGEVLSAEVVF------GKRRRLTVTVSDGTGNLTLRFFNFNQ 101
Query: 501 NRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYE 535
++ K + +K ++ +YE
Sbjct: 102 PYLKKQLKVGKRVAVYG-KVKRGKYGLEMVHPEYE 135
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.131 0.383
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,175,436
Number of extensions: 3610360
Number of successful extensions: 2942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2907
Number of HSP's successfully gapped: 74
Length of query: 786
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 681
Effective length of database: 6,280,432
Effective search space: 4276974192
Effective search space used: 4276974192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.1 bits)