RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15132
(786 letters)
>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding
replication protein A(RPA), single stranded DNA-binding
protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo
sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A
Length = 246
Score = 198 bits (503), Expect = 2e-58
Identities = 103/209 (49%), Positives = 152/209 (72%), Gaps = 2/209 (0%)
Query: 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNR 502
PI SL+PYQ+KWTI ARVTNK+ IR W+N+RG GKLFS++L+DESGEIRAT FN++ ++
Sbjct: 9 VPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVDK 68
Query: 503 FHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCF 562
F +IE +KVYY S TLK ANK+F+++ NDYEM+F + T+V+PC +D ++P+V++ F
Sbjct: 69 FFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDDH--HLPTVQFDF 126
Query: 563 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG 622
+ + S D +D++G+C + + +T ++N + KR+I L+D S VT TLWG
Sbjct: 127 TGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWG 186
Query: 623 KEAETFDASNKPVIAVKAARVSEFQGNLL 651
++A+ FD S +PV+A+K ARVS+F G L
Sbjct: 187 EDADKFDGSRQPVLAIKGARVSDFGGRSL 215
Score = 129 bits (326), Expect = 5e-34
Identities = 67/158 (42%), Positives = 109/158 (68%), Gaps = 3/158 (1%)
Query: 5 PANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLG 64
ANK+F+++ NDYEM+F + T+V+PC +D ++P+V++ F + + S D +D++G
Sbjct: 88 IANKQFTAVKNDYEMTFNNETSVMPCEDDH--HLPTVQFDFTGIDDLENKSKDSLVDIIG 145
Query: 65 VCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAA 124
+C + + +T ++N + KR+I L+D S VT TLWG++A+ FD S +PV+A+K A
Sbjct: 146 ICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA 205
Query: 125 RVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQ 162
RVS+F GG++LS+ SS + NPDIPE +KL+GWF +
Sbjct: 206 RVSDF-GGRSLSVLSSSTIIANPDIPEAYKLRGWFDAE 242
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding
protein; NMR {Saccharomyces cerevisiae}
Length = 114
Score = 155 bits (393), Expect = 8e-45
Identities = 50/108 (46%), Positives = 75/108 (69%)
Query: 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNR 502
I LSPYQN WTIKARV+ K I+ W+N RG GKLF+++ LD SGEIRAT FND +
Sbjct: 5 FAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDTSGEIRATAFNDFATK 64
Query: 503 FHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNED 550
F++++++ KVYY+S L+PA +F+++ + YE++ T + C ++
Sbjct: 65 FNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDE 112
Score = 43.0 bits (101), Expect = 3e-05
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 5 PANKKFSSINNDYEMSFTHSTTVIPCNED 33
PA +F+++ + YE++ T + C ++
Sbjct: 84 PAKPQFTNLTHPYELNLDRDTVIEECFDE 112
>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB,
ssDNA binding protein, OB-fold; 2.80A {Homo sapiens}
SCOP: b.40.4.3
Length = 181
Score = 149 bits (377), Expect = 9e-42
Identities = 70/152 (46%), Positives = 92/152 (60%), Gaps = 5/152 (3%)
Query: 179 GGAAGNLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNN 238
GG+ N + E++ + LG GDK DY S + R N Y+ACP+QDCNKKVIDQ N
Sbjct: 1 GGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPTQDCNKKVIDQQN 60
Query: 239 GMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP 298
G+YRCEKC+ EF F YR+IL V I D+ + WVT FQ AE+ILG A +GE + +
Sbjct: 61 GLYRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDKNE 120
Query: 299 -----ALKKALFTQYIFRLRAKLEHYNGTKKI 325
+ A F +IFR+R K+E YN +I
Sbjct: 121 QAFEEVFQNANFRSFIFRVRVKVETYNDESRI 152
Score = 144 bits (363), Expect = 8e-40
Identities = 66/136 (48%), Positives = 85/136 (62%), Gaps = 5/136 (3%)
Query: 655 EIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKE 714
E++ + LG GDK DY S + R N Y+ACP+QDCNKKVIDQ NG+YRCEKC+ E
Sbjct: 12 EVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPTQDCNKKVIDQQNGLYRCEKCDTE 71
Query: 715 FNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP-----ALKKAL 769
F F YR+IL V I D+ + WVT FQ AE+ILG A +GE + + + A
Sbjct: 72 FPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDKNEQAFEEVFQNAN 131
Query: 770 FTQYIFRLRAKLEHYN 785
F +IFR+R K+E YN
Sbjct: 132 FRSFIFRVRVKVETYN 147
Score = 28.1 bits (62), Expect = 8.5
Identities = 12/111 (10%), Positives = 32/111 (28%), Gaps = 10/111 (9%)
Query: 479 LFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSF 538
+ S+++ D T F + + + + + + F + N F
Sbjct: 80 ILSVNIADFQENQWVTCFQESAEAILGQNAAY-LGELKDKNEQAFEEVFQNANF-RSFIF 137
Query: 539 THSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAEL 589
+ + + +K + + + E L + I + L
Sbjct: 138 -----RVRVKVETYNDESRIKA---TVMDVKPVDYREYGRRLVMSIRRSAL 180
>3u50_C Telomerase-associated protein 82; TEB1, processivity factor, DNA
BIND protein; 2.50A {Tetrahymena thermophila}
Length = 172
Score = 131 bits (331), Expect = 1e-35
Identities = 24/149 (16%), Positives = 54/149 (36%), Gaps = 18/149 (12%)
Query: 192 QDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFN 251
Q Q +G K ++ ++ + + Y C K V+ + + CE C + F
Sbjct: 13 QAQASEIGQKKEFYVYGNLVSIQMKNKLYYYRCT--CQGKSVLKYHGDSFFCESCQQ-FI 69
Query: 252 TFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP------------- 298
L+L + D T ++ V +F ++ ++ +
Sbjct: 70 NPQVHLMLRAFVQDSTGTIPVMIFDQQSSQLINQIDPSIHVQEAGQYVKNCIENGQEEII 129
Query: 299 --ALKKALFTQYIFRLRAKLEHYNGTKKI 325
K F ++IF ++ + + +N ++I
Sbjct: 130 RQLFSKLDFARFIFEIQFENKEFNNEQEI 158
Score = 128 bits (322), Expect = 2e-34
Identities = 23/144 (15%), Positives = 51/144 (35%), Gaps = 18/144 (12%)
Query: 657 QDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFN 716
Q Q +G K ++ ++ + + Y C K V+ + + CE C + F
Sbjct: 13 QAQASEIGQKKEFYVYGNLVSIQMKNKLYYYRCT--CQGKSVLKYHGDSFFCESCQQ-FI 69
Query: 717 TFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP------------- 763
L+L + D T ++ V +F ++ ++ +
Sbjct: 70 NPQVHLMLRAFVQDSTGTIPVMIFDQQSSQLINQIDPSIHVQEAGQYVKNCIENGQEEII 129
Query: 764 --ALKKALFTQYIFRLRAKLEHYN 785
K F ++IF ++ + + +N
Sbjct: 130 RQLFSKLDFARFIFEIQFENKEFN 153
Score = 28.1 bits (62), Expect = 8.2
Identities = 13/100 (13%), Positives = 32/100 (32%), Gaps = 13/100 (13%)
Query: 479 LFSIDLLDESGEIRATMFNDECNRF-----HDMIEKDKVYYISNCTLKPANKKFSSINND 533
+ + D +G I +F+ + ++ + ++ Y+ NC + + +
Sbjct: 76 MLRAFVQDSTGTIPVMIFDQQSSQLINQIDPSIHVQEAGQYVKNCIENGQEEIIRQLFSK 135
Query: 534 YEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISP 573
+ F I E N + Y + +I
Sbjct: 136 --LDFARFIFEIQFENKEFNNEQEIAY------KVLKIEK 167
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A
{Sulfolobus solfataricus} SCOP: b.40.4.3
Length = 119
Score = 92.2 bits (229), Expect = 2e-22
Identities = 17/114 (14%), Positives = 40/114 (35%), Gaps = 11/114 (9%)
Query: 445 IVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFH 504
+ +L P + RV + R+ G + + DE+G ++ T++
Sbjct: 5 VGNLKPNMESVNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKHA---- 60
Query: 505 DMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSV 558
I++ +V I N ++ +++ T + +ED +
Sbjct: 61 GSIKEGQVVKIENA-------WTTAFKGQVQLNAGSKTKIAEASEDGFPESSQI 107
>2b29_A Replication protein A 70 kDa DNA-binding subunit; 1.60A {Homo
sapiens} SCOP: b.40.4.3 PDB: 2b3g_A 1ewi_A
Length = 123
Score = 83.4 bits (206), Expect = 3e-19
Identities = 33/76 (43%), Positives = 47/76 (61%), Gaps = 4/76 (5%)
Query: 327 DGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGVSSGSATNRSVLIILELNIIK 386
DG+N S MLATQLN ++ + LS + QI R+IV+ + G R V+I++EL ++K
Sbjct: 51 DGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDG----RRVVILMELEVLK 106
Query: 387 PGTEIGFKIGNPQPLN 402
+G KIGNP P N
Sbjct: 107 SAEAVGVKIGNPVPYN 122
>2k50_A Replication factor A related protein; uncharacterized protein,
structural genomics, PSI-2; NMR
{Methanothermobacterthermautotrophicus str}
Length = 115
Score = 77.7 bits (191), Expect = 2e-17
Identities = 23/119 (19%), Positives = 42/119 (35%), Gaps = 9/119 (7%)
Query: 437 APVVQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATM 495
P + I L + RV + R + +G GKL ++ + D++GE+RA
Sbjct: 2 KPEHRMDTISKLEEGAE-TPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVF 60
Query: 496 FNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGN 554
+ + E D V I + ++ E +TV + E +
Sbjct: 61 WTENIKLLKKFREGD-VIRIKDVNIRGGF------GGRKEAHLMPRSTVEVLDPLEHHH 112
>3dm3_A Replication factor A; probably plays AN essential for replication
of the chromosome, DNA recombination and repair; 2.40A
{Methanocaldococcus jannaschii}
Length = 105
Score = 48.1 bits (114), Expect = 5e-07
Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDE 499
T+ I LSP T + V + PI+E+ A GS GKL S + DE+G IR T++++
Sbjct: 4 DTYNIGELSPGMT-ATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNL 62
Query: 500 CN 501
+
Sbjct: 63 TD 64
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 52.5 bits (125), Expect = 5e-07
Identities = 107/800 (13%), Positives = 211/800 (26%), Gaps = 280/800 (35%)
Query: 16 DYEMSFTHST--TVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELS 73
D+E ++ ED FV ++ D+ + E+
Sbjct: 8 DFETGEHQYQYKDILSVFEDA----------FVDNFDCKDVQ-----DMPKSILSKEEID 52
Query: 74 SVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGK 133
+ + + R + Q + E N + + + Q
Sbjct: 53 HIIMSKDAVSGTLRLFWTLLSKQEEMVQKF----VEEVLRINYKFLM---SPIKTEQRQP 105
Query: 134 TLSLSM--SSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQ-RTG-------------GM 177
++ M L D F+ +R +P + R G+
Sbjct: 106 SMMTRMYIEQRDRLYNDNQV-------FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV 158
Query: 178 GGGAAGNLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQN 237
G +G K + + V + KV
Sbjct: 159 LG--SG-----------------K----TWV-ALDVCL--------------SYKV---- 176
Query: 238 NGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQ-NEAESILGVTAQEVGESTED 296
+C +F F W+ L N E++L
Sbjct: 177 -------QCKMDFKIF-----------------WLNLKNCNSPETVL------------- 199
Query: 297 HPALKKALFTQYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIV 356
+ + L Q ++ +H + I + I+S + +L ++
Sbjct: 200 --EMLQKLLYQIDPNWTSRSDH---SSNIK--LRIHS---IQAELRRLLKS--------- 240
Query: 357 QIKRYIVSGVSSGSATNRSVLIIL----ELNIIKPGTEIGFKIGNPQPLNTNTDNSSTQQ 412
K Y L++L F + + L T T
Sbjct: 241 --KPY-----------ENC-LLVLLNVQNAKAWNA-----FNLSC-KILLTTRFKQVTDF 280
Query: 413 TPAATNTNGSNGVHNNVAIPRQASAPVVQTHPIVSLSPYQNKWTIKARVTNKTPI---RE 469
AAT T+ + H ++L+P + K ++ + + P RE
Sbjct: 281 LSAATTTH------------------ISLDHHSMTLTPDEVK-SLLLKYLDCRPQDLPRE 321
Query: 470 WNNARGSGKLFSIDLLDESGEIRATMFNDECNRFH--DMIEKDKV-YYISNC--TLKPAN 524
+ + ++ A D + + DK+ I + L+PA
Sbjct: 322 ---VL-TTNPRRLSII-------AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA- 369
Query: 525 KKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIA----EISPDENIDVL 580
+Y F +V P +P ++ ++ + + V+
Sbjct: 370 --------EYRKMF-DRLSVFP--PS-------AH---IPTILLSLIWFDVIKSDVMVVV 408
Query: 581 GVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTL---------WGKEAETFDAS 631
S V + + T I L + + L K ++ D
Sbjct: 409 NKLHK---YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI 465
Query: 632 NKPV-------IA--VKAARVSEFQGNLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGS 682
+ I +K E + L R + + R + Q R
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPE---RMTLFRMV------------FLDFRFLEQKIRHD 510
Query: 683 NTTYKACPS-----QDCN--KKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSV 735
+T + A S Q K I N+ Y E+ F ++ ++ +T+ +
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYICDNDPKY--ERLVNAILDFLPKIEENLICSKYTDLL 568
Query: 736 WVTLFQNEAESILGVTAQEV 755
+ L E E+I ++V
Sbjct: 569 RIAL-MAEDEAIFEEAHKQV 587
>3e0e_A Replication protein A; structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium, NESG; 1.60A {Methanococcus maripaludis} PDB:
2k5v_A
Length = 97
Score = 44.5 bits (105), Expect = 6e-06
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 442 THPIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRATMFNDEC 500
+ I L P TI A V P +E++ G+ G+L S+ L D++G IR T++N+
Sbjct: 2 NYKISELMP-NLSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELA 60
Query: 501 N 501
+
Sbjct: 61 D 61
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold,
structural genomics, PSI-2, protein structure
initiative; NMR {Thermoplasma acidophilum}
Length = 106
Score = 41.4 bits (97), Expect = 9e-05
Identities = 15/106 (14%), Positives = 38/106 (35%), Gaps = 15/106 (14%)
Query: 445 IVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFH 504
I +S ++ ++T +E+ + + ++ + D++ IR + F +
Sbjct: 6 IRDVSLSTPYVSVIGKITGIHK-KEYESDGTTKSVYQGYIEDDTARIRISSFGKQ----- 59
Query: 505 DMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNED 550
++ V I N + N +S S+ + N +
Sbjct: 60 --LQDSDVVRIDNARVA-------QFNGYLSLSVGDSSRIESVNVN 96
Score = 38.3 bits (89), Expect = 0.001
Identities = 24/107 (22%), Positives = 49/107 (45%), Gaps = 11/107 (10%)
Query: 47 PLKTIAEISP-DENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG 105
L I ++S + V+G + +++ T + D + A + ++ +G
Sbjct: 2 DLVKIRDVSLSTPYVSVIGKIT---GIHKKEYESDGTTKSVYQGYIEDDT-ARIRISSFG 57
Query: 106 KEAETFDASNKPVIAVKAARVSEFQGGKTLSL-SMSSVLSLNPDIPE 151
K+ + D V+ + ARV++F G +LS+ S + S+N +IP
Sbjct: 58 KQLQDSD-----VVRIDNARVAQFNGYLSLSVGDSSRIESVNVNIPL 99
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 43.1 bits (101), Expect = 4e-04
Identities = 44/286 (15%), Positives = 78/286 (27%), Gaps = 132/286 (46%)
Query: 194 QQLGMG--------------DKADYC-------SVRGIIQVFRGSNTTYKACPSQDCNKK 232
Q+ GMG ++AD S+ I+ +N K
Sbjct: 1627 QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVI----NNPVNLTIHFGGEKGK 1682
Query: 233 VIDQN----------NGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESI 282
I +N +G + EK KE N + F++E +
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT----------------FRSEKG-L 1725
Query: 283 LGVT--AQEVGESTEDHPALKKALFTQY-IFR-LRAK-------------------LEHY 319
L T Q PAL + F L++K L
Sbjct: 1726 LSATQFTQ---------PAL---TLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASL 1773
Query: 320 NGTKKIPDGVNI-------------------NSFAMLATQLNDIITDGT----------L 350
I V + +++ M+A + + +
Sbjct: 1774 ADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV 1833
Query: 351 SEFT--IVQI-------KRYIVSGVSSGSATNRSV-LIILELNIIK 386
+ T +V+I ++Y+ +G R++ + LN IK
Sbjct: 1834 GKRTGWLVEIVNYNVENQQYVAAG------DLRALDTVTNVLNFIK 1873
Score = 43.1 bits (101), Expect = 5e-04
Identities = 69/455 (15%), Positives = 138/455 (30%), Gaps = 164/455 (36%)
Query: 3 AAPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKY---CFV--PLKTIAEI--- 54
+A + D E FT ++ E+ N P Y + PL + ++
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENP-SNTPDKDYLLSIPISCPLIGVIQLAHY 249
Query: 55 ---------SPDENIDVL--------GVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQA 97
+P E L G+ + A ++ + + + +
Sbjct: 250 VVTAKLLGFTPGELRSYLKGATGHSQGL-VTAVAIAE--TDSWE--------SFFVSVRK 298
Query: 98 SVTMTLW-GKEA-ETFDASNKPVIAVKAARVSEF-QGGKTLSLSMSSVLSLNPDIPECHK 154
++T+ + G E + P ++ + + + + + + M S+ +L + + +
Sbjct: 299 AITVLFFIGVRCYEAY-----PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY- 352
Query: 155 LQGWFSTQTNTRFEPVSQRTG-GMGGGA-----AGNLLLMREIQDQQLGMGDKADYCSVR 208
+TN+ P ++ + GA +G S+
Sbjct: 353 -----VNKTNSHL-PAGKQVEISLVNGAKNLVVSGPPQ-------------------SLY 387
Query: 209 GIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTN 268
G+ R KA D ++ + R K + F LPV
Sbjct: 388 GLNLTLRK----AKAPSGLDQSRIPFSE-----RKLKFSNRF--------LPV------- 423
Query: 269 SVWVTL-FQNEAESILGVTAQEVGESTEDH-PALKKALFTQYIF-RLRAKLEHYNGTK-K 324
F H L A + I L +N +
Sbjct: 424 ----ASPF---------------------HSHLLVPA--SDLINKDLVKNNVSFNAKDIQ 456
Query: 325 IP-----DGVNINSF-AMLATQLNDIITDG-----TLSEFTIVQIKRYIVS---GVSSGS 370
IP DG ++ ++ ++ D I T ++F +I+ G +SG
Sbjct: 457 IPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKA----THILDFGPGGASGL 512
Query: 371 A--TNRSV------LII---LELNIIKPGTEIGFK 394
T+R+ +I+ L++N P + GFK
Sbjct: 513 GVLTHRNKDGTGVRVIVAGTLDIN---PDDDYGFK 544
Score = 39.3 bits (91), Expect = 0.006
Identities = 31/169 (18%), Positives = 48/169 (28%), Gaps = 77/169 (45%)
Query: 647 QGNLLLMREIQDQQLGMG--------------DKADYC-------SVRGIIQVFRGSNTT 685
QG+ Q+ GMG ++AD S+ I+ +N
Sbjct: 1624 QGS---------QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVI----NNPV 1670
Query: 686 YKACPSQDCNKKVIDQN----------NGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSV 735
K I +N +G + EK KE N +
Sbjct: 1671 NLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT------------ 1718
Query: 736 WVTLFQNEAESILGVT--AQEVGESTEDHPALKKALFTQY-IFR-LRAK 780
F++E +L T Q PAL + F L++K
Sbjct: 1719 ----FRSEKG-LLSATQFTQ---------PAL---TLMEKAAFEDLKSK 1750
Score = 38.1 bits (88), Expect = 0.015
Identities = 79/481 (16%), Positives = 134/481 (27%), Gaps = 181/481 (37%)
Query: 273 TLF--QNEAESILGVTAQEVGESTEDHPALKKALFTQYIFRLRAKLEHYNGTKKI-PDGV 329
+F Q + +E+ + + + L L L + +K+ G+
Sbjct: 158 AIFGGQGNTDDYF----EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL 213
Query: 330 NINSFAMLATQL--NDIITDGTLSEF---TIVQIKRYIVSGVSSG-----------SATN 373
NI + + D + +S ++Q+ Y+V+ G AT
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPIS-CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATG 272
Query: 374 RSVLIILELNIIKPGT------------EIGFKIG------------NPQPLNTNTDNSS 409
S ++ + I + + + F IG P L + +N+
Sbjct: 273 HSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE 332
Query: 410 TQQTP----------------AATNTNGSNGVHNNVAI-----PRQASAPVVQTHPIVSL 448
+P TN++ G V I + VV + P SL
Sbjct: 333 GVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ--VEISLVNGAKNL---VV-SGPPQSL 386
Query: 449 SPYQ-NKW--TIKARVT---NKTPIREWNNARGSGKL-FSIDLLDESGEIRATMFNDECN 501
Y N KA ++ P E R KL FS L + +
Sbjct: 387 --YGLNLTLRKAKAPSGLDQSRIPFSE----R---KLKFSNRFL----PVAS-------- 425
Query: 502 RFHDMIEKDKVYYISNCTLKPANKKFSSINND---YEMSFTHSTTVIPCNEDEVGNMPSV 558
FH + L PA+ IN D +SF IP V
Sbjct: 426 PFHSHL------------LVPASDL---INKDLVKNNVSFNAKDIQIP-----V------ 459
Query: 559 KYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDIT--LVDQSQASV 616
Y D ++L ++G I+ +VD +
Sbjct: 460 -YDTF---------------------DGSDLRVLSG----------SISERIVDC---II 484
Query: 617 TMTL-WGKEAET-------FDASNKPVIAVKAARVSEFQGNLLLMREIQDQQLGMGDKAD 668
+ + W + F + V R + G +R I L + D
Sbjct: 485 RLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTG----VRVIVAGTLDINPDDD 540
Query: 669 Y 669
Y
Sbjct: 541 Y 541
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 33.1 bits (75), Expect = 0.23
Identities = 10/46 (21%), Positives = 14/46 (30%), Gaps = 17/46 (36%)
Query: 224 CPSQDCNKK----VIDQNNGMYRCEKC-----------NKEFNTFT 254
CP +C V + G C C E+ TF+
Sbjct: 24 CP--ECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFS 67
Score = 33.1 bits (75), Expect = 0.23
Identities = 10/46 (21%), Positives = 14/46 (30%), Gaps = 17/46 (36%)
Query: 689 CPSQDCNKK----VIDQNNGMYRCEKC-----------NKEFNTFT 719
CP +C V + G C C E+ TF+
Sbjct: 24 CP--ECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFS 67
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.5 bits (70), Expect = 0.58
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 16/44 (36%)
Query: 81 QKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAA 124
+K +K+ L QAS + L+ D++ P +A+KA
Sbjct: 18 EKQALKK---L----QAS--LKLYAD-----DSA--PALAIKAT 45
Score = 31.5 bits (70), Expect = 0.58
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 16/44 (36%)
Query: 598 QKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAA 641
+K +K+ L QAS + L+ D++ P +A+KA
Sbjct: 18 EKQALKK---L----QAS--LKLYAD-----DSA--PALAIKAT 45
Score = 29.5 bits (65), Expect = 2.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 307 QYIFRLRAKLEHYNGTKKIPDGVNINSFAMLAT 339
Q + +L+A L+ Y D + A+ AT
Sbjct: 20 QALKKLQASLKLYA-----DDSA--PALAIKAT 45
>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural
genomics, PSI-2, protein structure initiative; NMR
{Escherichia coli} SCOP: g.41.18.1
Length = 101
Score = 30.0 bits (67), Expect = 0.97
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 224 CPSQDCNKKVIDQNNGMYRCEKCNKEF 250
CP C + V+DQ+NG RC C +
Sbjct: 35 CP--QC-QHVLDQDNGHARCRSCGEFI 58
Score = 30.0 bits (67), Expect = 0.97
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 689 CPSQDCNKKVIDQNNGMYRCEKCNKEF 715
CP C + V+DQ+NG RC C +
Sbjct: 35 CP--QC-QHVLDQDNGHARCRSCGEFI 58
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.7 bits (66), Expect = 2.5
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 24/73 (32%)
Query: 466 PIREW---NNARGSGKLFSIDLLDESGEIR-------ATMFNDECNRFHD-MIEKDKVYY 514
IR+W R + LD + ++ A +E N+ +EK+K+
Sbjct: 86 SIRKWREEQRKR-------LQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI-- 136
Query: 515 ISNCTLKPANKKF 527
+N + A+K F
Sbjct: 137 -NN---RIADKAF 145
>2hpi_A DNA polymerase III alpha subunit; POL-beta-like
nucleotidyltransferase fold, transferase; HET: DNA; 3.00A
{Thermus aquaticus} PDB: 2hpm_A* 3e0d_A*
Length = 1220
Score = 30.7 bits (70), Expect = 2.7
Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 4/87 (4%)
Query: 430 AIPRQASAPVVQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESG 489
+ AS + + V P + K + V + G + L DE+G
Sbjct: 1020 GLREVASCTIEELSEFVRELPGKPKVLLSGMVEE---VVRKPTRSGG-MMARFTLSDETG 1075
Query: 490 EIRATMFNDECNRFHDMIEKDKVYYIS 516
+ +F +++D +
Sbjct: 1076 ALEVVVFGRAYEGVSPKLKEDIPLLVL 1102
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 30.3 bits (69), Expect = 2.7
Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 6/57 (10%)
Query: 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFN 497
+ + L P K T + ++ + + + + + L D + FN
Sbjct: 155 KIFKLNDLLP-GEKVTTQGKIVSVETKK-----FQNMNILTAVLSDGLVHVPLKWFN 205
>2ej4_A Zinc finger protein ZIC 3; ZF-C2H2 domain, zinc binding, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 95
Score = 28.4 bits (63), Expect = 2.8
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 216 GSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNT 252
GS+ + Q+ + K ID+ + C++ F+T
Sbjct: 1 GSSGSSGQPIKQELSCKWIDEAQLSRPKKSCDRTFST 37
Score = 28.4 bits (63), Expect = 2.8
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 681 GSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNT 717
GS+ + Q+ + K ID+ + C++ F+T
Sbjct: 1 GSSGSSGQPIKQELSCKWIDEAQLSRPKKSCDRTFST 37
>3ebe_A Protein MCM10 homolog; OB-fold, zinc finger, CCCH, DNA replication,
metal-binding, zinc-finger, replication; 2.30A {Xenopus
laevis} PDB: 3h15_A
Length = 200
Score = 29.5 bits (66), Expect = 3.0
Identities = 16/107 (14%), Positives = 30/107 (28%), Gaps = 10/107 (9%)
Query: 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYY 514
W + K + NN + DL D I +F D + V
Sbjct: 58 WVTFGVIVKKITPQSSNNGKTFSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGT-VIG 116
Query: 515 ISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYC 561
+ N + + +S + V+ +G+ + C
Sbjct: 117 LLNANPMKPKEGTDEVC----LSVDNPQKVL-----LMGDAVDLGTC 154
>1umu_A UMUD'; induced mutagenesis, SOS mutagenesis, DNA repair, beta-
lactamase cleavage reaction, LEXA repressor, lambda CI;
2.50A {Escherichia coli} SCOP: b.87.1.1 PDB: 1i4v_A
1ay9_A
Length = 116
Score = 28.3 bits (64), Expect = 3.8
Identities = 10/55 (18%), Positives = 16/55 (29%), Gaps = 11/55 (20%)
Query: 487 ESGEIRATMFNDE--CNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFT 539
G+I + E + + V L P N +S I E +
Sbjct: 57 SHGDIVIAAVDGEFTVKKLQ---LRPTVQ------LIPMNSAYSPITISSEDTLD 102
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural
genomics, PSI-2, protein structure initiative; NMR
{Salmonella typhimurium LT2}
Length = 81
Score = 27.6 bits (61), Expect = 4.0
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 224 CPSQDCNKKVIDQNNGMYRCEKCNKEFN 251
CP C +++N CE C K+F+
Sbjct: 5 CP--VC-HHALERNGDTAHCETCAKDFS 29
Score = 27.6 bits (61), Expect = 4.0
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 689 CPSQDCNKKVIDQNNGMYRCEKCNKEFN 716
CP C +++N CE C K+F+
Sbjct: 5 CP--VC-HHALERNGDTAHCETCAKDFS 29
>3ixv_A Hemocyanin AA6 chain; HC, phenolxoidase activity, tyrosinase (TY),
catecholoxidase (CO), enzyme, SDS, cryo-EM, single
particle analysis; 6.80A {Androctonus australis} PDB:
3ixw_A
Length = 626
Score = 29.5 bits (66), Expect = 5.2
Identities = 7/50 (14%), Positives = 14/50 (28%)
Query: 306 TQYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTI 355
+ Y + GV + ++ + N I T S +
Sbjct: 365 DNIFQEHKKSFHPYTKEELSFPGVEVVGVSINSKTANVITTLIKESLLEL 414
>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca
cleavage, DNA damage, DNA repair, DNA replication,
DNA-BIND hydrolase; 1.37A {Thermotoga maritima}
Length = 196
Score = 28.3 bits (64), Expect = 8.3
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 10/46 (21%)
Query: 487 ESGEIRATMFNDE--CNRFHDMIEKDKVYYISNCTLKPANKKFSSI 530
++G+I A M + E +F+ D V L+PAN++ SS+
Sbjct: 139 QNGDIVAAMVDGEVTLAKFY--QRGDTVE------LRPANREMSSM 176
>1tm9_A GI3844938, hypothetical protein Mg354; all alpha helical protein,
structural genomics, PSI, protein structure initiative;
NMR {Mycoplasma genitalium} SCOP: a.225.1.1
Length = 137
Score = 27.8 bits (61), Expect = 8.6
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 30 CNEDEVGNMPSVKYCFVPLKTIAEISPDEN--IDVLGVCIDAAELSSVTGKTNQ 81
C+ E SV P+K I EI+ DEN I++ + ++ + S G T Q
Sbjct: 29 CSTRESDTFSSVDVPLEPIKNIIEITKDENQQIEITKIAVNNIKTLSSVGATGQ 82
Score = 27.8 bits (61), Expect = 8.6
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 547 CNEDEVGNMPSVKYCFVPLKTIAEISPDEN--IDVLGVCIDAAELSSVTGKTNQ 598
C+ E SV P+K I EI+ DEN I++ + ++ + S G T Q
Sbjct: 29 CSTRESDTFSSVDVPLEPIKNIIEITKDENQQIEITKIAVNNIKTLSSVGATGQ 82
>3hhs_B Propo-P1, phenoloxidase subunit 1; alpha helix, beta strand,
melanin biosynthesis, metal-bindin monooxygenase,
oxidoreductase, secreted; 1.97A {Manduca sexta}
Length = 684
Score = 28.4 bits (63), Expect = 10.0
Identities = 9/49 (18%), Positives = 17/49 (34%)
Query: 307 QYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTI 355
+ KL Y + GV ++S + + N + T S +
Sbjct: 410 DVFNIYKEKLTPYTNERLDFPGVRVSSVGIEGARPNTLRTLWQQSTVEL 458
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.131 0.383
Gapped
Lambda K H
0.267 0.0540 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 11,508,641
Number of extensions: 680238
Number of successful extensions: 1952
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1934
Number of HSP's successfully gapped: 49
Length of query: 786
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 685
Effective length of database: 3,881,772
Effective search space: 2659013820
Effective search space used: 2659013820
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: 61 (27.7 bits)