RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3603
(264 letters)
>1wjj_A Hypothetical protein F20O9.120; DNA-binding protein-related,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Arabidopsis
thaliana} SCOP: b.40.4.3
Length = 145
Score = 100 bits (250), Expect = 8e-27
Identities = 24/124 (19%), Positives = 47/124 (37%), Gaps = 13/124 (10%)
Query: 27 KKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKEN-------------REVRTLKVAD 73
K++ + V ++ L G +T V++ + V + + + D
Sbjct: 11 KRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGD 70
Query: 74 STACINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNEN 133
T CI + ++ L+ PG V L +++ + L K G IE G E+
Sbjct: 71 ETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKED 130
Query: 134 LDMS 137
++S
Sbjct: 131 NNLS 134
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A
{Sulfolobus solfataricus} SCOP: b.40.4.3
Length = 119
Score = 95.3 bits (237), Expect = 4e-25
Identities = 22/112 (19%), Positives = 48/112 (42%), Gaps = 3/112 (2%)
Query: 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVTLK---ENREVRTLKVADSTACINLSLWDEPG 87
M+ + +L +++VNVT VL+ S ++ R + V D T + L+LW +
Sbjct: 1 MEEKVGNLKPNMESVNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKHA 60
Query: 88 ALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIP 139
+ G +V++ + ++ + L + I + E + + + P
Sbjct: 61 GSIKEGQVVKIENAWTTAFKGQVQLNAGSKTKIAEASEDGFPESSQIPENTP 112
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold,
structural genomics, PSI-2, protein structure
initiative; NMR {Thermoplasma acidophilum}
Length = 106
Score = 75.7 bits (186), Expect = 8e-18
Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 5/93 (5%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPRVTLKENRE--VRTLKVADSTACINLSLWDEPGALLHP 92
I+D+ + V+V + I + + V + D TA I +S + + L
Sbjct: 6 IRDVSLSTPYVSVIGKITGIHKKEYESDGTTKSVYQGYIEDDTARIRISSFGKQ---LQD 62
Query: 93 GDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125
D+VR+ + L+L S IE +
Sbjct: 63 SDVVRIDNARVAQFNGYLSLSVGDSSRIESVNV 95
>2k50_A Replication factor A related protein; uncharacterized protein,
structural genomics, PSI-2; NMR
{Methanothermobacterthermautotrophicus str}
Length = 115
Score = 69.6 bits (170), Expect = 2e-15
Identities = 23/108 (21%), Positives = 38/108 (35%), Gaps = 9/108 (8%)
Query: 27 KKEAMDVYIKDLHVGIKNVNVTCIVLDISPR--VTLKENRE--VRTLKVADSTACINLSL 82
K E I L G VT V+ IS T ++ RE + + +AD T +
Sbjct: 2 KPEHRMDTISKLEEG-AETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVF 60
Query: 83 WDEPGAL---LHPGDIVRLTKCYAQI-WRNCLTLYSSKSGLIEKIGEF 126
W E L GD++R+ + + + +E +
Sbjct: 61 WTENIKLLKKFREGDVIRIKDVNIRGGFGGRKEAHLMPRSTVEVLDPL 108
>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 = 68.8 bits (168), Expect = 2e-15
Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 7/97 (7%)
Query: 31 MDVYIKDLHVGIKNVNVTCIVLDISP--RVTLKENRE--VRTLKVADSTACINLSLWDEP 86
M+ I +L + + V+ P + K+ + +++L + D T I +LW+E
Sbjct: 1 MNYKISELMPNLSGT-INAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNEL 59
Query: 87 GAL-LHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEK 122
+ GDI + Y + + L + G+IEK
Sbjct: 60 ADFEVKKGDIAEV-SGYVKQGYSGLEISVDNIGIIEK 95
>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 = 63.5 bits (154), Expect = 3e-13
Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 6/96 (6%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPRVTLK----ENREVRTLKVADSTACINLSLWDEPGAL- 89
I +L G V+ P K ++++ V D T I ++LWD +
Sbjct: 8 IGELSPG-MTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTDID 66
Query: 90 LHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125
+ GD VR+ + + L ++ +++K +
Sbjct: 67 VGRGDYVRVRGYIREGYYGGLECTANYVEILKKGEK 102
>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel,
structural genomics, PSI-2, protein structure
initiative; NMR {Methanosarcina mazei} PDB: 2ken_A
Length = 109
Score = 48.0 bits (114), Expect = 1e-07
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 4/92 (4%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGA-LLHPG 93
I D+ + N+ V+ + + + D T I ++W LL G
Sbjct: 8 IVDIVENGQWANLKAKVIQLWEN---THESISQVGLLGDETGIIKFTIWKNAELPLLEQG 64
Query: 94 DIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125
+ L + + + +K+ IEK+ E
Sbjct: 65 ESYLLRSVVVGEYNDRFQVQVNKNSSIEKLSE 96
>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded
DNA, transcription/DNA complex; 1.73A {Homo sapiens}
SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A
Length = 294
Score = 34.7 bits (79), Expect = 0.022
Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 6/90 (6%)
Query: 33 VYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVAD-STACINLSLWDEPGALL- 90
+ L G VNV +V P K + + D + + L+ L
Sbjct: 7 TPLNQLKGG-TIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALP 65
Query: 91 ---HPGDIVRLTKCYAQIWRNCLTLYSSKS 117
GDIVR + Q+++ +S
Sbjct: 66 IIYKNGDIVRFHRLKIQVYKKETQGITSSG 95
>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 = 33.1 bits (75), Expect = 0.093
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 130 FNENLDMSIPIPNLPVNAPQS-------ANG---NSNPGNMNNSGNNKGNMRPNPIDRDV 179
F + SI ++ +N P + G N M G ++ I +++
Sbjct: 1653 FKDTYGFSIL--DIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEI 1710
Query: 180 NR----YSNNPDKGSSSSTQNT 197
N Y+ +KG S+TQ T
Sbjct: 1711 NEHSTSYTFRSEKGLLSATQFT 1732
>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 = 30.6 bits (68), Expect = 0.57
Identities = 25/196 (12%), Positives = 52/196 (26%), Gaps = 72/196 (36%)
Query: 13 KNHGMRAER-KEINRKK--EAMDVYIKDLH----------VGI--KNVNVTCIVLDISPR 57
++ + K +N K ++ + L + + + ++ I+L +
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL--- 394
Query: 58 VTL---KENREVRTLKVADSTACINLSL---WDEPGAL-LHPGDIVRLTKC----YAQIW 106
+ +V V + SL + + + I K +
Sbjct: 395 --IWFDVIKSDVM--VVVNK--LHKYSLVEKQPKESTISIP--SIYLELKVKLENEYALH 446
Query: 107 RNCLTLYS---------------------------SKSGLIEKIGEFCMVFNENLDMS-- 137
R+ + Y+ E++ F MVF LD
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDFRFL 503
Query: 138 ---IPIPNLPVNAPQS 150
I + NA S
Sbjct: 504 EQKIRHDSTAWNASGS 519
>2yzy_A Putative uncharacterized protein TTHA1012; uncharacterized
conserved protein, structural genomics, UNKN function,
NPPSFA; 1.60A {Thermus thermophilus}
Length = 200
Score = 29.4 bits (65), Expect = 0.78
Identities = 9/63 (14%), Positives = 19/63 (30%), Gaps = 3/63 (4%)
Query: 186 PDKGSSSSTQNTWVTWDQLLPVKFQFFSSSS---RTLKFSNFECGVYLDMCLRRRTSHSH 242
+ + ++ P++F F LK F+ + L+R +
Sbjct: 137 SKENQGFAAMELYILKADPRPLRFVFLDEKGKVLADLKVVEFKRTNLTEAQLKRYPKDAQ 196
Query: 243 WFR 245
R
Sbjct: 197 VVR 199
>3k2k_A Putative carboxypeptidase; structural genomics, joint center
structural genomics, JCSG, protein structure initiative;
2.49A {Burkholderia mallei atcc 23344}
Length = 403
Score = 29.4 bits (65), Expect = 1.2
Identities = 16/88 (18%), Positives = 25/88 (28%)
Query: 159 NMNNSGNNKGNMRPNPIDRDVNRYSNNPDKGSSSSTQNTWVTWDQLLPVKFQFFSSSSRT 218
NMN G+ GN+R N ++NR PD S + F
Sbjct: 233 NMNPDGSVHGNLRTNAAGANLNREWMEPDAERSPEVLVVRDAIHAIGCDLFFDIHGDEDL 292
Query: 219 LKFSNFECGVYLDMCLRRRTSHSHWFRL 246
+ ++R S +
Sbjct: 293 PYVFAAGSEMLPGFTEQQRVEQSAFIDS 320
>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 = 27.6 bits (60), Expect = 3.2
Identities = 6/46 (13%), Positives = 17/46 (36%), Gaps = 16/46 (34%)
Query: 20 ERKEINRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENRE 65
E++ + + + ++ +Y D +P + +K E
Sbjct: 18 EKQALKKLQASLKLYAD----------------DSAPALAIKATME 47
>1qzg_A Protection of telomeres protein 1; protrein-DNA complex,
single-stranded telomeric DNA, DNA binding protein/DNA
complex; HET: TMP; 1.90A {Schizosaccharomyces pombe}
SCOP: b.40.4.3 PDB: 1qzh_A
Length = 187
Score = 27.4 bits (60), Expect = 3.5
Identities = 21/108 (19%), Positives = 42/108 (38%), Gaps = 14/108 (12%)
Query: 45 VNVTCIVLDIS-PRVTLKENRE-VRTLKVAD-----STACINLSLWDEPGALL----HPG 93
VN+ IV D + R +L ++ V T+ + D S+ + + L+ + G L G
Sbjct: 45 VNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDLPVIKQVG 104
Query: 94 DIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIPIP 141
+ L + + +R+ S + + + + D P P
Sbjct: 105 QPLLLHQITLRSYRDRTQGLSKDQ---FRYALWPDFSSNSKDTLCPQP 149
>2zp2_A Kinase A inhibitor; KIPI, histidine kinase inhibitor, ATP-binding,
nucleotide- binding, protein kinase inhibitor,
sporulation; 3.01A {Bacillus subtilis}
Length = 141
Score = 27.2 bits (61), Expect = 3.7
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 80 LSLWD---EPGALLHPGDIVR 97
L+L+ P LL GDIV+
Sbjct: 104 LALFRPQENPPTLLRAGDIVK 124
>2boa_A Carboxypeptidase A4; metalloprocarboxypeptidase, X-RAY zymogen,
metalloprotease, exopropeptidase, hydrolase; HET: NAG;
2.20A {Homo sapiens} SCOP: c.56.5.1 d.58.3.1
Length = 404
Score = 27.9 bits (62), Expect = 3.7
Identities = 8/40 (20%), Positives = 19/40 (47%)
Query: 57 RVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIV 96
R+ ++ E+ L ++ + L+ W P + P D++
Sbjct: 11 RINVRNGDEISKLSQLVNSNNLKLNFWKSPSSFNRPVDVL 50
>3mml_B Allophanate hydrolase subunit 1; structural genomics, PSI-2,
protein structure initiative, tuberculosis structural
genomics consortium; 2.50A {Mycobacterium smegmatis}
Length = 228
Score = 27.7 bits (62), Expect = 3.7
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 80 LSLWD---EPGALLHPGDIVR 97
++D + ALL PG V+
Sbjct: 203 AVMFDVNRDKPALLTPGMWVQ 223
>2phc_B Uncharacterized protein PH0987; structural genomics, southeas
collaboratory for structural genomics, secsg, PSI,
protein initiative; 2.29A {Pyrococcus horikoshii} SCOP:
b.62.1.4 d.74.5.1
Length = 225
Score = 27.7 bits (62), Expect = 3.7
Identities = 6/21 (28%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 80 LSLWD---EPGALLHPGDIVR 97
L ++ P +++ PGD V+
Sbjct: 187 LRTFNPGKVPPSIVLPGDYVK 207
>3l2n_A Peptidase M14, carboxypeptidase A; putative carboxypeptidase A,
structural genomics, joint CENT structural genomics,
JCSG; 2.39A {Shewanella denitrificans}
Length = 395
Score = 27.8 bits (61), Expect = 3.8
Identities = 12/60 (20%), Positives = 20/60 (33%)
Query: 159 NMNNSGNNKGNMRPNPIDRDVNRYSNNPDKGSSSSTQNTWVTWDQLLPVKFQFFSSSSRT 218
NMN G+ +G++R N + ++NR P S + F
Sbjct: 224 NMNPDGSVRGHLRTNAVGANLNREWQTPSLERSPEVYYVVNKMHETGVDLFYDVHGDEGL 283
>1whz_A Hypothetical protein; alpha and beta protein, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
unknown function; 1.52A {Thermus thermophilus} SCOP:
d.50.3.2
Length = 70
Score = 25.8 bits (57), Expect = 4.1
Identities = 7/32 (21%), Positives = 11/32 (34%), Gaps = 5/32 (15%)
Query: 235 RRRTSHSHWFRLTAE-----KHSGEIRPGTVR 261
+ H + HSGE+ GT +
Sbjct: 23 MAKGGHRLYTHPDGRIVVVPFHSGELPKGTFK 54
>1dgf_A Catalase; heme, NADPH, hydrogen peroxide, oxidoreductase; HET: HEM
NDP; 1.50A {Homo sapiens} SCOP: e.5.1.1 PDB: 1dgg_A*
1f4j_A* 1qqw_A* 1dgh_A* 1dgb_A* 3rgp_A* 3re8_A* 3rgs_A*
3nwl_A* 4blc_A* 1th2_A* 1th3_A* 1th4_A* 1tgu_A* 7cat_A*
8cat_A*
Length = 497
Score = 27.2 bits (61), Expect = 5.8
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 143 LPVNAPQSANGNSNP--GNMNNSGNNKGNMRPN 173
+PVN P A + G M N G PN
Sbjct: 369 IPVNCPYRARVANYQRDGPMCMQDNQGG--APN 399
>1aye_A PCPA2, procarboxypeptidase A2; serine protease, zymogen,
hydrolase; 1.80A {Homo sapiens} SCOP: c.56.5.1 d.58.3.1
PDB: 1o6x_A
Length = 401
Score = 27.0 bits (60), Expect = 7.3
Identities = 4/40 (10%), Positives = 12/40 (30%)
Query: 57 RVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIV 96
+ +++ L ++ + L W P +
Sbjct: 11 EIVPSNEEQIKNLLQLEAQEHLQLDFWKSPTTPGETAHVR 50
>2o0a_A S.cerevisiae chromosome XVI reading frame ORF YPL253C; VIK1, motor
homology domain, kinesin, motor domain,
microtubule-binding; 1.60A {Saccharomyces cerevisiae}
Length = 298
Score = 26.8 bits (58), Expect = 7.3
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 225 ECGVYLDMCLRRRTSHS 241
E VY DMCL ++ + +
Sbjct: 79 EYSVYHDMCLNQKKNFN 95
>1pca_A Procarboxypeptidase A PCPA; hydrolase(C-terminal peptidase); HET:
CIT; 2.00A {Sus scrofa} SCOP: d.58.3.1 PDB: 1pyt_A
Length = 403
Score = 26.7 bits (59), Expect = 8.5
Identities = 8/40 (20%), Positives = 18/40 (45%)
Query: 57 RVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIV 96
R+++ + +V+ +K + + L W P P D+
Sbjct: 12 RISVDDEAQVQKVKELEDLEHLQLDFWRGPARPGFPIDVR 51
>4a37_A Metallo-carboxypeptidase; metallo-protease, hydrolase; 1.60A
{Pseudomonas aeruginosa} PDB: 4a38_A 4a39_A*
Length = 388
Score = 26.6 bits (58), Expect = 8.6
Identities = 13/37 (35%), Positives = 16/37 (43%)
Query: 159 NMNNSGNNKGNMRPNPIDRDVNRYSNNPDKGSSSSTQ 195
NMN G GN+R N +D+NR P S
Sbjct: 219 NMNPDGAFHGNLRTNAAGQDLNRAWLEPSAERSPEVW 255
>4etp_B Spindle POLE BODY-associated protein VIK1; kinesin motor protein,
kinesin motor homology domain, karyog mitosis,
microtubules; HET: ADP EBC; 2.30A {Saccharomyces
cerevisiae} PDB: 1u0i_A
Length = 333
Score = 26.4 bits (57), Expect = 9.9
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 225 ECGVYLDMCLRRRTSHS 241
E VY DM L ++ + +
Sbjct: 114 EYSVYHDMALNQKKNFN 130
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
0.317 0.133 0.416
Gapped
Lambda K H
0.267 0.0415 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,017,727
Number of extensions: 223858
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 463
Number of HSP's successfully gapped: 33
Length of query: 264
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 172
Effective length of database: 4,133,061
Effective search space: 710886492
Effective search space used: 710886492
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 (21.7 bits)
S2: 56 (26.2 bits)