RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5840
(132 letters)
>1nlq_A Nucleoplasmin-like protein; DNLP, chaperone, histone binding, X-RAY
crystallography, ligand binding; 1.50A {Drosophila
melanogaster} SCOP: b.121.3.1
Length = 108
Score = 80.4 bits (198), Expect = 5e-21
Identities = 32/75 (42%), Positives = 47/75 (62%), Gaps = 3/75 (4%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTF 60
+ + Q ++GA AKE E +VVEV +++PI VLKA G D+ F + VTF
Sbjct: 32 LVIKQILLGAEAKENEFNVVEVNTPK--DSVQIPIAVLKA-GETRAVNPDVEFYESKVTF 88
Query: 61 KLVKGSGPIYLFGNH 75
KL+KGSGP+Y+ G++
Sbjct: 89 KLIKGSGPVYIHGHN 103
>1k5j_A Nucleoplasmin core; beta-barrel, jellyroll, beta-bulge, pentamer,
chaperone; 2.30A {Xenopus laevis} SCOP: b.121.3.1 PDB:
2vtx_A 2vtx_J
Length = 124
Score = 77.1 bits (189), Expect = 2e-19
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTF 60
+ L +G AK+ E H+VE+ A+ +PI LK + A + + PPVTF
Sbjct: 45 LALRTVCLGDKAKD-EFHIVEIVTQEEGAEKSVPIATLKP-SILPMATMVGIELTPPVTF 102
Query: 61 KLVKGSGPIYLFGNHSVGTGE 81
+L GSGP+Y+ G H +
Sbjct: 103 RLKAGSGPLYISGQHVAMEED 123
>1xe0_A Nucleophosmin; drosophila nucleoplasmin-like protein (DNLP),
nucleoplasmin (NP), histone binding, X-RAY
crystallography, chaperone; 1.70A {Xenopus laevis} SCOP:
b.121.3.1 PDB: 1xb9_A 2p1b_A
Length = 114
Score = 75.8 bits (186), Expect = 4e-19
Identities = 29/82 (35%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRAD-IKLPIVVLKAAGVNNHAPLDLLFPDPPVT 59
+ L +GA+AK+ E+HVVE E + + IK+ + LK V L PPV
Sbjct: 34 LSLRTVSLGASAKD-ELHVVEAEGINYEGKTIKIALASLKP-SVQPTVSLGGFEITPPVI 91
Query: 60 FKLVKGSGPIYLFGNHSVGTGE 81
+L GSGP+Y+ G H V +
Sbjct: 92 LRLKSGSGPVYVSGQHLVALED 113
>3t30_B Nucleoplasmin-2; beta-barrel jelly roll topology, histone
chaperone, H2A-H2B H3-H4 tetramer, oocytes and early
embryos, chaperone; 1.90A {Homo sapiens}
Length = 110
Score = 67.8 bits (165), Expect = 5e-16
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRAD---IKLPIVVLKAAGVNNHAPLDLLFPDPP 57
+ L +G AKE E+H VE+ + D + I L+A+ + + + + PP
Sbjct: 32 LLLHTICLGEKAKE-EMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLS-PP 89
Query: 58 VTFKLVKGSGPIYLFGNHSV 77
VTF+L GSGP++L G
Sbjct: 90 VTFQLRAGSGPVFLSGQERY 109
>1xzp_A Probable tRNA modification GTPase TRME; GTP-binding, THF-binding,
hydrolase; 2.30A {Thermotoga maritima} SCOP: a.24.25.1
c.37.1.8 d.250.1.2 PDB: 1xzq_A* 1xzp_B 1xzq_B*
Length = 482
Score = 28.3 bits (64), Expect = 0.73
Identities = 6/34 (17%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 95 DFSEEEVDESEILSKNLSQ-KFQVSSLLLSFKVG 127
D+ +E + + L + K +++ L G
Sbjct: 204 DYPDEIETNTGEVVTRLERIKEKLTEELKKADAG 237
>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP-
binding, hydrolase, magnesium, metal-binding,
nucleotide- binding, potassium; HET: GDP FON; 2.95A
{Chlorobium tepidum} PDB: 3gei_A*
Length = 476
Score = 27.9 bits (63), Expect = 0.98
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 95 DFSEEEVDE---SEILSKNLSQKFQVSSLLLSFKVG 127
DFSEE+V+ E+ + + + +V+ L+ S++ G
Sbjct: 192 DFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHG 227
>1ej6_B Lambda1; icosahedral, non-equivalence, dsRNA virus, methylase,
methyltransferase, guanylyltransferase, zinc finger,
icosahedral virus; 3.60A {Reovirus SP} SCOP: i.7.1.1 PDB:
2cse_V
Length = 1275
Score = 27.9 bits (61), Expect = 1.4
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 10/59 (16%)
Query: 35 IVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGSGPIYLFGNHSV-----GTGEPMGEDDD 88
I++ + + +PL PP + + +++FG PM D+
Sbjct: 1045 IIIGRVQSTHLWSPLA-----PPPDLVFDRDTPGVHIFGRDCRISFGMNGAAPMIRDET 1098
>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 142
Score = 27.0 bits (59), Expect = 1.4
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 85 EDDDEESIDEDFSEEEVDESEILSKNLSQKFQVSS 119
E+D+ +D EEEVDE E++ +N + VS
Sbjct: 5 EEDEAFGMDGAVMEEEVDELEMIDENGQSQQGVSH 39
>3iyl_X VP3; non-enveloped virus, membrane penetration protein, autocleav
myristol group, icosahedral virus; HET: MYR; 3.30A {Grass
carp reovirus} PDB: 3k1q_C 3k1q_B
Length = 1214
Score = 27.5 bits (60), Expect = 1.4
Identities = 11/59 (18%), Positives = 20/59 (33%), Gaps = 10/59 (16%)
Query: 35 IVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGSGPIYLFGNHSV-----GTGEPMGEDDD 88
+ +++ A N +P+ P V+G + + G EP DD
Sbjct: 982 LYLVQTATNGNWSPMA-----PVAAPPFVRGGPNVRVVGRFGTIVPRPNGLEPQLIDDG 1035
>2ayu_A Nucleosome assembly protein; histone chaperone; 3.00A
{Saccharomyces cerevisiae} SCOP: d.305.1.1 PDB: 2z2r_A
Length = 417
Score = 26.8 bits (58), Expect = 2.8
Identities = 6/27 (22%), Positives = 15/27 (55%)
Query: 79 TGEPMGEDDDEESIDEDFSEEEVDESE 105
TG + + +E+ + D E+E ++ +
Sbjct: 361 TGAALEFEFEEDEEEADEDEDEEEDDD 387
Score = 25.3 bits (54), Expect = 8.6
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 78 GTGEPMGEDDDEESIDEDFSEEEVDESE 105
G ++DEE DED EEE D+
Sbjct: 362 GAALEFEFEEDEEEADEDEDEEEDDDHG 389
>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 = 26.4 bits (57), Expect = 3.5
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 81 EPMGEDDD----EESIDEDFSEEEVDESEILSKNLSQKFQVSSLLLS 123
+ ++ D ++ S+EE+D + +S ++ LLS
Sbjct: 27 DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73
Score = 26.0 bits (56), Expect = 4.7
Identities = 23/121 (19%), Positives = 37/121 (30%), Gaps = 30/121 (24%)
Query: 34 PIVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGSGPIYLFG----NHSVGTGEP------- 82
P + L+ A L L P V V GSG ++ ++ V
Sbjct: 136 PYLKLRQA-------LLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188
Query: 83 MGEDDDEES-----------IDEDFSEEEVDESEILSKNLSQKFQVSSLLLSFKVGIECL 131
+ + E+ ID +++ D S + + LL K CL
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRS-DHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
Query: 132 L 132
L
Sbjct: 248 L 248
Score = 26.0 bits (56), Expect = 5.0
Identities = 3/12 (25%), Positives = 6/12 (50%)
Query: 27 FRADIKLPIVVL 38
F +P ++L
Sbjct: 381 FPPSAHIPTILL 392
Score = 26.0 bits (56), Expect = 6.0
Identities = 19/139 (13%), Positives = 38/139 (27%), Gaps = 44/139 (31%)
Query: 6 AVIGANAKEGEVH---VVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDL--------LFP 54
++I + ++G V I+ + VL+ P + +FP
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE--------PAEYRKMFDRLSVFP 382
Query: 55 D----PPVTFKLVKGSGPIYLFGNHSVGTGEPMGEDDDEESIDEDFSEEEVDESEILSKN 110
P + L+ D +S + S + +
Sbjct: 383 PSAHIPTILLSLIWF---------------------DVIKSDVMVVVNKLHKYSLVEKQP 421
Query: 111 LSQKFQVSSLLLSFKVGIE 129
+ S+ L KV +E
Sbjct: 422 KESTISIPSIYLELKVKLE 440
>2joz_A Hypothetical protein YXEF; structure, GFT, NESG, lipoprotein,
structural genomics, PSI-2, protein structure
initiative; NMR {Bacillus subtilis} SCOP: b.60.1.1
Length = 135
Score = 25.6 bits (55), Expect = 3.9
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 10/90 (11%)
Query: 16 EVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDP--PVTFKLVKGSGPIYLFG 73
E VVE E M R +++LP + K + +++ + P P+ L +G ++
Sbjct: 42 EDEVVETEVMEGRGEVQLPFMAYKVISQSTDGSIEIQYLGPYYPLKSTLKRGENGTLIW- 100
Query: 74 NHSVGTGEPMGEDDDEESIDEDFSEEEVDE 103
E G+ I+ EE DE
Sbjct: 101 -------EQNGQRKTMTRIESKTGREEKDE 123
>3c1d_A Protein ORAA, regulatory protein RECX; tandem repeats,
helix-turn-helix, cytoplasm, DNA damage, DNA repair, SOS
response, DNA binding protein; 1.80A {Escherichia coli}
Length = 159
Score = 25.4 bits (56), Expect = 4.8
Identities = 4/28 (14%), Positives = 14/28 (50%)
Query: 88 DEESIDEDFSEEEVDESEILSKNLSQKF 115
E+ ++ E ++D + + ++K+
Sbjct: 95 SREATEKAMREADIDWAALARDQATRKY 122
>3fs3_A Nucleosome assembly protein 1, putative; protein localization,
histone recognition, structural analysis, CHA; 2.30A
{Plasmodium falciparum} PDB: 3hfd_A 3gyw_A 3gyv_A
Length = 359
Score = 26.1 bits (56), Expect = 5.0
Identities = 4/27 (14%), Positives = 9/27 (33%)
Query: 79 TGEPMGEDDDEESIDEDFSEEEVDESE 105
G + + + D D S + +
Sbjct: 290 LGIIIESESNSIVSDVDSSYSSSENNS 316
>3etv_A Protein transport protein TIP20,linker,protein transport protein
DSL1; TIP20P-DSL1P complex, endoplasmic reticulum,
ER-golgi transport; 1.94A {Saccharomyces cerevisiae}
PDB: 3etu_A
Length = 355
Score = 25.9 bits (56), Expect = 5.7
Identities = 9/53 (16%), Positives = 16/53 (30%), Gaps = 1/53 (1%)
Query: 79 TGEPMGEDDDEESIDEDFSEEEVDESEILSKNLSQKFQVSSLLLSFKVGIECL 131
G S D + E + L+ + K +L+ K + L
Sbjct: 40 ASNDTGGGSGGGSDSSDLLQREAILANELNILDNLK-TFLNLIKEVKTNLNIL 91
>2pok_A Peptidase, M20/M25/M40 family; M20 family peptidase, metallo
protein, MCSG, structural GENO PSI-2, protein structure
initiative; HET: BGC; 1.90A {Streptococcus pneumoniae}
Length = 481
Score = 25.7 bits (57), Expect = 6.2
Identities = 12/91 (13%), Positives = 27/91 (29%), Gaps = 14/91 (15%)
Query: 3 LFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIV-VLKAAGVNNHAPLDLLFPDPPVTFK 61
+ + N + + M +R+D+ P + + +P
Sbjct: 371 KIRKQLDKNGFDKVELYYTLGEMSYRSDMSAPAILNVIEL-------AKKFYPQGVSVLP 423
Query: 62 LVKGSGPIYLF----GNHSVGTGEPMGEDDD 88
G+GP++ V G +G +
Sbjct: 424 TTAGTGPMHTVFDALEVPMVAFG--LGNANS 452
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding;
HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP:
a.4.13.2
Length = 243
Score = 25.6 bits (57), Expect = 6.2
Identities = 7/50 (14%), Positives = 13/50 (26%), Gaps = 8/50 (16%)
Query: 58 VTFKLVKGSGPIYLFGNHSVGTGEPMGEDDDEESIDEDFSEEEVDESEIL 107
V P + E + E+D + D + + S
Sbjct: 147 VVLAQEAVRLPTSIH--------ETVYENDGDPITLLDQIADADEASWFD 188
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 0.138 0.388
Gapped
Lambda K H
0.267 0.0545 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,038,826
Number of extensions: 122060
Number of successful extensions: 379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 358
Number of HSP's successfully gapped: 39
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
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: 52 (24.2 bits)