RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8399
(167 letters)
>1dzl_A Late major capsid protein L1; icosahedral; 3.50A {Human
papillomavirus type 16} SCOP: b.121.6.1
Length = 505
Score = 33.6 bits (77), Expect = 0.021
Identities = 10/62 (16%), Positives = 22/62 (35%)
Query: 62 NRHYTMHNNRNHSMYHAWNDNRNHSMYDNTRNNNRHYTMHNNRNHSMYNTRNINRNHSMY 121
N+ Y + + H+ W + ++ D TR+ N + + + Y N
Sbjct: 308 NKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHG 367
Query: 122 KN 123
+
Sbjct: 368 EE 369
>3oae_A Late major capsid protein L1; jelly roll, receptor HSPG, virus
capsid, VIR protein; HET: JHM IDS; 2.80A {Human
papillomavirus} PDB: 2r5h_A 2r5j_A 2r5k_A
Length = 428
Score = 33.2 bits (76), Expect = 0.030
Identities = 10/62 (16%), Positives = 22/62 (35%)
Query: 62 NRHYTMHNNRNHSMYHAWNDNRNHSMYDNTRNNNRHYTMHNNRNHSMYNTRNINRNHSMY 121
N+ Y + + H+ W + ++ D TR+ N + + + Y N
Sbjct: 291 NKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHG 350
Query: 122 KN 123
+
Sbjct: 351 EE 352
>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc
finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus
musculus} PDB: 3av5_A* 3av6_A*
Length = 1330
Score = 33.4 bits (75), Expect = 0.035
Identities = 12/130 (9%), Positives = 36/130 (27%), Gaps = 4/130 (3%)
Query: 14 YNNRNHSMYDNTRNNNRHYAMYINRNHYMYNTRNNNRIHPM----YDNTRNNNRHYTMHN 69
YN S + + + + + + R+ + + R+
Sbjct: 1101 YNGEPLSWFQRQLRGSHYQPILRDHICKDMSPLVAARMRHIPLFPGSDWRDLPNIQVRLG 1160
Query: 70 NRNHSMYHAWNDNRNHSMYDNTRNNNRHYTMHNNRNHSMYNTRNINRNHSMYKNTGNNNR 129
+ + + + + Y +T + + + + +TGN +
Sbjct: 1161 DGVIAHKLQYTFHDVKNGYSSTGALRGVCSCAEGKACDPESRQFSTLIPWCLPHTGNRHN 1220
Query: 130 HYSMYINRNH 139
H++ R
Sbjct: 1221 HWAGLYGRLE 1230
>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 = 31.0 bits (69), Expect = 0.18
Identities = 23/159 (14%), Positives = 40/159 (25%), Gaps = 40/159 (25%)
Query: 1 MHNNRNHSMYHAWYNNRNHSMYD-------NTRNNNRHYAMYINRNHYMYNTRNNNRIHP 53
++ +S+ S+ N + ++ YN +
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH----YNIP---KTFD 460
Query: 54 MYDNTRNNNRHYTMHNNRNHSMYHAWNDNRNHSM------YDNTR---NNNRHYTMHNNR 104
D Y +H +H N M + + R RH + N
Sbjct: 461 SDDLIPPYLDQYFY----SHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNA 516
Query: 105 NHSMYNTRNINRNHSMYKNTGNNNRHYSMYINRNHSMYT 143
+ S+ NT + Y YI N Y
Sbjct: 517 SGSILNTLQ-------------QLKFYKPYICDNDPKYE 542
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.25
Identities = 4/20 (20%), Positives = 9/20 (45%), Gaps = 1/20 (5%)
Query: 11 HAWYNNRNHSMYDNTRNNNR 30
W ++ + + + NNR
Sbjct: 121 EEWNQRQSEQV-EKNKINNR 139
>1ddw_A GLGF-domain protein homer; pleckstrin homology domain fold,
signaling protein; 1.70A {Rattus norvegicus} SCOP:
b.55.1.4 PDB: 1ddv_A 2p8v_A 1i7a_A*
Length = 120
Score = 29.3 bits (65), Expect = 0.31
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 40 HYMYNTRNNN-RIHPMYDNTRNNNR--HYTMHNNRNHSMYHAWNDNRNHSMY 88
Y Y++ N RI + + N M + + W D+R +++Y
Sbjct: 35 SYFYDSTRNVYRIISLDGSKAIINSTITPNMTFTKTSQKFGQWADSRANTVY 86
>3fef_A Putative glucosidase LPLD; gulosidase, structural genomics, unknown
function, glycosidase, hydrolase, manganese,
metal-binding, NAD, PSI- 2; 2.20A {Bacillus subtilis}
Length = 450
Score = 30.1 bits (67), Expect = 0.35
Identities = 14/148 (9%), Positives = 29/148 (19%), Gaps = 6/148 (4%)
Query: 1 MHNNRNHSMYHAWYNNRNHSMYDNTRNNNRHY----AMYINRNHYMYNTRNNNRIHPMYD 56
Y A + + + ++ + R R
Sbjct: 253 RVAFDLFETYGAIPAAGDRHLAEFLPGPYLKQPEVWKFHLTPISFRKQDRAEKRQETERL 312
Query: 57 NTRNNNRHYTMHNNRNHSMYHAWNDNRNHSMYDNTRNNNRHYTMHNNRNHSMYNTRNINR 116
+ ++ A N N + + + I R
Sbjct: 313 IVQQRGVAEKASGEEGVNIIAALLGLGELVTNVNMPNQGQVLNLPI--QAIVETNAFITR 370
Query: 117 NHSMYKNTGNNNRHYSMYINRNHSMYTL 144
N +G + M R+ S
Sbjct: 371 NRVQPILSGALPKGVEMLAARHISNQEA 398
>2r5i_A L1 protein; HPV18, pentamer, structure, type specific epitope,
capsid, capsid protein, virion; 3.40A {Human
papillomavirus type 18} PDB: 3ofl_A*
Length = 428
Score = 29.7 bits (67), Expect = 0.45
Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 1/63 (1%)
Query: 62 NRHYTMHNNRNHSMYHAWNDNRNHSMYDNTRNNNRHYTMHNNRNH-SMYNTRNINRNHSM 120
N+ Y +H + H+ W++ ++ D TR+ N Y+ +
Sbjct: 289 NKPYWLHKAQGHNNGVCWHNQLFVTVVDTTRSTNLTICASTQSPVPGQYDATKFKQYSRH 348
Query: 121 YKN 123
+
Sbjct: 349 VEE 351
>3hnc_A Ribonucleoside-diphosphate reductase large subuni; oxidoreductase,
ribonucleotide reductase, allosteric enzyme, binding,
DNA replication; HET: TTP; 2.41A {Homo sapiens} PDB:
3hnd_A* 3hne_A* 3hnf_A*
Length = 792
Score = 28.3 bits (63), Expect = 1.5
Identities = 9/87 (10%), Positives = 26/87 (29%), Gaps = 12/87 (13%)
Query: 57 NTRNNNRHYTMHNNRNHSMYHAWNDNRNH-----------SMYDNTRNNNRHYTMHNNRN 105
N ++N ++ N +++ +MY + + +
Sbjct: 412 NRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTK 471
Query: 106 HSMYNTRN-INRNHSMYKNTGNNNRHY 131
+ N I+ N+ +N+ +
Sbjct: 472 VVVRNLNKIIDINYYPVPEACLSNKRH 498
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 26.3 bits (58), Expect = 6.4
Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 6/82 (7%)
Query: 37 NRNHYMYNTRNNNRIHPMYDNTRNNNRHYTMHNNRNHSMYHAWNDNRNHS--MYDNTRNN 94
M+ R+ + + ++ + R + Y+ + NR++ + + NN
Sbjct: 501 PIGKAMFEIRDYSSRDGNNKSYDYDDDS--EISFRGNKNYNNRSQNRDYDDEPFRRSNNN 558
Query: 95 NRHYTMHNNRNHSMYNTRNINR 116
R ++ N++N+ Y++RN N
Sbjct: 559 RRSFSRSNDKNN--YSSRNSNI 578
>1i2h_A PSD-ZIP45(homer-1C/VESL-1L); enabled VAsp homology 1 domain,
signaling protein; 1.80A {Rattus norvegicus} SCOP:
b.55.1.4
Length = 168
Score = 25.6 bits (55), Expect = 7.1
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 40 HYMYNTRNNN-RIHPMYDN--TRNNNRHYTMHNNRNHSMYHAWNDNRNHSMY 88
Y Y++ N RI + + N+ M + + W D+R +++Y
Sbjct: 40 SYFYDSTRNVYRIISLDGSKAIINSTITPNMTFTKTSQKFGQWADSRANTVY 91
>3iyj_F Major capsid protein L1; bovine papillomavirus BPV1, single
cryo-EM, high resolution, late protein, VIR virus; 4.20A
{Bovine papillomavirus type 1}
Length = 495
Score = 25.5 bits (56), Expect = 9.6
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 62 NRHYTMHNNRNHSMYHAWNDNRNHSMYDNTRNNNRHYTMHNNRNH-SMYNTRNIN 115
NR Y + + + AWN+ ++ DNTR N ++ ++ + Y++ N
Sbjct: 305 NRPYWLFRAQGMNNGIAWNNLLFLTVGDNTRGTNLTISVASDGTPLTEYDSSKFN 359
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
0.321 0.129 0.421
Gapped
Lambda K H
0.267 0.0480 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,453,503
Number of extensions: 128031
Number of successful extensions: 469
Number of sequences better than 10.0: 1
Number of HSP's gapped: 422
Number of HSP's successfully gapped: 121
Length of query: 167
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 80
Effective length of database: 4,272,666
Effective search space: 341813280
Effective search space used: 341813280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.2 bits)