RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6932
(150 letters)
>1jid_A Signal recognition particle 19 kDa protein; signal recognition
particle (SRP), protein-RNA complex, GGAG tetraloop,
signaling protein/RNA complex; HET: 5BU A23; 1.80A {Homo
sapiens} SCOP: d.201.1.1 PDB: 3ktv_B* 1mfq_B* 1ry1_B*
2go5_B 2j37_B
Length = 128
Score = 143 bits (363), Expect = 2e-45
Identities = 62/128 (48%), Positives = 86/128 (67%), Gaps = 1/128 (0%)
Query: 1 MATIDTKKHTDVERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKY 60
MA + D +R++CIYPAY+N KKT+AEGRRIP +KAV+NPT +I DV S GL
Sbjct: 1 MACAAARSPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNV 60
Query: 61 HIE-NKLYPREISKEHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGALIPKLKSRQG 119
+E NK+Y RE +++ RGR RVQLK +DGS FP+R++VML+ +IPKLK+R
Sbjct: 61 FLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ 120
Query: 120 KQANSEQN 127
+ + +
Sbjct: 121 LEHHHHHH 128
>3dlu_A SRP19, signal recognition particle 19 kDa protein; protein-RNA,
cytoplasm, ribonucleoprotein, RNA-binding, RNA binding
protein; 1.80A {Pyrococcus furiosus} PDB: 3dlv_B
Length = 106
Score = 95.7 bits (238), Expect = 1e-26
Identities = 19/108 (17%), Positives = 44/108 (40%), Gaps = 11/108 (10%)
Query: 16 VCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHI--ENKLYPREISK 73
++P+ ++ + + GR +P++ AV++P ++I K E+KL PR
Sbjct: 4 FVVWPSELDSRLSRKYGRIVPRSIAVESPRVEEIVRAAEELKFKVIRVEEDKLNPRLSGI 63
Query: 74 EHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGALIPKLKSRQGKQ 121
+ +R + L++ G + + + I + + R
Sbjct: 64 DEELRTFGMIVLESPYG---------KSKSLKLIAQKIREFRRRSAGT 102
>1kvn_A SRP19; RNA binding protein; NMR {Archaeoglobus fulgidus} SCOP:
d.201.1.1 PDB: 1kvv_A
Length = 104
Score = 92.9 bits (231), Expect = 1e-25
Identities = 27/117 (23%), Positives = 55/117 (47%), Gaps = 14/117 (11%)
Query: 14 RWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIENKLYPREISK 73
+ ++ ++ KK+ AEGRRIP+ AV N ++ + GLK+ E K YP+
Sbjct: 2 KESVVWTVNLDSKKSRAEGRRIPRRFAVPNVKLHELVEASKELGLKFRAEEKKYPKS--- 58
Query: 74 EHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGALIPKLKSRQGKQANSEQNQQR 130
GR V+ + T+ +M+ L I +++ ++ +Q ++ +++
Sbjct: 59 WWEEGGRVVVEKRG-----------TKTKLMIELARKIAEIREQKREQKKDKKKKKK 104
>1lng_A SRP19, signal recognition particle 19 kDa protein; protein-RNA
complex, signaling protein/RNA complex; 2.30A
{Methanocaldococcus jannaschii} SCOP: d.201.1.1 PDB:
2v3c_A 3ndb_A 1l9a_A*
Length = 87
Score = 89.0 bits (221), Expect = 2e-24
Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 4/80 (5%)
Query: 16 VCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIE-NKLYPREISKE 74
+ I+P+YI++KK+ EGR++P+ A++ P+ KDI+ L GL+ I +K YPR+
Sbjct: 1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQ---H 57
Query: 75 HFVRGRARVQLKNDDGSPVN 94
+ G V K + +
Sbjct: 58 WEICGCVEVDYKGNKLQLLK 77
>3ktw_A SRP19, signal recognition particle 19 kDa protein;
ribonucleoprotein complex, RNA-RNA tertiary
interactions, AS loop, 7S RNA; 3.20A {Sulfolobus
solfataricus}
Length = 109
Score = 43.4 bits (102), Expect = 2e-06
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 13 ERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIE-NKLYPREI 71
E + I+P+Y T ++GRR+ + +++ L GL + NK YPR
Sbjct: 16 ENRIVIWPSYFF-SPTRSKGRRLARI--PYKIKTEELVSTLRELGLDPIVIENKKYPR-- 70
Query: 72 SKEHFVRGRARVQ 84
+ + V+
Sbjct: 71 --DRKINFLIAVK 81
>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 = 34.4 bits (78), Expect = 0.009
Identities = 23/154 (14%), Positives = 45/154 (29%), Gaps = 40/154 (25%)
Query: 4 IDTKKHTDVERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLS--TTGLKYH 61
D K D+ + + + E I +K + T + +LS ++
Sbjct: 33 FDCKDVQDMPKSIL----------SKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF 82
Query: 62 IENKL---YP------------REISKEHFVRGRARVQLKNDDGSPVNPDFPTREAVMLH 106
+E L Y + ++ R R+ +D +R L
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY---NDNQVFAKYNVSRLQPYLK 139
Query: 107 LGALIPKLKSRQGKQANSEQNQQRDLSGGGGGGK 140
L + +L+ + + G G GK
Sbjct: 140 LRQALLELRPAKNVL----------IDGVLGSGK 163
>3db3_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA
repair, tandem tudor domains, LI metal binding, DNA
replication; HET: M3L; 2.40A {Homo sapiens} PDB: 3db4_A
2l3r_A*
Length = 161
Score = 29.2 bits (65), Expect = 0.38
Identities = 18/76 (23%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 34 RIPKAKAVDNPTYKDIDDVLSTTGLKYHIENKLYPREIS---KEHFVRGRARVQLKNDD- 89
R+ + + + YH++ YP VR RAR +K D
Sbjct: 34 RVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDL 93
Query: 90 --GSPV----NPDFPT 99
G V NPD P
Sbjct: 94 EVGQVVMLNYNPDNPK 109
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
0.315 0.135 0.397
Gapped
Lambda K H
0.267 0.0573 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,288,412
Number of extensions: 127138
Number of successful extensions: 194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 9
Length of query: 150
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 65
Effective length of database: 4,328,508
Effective search space: 281353020
Effective search space used: 281353020
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: 42 (22.0 bits)
S2: 53 (24.5 bits)