RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8562
(205 letters)
>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S
rRNA-protein complex, cadmium IONS, ribosome; 2.30A
{Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T
2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z
2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z
2wrl_Z 2wro_Z ...
Length = 206
Score = 170 bits (433), Expect = 5e-54
Identities = 48/200 (24%), Positives = 98/200 (49%), Gaps = 10/200 (5%)
Query: 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
++ A+ R+ + S LR+ GK+PG++Y + + K+ ++ ++ + H I+
Sbjct: 3 YRLKAYYREGEKPS---ALRRAGKLPGLMYNRHLNR-KVYVDLVEFDKVFRQASIHHVIV 58
Query: 61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
G+ L+R L ++ H DF + E + + VPL F+ + V+
Sbjct: 59 LELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDE-PVEMYVPLRFVGT--PAGVRAGG 115
Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
++ + D+ + P+N+P+FIE+++ +E+ S+H SD+KLP GV + + TIA
Sbjct: 116 -VLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAV--SPEETIA 172
Query: 181 TAIIPVNTLESDNNSSIEKE 200
+ P + + ++ E
Sbjct: 173 AVVPPEDVEKLAEEAAAEVA 192
>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T*
1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S*
3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z
1pnu_T 1pny_T 1vor_W ...
Length = 237
Score = 159 bits (403), Expect = 4e-49
Identities = 34/179 (18%), Positives = 79/179 (44%), Gaps = 9/179 (5%)
Query: 16 SRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYG-KVELVLLR 74
+ + + Y ++ V +++ A ++++ + + ++ + G + L++
Sbjct: 10 PKQKLDESMIAAVAYNK-ENNVSFALDRKAFDRAFRQQST-TGLFDITVEGGETFPALVK 67
Query: 75 NFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISC 134
Q+ K+ +H DF V + + V VP+H S ++ V+ +L I
Sbjct: 68 AVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEV-QGGLVDIVVHNLQIVA 124
Query: 135 L-PKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPVNTLESD 192
P+ +P+ + +++ KM + I DIKLP G ++ + + T+ + + P T E
Sbjct: 125 PGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLA--ADPELTVVSVLPPRLTAEEL 181
>1b75_A Protein (50S ribosomal protein L25); RNA-binding protein, RNA
binding protein; NMR {Escherichia coli} SCOP: b.53.1.1
PDB: 1d6k_A 1dfu_P 1giy_V 1ml5_v* 1p85_T 1p86_T 1vs6_V
1vs8_V 1vt2_V 2aw4_V 2awb_V 2gya_T 2gyc_T 2i2t_V 2i2v_V
2j28_V 2qam_V* 2qao_V* 2qba_V* 2qbc_V* ...
Length = 94
Score = 118 bits (297), Expect = 6e-35
Identities = 34/91 (37%), Positives = 50/91 (54%)
Query: 2 KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
I A RK++G SR LR K P IIYGG + P+ I ++H+ + + K F+S +L
Sbjct: 3 TINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLT 62
Query: 62 LEIYGKVELVLLRNFQLHAYKKLVLHADFQR 92
+ + GK V ++ Q H YK + H DF R
Sbjct: 63 IVVDGKEIKVKAQDVQRHPYKPKLQHIDFVR 93
>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 = 0.057
Identities = 36/208 (17%), Positives = 60/208 (28%), Gaps = 78/208 (37%)
Query: 14 SFSRNLRKIGKVPG-----IIYGGNKDPVKISMNHNMIYHALKKET--FHSSILNLEIYG 66
+ LRK G I + K +K S + FHS +L
Sbjct: 388 GLNLTLRKAKAPSGLDQSRIPFSERK--LKFSNRFLPV-------ASPFHSHLLV----P 434
Query: 67 KVELVLL----RNFQLHAYKKL---VLH----ADFQRVDTEKKIHVKVPLHFINSEISPA 115
+L+ N +A K + V +D + + IS
Sbjct: 435 ASDLINKDLVKNNVSFNA-KDIQIPVYDTFDGSDLRVLSG---------------SISE- 477
Query: 116 VKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVS----VIH 171
++ CII LP + E + H+ D P G S + H
Sbjct: 478 -RIVDCII----------RLP--------VKWETTTQFKATHILDFG-PGGASGLGVLTH 517
Query: 172 STEEDPTIAT--AIIPVNTLESDNNSSI 197
++ T +I TL+ + +
Sbjct: 518 RNKD----GTGVRVIVAGTLDINPDDDY 541
>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 = 0.11
Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 91 QRVDTEKKIHVKVPLHFINSEISPAVKLNSCI 122
Q + KK+ + L+ +S +PA+ + + +
Sbjct: 20 QAL---KKLQASLKLYADDS--APALAIKATM 46
>1xv2_A ALDC, hypothetical protein, similar to alpha- acetolactate
decarboxylase; structural genomics, MCSG; 2.00A
{Staphylococcus aureus subsp} SCOP: d.290.1.1
Length = 237
Score = 28.0 bits (62), Expect = 2.3
Identities = 22/140 (15%), Positives = 45/140 (32%), Gaps = 29/140 (20%)
Query: 43 HNMIYHALKKETFHSSILNLEIYGKVELVLLRNF--QLHAYKKLVLHADFQRVDTEKKIH 100
I + + E + ++IYG + + +R Q Y +L+ A Q + + I
Sbjct: 99 FAQIKNEMLSE---NLFSAVKIYGTFKHMHVRMMPAQQPPYTRLIDSARRQPEEKRQDIR 155
Query: 101 --------------VKVP---LHFINSEISPAVKLNSCIISNV------ISDLYISCLPK 137
V +HF + E + + + +V P
Sbjct: 156 GAIVGFFTPELFHGVGSAGFHIHFADDERAYGGHVLDFEVDDVVVEIQNFETFQQH-FPV 214
Query: 138 NLPKFIEINLEKMEVNTSIH 157
N F++ ++ +V I
Sbjct: 215 NNETFVKAKIDYKDVAEEIR 234
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 0.134 0.374
Gapped
Lambda K H
0.267 0.0490 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,966,915
Number of extensions: 168856
Number of successful extensions: 211
Number of sequences better than 10.0: 1
Number of HSP's gapped: 204
Number of HSP's successfully gapped: 18
Length of query: 205
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 116
Effective length of database: 4,216,824
Effective search space: 489151584
Effective search space used: 489151584
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: 55 (25.5 bits)