RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9422
(211 letters)
>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 148
Score = 78.3 bits (192), Expect = 9e-19
Identities = 45/115 (39%), Positives = 59/115 (51%)
Query: 97 RSLFKGHHQFNIHQRHLTAFSIVLNMNMGIVRRSEERRVGEEGRLLNMNMGIVRSATGRQ 156
+ HH+ N + H F V + + R + + R +
Sbjct: 34 NAGGMHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLDKPWTLVSEQTRVNAAKN 93
Query: 157 VLLALTSLLVDIAGYYKVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVLTA 211
+ V +GYYKVLGKG++PKQPVIVKAKFFS+ AEEKIK+VGGACVL A
Sbjct: 94 KTGVAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKSVGGACVLVA 148
>3iz5_O 60S ribosomal protein L27A (L15P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_O
Length = 144
Score = 74.3 bits (182), Expect = 3e-17
Identities = 28/44 (63%), Positives = 36/44 (81%), Gaps = 1/44 (2%)
Query: 169 AGYYKVLGKGRI-PKQPVIVKAKFFSKLAEEKIKAVGGACVLTA 211
GY KVLGKG + P++P++VKAK SK+AE+KIKA GGA +LTA
Sbjct: 101 FGYTKVLGKGMLPPERPIVVKAKLISKVAEKKIKAAGGAVLLTA 144
>4a17_K L29, RPL27A, 60S ribosomal protein L27A; eukaryotic ribosome,
ribosome, eukaryotic initiation factor 60S, translation,
large ribosomal subunit; 3.52A {Tetrahymena thermophila}
PDB: 4a1a_K 4a1c_K 4a1e_K
Length = 149
Score = 74.4 bits (182), Expect = 3e-17
Identities = 33/43 (76%), Positives = 39/43 (90%)
Query: 169 AGYYKVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVLTA 211
AG++KVLGKGR+P QPV+VKAK+FSK AE +I AVGGACVLTA
Sbjct: 107 AGFFKVLGKGRLPNQPVVVKAKYFSKTAERRIVAVGGACVLTA 149
>3o58_Y 60S ribosomal protein L28; ribosomal RNA and proteins, ribosome;
4.00A {Saccharomyces cerevisiae} PDB: 3o5h_Y 3izc_O
3izs_O 3u5e_a 3u5i_a 1s1i_V 3jyw_V
Length = 149
Score = 74.0 bits (181), Expect = 4e-17
Identities = 31/43 (72%), Positives = 34/43 (79%)
Query: 169 AGYYKVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVLTA 211
AGY K+LGKGRIP PVIVKA+F SKLAEEKI+A GG L A
Sbjct: 107 AGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA 149
>1vq8_L 50S ribosomal protein L15P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.12.1.1 PDB: 1vq4_L*
1vq5_L* 1vq6_L* 1vq7_L* 1s72_L* 1vq9_L* 1vqk_L* 1vql_L*
1vqm_L* 1vqn_L* 1vqo_L* 1vqp_L* 1yhq_L* 1yi2_L* 1yij_L*
1yit_L* 1yj9_L* 1yjn_L* 1yjw_L* 2otj_L* ...
Length = 165
Score = 60.2 bits (146), Expect = 8e-12
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 157 VLLALTSLLVDIAGYYKVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVLT 210
V + D A Y KVLG G++ + + + A FS+ A EK++ GG+ LT
Sbjct: 92 VDVRDVVEEADDADYVKVLGAGQV-RHELTLIADDFSEGAREKVEGAGGSVELT 144
>2zjr_I 50S ribosomal protein L15; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.12.1.1 PDB: 1nwx_J* 1nwy_J* 1sm1_J*
1xbp_J* 2zjp_I* 2zjq_I 1nkw_J 3cf5_I* 3dll_I* 3pio_I*
3pip_I* 1pnu_J 1pny_J 1vor_M 1vou_M 1vow_M 1voy_M 1vp0_M
Length = 156
Score = 42.9 bits (102), Expect = 1e-05
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 173 KVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVLTA 211
K+L G I + V V S A + ++A GG VL
Sbjct: 107 KLLASGEI-SRAVTVHVDAASAAAIKAVEAAGGRVVLPE 144
>3bbo_N Ribosomal protein L15; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 257
Score = 43.3 bits (102), Expect = 2e-05
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 173 KVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVLTA 211
K+L G + + + +KA FS A+EK++ G + ++
Sbjct: 184 KILADGEL-SKKLTIKAGAFSTSAKEKLEYAGCSLIVLP 221
>3v2d_P 50S ribosomal protein L15; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_J 2hgj_O 2hgq_O 2hgu_O 1vsa_J 2j03_P 2jl6_P 2jl8_P
2v47_P 2v49_P 2wdi_P 2wdj_P 2wdl_P 2wdn_P 2wh2_P 2wh4_P
2wrj_P 2wrl_P 2wro_P 2wrr_P ...
Length = 150
Score = 41.0 bits (97), Expect = 5e-05
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 173 KVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGACVL 209
K+LG+G +P+ V A FSK A EK+KA GG VL
Sbjct: 113 KILGEGEA--KPLKVVAHAFSKSALEKLKAAGGEPVL 147
>3r8s_L 50S ribosomal protein L15; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_L 2wwq_L 3oat_L* 3oas_L* 3ofd_L 3ofc_L 3ofr_L*
3ofz_L* 3og0_L 3ofq_L 3r8t_L 3i1n_L 1p85_J 1p86_J 1vs8_L
1vs6_L 2aw4_L 2awb_L 1vt2_L 2i2v_L ...
Length = 143
Score = 40.9 bits (97), Expect = 5e-05
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 173 KVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGAC 207
KV+ G + PV V+ +K A I+A GG
Sbjct: 108 KVILAGEV-TTPVTVRGLRVTKGARAAIEAAGGKI 141
>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 = 41.0 bits (95), Expect = 2e-04
Identities = 41/248 (16%), Positives = 70/248 (28%), Gaps = 84/248 (33%)
Query: 9 KSLLLLICFESWQQEHVK-----------------FKTE-VGPG--TPNFKDRR-VLIQG 47
+L L S Q+E V+ KTE P T + ++R L
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYND 122
Query: 48 TQNFKVHQNRTRQEHV-KLCERLKSTPPGPADRKLWIS---MTANGKYFHVGKRSLFKGH 103
Q F + N +R + KL + L P + + G GK +
Sbjct: 123 NQVFAKY-NVSRLQPYLKLRQALLELRPAK-----NVLIDGVL--G----SGKTWV---- 166
Query: 104 HQFNIHQRHLTAFSIVLNMNMGIVRRSEERRVGEEGRLLNMNMGIVRSATGRQVLLALTS 163
L+ V S + + + ++ +N+ S VL L
Sbjct: 167 ---------------ALD-----VCLSYKVQCKMDFKIFWLNLKNCNSP--ETVLEMLQK 204
Query: 164 LLVDIAGYYKVLGKG--RIPKQPVIVKAKFFSKLAEEK----------------IKAVGG 205
LL I + I + ++A+ L + A
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL 264
Query: 206 AC---VLT 210
+C + T
Sbjct: 265 SCKILLTT 272
Score = 38.3 bits (88), Expect = 0.001
Identities = 29/175 (16%), Positives = 49/175 (28%), Gaps = 41/175 (23%)
Query: 37 NFKDRRVLIQGTQ-NFKVHQNRTRQEHVKLCERLKSTPPGPADRKLW-ISMTANGKYFHV 94
K+ + I KV H + + P + +YF+
Sbjct: 420 QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNI----PKTFDSDDLIPPYLDQYFY- 474
Query: 95 GKRSLFKGHHQFNIHQRHLTA-FSIVLNMNMGIVRRSEERRVGEEGRLLNMNMGIVRSAT 153
GHH NI F +V ++ + + I +T
Sbjct: 475 ----SHIGHHLKNIEHPERMTLFRMVF-LDFRFLEQK-----------------IRHDST 512
Query: 154 GRQVLLALTSLLVDIAGYYKVLGKGRI----PKQPVIVKA--KFFSKLAEEKIKA 202
++ + L + Y K I PK +V A F K+ E I +
Sbjct: 513 AWNASGSILNTLQQLKFY-----KPYICDNDPKYERLVNAILDFLPKIEENLICS 562
>1vq8_O 50S ribosomal protein L18E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.12.1.1 PDB: 1vq4_O*
1vq5_O* 1vq6_O* 1vq7_O* 1s72_O* 1vq9_O* 1vqk_O* 1vql_O*
1vqm_O* 1vqn_O* 1vqo_O* 1vqp_O* 1yhq_O* 1yi2_O* 1yij_O*
1yit_O* 1yj9_O* 1yjn_O* 1yjw_O* 2otj_O* ...
Length = 116
Score = 35.8 bits (83), Expect = 0.002
Identities = 18/34 (52%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 173 KVLGKGRIPKQPVIVKAKFFSKLAEEKIKAVGGA 206
KVLG G + K V V A FS AE KI VG A
Sbjct: 64 KVLGSGVLQK-DVTVAAVDFSGTAETKIDQVGEA 96
>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 = 32.2 bits (72), Expect = 0.058
Identities = 10/30 (33%), Positives = 11/30 (36%), Gaps = 5/30 (16%)
Query: 59 RQEHVKLCERLKSTPPG--PADRKLWISMT 86
+Q KL LK PA L I T
Sbjct: 19 KQALKKLQASLKLYADDSAPA---LAIKAT 45
>3jyw_O 60S ribosomal protein L18(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_O
Length = 121
Score = 28.8 bits (64), Expect = 0.56
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 173 KVLGKGRIPKQP-VIVKAKFFSKLAEEKIKAVGGACV 208
V RI + P V A F+ A KI GG C+
Sbjct: 66 TVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGECI 102
>4a17_N RPL18, 60S ribosomal protein L5; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_N 4a1c_N 4a1e_N
Length = 181
Score = 28.8 bits (64), Expect = 1.0
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 173 KVLGKGRIPKQP-VIVKAKFFSKLAEEKIKAVGGACV 208
V R+ P + V A F++ A ++I A GG C+
Sbjct: 86 TVTNDERLLTVPKLTVCALKFTETARKRILAAGGKCL 122
>3b21_A ORF169B, OSPI; bacterial protein, effector, type 3 secretion SYST
unknown function; 2.01A {Shigella flexneri}
Length = 220
Score = 28.6 bits (63), Expect = 1.2
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 32 GP-GTPNFKDRRVLIQGTQNFKVHQNRTRQEHVKLCERLKSTPPGPADRKLWISMT 86
GP G+P F V +QGT ++ H KL E L S G D+ ++ T
Sbjct: 1 GPLGSPEFMINGVSLQGTAGYEAHTEEGNVNVKKLLESLNSKSLGDMDKDSELAAT 56
>3izc_R 60S ribosomal protein RPL18 (L18E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_R
3o58_R 3o5h_R 3u5e_Q 3u5i_Q
Length = 186
Score = 28.4 bits (63), Expect = 1.4
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 173 KVLGKGRIPKQP-VIVKAKFFSKLAEEKIKAVGGACV 208
V RI + P V A F+ A KI GG C+
Sbjct: 86 TVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGECI 122
>2qrj_A Saccharopine dehydrogenase, NAD+, L-lysine- forming; sulfate,
rossmann fold, alpha-aminoadipate pathway, fungal lysine
biosynthesis; 1.60A {Saccharomyces cerevisiae} PDB:
2qrk_A* 2qrl_A* 2q99_A 3ugk_A 3uh1_A* 3uha_A*
Length = 394
Score = 28.1 bits (62), Expect = 2.1
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 102 GHHQFNIHQRHLTAFSIVLNMN-MGIVRRSE----ERRVG 136
GHH + H H + +M + + R+E E R
Sbjct: 2 GHHHHHHHHHHSSGHIEGRHMAAVTLHLRAETKPLEARAA 41
>2zkr_o 60S ribosomal protein L18; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 188
Score = 27.3 bits (60), Expect = 2.8
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 173 KVLGKGRIPKQP-VIVKAKFFSKLAEEKIKAVGGACV 208
V RI + P + V A S A +I GG +
Sbjct: 85 TVTDDVRILEVPKLKVCALRVSSRARSRILKAGGKIL 121
>4aco_A Centromere DNA-binding protein complex CBF3 subun; 1.89A
{Saccharomyces cerevisiae}
Length = 956
Score = 27.4 bits (59), Expect = 4.8
Identities = 10/42 (23%), Positives = 22/42 (52%)
Query: 38 FKDRRVLIQGTQNFKVHQNRTRQEHVKLCERLKSTPPGPADR 79
+K+R+ +++ H++ R + V +CE+L+ G R
Sbjct: 890 YKERKSIVEFYIYLVNHESLDRYKAVDICEKLRDQNEGSFSR 931
>2kav_A Sodium channel protein type 2 subunit alpha; voltage-gated sodium
channel, alternative splicing, disease epilepsy,
glycoprotein, ION transport; NMR {Homo sapiens} PDB:
2kbi_A
Length = 129
Score = 25.9 bits (57), Expect = 6.8
Identities = 4/35 (11%), Positives = 10/35 (28%), Gaps = 5/35 (14%)
Query: 109 HQRHLTAFSIVLNM-----NMGIVRRSEERRVGEE 138
H H ++ + N + + E+
Sbjct: 6 HHHHHSSGLVPRGSHMASENFSVATEESAEPLSED 40
>3ks4_A Polymerase cofactor VP35; RNA-binding protein, protein-RNA complex,
interferon, HOST cytoplasm, interferon antiviral system
evasion; 2.40A {Reston ebolavirus} PDB: 3ks8_A
Length = 184
Score = 26.3 bits (57), Expect = 6.9
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 12/69 (17%)
Query: 24 HVKFKTEVGPGTPNFKDRRVLIQGTQNFKVHQN--------RTRQEHVKLCE-RLKSTPP 74
H +F+ + G + LIQ T+ + Q+ R+R + + C+ L+ PP
Sbjct: 104 HAEFQASLADG---DSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPP 160
Query: 75 GPADRKLWI 83
P + W+
Sbjct: 161 SPKIDRGWV 169
>4gh9_A Polymerase cofactor VP35; viral polymerase, interferon inhibition,
double stranded VIR viral protein,RNA binding protein;
1.65A {Marburg virus}
Length = 146
Score = 25.5 bits (55), Expect = 8.7
Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 17/97 (17%)
Query: 1 MPSGCLPLKSLLLLICFESWQQE-----HVKFKTEVGPGTPNFKDRRVLIQGTQNFKVHQ 55
+P P L ++ +++ F + G + L + ++ F
Sbjct: 38 LPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEG---ENAQAALTRLSRTFDAFL 94
Query: 56 N--------RTRQEHVKLCE-RLKSTPPGPADRKLWI 83
+ Q + C+ L++ PP P K W+
Sbjct: 95 GVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWV 131
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
0.323 0.138 0.413
Gapped
Lambda K H
0.267 0.0488 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,187,057
Number of extensions: 183395
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 326
Number of HSP's successfully gapped: 25
Length of query: 211
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 122
Effective length of database: 4,216,824
Effective search space: 514452528
Effective search space used: 514452528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.5 bits)