RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16262
(222 letters)
>1vi6_A 30S ribosomal protein S2P; structural genomics, ribosome; 1.95A
{Archaeoglobus fulgidus} SCOP: c.23.15.1 PDB: 1vi5_A
Length = 208
Score = 296 bits (761), Expect = e-103
Identities = 61/192 (31%), Positives = 109/192 (56%), Gaps = 5/192 (2%)
Query: 1 MSGGLDILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLL 60
+ + L L A HIG++ M+++++K R DG+++L++R+ E++ +
Sbjct: 3 LEKEYEYL----VPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRV 58
Query: 61 AARAIVAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPR 120
AA+ + E P+ + ++++R + V F+ G+ I GRF PG TN + + +REP
Sbjct: 59 AAKFLSRYE-PSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPE 117
Query: 121 LLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
++ V DP D Q ++EA V IPV+A C++ + VD+ IP NNK ++ +++WLLAR
Sbjct: 118 VVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAR 177
Query: 181 EVLRFRGVIGPD 192
E+ + RG
Sbjct: 178 EIAKIRGQDFTY 189
>3u5c_A 40S ribosomal protein S0-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_A 3o30_A 3o2z_A 3u5g_A 3jyv_B* 1s1h_B
Length = 252
Score = 289 bits (742), Expect = e-100
Identities = 111/187 (59%), Positives = 138/187 (73%)
Query: 6 DILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAI 65
L +D +L A TH+G+ N E YV+ R DGVH++N+ +TWEKL+LAAR I
Sbjct: 5 ATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAARII 64
Query: 66 VAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPRLLVVT 125
AI +P DV ISSR GQRAVLKFA++TGATPIAGRFTPG+FTN I +F+EPRL++VT
Sbjct: 65 AAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLVIVT 124
Query: 126 DPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRF 185
DP +D Q I EA+YVNIPVIA + +SP FVD+AIPCNN+ HSIGL+W+LLAREVLR
Sbjct: 125 DPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREVLRL 184
Query: 186 RGVIGPD 192
RG +
Sbjct: 185 RGALVDR 191
>2zkq_b 40S ribosomal protein SA; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 295
Score = 291 bits (745), Expect = e-100
Identities = 146/192 (76%), Positives = 168/192 (87%)
Query: 1 MSGGLDILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLL 60
MSG LD+L +KE+DV K L A TH+G N D+QMEQY+YKR++DG++I+NL+RTWEKLLL
Sbjct: 1 MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL 60
Query: 61 AARAIVAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPR 120
AARAIVAIE+PADV VISSR GQRAVLKFA+ TGATPIAGRFTPG FTNQIQAAFREPR
Sbjct: 61 AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR 120
Query: 121 LLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
LLVVTDP DHQP+TEA+YVN+P IA CNT+SPLR+VDIAIPCNNK HS+GLMWW+LAR
Sbjct: 121 LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR 180
Query: 181 EVLRFRGVIGPD 192
EVLR RG I +
Sbjct: 181 EVLRMRGTISRE 192
>2xzm_B RPS0E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_B
Length = 241
Score = 282 bits (724), Expect = 1e-97
Identities = 86/186 (46%), Positives = 126/186 (67%), Gaps = 1/186 (0%)
Query: 8 LSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLLAARAIVA 67
K+DD+ ++L + H + N + QM++Y+ + +G+H +N+ TW+K+ LAAR I A
Sbjct: 3 TQRKQDDIKRLLASNCHQATINLNNQMKRYISHKGVNGIHYINIEETWQKIKLAARVIAA 62
Query: 68 IEHPADVFVISSRPIGQRAVLKFASYTGATPIAG-RFTPGAFTNQIQAAFREPRLLVVTD 126
++HP DV V+ SR GQRA +KFA YT + R+TPG TN + EPR+L+VTD
Sbjct: 63 VQHPEDVMVVCSRIYGQRAAIKFAGYTHCKSTSSSRWTPGTLTNYQTLKYEEPRVLIVTD 122
Query: 127 PHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFR 186
P +D Q I EA+YVNIPVIA C+++SPL +VD+ IPCNN+S SI +++W++AREV R
Sbjct: 123 PRSDFQAIKEASYVNIPVIALCDSDSPLAYVDVVIPCNNRSTESISMIYWMIAREVKILR 182
Query: 187 GVIGPD 192
G + D
Sbjct: 183 GELSKD 188
>3iz6_A 40S ribosomal protein SA (S2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 305
Score = 282 bits (721), Expect = 3e-96
Identities = 120/192 (62%), Positives = 146/192 (76%)
Query: 1 MSGGLDILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLL 60
LS +E D+ ML A H+G++N D+QME+YVYKRR DG++I+NL +TWEKL L
Sbjct: 5 GGAAARALSQREQDIQMMLAADVHLGTKNCDFQMERYVYKRRTDGIYIINLGKTWEKLQL 64
Query: 61 AARAIVAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPR 120
AAR IVAIE+P D+ V S+RP GQRAVLKFA YTGA IAGR TPG FTNQ+Q +F EPR
Sbjct: 65 AARVIVAIENPQDIIVQSARPYGQRAVLKFAQYTGAHAIAGRHTPGTFTNQLQTSFSEPR 124
Query: 121 LLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
LL++TDP TDHQPI E+A NIP IAFC+T+SP+R+VDI IP NNK SIG ++WLLAR
Sbjct: 125 LLILTDPRTDHQPIKESALGNIPTIAFCDTDSPMRYVDIGIPANNKGKQSIGCLFWLLAR 184
Query: 181 EVLRFRGVIGPD 192
VL+ RG I P
Sbjct: 185 MVLQMRGTILPG 196
>3bch_A 40S ribosomal protein SA; laminin receptor, P40 ribosomal protein,
acetylation, cytoplasm, phosphorylation, polymorphism;
2.15A {Homo sapiens}
Length = 253
Score = 276 bits (707), Expect = 9e-95
Identities = 145/192 (75%), Positives = 167/192 (86%)
Query: 1 MSGGLDILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGVHILNLRRTWEKLLL 60
SG LD+L +KE+DV K L A TH+G N D+QMEQY+YKR++DG++I+NL+RTWEKLLL
Sbjct: 34 SSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL 93
Query: 61 AARAIVAIEHPADVFVISSRPIGQRAVLKFASYTGATPIAGRFTPGAFTNQIQAAFREPR 120
AARAIVAIE+PADV VISSR GQRAVLKFA+ TGATPIAGRFTPG FTNQIQAAFREPR
Sbjct: 94 AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR 153
Query: 121 LLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
LLVVTDP DHQP+TEA+YVN+P IA CNT+SPLR+VDIAIPCNNK HS+GLMWW+LAR
Sbjct: 154 LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR 213
Query: 181 EVLRFRGVIGPD 192
EVLR RG I +
Sbjct: 214 EVLRMRGTISRE 225
>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 = 45.0 bits (106), Expect = 1e-05
Identities = 42/223 (18%), Positives = 64/223 (28%), Gaps = 68/223 (30%)
Query: 4 GLDILS-LKEDDVTKMLGAQTHIGSENSDY--------------QMEQYVYKRRNDGVHI 48
GL+IL L+ T + DY Q+ YV + G
Sbjct: 212 GLNILEWLENPSNTP-----------DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
Query: 49 LNLRR------TWEKLLLAARAIVAIEHPADVFVISSRPIGQRAVLKFASYTG-----AT 97
LR + L+ A AI A + F +S R + + G A
Sbjct: 261 GELRSYLKGATGHSQGLVTAVAI-AETDSWESFFVSV-----RKAITVLFFIGVRCYEAY 314
Query: 98 PIAGRFTPGAFTNQIQAAFREPR-LLVVTDPHTDHQPITEAAYVN--IP-----VIAFCN 149
P P + ++ P +L +++ T Q N +P I+ N
Sbjct: 315 PNTS-LPPSILEDSLENNEGVPSPMLSISNL-TQEQVQDYVNKTNSHLPAGKQVEISLVN 372
Query: 150 TESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRGVIGPD 192
V ++ P P S L L R P
Sbjct: 373 --GAKNLV-VSGP-----PQS-------LYGLNLTLRKAKAPS 400
>3bbn_B Ribosomal protein S2; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 231
Score = 43.3 bits (103), Expect = 2e-05
Identities = 16/65 (24%), Positives = 30/65 (46%)
Query: 119 PRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLL 178
P ++++ D ++ + E + IP I +T DI+IP N+ + SI L+ L
Sbjct: 158 PDIVIIVDQQEEYTALRECITLGIPTICLIDTNCNPDLADISIPANDDAIASIRLILTKL 217
Query: 179 AREVL 183
+
Sbjct: 218 VFAIC 222
Score = 31.3 bits (72), Expect = 0.16
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 34 MEQYVYKRRNDGVHILNLRRTWEKL 58
M Y+ + G+HI+NL RT L
Sbjct: 27 MSPYISAKCK-GIHIINLTRTARFL 50
>2vqe_B 30S ribosomal protein S2; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: c.23.15.1 PDB: 1gix_E*
1hnw_B* 1hnx_B* 1hnz_B* 1hr0_B 1ibk_B* 1ibl_B* 1ibm_B
1j5e_B 1jgo_E* 1jgp_E* 1jgq_E* 1ml5_E* 1n32_B* 1n33_B*
1n34_B 1n36_B 1xmo_B* 1xmq_B* 1xnq_B* ...
Length = 256
Score = 43.0 bits (102), Expect = 2e-05
Identities = 21/65 (32%), Positives = 32/65 (49%)
Query: 119 PRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLL 178
P + V DP + + EA + IPVIA +T+S VD IP N+ + SI L+
Sbjct: 159 PDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRA 218
Query: 179 AREVL 183
++
Sbjct: 219 VDLII 223
Score = 31.8 bits (73), Expect = 0.12
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 34 MEQYVYKRRNDGVHILNLRRTWEKLLLAARAI 65
+Y+Y RN G+HI++L++T E+L R I
Sbjct: 28 FARYIYAERN-GIHIIDLQKTMEELERTFRFI 58
>3r8n_B 30S ribosomal protein S2; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_B 3fih_B* 2wwl_B 3oar_B 3oaq_B 3ofb_B
3ofa_B 3ofp_B 3ofx_B 3ofy_B 3ofo_B 3r8o_B 4a2i_B 3i1m_B
1vs7_B* 3e1a_B 3e1c_B 1vs5_B 3i1o_B 3i1q_B ...
Length = 218
Score = 41.7 bits (99), Expect = 5e-05
Identities = 22/65 (33%), Positives = 30/65 (46%)
Query: 119 PRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLL 178
P L V D +H I EA + IPV A +T S VD IP N+ + ++ L +
Sbjct: 150 PDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAV 209
Query: 179 AREVL 183
A V
Sbjct: 210 AATVR 214
Score = 30.9 bits (71), Expect = 0.23
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 34 MEQYVYKRRNDGVHILNLRRTWEKLLLAARAI 65
M+ +++ RN VHI+NL +T A +
Sbjct: 19 MKPFIFGARN-KVHIINLEKTVPMFNEALAEL 49
>3c9g_A UPF0200/UPF0201 protein AF_1395; uncharacterized UPF0201 protein
AF_135, structural genomics, PSI-II, dimer; 2.30A
{Archaeoglobus fulgidus dsm 4304}
Length = 142
Score = 28.7 bits (64), Expect = 0.81
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 137 AAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
A V+ I FC+ + L + + NN + ++
Sbjct: 90 TATVS--RINFCDENAVLSPIKVTFRLNN--IPFSRFLDYIAPE 129
>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription
factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter
litoralis}
Length = 258
Score = 27.6 bits (61), Expect = 2.7
Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 18/63 (28%)
Query: 97 TPIAGRFTPGAFTNQIQAAFREPRLL-----------VVTDPHTDHQPITEAAYVNIPVI 145
PI G PGA +++ + + VV+DP P+ +N
Sbjct: 41 RPIDGSGAPGADDTRVEVQ-PPAQWVLDLIEASPIASVVSDPRLADNPLI---AIN---Q 93
Query: 146 AFC 148
AF
Sbjct: 94 AFT 96
>3txv_A Probable tagatose 6-phosphate kinase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.80A {Sinorhizobium meliloti}
Length = 450
Score = 27.3 bits (60), Expect = 4.4
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 11 KEDDVTKMLGAQTHIGSE--NSDYQMEQYVYKRRNDGVHILNL 51
+ + ++ LG + E ++DYQ + + DG IL +
Sbjct: 246 RAEKLSATLGQLHGMVFEAHSTDYQTPDALRELVADGFAILKV 288
>3t43_A HIV epitope-scaffold 4E10_1XIZA_S0_006_C; putative
phosphotransferase system, transferase; 1.95A
{Artificial gene}
Length = 162
Score = 25.8 bits (57), Expect = 7.9
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 6/30 (20%)
Query: 127 PHTDHQPITEAAYVNIPVIAFCNTESPLRF 156
PHTD + YV I+ P+ F
Sbjct: 49 PHTD------SKYVRQNAISVGILAEPVNF 72
>2f2h_A Putative family 31 glucosidase YICI; BETA8alpha8 barrel, hydrolase;
HET: MPO XTG; 1.95A {Escherichia coli} SCOP: b.150.1.1
b.30.5.11 b.71.1.4 c.1.8.13 PDB: 1xsj_A 1xsi_A 1xsk_A*
1we5_A*
Length = 773
Score = 26.6 bits (59), Expect = 9.1
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 15/80 (18%)
Query: 128 HTDHQPITEAAYVNIPVI-------AFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAR 180
+ D TE AY NIP N + F ++ +K + + +
Sbjct: 183 NRDGGTSTEQAYKNIPFYMTNRGYGVLVNHPQCVSF-EVGSEKVSK-------VQFSVES 234
Query: 181 EVLRFRGVIGPDYLTILGTY 200
E L + + GP +L Y
Sbjct: 235 EYLEYFVIDGPTPKAVLDRY 254
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 0.139 0.427
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,577,640
Number of extensions: 216841
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 468
Number of HSP's successfully gapped: 27
Length of query: 222
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,188,903
Effective search space: 552935196
Effective search space used: 552935196
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 (21.9 bits)
S2: 55 (25.3 bits)