RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4234
(177 letters)
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*
Length = 197
Score = 122 bits (306), Expect = 1e-35
Identities = 94/173 (54%), Positives = 116/173 (67%), Gaps = 41/173 (23%)
Query: 5 RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
R P +SKTY TP+RPYE +RLD ELK+ GE+GL+NK+E++R+ + L+KIR+AAR+LLT
Sbjct: 3 RAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTR 62
Query: 65 DEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLV 124
DEK+ +RLFEG NAL+RRLV
Sbjct: 63 DEKDPKRLFEG-----------------------------------------NALIRRLV 81
Query: 125 RIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
R+GVL E + KLDYVL LK+EDFLERRLQTQV+KLGLAKS+HHARVLI QRHI
Sbjct: 82 RVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHI 134
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Length = 181
Score = 120 bits (301), Expect = 5e-35
Identities = 92/173 (53%), Positives = 106/173 (61%), Gaps = 41/173 (23%)
Query: 5 RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
+ SKTY TPRRPYEK RLD E+K+IG +GL+NKREVWRV+ LAK RKAARELLTL
Sbjct: 3 KTYINTSKTYSTPRRPYEKERLDNEMKLIGTFGLKNKREVWRVQMILAKFRKAARELLTL 62
Query: 65 DEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLV 124
D K+ RRLFEG +ALLRR+
Sbjct: 63 DPKDPRRLFEG-----------------------------------------SALLRRMF 81
Query: 125 RIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
+ G+L E KLDYVLGL I +ERRLQT+VFKL LA SIHH+RVLIRQRHI
Sbjct: 82 KYGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLANSIHHSRVLIRQRHI 134
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 195
Score = 114 bits (285), Expect = 2e-32
Identities = 94/175 (53%), Positives = 109/175 (62%), Gaps = 43/175 (24%)
Query: 5 RVPSVHSKTYVT--PRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELL 62
R P +SKTY T PRRPYEK RLD ELK++GEYGLR KRE+WRV+YAL++IR AR LL
Sbjct: 3 RAPRTYSKTYSTKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNNARHLL 62
Query: 63 TLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRR 122
TLDEK RR+FEG ALLRR
Sbjct: 63 TLDEKNPRRIFEG-----------------------------------------EALLRR 81
Query: 123 LVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
+ R G+L + + KLDYVL L +E+FL RRLQT VFK G+AKSIHHARVLIRQRHI
Sbjct: 82 MNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGMAKSIHHARVLIRQRHI 136
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog;
S4 domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 71
Score = 58.5 bits (142), Expect = 2e-12
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 144 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
RRL T + KL +A+ + A + Q H+
Sbjct: 2 SSGSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHV 35
>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 = 39.8 bits (92), Expect = 2e-04
Identities = 25/137 (18%), Positives = 52/137 (37%), Gaps = 31/137 (22%)
Query: 30 LKIIGEYGLRNKREVW-RVKY----ALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVR 84
L II E +R+ W K+ L I +++ L L+ E R++F+ ++
Sbjct: 330 LSIIAES-IRDGLATWDNWKHVNCDKLTTIIESS--LNVLEPAEYRKMFDRLSVFPPSAH 386
Query: 85 I--GVLDESRMKLDYVL-GLKIEDFLERRLQTQVSNALLRR-----LVRI-GVLDESRMK 135
I +L ++ I+ + + +L+ + + I + E ++K
Sbjct: 387 IPTILLS--------LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVK 438
Query: 136 LDYVLGLKIEDFLERRL 152
L+ E L R +
Sbjct: 439 LEN------EYALHRSI 449
Score = 36.8 bits (84), Expect = 0.003
Identities = 33/170 (19%), Positives = 51/170 (30%), Gaps = 61/170 (35%)
Query: 4 NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAAREL-- 61
R PS+ ++ Y+ R RL + ++ K V R++ K+R+A EL
Sbjct: 102 QRQPSMMTRMYIEQRD-----RLYNDNQVF------AKYNVSRLQ-PYLKLRQALLELRP 149
Query: 62 ----------------LTL----DEKEQRRLFEG------------NALLRRL----VRI 85
+ L K Q ++ +L L +I
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 86 GVLDESRMKLDYVLGLKIEDFLE--RRL--QTQVSNALLRRLVRIGVLDE 131
SR + L+I RRL N LL VL
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL-------VLLN 252
Score = 29.1 bits (64), Expect = 0.86
Identities = 27/150 (18%), Positives = 51/150 (34%), Gaps = 25/150 (16%)
Query: 25 RLDQELKIIGEYGLRNKREVWRVKYALAKI---RKAARELLTLDE---KEQRRLFEGNAL 78
++D ++ K + ++ L ++ + LL L + F +
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC- 266
Query: 79 LRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDY 138
+ L+ +R K ++ DFL T +S L DE + L
Sbjct: 267 -KILL------TTRFK-------QVTDFLSAATTTHIS---LDHHSMTLTPDEVKSLLLK 309
Query: 139 VLGLKIEDFLERRLQTQVFKLGL-AKSIHH 167
L + +D L T +L + A+SI
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRD 339
>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 = 34.9 bits (79), Expect = 0.005
Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 25/47 (53%)
Query: 66 EKEQRRLFEGNALLRRLVRIGVLDESRMKLDY------VLGLK--IE 104
EK+ L++L ++ +KL Y L +K +E
Sbjct: 18 EKQA---------LKKL-------QASLKL-YADDSAPALAIKATME 47
Score = 30.7 bits (68), Expect = 0.17
Identities = 8/34 (23%), Positives = 15/34 (44%), Gaps = 16/34 (47%)
Query: 120 LRRLVRIGVLDESRMKLDY------VLGLK--IE 145
L++L ++ +KL Y L +K +E
Sbjct: 22 LKKL-------QASLKL-YADDSAPALAIKATME 47
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 201
Score = 34.8 bits (81), Expect = 0.007
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 148 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL +F+LG+A +I AR L+ RHI
Sbjct: 87 LEMRLDNILFRLGMAPTIPGARQLVNHRHI 116
>3r8n_D 30S ribosomal protein S4; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D*
2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D*
2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D*
...
Length = 205
Score = 34.5 bits (80), Expect = 0.008
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 147 FLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL V+++G + AR L+ + I
Sbjct: 92 LLEGRLDNVVYRMGFGATRAEARQLVSHKAI 122
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D*
1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D*
1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G
2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...
Length = 209
Score = 34.6 bits (80), Expect = 0.008
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 147 FLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL V++LG A S AR L+R HI
Sbjct: 96 LLESRLDNVVYRLGFAVSRRQARQLVRHGHI 126
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology,
possible helix-turn-helix motif, ribosome; NMR
{Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB:
1c06_A 1eg0_A 1qd7_C
Length = 159
Score = 34.0 bits (79), Expect = 0.011
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 148 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL V++LGLA++ AR L+ HI
Sbjct: 49 LESRLDNLVYRLGLARTRRQARQLVTHGHI 78
>3gwf_A Cyclohexanone monooxygenase; flavoprotein biocatalysis
baeyer-villiger oxidation green CH monooxygenase,
oxidoreductase; HET: FAD NAP; 2.20A {Rhodococcus SP}
PDB: 3gwd_A* 3ucl_A*
Length = 540
Score = 29.8 bits (68), Expect = 0.52
Identities = 13/116 (11%), Positives = 34/116 (29%), Gaps = 7/116 (6%)
Query: 11 SKTYVTPR--RPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
+ Y P RP ++ + E + ++ +++ E+E
Sbjct: 210 TPQYSVPVGNRPVNPEQIAEIKADYDRI-----WERAKNSAVAFGFEESTLPAMSVSEEE 264
Query: 69 QRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLV 124
+ R+F+ R + D F+ ++ + + R +
Sbjct: 265 RNRIFQEAWDHGGGFRFMFGTFGDIATDEAANEAAASFIRAKVAEIIEDPETARKL 320
>2vjq_A Formyl-coenzyme A transferase; class III COA transferase; HET: EPE;
1.8A {Oxalobacter formigenes} PDB: 2vjp_A 2vjm_A*
2vjl_A* 2vjk_A* 1p5h_A 1p5r_A* 2vjn_A* 1t4c_A* 2vjo_A*
2vjm_B* 1vgr_A* 1t3z_A* 1t4c_B* 1vgq_A*
Length = 428
Score = 27.6 bits (62), Expect = 2.7
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 16/46 (34%)
Query: 62 LTLDEKEQRRLFEGNALLRRLV----------RIGVLDESRMKLDY 97
+ LD K EG LL +++ G LD RM +
Sbjct: 70 IELDMKTP----EGKELLEQMIKKADVMVENFGPGALD--RMGFTW 109
>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 = 27.3 bits (60), Expect = 3.4
Identities = 22/152 (14%), Positives = 45/152 (29%), Gaps = 54/152 (35%)
Query: 2 VNNRVPSVHSKTYV----TPRR------PYEKARLDQEL-KIIGEYGLRNKREVWRVKYA 50
N+ +P+ + + + P L+ L K GL + R+ ++
Sbjct: 356 TNSHLPA-GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGL----DQSRIPFS 410
Query: 51 LAKIR-----------------KAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRM 93
K++ A +L+ D + F + +I V D
Sbjct: 411 ERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDI-----QIPVYD---- 461
Query: 94 KLDYVLGLKIEDFLERRLQTQVSNALLRRLVR 125
D L+ +S ++ R+V
Sbjct: 462 ---------TFD--GSDLRV-LSGSISERIVD 481
>4ap3_A Steroid monooxygenase; oxidoreductase, baeyer-villiger; HET: FAD
NAP; 2.39A {Rhodococcus rhodochrous} PDB: 4aox_A*
4aos_A* 4ap1_A*
Length = 549
Score = 27.2 bits (61), Expect = 3.5
Identities = 20/119 (16%), Positives = 40/119 (33%), Gaps = 15/119 (12%)
Query: 11 SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQR 70
S Y P LD + + +R + R + R + L + E+E+R
Sbjct: 223 SANYSIPAG---NVPLDDATRAEQKANYAERRRLSRESGGGSPHRPHPKSALEVSEEERR 279
Query: 71 RLFE-----GNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLV 124
++E G L + + D + F E +++ V + + L+
Sbjct: 280 AVYEERWKLGGVLFSKAFPDQLTDPAANDT-------ARAFWEEKIRAVVDDPAVAELL 331
>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic
aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo
sapiens} PDB: 2xiq_A* 3bic_A
Length = 762
Score = 26.6 bits (59), Expect = 5.0
Identities = 4/23 (17%), Positives = 11/23 (47%)
Query: 38 LRNKREVWRVKYALAKIRKAARE 60
+++ R+ + LA + + A
Sbjct: 511 IKSSRDQALAERCLAALTECAAS 533
>3ubm_A COAT2, formyl-COA:oxalate COA-transferase; HET: COA; 1.99A
{Acetobacter aceti}
Length = 456
Score = 26.5 bits (59), Expect = 6.2
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 16/46 (34%)
Query: 62 LTLDEKEQRRLFEGNALLRRLV----------RIGVLDESRMKLDY 97
+ L+ K EG A+ + + R G ++ RM +
Sbjct: 96 VELNTKTP----EGKAVFEKCIKWADILLENFRPGAME--RMGFTW 135
>1q7e_A Hypothetical protein YFDW; structural genomics, intertwined dimer,
PSI, protein structu initiative; HET: MSE; 1.60A
{Escherichia coli} SCOP: c.123.1.1 PDB: 1pqy_A* 1q6y_A*
1pt7_A 1pt5_A 1pt8_A*
Length = 428
Score = 26.4 bits (59), Expect = 6.7
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 16/46 (34%)
Query: 62 LTLDEKEQRRLFEGNALLRRLV----------RIGVLDESRMKLDY 97
+ L+ K EG ++ +L+ G +D M +
Sbjct: 72 IELNTKTA----EGKEVMEKLIREADILVENFHPGAID--HMGFTW 111
>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition,
kinase-INH complex, rubredoxin fold, TPR domain,
transferase; HET: AXX; 2.40A {Mycobacterium
tuberculosis}
Length = 681
Score = 26.4 bits (58), Expect = 7.0
Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 12/90 (13%)
Query: 50 ALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLD---ESRMKLDYVLGLKIEDF 106
+IR AAR + L E R L +R LV G LD +++ +++LG F
Sbjct: 588 TEEQIRDAARRVEALPPTEPRVL-----QIRALVLGGALDWLKDNKASTNHILGF---PF 639
Query: 107 LERRLQTQVSNALLRRLVRIGVLDESRMKL 136
L+ V + LR L R+ R L
Sbjct: 640 TSHGLRLGVEAS-LRSLARVAPTQRHRYTL 668
>1yvr_A RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein, 60 kDa; heat
repeat, VON willebrand factor A, rossmann fold, midas
motif', RNA binding protein; 1.95A {Xenopus laevis}
SCOP: a.118.25.1 c.62.1.5 PDB: 1yvp_A 2i91_A
Length = 538
Score = 26.4 bits (57), Expect = 7.5
Identities = 16/138 (11%), Positives = 46/138 (33%)
Query: 3 NNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELL 62
+ + ++ R ++ L ++ +Y + +EV + + L
Sbjct: 168 VTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLK 227
Query: 63 TLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRR 122
L+ E+ + + + L+ L + ++ +I L + + L +
Sbjct: 228 YLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGK 287
Query: 123 LVRIGVLDESRMKLDYVL 140
+ VL + ++ V
Sbjct: 288 MTADSVLAPASSEVSSVC 305
>1req_A Methylmalonyl-COA mutase; isomerase, intramolecular transferase;
HET: B12 DCA; 2.00A {Propionibacterium freudenreichii
subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 2req_A*
3req_A* 4req_A* 6req_A* 7req_A* 5req_A* 1e1c_A*
Length = 727
Score = 26.2 bits (58), Expect = 8.1
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 38 LRNKREVWRVKYALAKIRKAARELLTLDEKE 68
LR +R+ +VK AL KI AA D
Sbjct: 498 LRAERDPEKVKAALDKITWAAGNPDDKDPDR 528
>3mml_B Allophanate hydrolase subunit 1; structural genomics, PSI-2,
protein structure initiative, tuberculosis structural
genomics consortium; 2.50A {Mycobacterium smegmatis}
Length = 228
Score = 25.4 bits (56), Expect = 9.3
Identities = 13/70 (18%), Positives = 19/70 (27%), Gaps = 12/70 (17%)
Query: 47 VKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGV----LDESRMKLDYV---L 99
VK A + + R+ L + R V I V D L V
Sbjct: 69 VKLAGPRYQAPTRQRLGKLRVRPEAITHQPPGDRVDVTIDVVYDGAD-----LHEVASLT 123
Query: 100 GLKIEDFLER 109
G+ +
Sbjct: 124 GMTPAQVIAA 133
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
0.325 0.141 0.390
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,857,066
Number of extensions: 176560
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 53
Length of query: 177
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 90
Effective length of database: 4,272,666
Effective search space: 384539940
Effective search space used: 384539940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.4 bits)