RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7992
(131 letters)
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Length = 181
Score = 129 bits (325), Expect = 3e-39
Identities = 85/132 (64%), Positives = 100/132 (75%), Gaps = 5/132 (3%)
Query: 5 RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
+ SKTY TPRRPYEK RLD E+K+IG +GL+NKREVWRV+ LAK RKAARELLTL
Sbjct: 3 KTYINTSKTYSTPRRPYEKERLDNEMKLIGTFGLKNKREVWRVQMILAKFRKAARELLTL 62
Query: 65 DEKE-----HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119
D K+ +ALLRR+ + G+L E + KLDYV GL I +ERRLQT+VFKL LA SI
Sbjct: 63 DPKDPRRLFEGSALLRRMFKYGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLANSI 122
Query: 120 HHARVLIRQRHI 131
HH+RVLIRQRHI
Sbjct: 123 HHSRVLIRQRHI 134
>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 = 129 bits (326), Expect = 3e-39
Identities = 89/132 (67%), Positives = 109/132 (82%), Gaps = 5/132 (3%)
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 DEKE-----HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119
DEK+ NAL+RRLVR+GVL E K KLDYV LK+EDFLERRLQTQV+KLGLAKS+
Sbjct: 63 DEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSV 122
Query: 120 HHARVLIRQRHI 131
HHARVLI QRHI
Sbjct: 123 HHARVLITQRHI 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 = 123 bits (310), Expect = 7e-37
Identities = 88/134 (65%), Positives = 102/134 (76%), Gaps = 7/134 (5%)
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 TLDEKE-----HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAK 117
TLDEK ALLRR+ R G+L + + KLDYV L +E+FL RRLQT VFK G+AK
Sbjct: 63 TLDEKNPRRIFEGEALLRRMNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGMAK 122
Query: 118 SIHHARVLIRQRHI 131
SIHHARVLIRQRHI
Sbjct: 123 SIHHARVLIRQRHI 136
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog;
S4 domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 71
Score = 58.1 bits (141), Expect = 9e-13
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
RRL T + KL +A+ + A + Q H+
Sbjct: 2 SSGSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHV 35
>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 = 0.003
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 102 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
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 = 34.9 bits (81), Expect = 0.003
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 101 FLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
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 = 34.9 bits (81), Expect = 0.003
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 101 FLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
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 = 0.005
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 102 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
LE RL V++LGLA++ AR L+ HI
Sbjct: 49 LESRLDNLVYRLGLARTRRQARQLVTHGHI 78
>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 = 34.1 bits (77), Expect = 0.009
Identities = 18/109 (16%), Positives = 32/109 (29%), Gaps = 41/109 (37%)
Query: 25 RLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLD 84
++D ++ K + ++ L R LL K + N LL VL
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAEL-------RRLLK--SKPYENCLL-------VLL 251
Query: 85 ESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI--RQRHI 131
V K + F L ++L+ R + +
Sbjct: 252 N-------VQNAKAWN---------AFNLS-------CKILLTTRFKQV 277
Score = 30.6 bits (68), Expect = 0.13
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 4 NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAAREL 61
R PS+ ++ Y+ R RL + ++ K V R++ K+R+A EL
Sbjct: 102 QRQPSMMTRMYIEQRD-----RLYNDNQVF------AKYNVSRLQ-PYLKLRQALLEL 147
>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 = 29.9 bits (66), Expect = 0.18
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 14/41 (34%)
Query: 66 EKEHRNALLRRLVRIGVLDESKMKL---DYVWGLKIEDFLE 103
EK+ L++L ++ +KL D L I+ +E
Sbjct: 18 EKQA----LKKL-------QASLKLYADDSAPALAIKATME 47
>3nz2_A Hexapeptide-repeat containing-acetyltransferase; structural
genomics, center for structural genomics of infec
diseases, csgid; HET: ACO; 2.35A {Vibrio cholerae o1
biovar eltor} PDB: 3ect_A*
Length = 195
Score = 27.5 bits (62), Expect = 1.2
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 4/32 (12%)
Query: 51 LAKIRKAARELL----TLDEKEHRNALLRRLV 78
+ +R A L ++ R AL R L
Sbjct: 25 IEALRSQAGRLKLEINQSLDEAERYALQRELF 56
>3srt_A Maltose O-acetyltransferase; structural genomics, the center
structural genomics of infectious diseases, csgid;
2.50A {Clostridium difficile}
Length = 188
Score = 26.7 bits (60), Expect = 1.8
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 51 LAKIRKAARELL------TLDEKEHRNALLRRLV 78
L K R+ ++L DE E R +LR+L
Sbjct: 23 LVKEREYCKKLTRLFNNTLEDEYEKREDILRQLF 56
>3hjj_A Maltose O-acetyltransferase; LEFT-handed beta-helix,
acyltransferase, struct genomics; 2.15A {Bacillus
anthracis} PDB: 3igj_A*
Length = 190
Score = 26.7 bits (60), Expect = 2.0
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 6/34 (17%)
Query: 51 LAKIRKAARELL------TLDEKEHRNALLRRLV 78
L R A+ L E R LL +L+
Sbjct: 24 LVADRVEAKRLTRLYNEAVETGDERRFTLLNQLL 57
>2p2o_A Maltose transacetylase; GK1921, GKA001001921.1, geobacillus
kaustophilus structural genomics, PSI; 1.74A
{Geobacillus kaustophilus} PDB: 2ic7_A
Length = 185
Score = 26.3 bits (59), Expect = 2.4
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 51 LAKIRKAARELL------TLDEKEHRNALLRRLV 78
L K R+ AR L+ E + R LL+ L
Sbjct: 21 LVKERERARRLVRLYNETLETEYDKRTGLLKELF 54
>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 = 2.6
Identities = 4/23 (17%), Positives = 11/23 (47%)
Query: 38 LRNKREVWRVKYALAKIRKAARE 60
+++ R+ + LA + + A
Sbjct: 511 IKSSRDQALAERCLAALTECAAS 533
>3ftt_A Putative acetyltransferase sacol2570; galactoside
O-acetyltransferase, enzyme, structural genomics,
acyltransferase; 1.60A {Staphylococcus aureus subsp}
PDB: 3v4e_A*
Length = 199
Score = 26.3 bits (59), Expect = 2.7
Identities = 6/34 (17%), Positives = 11/34 (32%), Gaps = 6/34 (17%)
Query: 51 LAKIRKAARELL------TLDEKEHRNALLRRLV 78
L R A+++ R L+ +L
Sbjct: 21 LINERARAKDICFELNHTRPSATNKRKELIDQLF 54
>1krr_A Galactoside O-acetyltransferase; LEFT-handed parallel beta helix;
HET: ACO; 2.50A {Escherichia coli} SCOP: b.81.1.3 PDB:
1kqa_A* 1kru_A* 1krv_A*
Length = 203
Score = 26.4 bits (59), Expect = 2.9
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 51 LAKIRKAARELL------TLDEKEHRNALLRRLV 78
L + R + L+ E E R +L++ +
Sbjct: 22 LPEKRLRGKTLMYEFNHSHPSEVEKRESLIKEMF 55
>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 = 4.1
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 38 LRNKREVWRVKYALAKIRKAARELLTLDEKE 68
LR +R+ +VK AL KI AA D
Sbjct: 498 LRAERDPEKVKAALDKITWAAGNPDDKDPDR 528
>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 = 25.8 bits (56), Expect = 5.8
Identities = 25/144 (17%), Positives = 45/144 (31%), Gaps = 57/144 (39%)
Query: 9 VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL-DEK 67
+H+ A+L QE + L +E+ + AR + +K
Sbjct: 101 IHALA----------AKLLQEN----DTTLVKTKELIKNYIT-------ARIMAKRPFDK 139
Query: 68 EHRNALLR-------RLVRI----GV----LDESKMKL-----DYVWGLKIEDFLER--- 104
+ +AL R +LV I G +E L Y + + D ++
Sbjct: 140 KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEE----LRDLYQTY--HVLVGDLIKFSAE 193
Query: 105 RLQTQVFKLGLAKSIHHARVLIRQ 128
L L ++ A + Q
Sbjct: 194 TLSE------LIRTTLDAEKVFTQ 211
>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 = 25.6 bits (56), Expect = 7.1
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 50 ALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLD 84
+IR AAR + L E R +R LV G LD
Sbjct: 588 TEEQIRDAARRVEALPPTEPRVLQIRALVLGGALD 622
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
0.324 0.139 0.399
Gapped
Lambda K H
0.267 0.0520 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,112,002
Number of extensions: 121935
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 32
Length of query: 131
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,384,350
Effective search space: 210448800
Effective search space used: 210448800
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: 52 (24.3 bits)