RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8077
(223 letters)
>2xzm_I RPS16E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_I
Length = 145
Score = 117 bits (296), Expect = 6e-34
Identities = 52/107 (48%), Positives = 75/107 (70%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLEMIEPKLLQYKLQEPILLLGKDKFAGVDIRVRVNGGG 139
K+A AVA + GKG L+V+G P++MI P++LQ K+ EPILLLG+ KFA +DIR+RV G G
Sbjct: 16 KNAVAVASVRPGKGLLKVNGSPIDMINPQILQAKIYEPILLLGQQKFANLDIRIRVRGSG 75
Query: 140 HVAQIYAIRQAISKALVAYYQKCKQATGLLGTEKMLVKSTLTLLGKD 186
+ +Q+YAIRQA+SK +VAY+ K ++ L++ +LL D
Sbjct: 76 YTSQVYAIRQALSKGIVAYHAKYVDENSKREIKEQLMQYDRSLLVAD 122
Score = 71.1 bits (175), Expect = 5e-16
Identities = 26/53 (49%), Positives = 38/53 (71%)
Query: 171 TEKMLVKSTLTLLGKDKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAYYQK 223
+ + + LLG+ KFA +DIR+RV G G+ +Q+YAIRQA+SK +VAY+ K
Sbjct: 45 ILQAKIYEPILLLGQQKFANLDIRIRVRGSGYTSQVYAIRQALSKGIVAYHAK 97
>3u5c_Q RP61R, 40S ribosomal protein S16-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_I 3o30_J 3o2z_J 3u5g_Q 1s1h_I
3jyv_I*
Length = 143
Score = 115 bits (291), Expect = 3e-33
Identities = 52/82 (63%), Positives = 72/82 (87%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLEMIEPKLLQYKLQEPILLLGKDKFAGVDIRVRVNGGG 139
KSATAVA+ K GKG ++V+G P+ ++EP++L++K+ EP+LL+G DKF+ +DIRVRV GGG
Sbjct: 14 KSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSNIDIRVRVTGGG 73
Query: 140 HVAQIYAIRQAISKALVAYYQK 161
HV+Q+YAIRQAI+K LVAY+QK
Sbjct: 74 HVSQVYAIRQAIAKGLVAYHQK 95
Score = 70.4 bits (173), Expect = 9e-16
Identities = 33/53 (62%), Positives = 41/53 (77%)
Query: 171 TEKMLVKSTLTLLGKDKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAYYQK 223
+ V L L+G DKF+ +DIRVRV GGGHV+Q+YAIRQAI+K LVAY+QK
Sbjct: 43 ILRFKVYEPLLLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQK 95
>2zkq_i 40S ribosomal protein S16E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 146
Score = 114 bits (288), Expect = 1e-32
Identities = 71/107 (66%), Positives = 85/107 (79%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLEMIEPKLLQYKLQEPILLLGKDKFAGVDIRVRVNGGG 139
K+ATAVA+CK G G ++V+GRPLEMIEP+ LQYKL EP+LLLGK++FAGVDIRVRV GGG
Sbjct: 17 KTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRVRVKGGG 76
Query: 140 HVAQIYAIRQAISKALVAYYQKCKQATGLLGTEKMLVKSTLTLLGKD 186
HVAQIYAIRQ+ISKALVAYYQK + +L++ TLL D
Sbjct: 77 HVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVAD 123
Score = 68.0 bits (167), Expect = 7e-15
Identities = 38/51 (74%), Positives = 44/51 (86%)
Query: 173 KMLVKSTLTLLGKDKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAYYQK 223
+ + + LLGK++FAGVDIRVRV GGGHVAQIYAIRQ+ISKALVAYYQK
Sbjct: 48 QYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQK 98
>3iz6_I 40S ribosomal protein S16 (S9P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 149
Score = 114 bits (287), Expect = 1e-32
Identities = 53/107 (49%), Positives = 74/107 (69%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLEMIEPKLLQYKLQEPILLLGKDKFAGVDIRVRVNGGG 139
K+A AV+YCK G+G ++V+G P+E+I P++L+ K EPILL G+ +F +D+R+RV GGG
Sbjct: 20 KTAVAVSYCKPGRGLIKVNGVPIELIRPEMLRLKAFEPILLAGRSRFKDIDMRIRVRGGG 79
Query: 140 HVAQIYAIRQAISKALVAYYQKCKQATGLLGTEKMLVKSTLTLLGKD 186
+QIYAIRQAI+KALVAYYQK + + + TLL D
Sbjct: 80 KTSQIYAIRQAIAKALVAYYQKYVDEASKKEVKDIFARYDRTLLVAD 126
Score = 70.0 bits (172), Expect = 2e-15
Identities = 28/53 (52%), Positives = 38/53 (71%)
Query: 171 TEKMLVKSTLTLLGKDKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAYYQK 223
++ + L G+ +F +D+R+RV GGG +QIYAIRQAI+KALVAYYQK
Sbjct: 49 MLRLKAFEPILLAGRSRFKDIDMRIRVRGGGKTSQIYAIRQAIAKALVAYYQK 101
>3r8n_I 30S ribosomal protein S9; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_I 3fih_I* 3iy8_I 2wwl_I 3oar_I 3oaq_I
3ofb_I 3ofa_I 3ofp_I 3ofx_I 3ofy_I 3ofo_I 3r8o_I 4a2i_I
2qal_I* 1p6g_I 1p87_I 2aw7_I 2avy_I 2i2u_I ...
Length = 127
Score = 62.1 bits (152), Expect = 8e-13
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 5/81 (6%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLEMIEP-KLLQYKLQEPILLLGK-DKFAGVDIRVRVNG 137
KS+ A + K G G + ++ R LE + + +++P+ L+ +K D+ + V G
Sbjct: 10 KSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKL---DLYITVKG 66
Query: 138 GGHVAQIYAIRQAISKALVAY 158
GG Q AIR I++AL+ Y
Sbjct: 67 GGISGQAGAIRHGITRALMEY 87
Score = 44.4 bits (106), Expect = 3e-06
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 171 TEKMLVKSTLTLLGK-DKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAY 220
T +M+V+ L L+ +K D+ + V GGG Q AIR I++AL+ Y
Sbjct: 40 TARMVVRQPLELVDMVEKL---DLYITVKGGGISGQAGAIRHGITRALMEY 87
>2vqe_I 30S ribosomal protein S9, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.14.1.1
PDB: 1gix_L* 1hnw_I* 1hnx_I* 1hnz_I* 1hr0_I 1i94_I*
1i95_I* 1i96_I* 1i97_I* 1ibk_I* 1ibl_I* 1ibm_I 1j5e_I
1jgo_L* 1jgp_L* 1jgq_L* 1ml5_L* 1n32_I* 1n33_I* 1n34_I
...
Length = 128
Score = 61.7 bits (151), Expect = 1e-12
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLEMIEP-KLLQYKLQEPILLLGK-DKFAGVDIRVRVNG 137
K A A + + G G + V+G+ + EP+ + +F D + V G
Sbjct: 11 KEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRF---DAYITVRG 67
Query: 138 GGHVAQIYAIRQAISKALVAY 158
GG QI AI+ I++ALV Y
Sbjct: 68 GGKSGQIDAIKLGIARALVQY 88
Score = 44.4 bits (106), Expect = 3e-06
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 171 TEKMLVKSTLTLLGK-DKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAY 220
+ L + +F D + V GGG QI AI+ I++ALV Y
Sbjct: 41 VRAVAALEPLRAVDALGRF---DAYITVRGGGKSGQIDAIKLGIARALVQY 88
>3bbn_I Ribosomal protein S9; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 197
Score = 62.5 bits (152), Expect = 2e-12
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 80 KSATAVAYCKEGKGNLRVDGRPLE--MIEPKLLQYKLQEPILLLGK-DKFAGVDIRVRVN 136
K A A +EG G ++ R + + L ++ P+ LG + D+ V+ +
Sbjct: 79 KCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYVKTPLATLGYETNY---DVFVKAH 135
Query: 137 GGGHVAQIYAIRQAISKALVAY 158
GGG Q AI +++AL+
Sbjct: 136 GGGLSGQAQAISLGVARALLKV 157
Score = 45.5 bits (108), Expect = 2e-06
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 171 TEKMLVKSTLTLLGK-DKFAGVDIRVRVNGGGHVAQIYAIRQAISKALVAY 220
VK+ L LG + D+ V+ +GGG Q AI +++AL+
Sbjct: 110 LWLQYVKTPLATLGYETNY---DVFVKAHGGGLSGQAQAISLGVARALLKV 157
>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA
processing, artemis, V(D)J recombination, double-strand
break repair; 2.50A {Saccharomyces cerevisiae} SCOP:
d.157.1.10
Length = 717
Score = 30.5 bits (68), Expect = 0.42
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 3/46 (6%)
Query: 52 RVDGRPLEMIEPKLLQYKLQEPILLLGTKSATAVAYCKEGKGNLRV 97
VD R +I P L K+ +L + K K N+ V
Sbjct: 663 LVDQRSASIIWPSLKSRKI---VLSAPKQIQNEEITAKLIKKNIEV 705
>3uf6_A LMO1369 protein; structural genomics, the center for structural
genomics of I diseases, csgid, unknown function,
transferase; HET: COD; 1.80A {Listeria monocytogenes}
PDB: 3tng_A* 3u9e_A*
Length = 291
Score = 29.8 bits (68), Expect = 0.68
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 10 AIKSVQVFGRKPPKVAIKS-VQVFGRK--KSATAVAYCKEGKGNLRVDGRPL 58
A+ G PK+A+ S V+ K + A + + V G PL
Sbjct: 155 ALAVAHQIGITNPKIALLSAVEEVTAKMPSTLEAQEVVQHFGNQISVSG-PL 205
>4g22_A Hydroxycinnamoyl-COA shikimate/quinate hydroxycinnamoyltransferase;
BAHD superfamily; 1.70A {Coffea canephora} PDB: 4g2m_A
4g0b_A
Length = 439
Score = 28.9 bits (65), Expect = 1.5
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 134 RVNGGGHVAQIYAIRQAISKALVAYY 159
R G + ++ A+S+ALV +Y
Sbjct: 48 RPTGSSNFFDAKVLKDALSRALVPFY 73
Score = 28.9 bits (65), Expect = 1.5
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 196 RVNGGGHVAQIYAIRQAISKALVAYY 221
R G + ++ A+S+ALV +Y
Sbjct: 48 RPTGSSNFFDAKVLKDALSRALVPFY 73
>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 = 28.0 bits (61), Expect = 1.6
Identities = 8/31 (25%), Positives = 17/31 (54%), Gaps = 10/31 (32%)
Query: 8 KVAIK----SVQVFGRKP---PKVAIK-SVQ 30
K A+K S++++ P +AIK +++
Sbjct: 19 KQALKKLQASLKLYA--DDSAPALAIKATME 47
Score = 27.2 bits (59), Expect = 2.9
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 62 EPKLLQYKLQEPILLLGTKSATAVA 86
E + L+ KLQ + L SA A+A
Sbjct: 18 EKQALK-KLQASLKLYADDSAPALA 41
>1i7n_A Synapsin II; synapse, phosphorylation, neuropeptide; 1.90A {Rattus
norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1i7l_A 1auv_A
1aux_A*
Length = 309
Score = 28.2 bits (62), Expect = 2.2
Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 18/126 (14%)
Query: 85 VAYCKEGKGNLRVD-GRPLEMIEPKLL---QYKLQEPILLLGKDKFAGVDIRVRVNGGGH 140
+ + G G ++V+ + I + Y EP + A DIRV+ G +
Sbjct: 159 IGHAHSGMGKVKVENHYDFQDIASVVALTQTYATAEPFID------AKYDIRVQKIGNNY 212
Query: 141 VAQIYAIRQAIS---KALVAYYQKCKQATGLLGTEKMLVKSTLTLLGKDKFAGVDIRVRV 197
A +R +IS K + + K+ V + + G V
Sbjct: 213 KA---YMRTSISGNWKTNTG--SAMLEQIAMSDRYKLWVDACSEMFGGLDICAVKAVHGK 267
Query: 198 NGGGHV 203
+G ++
Sbjct: 268 DGKDYI 273
>1wb1_A Translation elongation factor SELB; selenocysteine, protein
synthesis, selenium, ribosome; HET: GDP DXC; 3.0A
{Methanococcus maripaludis} SCOP: b.43.3.1 b.43.3.1
b.44.1.1 c.37.1.8 PDB: 1wb2_A* 1wb3_A*
Length = 482
Score = 27.8 bits (62), Expect = 3.0
Identities = 14/95 (14%), Positives = 30/95 (31%), Gaps = 16/95 (16%)
Query: 68 YKLQEPI-LLLGTKSATA-VAYCKEGKGNLRVDGRPLEMIEP---KLLQYKLQEPILLLG 122
+ + L +G A K+ + L + ++L+E +L
Sbjct: 307 LTPKMKVHLNVGMLIVPAVAVPFKKVTFGKTEENIILNEVISGNEXYXAFELEEKVLAEV 366
Query: 123 KDKFAGVDIR--------VRVNGGGHVAQIYAIRQ 149
D+ I +R+ G G + + I+
Sbjct: 367 GDRVL---ITRLDLPPTTLRIXGHGLIEEFKPIKD 398
>3f67_A Putative dienelactone hydrolase; alpha-beta-alpha sandwich,
structural genomics, PSI-2, prote structure initiative;
1.74A {Klebsiella pneumoniae subsp}
Length = 241
Score = 27.3 bits (61), Expect = 3.4
Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 17/89 (19%)
Query: 138 GGHVAQIYAIRQAISKALVAYYQKCKQATGLLGTEKMLVKSTLTLLGKDK------FAGV 191
GG + +YA KA VA+Y + K + + +
Sbjct: 125 GGRITWLYAAHNPQLKAAVAWY-----GKLVGEKSLNSPKHPVDIAVDLNAPVLGLYGAK 179
Query: 192 DIRVRVNGGGHVAQIYAIRQAISKALVAY 220
D + + +RQA+ A
Sbjct: 180 DASIP------QDTVETMRQALRAANATA 202
>3bf0_A Protease 4; bacterial, hydrolase, inner membrane, membrane,
transmembrane; 2.55A {Escherichia coli} PDB: 3bez_A
Length = 593
Score = 27.6 bits (61), Expect = 4.4
Identities = 7/41 (17%), Positives = 15/41 (36%), Gaps = 6/41 (14%)
Query: 124 DKFAGVDIRVRVNGGGHVAQIYAIRQAIS------KALVAY 158
G+ + ++ GG + I +A+ K + A
Sbjct: 86 RNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAV 126
Score = 27.6 bits (61), Expect = 4.4
Identities = 7/41 (17%), Positives = 15/41 (36%), Gaps = 6/41 (14%)
Query: 186 DKFAGVDIRVRVNGGGHVAQIYAIRQAIS------KALVAY 220
G+ + ++ GG + I +A+ K + A
Sbjct: 86 RNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAV 126
>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine,
structural genomics, NPPSFA; HET: CIT; 1.70A
{Methanosarcina mazei}
Length = 370
Score = 27.2 bits (61), Expect = 5.2
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 11/55 (20%)
Query: 95 LRVDGRPLEMIEP---KLLQYKLQEPILLLGKDKFAGVDIR-----VRVNGGGHV 141
+ VDG +E +P +L+ + + +D+F + R G
Sbjct: 318 ILVDGNEVEEAKPGSTCVLELSGNKKLAYSKQDRFL---LANLDLTQRFAAYGFS 369
>2p0a_A Synapsin-3, synapsin III; neurotransmitter release, schizophrenia,
vesicle T structural genomics, structural genomics
consortium, SGC, neuropeptide; HET: ANP; 1.90A {Homo
sapiens}
Length = 344
Score = 27.1 bits (59), Expect = 5.4
Identities = 20/127 (15%), Positives = 43/127 (33%), Gaps = 24/127 (18%)
Query: 87 YCKEGKGNLRVDGRP-LEMIEPKLLQYK----LQEPILLLGKDKFAGVDIRVRVNGGGHV 141
+ G G ++V+ + + I + K + I + DIR++ G +
Sbjct: 178 HAHAGMGKIKVENQLDFQDITSVVAMAKTYATTEAFID-------SKYDIRIQKIGSNYK 230
Query: 142 AQIYAIRQAISK-----ALVAYYQKCKQATGLLGTEKMLVKSTLTLLGKDKFAGVDIRVR 196
A +R +IS A ++ + ++ V S + G V
Sbjct: 231 A---YMRTSISGNWKANTGSAMLEQVA----MTERYRLWVDSCSEMFGGLDICAVKAVHS 283
Query: 197 VNGGGHV 203
+G ++
Sbjct: 284 KDGRDYI 290
>1mng_A Manganese superoxide dismutase; oxidoreductase(superoxide
acceptor); 1.80A {Thermus thermophilus} SCOP: a.2.11.1
d.44.1.1 PDB: 3mds_A
Length = 203
Score = 26.0 bits (58), Expect = 8.1
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 170 GTEKMLVKSTLTLLGKDKFAGVDIR--VRVNGGGHV 203
+ LL DI+ VR NGGGH+
Sbjct: 46 KYPYLHGVEVEVLLRHLAALPQDIQTAVRNNGGGHL 81
>2af4_C Phosphate acetyltransferase; PTA dimer with one COA ligand bound
PER monomer, acyltransferase; HET: COA; 2.15A
{Methanosarcina thermophila} SCOP: c.77.1.5 PDB: 1qzt_A*
2af3_C*
Length = 333
Score = 26.0 bits (58), Expect = 9.7
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 14/69 (20%)
Query: 12 KSVQVFGRKPPKVAIKSVQVFG------RKKSATAVAYCKEGKGNLRVDGRPLEM----- 60
K+ ++ + PKVA+ S G + + + +E ++ +DG E+
Sbjct: 192 KTFELLVQDVPKVAMLSYSTKGSAKSKLTEATIASTKLAQELAPDIAIDG---ELQVDAA 248
Query: 61 IEPKLLQYK 69
I PK+ K
Sbjct: 249 IVPKVAASK 257
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
0.319 0.137 0.385
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,321,189
Number of extensions: 199030
Number of successful extensions: 582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 37
Length of query: 223
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 133
Effective length of database: 4,188,903
Effective search space: 557124099
Effective search space used: 557124099
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.0 bits)