RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9436
(188 letters)
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 87.9 bits (218), Expect = 2e-22
Identities = 35/78 (44%), Positives = 47/78 (60%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M HK RG AL+RLKV+EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S VG
Sbjct: 81 MVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVG 140
Query: 125 WKYKTIVRHLERKRREKS 142
WK +
Sbjct: 141 WKAAAAAAAAAAAAAAAA 158
>4a17_I RPL13A, 60S ribosomal protein L13A; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_I 4a1c_I 4a1e_I
Length = 198
Score = 85.4 bits (211), Expect = 3e-21
Identities = 38/123 (30%), Positives = 58/123 (47%), Gaps = 10/123 (8%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M PHK +GA AL+RLK++EGIP Y R ++ V AL+ L+ R C +G +S VG
Sbjct: 86 MLPHKTPKGAAALERLKIFEGIPTPYDRVKKQVVVDALKVQRLRNSRPVCKLGDLSASVG 145
Query: 125 WKYKTIVRHLERKRREKSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKATFPLTKQINT 184
W +T++ LE KRR ++ + + A + ++
Sbjct: 146 WGKQTLIEKLEEKRRARAKTYHD----------KKVKQADARKKELAAPALKAIKDKLAQ 195
Query: 185 FGY 187
FGY
Sbjct: 196 FGY 198
>3izc_K 60S ribosomal protein RPL16 (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_K
3o58_P 3o5h_P 3u5e_O 3u5i_O
Length = 199
Score = 85.4 bits (211), Expect = 4e-21
Identities = 48/123 (39%), Positives = 67/123 (54%), Gaps = 10/123 (8%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M HK RG AL+RLKV+EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S VG
Sbjct: 87 MVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVG 146
Query: 125 WKYKTIVRHLERKRREKSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKATFPLTKQINT 184
WKY+ +V LE KR+ S E + A ++ + KQ+
Sbjct: 147 WKYEDVVAKLEAKRKVSSAEYYAKKRAFT--------KKVASANATAAES--DVAKQLAA 196
Query: 185 FGY 187
GY
Sbjct: 197 LGY 199
>3iz5_K 60S ribosomal protein L13A (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_K
Length = 206
Score = 84.3 bits (208), Expect = 1e-20
Identities = 46/123 (37%), Positives = 63/123 (51%), Gaps = 8/123 (6%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M PHK RG AL RLK YEG+PP Y R +R+ +P AL+ + L+PG YC +G++S EVG
Sbjct: 92 MIPHKTARGEAALARLKAYEGVPPPYDRTKRMVIPDALKVLRLQPGHRYCLLGQLSKEVG 151
Query: 125 WKYKTIVRHLERKRREKSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKATFPLTKQINT 184
W Y +R LE KR+EK+ L KA K ++ + +
Sbjct: 152 WNYADTIRELEEKRKEKAKVSYDRRKQLA--------KLRVKAEKAAEEKLGTQLEILAP 203
Query: 185 FGY 187
Y
Sbjct: 204 IKY 206
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 83.9 bits (207), Expect = 1e-20
Identities = 51/123 (41%), Positives = 72/123 (58%), Gaps = 8/123 (6%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M PHK RG AL RLKV++GIPP Y +++R+ VP AL+ V LKP R + +GR++HEVG
Sbjct: 87 MLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVG 146
Query: 125 WKYKTIVRHLERKRREKSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKATFPLTKQINT 184
WKY+ + LE KR+EK+ + + L K+A K V+K T+ + T
Sbjct: 147 WKYQAVTATLEEKRKEKAKIHYRKKKQLM--------RLRKQAEKNVEKKIDKYTEVLKT 198
Query: 185 FGY 187
G
Sbjct: 199 HGL 201
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 81.1 bits (201), Expect = 4e-20
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M P K DRG KA +RLKVY GIP ++ +Q + A + Y +VG ++ +G
Sbjct: 82 MLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETIVEAHVS--RLSRPKYVTVGEVAKFLG 139
Query: 125 WKY 127
K+
Sbjct: 140 GKF 142
>1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M
1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I*
1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K*
1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
Length = 145
Score = 68.0 bits (167), Expect = 3e-15
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 65 MTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124
M PHK RG +A + ++VY G P T+L + + ++G IS +G
Sbjct: 86 MLPHKKQRGREAFESVRVYLGNPYDEDGEV--LDGTSLDRL---SNIKFVTLGEISETLG 140
Query: 125 WKY 127
Sbjct: 141 ANK 143
>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 = 34.8 bits (79), Expect = 0.012
Identities = 28/132 (21%), Positives = 45/132 (34%), Gaps = 42/132 (31%)
Query: 28 IGHFDRKRKQARHESKIRAVEKLELFS--------IEN-------ARNQSESMTPHKLDR 72
IGH H I E++ LF +E A N S S+
Sbjct: 477 IGH---------HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN----- 522
Query: 73 GAKALKRLKVYEG-IPPKYARRQRLCVPTALRTVCLKPG----RS-YCSVGRIS--HEVG 124
L++LK Y+ I + +RL A+ K S Y + RI+ E
Sbjct: 523 ---TLQQLKFYKPYICDNDPKYERLV--NAILDFLPKIEENLICSKYTDLLRIALMAEDE 577
Query: 125 WKYKTIVRHLER 136
++ + ++R
Sbjct: 578 AIFEEAHKQVQR 589
Score = 26.7 bits (58), Expect = 5.2
Identities = 11/89 (12%), Positives = 30/89 (33%), Gaps = 15/89 (16%)
Query: 12 RLATLVTEKTTST-KRNIGHFDRKR-----KQARHESKIRAVEKLELFSIENAR--NQSE 63
RL + K ++ + R + E + ++ ++ + R N ++
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMT-RMYIEQRDRLYNDNQ 124
Query: 64 SMTPHKLDRGA------KALKRLKVYEGI 86
+ + R +AL L+ + +
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRPAKNV 153
>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 = 30.4 bits (68), Expect = 0.43
Identities = 26/131 (19%), Positives = 35/131 (26%), Gaps = 50/131 (38%)
Query: 44 IRAVEKLELFSIENARNQSESMTPH---KLDRGAKALKRLKVYEGIPPK--YARRQRLCV 98
I + + ++ N N L GAK L V G PP+ Y L
Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL----VVSG-PPQSLYG----LN- 390
Query: 99 PTALRTVCLKPGRSYCSVGRISHEVGWKYKTIVRHLERKRREKSIEKIKL---------- 148
LR G RI +R K+K
Sbjct: 391 -LTLRKAKAPSG---LDQSRIPF--------------SER------KLKFSNRFLPVASP 426
Query: 149 -HTVYLIPCLD 158
H+ L+P D
Sbjct: 427 FHSHLLVPASD 437
>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 = 27.6 bits (60), Expect = 1.8
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 16/37 (43%)
Query: 75 KALKRL----KVYEGIPPKYARRQRLCVPT-ALR-TV 105
+ALK+L K+Y A P A++ T+
Sbjct: 20 QALKKLQASLKLYA---DDSA-------PALAIKATM 46
Score = 26.1 bits (56), Expect = 6.3
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 26/47 (55%)
Query: 36 KQARHESKIRAVEKLE----LFSIENARNQSESMTPHKLDRGAKALK 78
KQA ++KL+ L++ ++A P A A+K
Sbjct: 19 KQA--------LKKLQASLKLYADDSA--------P------ALAIK 43
>2x8r_A Glycosyl hydrolase; peptidoglycan cleavage,
endo-N-acetylmuramidases, motif; 1.70A {Aspergillus
fumigatus}
Length = 210
Score = 27.0 bits (60), Expect = 3.7
Identities = 8/45 (17%), Positives = 13/45 (28%), Gaps = 2/45 (4%)
Query: 141 KSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKATFPLTKQINTF 185
K+ L LD E N + + + I+ F
Sbjct: 80 KNGGGWSDDNRTLPGMLDIEYNPYGATCYGLSHSQ--MVAWIHDF 122
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 26.0 bits (58), Expect = 6.8
Identities = 4/24 (16%), Positives = 9/24 (37%), Gaps = 3/24 (12%)
Query: 157 LDCESN---LTKKAGKQVKKATFP 177
+D ++ K + K +F
Sbjct: 218 IDVTTSQEQSGKPTNNDIHKNSFV 241
>1zvf_A 3-hydroxyanthranilate 3,4-dioxygenase; jellyroll beta-barrel,
oxidoreductase; 2.41A {Saccharomyces cerevisiae} SCOP:
b.82.1.20
Length = 176
Score = 25.7 bits (56), Expect = 9.2
Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 12/82 (14%)
Query: 99 PTALRTVCLKPGRSYCSVGRISHEVGWKYKTIVRHLERKRREKSIEKIKLHTVYLIPCLD 158
+ + G SY G + H T+ +E+ R +KI+ + C
Sbjct: 76 EPKFIDIIINEGDSYLLPGNVPHSPVRFADTVGIVVEQDRPGGENDKIRWY------CSH 129
Query: 159 CESNLTKKA------GKQVKKA 174
C + + G QVK+A
Sbjct: 130 CRQVVHESELQMLDLGTQVKEA 151
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 0.132 0.382
Gapped
Lambda K H
0.267 0.0586 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,662,589
Number of extensions: 146437
Number of successful extensions: 282
Number of sequences better than 10.0: 1
Number of HSP's gapped: 275
Number of HSP's successfully gapped: 25
Length of query: 188
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 100
Effective length of database: 4,244,745
Effective search space: 424474500
Effective search space used: 424474500
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: 54 (24.9 bits)