RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7821
(231 letters)
>4a17_L RPL15, ribosomal protein L15; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_L 4a1c_L 4a1e_L
Length = 204
Score = 153 bits (388), Expect = 5e-47
Identities = 77/238 (32%), Positives = 117/238 (49%), Gaps = 41/238 (17%)
Query: 1 MGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMGYRAKQGGK 60
MGAY+++ EL+RKKQSD+M +I R+R W+YRQL +H+A R +RPDKAR++GY+ K G
Sbjct: 1 MGAYKYLEELWRKKQSDLMSFILRLRTWEYRQLPVIHKASRSSRPDKARKLGYKNKDG-- 58
Query: 61 LPRSNTSSIMGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRM 120
I R+RV + + + + +P
Sbjct: 59 ----------------------------YAIWRVRVRRGGRKRPVSKGIVYGKPSSVGIN 90
Query: 121 GYRAKQVTLFSVQRYDVEEGNVQYPRVPTMNV--SAEDVVTSVFLKLLL-----AIRRDP 173
+ + +++ E + P + +N +D + +L AIR DP
Sbjct: 91 QLKFAR----NLRSCAEERVGKRVPELRVLNSYWVGQDGTYKFYEVILADPSHNAIRNDP 146
Query: 174 KVNWICKPVHKHREMRGLTSISKKSRGLGKGHGFAQTIGGSRHAAWVRRNTLELRRKR 231
++NWIC+ HKHRE+RGLTS +K RGL A+++ SR W R L+LRR R
Sbjct: 147 RINWICESAHKHRELRGLTSAGRKGRGLRVKGHRAKSLRTSRKGNWRARQMLKLRRYR 204
>3iz5_P 60S ribosomal protein L15 (L15E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_P 2zkr_m
Length = 204
Score = 148 bits (375), Expect = 5e-45
Identities = 84/238 (35%), Positives = 119/238 (50%), Gaps = 41/238 (17%)
Query: 1 MGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMGYRAKQGGK 60
MGAY+++SEL+R+KQSDVMR++ R+R W+YRQ + R RPTRPDKARR+GY+AKQG
Sbjct: 1 MGAYKYVSELWRRKQSDVMRFVQRVRCWEYRQQPAIVRLTRPTRPDKARRLGYKAKQG-- 58
Query: 61 LPRSNTSSIMGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRM 120
++R+RV + + + + +P
Sbjct: 59 ----------------------------YVVYRVRVRRGGRKRPVPKGIVYGKPKHQGIT 90
Query: 121 GYRAKQVTLFSVQRYDVEEGNVQYPRVPTMNV--SAEDVVTSVFLKLLL-----AIRRDP 173
+ ++ + + E + + +N ED F +L+ AIR DP
Sbjct: 91 QLKFQR----NKRSVAEERAGRKLGGLRVLNSYWVNEDSTYKYFEIILVDVAHSAIRNDP 146
Query: 174 KVNWICKPVHKHREMRGLTSISKKSRGLGKGHGFAQTIGGSRHAAWVRRNTLELRRKR 231
++NW+CKPVHKHRE+RGLTS KK RGL SR A W R T+ LRR R
Sbjct: 147 RINWLCKPVHKHRELRGLTSAGKKYRGLRGKGHTHHKARPSRRATWKRNQTVSLRRYR 204
>3jyw_L 60S ribosomal protein L15(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
3izc_P 3izs_P 3o58_O 3o5h_O 3u5e_N 3u5i_N 1s1i_L
Length = 192
Score = 138 bits (348), Expect = 4e-41
Identities = 87/227 (38%), Positives = 114/227 (50%), Gaps = 42/227 (18%)
Query: 2 GAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMGYRAKQGGKL 61
GAY+++ EL RKKQSDV+R++ R+RVW+YRQ +HRA RPTRPDKARR+GY+AKQG
Sbjct: 1 GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQG--- 57
Query: 62 PRSNTSSIMGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMG 121
I+R+RV R+ P+ K G
Sbjct: 58 ---------------------------FVIYRVRV---RRGNRKRPVPKGATYGKPTNQG 87
Query: 122 YRAKQVTLFSVQRYDVEEGNVQYPRVPTMNVS--AEDVVTSVFLKLLL-----AIRRDPK 174
+ S++ E + + +N +D F +L+ AIRRD +
Sbjct: 88 VNELKYQR-SLRATAEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDAR 146
Query: 175 VNWICKPVHKHREMRGLTSISKKSRGLGKGHGFAQTIGGSRHAAWVR 221
NWIC PVHKHRE RGLT+ KKSRG+ KGH F T G R W R
Sbjct: 147 YNWICDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRR-KTWKR 192
>1vq8_M 50S ribosomal protein L15E; 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: d.12.1.2 PDB: 1vq4_M*
1vq5_M* 1vq6_M* 1vq7_M* 1s72_M* 1vqn_M* 2otj_M* 2otl_M*
2qex_M* 2qa4_M* 1vqo_M* 1vq9_M* 1vql_M* 1vqm_M* 1vqk_M*
1vqp_M* 1yij_M* 1yi2_M* 1yit_M* 1yj9_M* ...
Length = 194
Score = 136 bits (345), Expect = 1e-40
Identities = 48/228 (21%), Positives = 82/228 (35%), Gaps = 43/228 (18%)
Query: 1 MGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMGYRAKQGGK 60
AY +I + + + + R ++R + R RPTR DKAR GY+AKQG
Sbjct: 2 RSAYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQG-- 59
Query: 61 LPRSNTSSIMGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRM 120
+ R+ V + R R +++R
Sbjct: 60 ----------------------------VIVARVSVRKGS-----ARKRRHKAGRRSKRQ 86
Query: 121 GYRAKQVTLFSVQRYDVEEGNVQYPRVPTMNV--SAEDVVTSVFLKLLL-----AIRRDP 173
G + +QR E + +P + +N +D +L+ AI+ D
Sbjct: 87 GVT-RITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPAIQNDD 145
Query: 174 KVNWICKPVHKHREMRGLTSISKKSRGLGKGHGFAQTIGGSRHAAWVR 221
++WIC R RGLT +++RGL ++ S + +
Sbjct: 146 DLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSNGGK 193
>1ffk_I Ribosomal protein L15E; ribosome assembly, RNA-RNA, protein-RNA,
protein-protein; 2.40A {Haloarcula marismortui} SCOP:
d.12.1.2
Length = 194
Score = 134 bits (338), Expect = 1e-39
Identities = 55/229 (24%), Positives = 101/229 (44%), Gaps = 45/229 (19%)
Query: 2 GAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMGYRAKQGGKL 61
Y +I E +++ + + R+ ++R+ + R PRPTR D+AR +GY+AK+G
Sbjct: 3 SMYAYIREAWKRPYEGYVGELMWHRLQKWRREPAVVRIPRPTRLDRARALGYKAKKG--- 59
Query: 62 PRSNTSSIMGAYRFISELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTRPDKARRMG 121
+ R+R+ + RA RP + K+++M
Sbjct: 60 ---------------------------IIVVRVRIRRGG-----RRATRPNKGRKSKKMM 87
Query: 122 YRAKQVTLFSVQRYDVEEGNVQYPRVPTMNVS--AEDVVTSVFLKLLL-----AIRRDPK 174
+ ++Q E N +YP + +N ED F +L+ AI+ DP+
Sbjct: 88 VNRRPRKK-NLQWIAEERANRKYPNMEVLNSYWVGEDGRYKWFEVILVDRDHPAIKSDPQ 146
Query: 175 VNWICKPVHKHREMRGLTSISKKSRGLGKGHGFAQTIGGSRHAAWVRRN 223
++W+ + + R RGLTS +K+RGL + A+ + S A + ++
Sbjct: 147 LSWVSR--TRGRVYRGLTSAGRKARGLRRKGRGAEKVRPSLRANFRKKR 193
>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 = 39.1 bits (90), Expect = 0.001
Identities = 37/255 (14%), Positives = 72/255 (28%), Gaps = 79/255 (30%)
Query: 4 YRF----ISELYRKKQSDVMRYI-HRIRVWQYRQLTTLHRAPRPTRPDKARRMGYRAKQG 58
Y+F I R+ YI R R++ Q+ + R K R+ +
Sbjct: 91 YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA 150
Query: 59 -----------GKLPRSNTSSIMGAYRFISELYR-KKQSDVMRY-IHRIRVWQYR----- 100
GK + + ++ K M + I + +
Sbjct: 151 KNVLIDGVLGSGK-------TWVAL-----DVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 101 --QLTTLHRAPRP---TRPDKARRMGYRAKQV-----TLFSVQRY-------DVEEGNVQ 143
L L P +R D + + R + L + Y NVQ
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL----NVQ 254
Query: 144 YPRV-PTMNVSAEDVVTSVFLKLLLAIRRDPKV-NWICKPVHKHREM----RGLTSISKK 197
+ N+S + ++T+ R +V +++ H + LT +
Sbjct: 255 NAKAWNAFNLSCKILLTT----------RFKQVTDFLSAATTTHISLDHHSMTLT--PDE 302
Query: 198 SRGLGKGHGFAQTIG 212
+ L + +
Sbjct: 303 VKSL-----LLKYLD 312
Score = 30.2 bits (67), Expect = 0.64
Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 28/166 (16%)
Query: 6 FISELYR--KKQSDVMRYIHRIRVWQYRQLTTLH-RAPRPTRPDK--ARRMGYRAKQGGK 60
I +Y K + + +HR V Y T P D+ +G+ K
Sbjct: 427 SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEH 486
Query: 61 LPRSNT-SSIMGAYRFI------SELYRKKQSDVMRYIHRIRVWQYRQLTTLHRAPRPTR 113
R + +RF+ ++ + +++ Y+ + P+ R
Sbjct: 487 PERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLK--FYKPYICDND-PKYER 543
Query: 114 PDKA-----RRMG---YRAK-----QVTLFSVQRYDVEEGNVQYPR 146
A ++ +K ++ L + EE + Q R
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
>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 = 35.8 bits (82), Expect = 0.010
Identities = 29/156 (18%), Positives = 58/156 (37%), Gaps = 50/156 (32%)
Query: 99 YRQLTTLHRAPRPTRPDKARRMGYRAKQVTLFSVQRY---------------------DV 137
Y TL +A P+ D++ R+ + +++ FS R+ D+
Sbjct: 387 YGLNLTLRKAKAPSGLDQS-RIPFSERKLK-FSN-RFLPVASPFHSHLLVPASDLINKDL 443
Query: 138 EEGNVQYP----RVP---TMNVSAEDV---VTSVFLKLLLAIRRDPKVNW--ICKPVHKH 185
+ NV + ++P T + D+ S+ +++ I R P V W + H
Sbjct: 444 VKNNVSFNAKDIQIPVYDTFD--GSDLRVLSGSISERIVDCIIRLP-VKWETTTQFKATH 500
Query: 186 ------REMRGLTSISKKSRGLGKGHGFAQTI-GGS 214
GL ++ +++ G G + I G+
Sbjct: 501 ILDFGPGGASGLGVLTHRNKD-GTG---VRVIVAGT 532
>1nf1_A NF1-333, protein (neurofibromin); type I neurofibromatosis, RAS,
GAP, signal transduction, cancer, growth regulation, GTP
hydrolysis; 2.50A {Homo sapiens} SCOP: a.116.1.2
Length = 333
Score = 28.2 bits (62), Expect = 2.7
Identities = 11/52 (21%), Positives = 19/52 (36%)
Query: 157 VVTSVFLKLLLAIRRDPKVNWICKPVHKHREMRGLTSISKKSRGLGKGHGFA 208
V +++FL+ + P I RGL +SK + + F
Sbjct: 187 VGSAMFLRFINPAIVSPYEAGILDKKPPPIIERGLKLMSKILQSIANHVLFT 238
>1obf_O Glyceraldehyde 3-phosphate dehydrogenase; glycolytic pathway,
oxidoreductase, free-NAD GAPDH; HET: PG4; 1.7A
{Achromobacter xylosoxidans} SCOP: c.2.1.3 d.81.1.1 PDB:
3gnq_A*
Length = 335
Score = 27.1 bits (61), Expect = 5.0
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 146 RVPTMNVSAEDVV 158
RVPT+NVS D+
Sbjct: 235 RVPTINVSIVDLS 247
>2x5j_O E4PDH, D-erythrose-4-phosphate dehydrogenase; oxidoreductase,
hydride transfer, aldehyde dehydrogenase, PY
biosynthesis; 2.30A {Escherichia coli} PDB: 2xf8_A*
2x5k_O*
Length = 339
Score = 27.1 bits (61), Expect = 5.4
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 146 RVPTMNVSAEDVV 158
RVPT+NV+A D+
Sbjct: 236 RVPTINVTAIDLS 248
>1wer_A P120GAP; GTPase activation, RAS, signal transduction, growth
regulation, cancer; 1.60A {Homo sapiens} SCOP: a.116.1.2
PDB: 1wq1_G*
Length = 334
Score = 27.0 bits (59), Expect = 6.1
Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 5/79 (6%)
Query: 129 LFSVQRYDVEEGNVQYPRVPTMNVSAEDVVTSVFLKLLLAIRRDPKVNWICKPVHKHREM 188
++ + V+ ++P TM V VFL+L+ +P++ I
Sbjct: 160 IYGCLQKSVQH---KWPTNTTMRTRV--VSGFVFLRLICPAILNPRMFNIISDSPSPIAA 214
Query: 189 RGLTSISKKSRGLGKGHGF 207
R L ++K + L F
Sbjct: 215 RTLILVAKSVQNLANLVEF 233
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 0.136 0.415
Gapped
Lambda K H
0.267 0.0539 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,633,907
Number of extensions: 205176
Number of successful extensions: 674
Number of sequences better than 10.0: 1
Number of HSP's gapped: 667
Number of HSP's successfully gapped: 35
Length of query: 231
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 141
Effective length of database: 4,188,903
Effective search space: 590635323
Effective search space used: 590635323
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: 56 (25.8 bits)