RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7621
(247 letters)
>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F
1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H
Length = 191
Score = 157 bits (400), Expect = 1e-48
Identities = 54/106 (50%), Positives = 71/106 (66%), Gaps = 3/106 (2%)
Query: 143 GFLYKMRAAYAHFPINCVTSEN--NTLLEIRNFLGEKYIRRVKMAPGVKVSNS-KQKDEL 199
G+ YKMR YAHFPIN E +E+RNFLG+K IR V + GV + S KDE+
Sbjct: 85 GYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGDKKIRNVPVRDGVTIEFSTNVKDEI 144
Query: 200 IIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKTTVVTD 245
++ GN +E+VS++AA +QQ V+NKDIRKFLDG+YVS K + D
Sbjct: 145 VLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIYVSHKGFITED 190
Score = 49.2 bits (118), Expect = 1e-07
Identities = 16/30 (53%), Positives = 21/30 (70%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
V NG +K +AA+RTV S + NM+ GVTK
Sbjct: 55 VAVHNGGRKHVAALRTVKSLVDNMITGVTK 84
>4a17_E RPL9, 60S ribosomal protein L9; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_E 4a1c_E 4a1e_E
Length = 188
Score = 156 bits (397), Expect = 3e-48
Identities = 50/104 (48%), Positives = 77/104 (74%), Gaps = 1/104 (0%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNS-KQKDELII 201
G+ +KM+ A+AHFPI +++ + +EI++FLGEK IRR++ PGVK+S ++K+ L +
Sbjct: 85 GYKFKMKLAFAHFPIQEAVAKDGSSIEIKHFLGEKRIRRIQALPGVKISRKDEEKNTLTL 144
Query: 202 EGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKTTVVTD 245
+G D+ NVS++ ALI QS VK KDIR+FLDG+YVS+K + +
Sbjct: 145 QGIDLNNVSQTCALIHQSCLVKEKDIRQFLDGIYVSDKRLAMNE 188
Score = 47.0 bits (112), Expect = 1e-06
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
+ ++KE A ++++ S I NM++GVT+
Sbjct: 55 LQIWQASRKERAVLQSIASQIKNMIRGVTE 84
>3iz5_F 60S ribosomal protein L9 (L6P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_F
Length = 190
Score = 156 bits (397), Expect = 4e-48
Identities = 66/105 (62%), Positives = 80/105 (76%), Gaps = 1/105 (0%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSK-QKDELII 201
G+ YKMR YAHFPIN + +NT +EIRNFLGEK +R+V M GV + S+ KDEL++
Sbjct: 86 GYRYKMRFVYAHFPINASITNSNTAIEIRNFLGEKKVRKVDMLEGVTILRSEKVKDELVL 145
Query: 202 EGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKTTVVTDA 246
+GNDIE VSRSAALI Q VKNKDIRKFLDG+YVS+K T+ DA
Sbjct: 146 DGNDIELVSRSAALINQKCHVKNKDIRKFLDGIYVSDKGTITEDA 190
Score = 47.7 bits (114), Expect = 5e-07
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 38 EETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
VD GT++ +AA+RT SH+ N++ GVTK
Sbjct: 51 GRKLQVDAWFGTRRTMAAIRTAISHVQNLITGVTK 85
>2zkr_e 60S ribosomal protein L9; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 192
Score = 155 bits (393), Expect = 1e-47
Identities = 79/104 (75%), Positives = 87/104 (83%), Gaps = 1/104 (0%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSK-QKDELII 201
GF YKMR+ YAHFPIN V EN +L+EIRNFLGEKYIRRV+M PGV S S+ QKDELI+
Sbjct: 87 GFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQAQKDELIL 146
Query: 202 EGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKTTVVTD 245
EGNDIE VS SAALIQQ+TTVKNKDIRKFLDG+YVSEK TV
Sbjct: 147 EGNDIELVSNSAALIQQATTVKNKDIRKFLDGIYVSEKGTVQQA 190
Score = 47.7 bits (114), Expect = 5e-07
Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
VD G +KE+A VRT+CSH+ NM+KGVT
Sbjct: 57 VDKWWGNRKELATVRTICSHVQNMIKGVTL 86
>1vq8_E 50S ribosomal protein L6P; 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.141.1.1 d.141.1.1 PDB:
1vq4_E* 1vq5_E* 1vq6_E* 1vq7_E* 1s72_E* 1vq9_E* 1vqk_E*
1vql_E* 1vqm_E* 1vqn_E* 1vqo_E* 1vqp_E* 1yhq_E* 1yi2_E*
1yij_E* 1yit_E* 1yj9_E* 1yjn_E* 1yjw_E* 2otj_E* ...
Length = 178
Score = 142 bits (360), Expect = 9e-43
Identities = 37/98 (37%), Positives = 54/98 (55%), Gaps = 4/98 (4%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIE 202
G+ Y M Y+HFP+ + + I NFLGEK RR + V +EL +
Sbjct: 80 GWEYGMEVFYSHFPMQVNVEGDE--VVIENFLGEKAPRRTTIHGDTDVE--IDGEELTVS 135
Query: 203 GNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKT 240
G DIE V ++AA I+Q T + +KD+R F DG+Y++ K
Sbjct: 136 GPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKP 173
Score = 49.5 bits (119), Expect = 1e-07
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
++ D K ++ + T SHI NM GVT+
Sbjct: 50 IESDEDNAKTMSTIGTFQSHIENMFHGVTE 79
>2cql_A OK/SW-CL.103, 60S ribosomal protein L9; N-terminal domain, alpha
and beta (A+B), structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.141.1.1
Length = 100
Score = 49.6 bits (119), Expect = 2e-08
Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
VD G +KE+A VRT+CSH+ NM+KGVT
Sbjct: 64 VDKWWGNRKELATVRTICSHVQNMIKGVTL 93
>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 = 38.1 bits (88), Expect = 0.002
Identities = 36/252 (14%), Positives = 68/252 (26%), Gaps = 106/252 (42%)
Query: 7 MIYQSF------FYEIPPDLNPGGGGGCLY-----LNKT--------------YR-WEET 40
MI+++ +I ++N L+ T + +
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSK 1750
Query: 41 FDVDCDN-------GTKKEIAAVRTVCSHISNMLKGVTKVKDCAVKVQQSTLDLLCEFLW 93
+ D G E AA+ L V ++ V+V
Sbjct: 1751 GLIPADATFAGHSLG---EYAAL--AS------LADVMSIES-LVEV------------- 1785
Query: 94 NVSLVLCTRNTLAQVF------------LLAL-----VLCMSVEKSFIVVYQKYTSTGGF 136
+ R QV ++A+ S E VV + TG
Sbjct: 1786 -----VFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
Query: 137 VCISFTGFLYKMRAAYAHFPINC-----VTSEN----NTLLEIRNFLGEKYIRRVKMAPG 187
V I Y N V + + +T+ + NF+ + I +++
Sbjct: 1841 VEI----------VNY-----NVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQ-- 1883
Query: 188 VKVSNSKQKDEL 199
+S + + L
Sbjct: 1884 KSLSLEEVEGHL 1895
Score = 37.0 bits (85), Expect = 0.006
Identities = 42/300 (14%), Positives = 69/300 (23%), Gaps = 126/300 (42%)
Query: 1 MCGHTFMIYQSFFYEIPPDLNP-------GGGGGCLYLNKTYRWEETFDVDCDNGTKKEI 53
H Y +I + NP GG G + + Y F+ D K E
Sbjct: 1649 ADNHFKDTYGFSILDIVIN-NPVNLTIHFGGEKGK-RIRENYS-AMIFETIVDGKLKTE- 1704
Query: 54 AAVRTVCSHISNMLKGVT-KVKDCAVKVQQSTLDLLCEFLWNVSLVLCTRNTLAQVFLLA 112
+ K + + ++ L T+ T Q A
Sbjct: 1705 -----------KIFKEINEHSTSYTFRSEKGLLSA-------------TQFT--QP---A 1735
Query: 113 LVLCMSV------EKSFIVVYQK---------YT---STGGFVCISFT---------GFL 145
L L M + ++ Y S +S G
Sbjct: 1736 LTL-MEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADV--MSIESLVEVVFYRGMT 1792
Query: 146 --------------YKMRA------------AYAHFPINCVTSENNTLLEIRNFLGEKYI 179
Y M A + + V L+EI N+
Sbjct: 1793 MQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY------ 1846
Query: 180 RRVKMAPGVKVSNS--KQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVS 237
N +Q + G D+ + + ++ DI + L S
Sbjct: 1847 ------------NVENQQ---YVAAG-DLRALDT-VTNVLNFIKLQKIDIIE----LQKS 1885
Score = 35.4 bits (81), Expect = 0.016
Identities = 30/141 (21%), Positives = 53/141 (37%), Gaps = 39/141 (27%)
Query: 118 SVEKSFIVVYQKYTSTGGFVCIS-----FTGFLYKMRAAYAHFPINCVTSENNTLLEI-- 170
S+E +V T F S F L + +A E T E+
Sbjct: 15 SLEHVLLV------PTASFFIASQLQEQFNKILPEPTEGFAA------DDEPTTPAELVG 62
Query: 171 RNFLGEKYIRRVKMAPGVKVSNSKQKDEL-----------IIEGNDIENVSRSAALIQQS 219
+ FLG Y+ + V+ S Q D++ +EGNDI ++ +
Sbjct: 63 K-FLG--YV-----SSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDT 114
Query: 220 TTVKNKD-IRKFLDGLYVSEK 239
T VK K+ I+ ++ ++++
Sbjct: 115 TLVKTKELIKNYITARIMAKR 135
>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 = 37.1 bits (85), Expect = 0.005
Identities = 34/283 (12%), Positives = 79/283 (27%), Gaps = 92/283 (32%)
Query: 34 TYR-----WEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKVKDCAVKVQQSTLDLL 88
Y+ +E+ F + D C + +M K + ++ +
Sbjct: 17 QYKDILSVFEDAFVDNFD-------------CKDVQDMPKSILSKEEIDHIIMSKDAVSG 63
Query: 89 CEFL-WNVSLVLCTRNT-LAQVFLLALVLCMSVEKSFIV----VYQKYTSTGGFVCISFT 142
L W L ++ + Q F+ + + + F++ Q+ S + I
Sbjct: 64 TLRLFW----TLLSKQEEMVQKFVEEV---LRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116
Query: 143 GFLYKMRAAYAHFPIN---CVTSENNTLLEIRNFLGEKYI-------------------- 179
LY +A + ++ LLE+R K +
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP---AKNVLIDGVLGSGKTWVALDVCLS 173
Query: 180 --RRVKMAPGV---KVSNSKQKDELI---------IEGNDIENVSRSAALIQQSTTVKNK 225
+ KM + + N + ++ I+ N S+ + + +++ +
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 226 DIRKF-----------LDGLYVSE---------KTTVVT-DAS 247
R L + ++ K + T
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQ 276
Score = 34.4 bits (78), Expect = 0.030
Identities = 30/287 (10%), Positives = 73/287 (25%), Gaps = 86/287 (29%)
Query: 6 FMIYQSFFYEIPPDLNPGGGGGC---------------LYLNKTYR---------WE--- 38
+ Q Y+I P+ L +K Y
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258
Query: 39 -ETFDVDC-------DNGTKKEIAAVRTVCSHISNMLKGVTKVKDCAVKVQQSTLDLLCE 90
F++ C ++A T + + +T + LL +
Sbjct: 259 WNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE---------VKSLLLK 309
Query: 91 FLWNVSLVL----CTRNTLAQVFLLALVLCMSVEKSFIVVYQKYTSTGGFVCISFTGFLY 146
+L L T N + ++A + + + + +
Sbjct: 310 YLDCRPQDLPREVLTTNPRR-LSIIAESI-----RDGLATWDNWKHVN----------CD 353
Query: 147 KMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNS------KQKDELI 200
K+ +N + E R + + R P + +
Sbjct: 354 KLTTIIESS-LNVLEPA-----EYR----KMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 201 IEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKTTVVTDAS 247
+ + N +L+++ + K+ + +Y+ K + + +
Sbjct: 404 VM--VVVNKLHKYSLVEK----QPKESTISIPSIYLELKVKLENEYA 444
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein
structure initiative; NMR {Salmonella typhimurium}
Length = 61
Score = 26.7 bits (60), Expect = 1.7
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 5/25 (20%)
Query: 49 TKKEIAA-----VRTVCSHISNMLK 68
T I+ ++TV +H NM++
Sbjct: 15 TNHGISEKLHISIKTVETHRMNMMR 39
>2yhf_A C-type lectin domain family 5 member A; immune system; 1.90A {Homo
sapiens}
Length = 118
Score = 27.3 bits (61), Expect = 2.2
Identities = 5/27 (18%), Positives = 8/27 (29%), Gaps = 3/27 (11%)
Query: 21 NPGGGGGCLYLNKTYRWEETFDVDCDN 47
N C + T ++ CD
Sbjct: 85 NQNQNFNCATIGLTKTFD---AASCDI 108
>4ffb_C Protein STU2; tubulin fold, heat repeats, cytoskeleton,
microtubule, tubul domain, hydrolase; HET: GTP; 2.88A
{Saccharomyces cerevisiae}
Length = 278
Score = 27.8 bits (61), Expect = 3.4
Identities = 7/51 (13%), Positives = 15/51 (29%), Gaps = 2/51 (3%)
Query: 73 VKDCAVKVQQSTLDLLCEFLWNVSLVLCTRNTLAQVFLLALVLCMSVEKSF 123
+ D V Q+ + L + + + + + VEK
Sbjct: 64 ITDSNVVAQEQAIVALNSLIDAFASSSLKNAHNITLI--STWTPLLVEKGL 112
>2asu_B Hepatocyte growth factor-like protein; serine proteinase,
beta-chain, MSP, HGFL, hydrolase; 1.85A {Homo sapiens}
Length = 234
Score = 26.8 bits (60), Expect = 6.6
Identities = 10/80 (12%), Positives = 26/80 (32%), Gaps = 19/80 (23%)
Query: 153 AHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELII---EGNDIENV 209
C +S + L +LG + P ++ + ++ G+ +
Sbjct: 38 RQ----CFSSCHMPLTGYEVWLGTLFQNPQHGEPSLQRVPVAK----MVCGPSGSQL--- 86
Query: 210 SRSAALIQQSTTVK-NKDIR 228
L++ +V N+ +
Sbjct: 87 ----VLLKLERSVTLNQRVA 102
>2bpd_A Dectin-1; receptor, beta-glucan, fungal recognition, C-type
lectin-like domain, CTLD, carbohydrate; 1.5A {Mus
musculus} PDB: 2bph_A 2bpe_A 2cl8_A*
Length = 142
Score = 26.3 bits (58), Expect = 6.9
Identities = 3/37 (8%), Positives = 12/37 (32%), Gaps = 4/37 (10%)
Query: 11 SFFYEIPPDLNPGGGGGCLYLNKTYRWEETFDVDCDN 47
+ F C++++ + ++ C+
Sbjct: 100 NSFQVRNAVPQESLLHNCVWIHGS-EV---YNQICNT 132
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
0.322 0.136 0.406
Gapped
Lambda K H
0.267 0.0509 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,637,523
Number of extensions: 203385
Number of successful extensions: 374
Number of sequences better than 10.0: 1
Number of HSP's gapped: 366
Number of HSP's successfully gapped: 28
Length of query: 247
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 156
Effective length of database: 4,160,982
Effective search space: 649113192
Effective search space used: 649113192
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 (21.9 bits)
S2: 56 (25.9 bits)