RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16179
(145 letters)
>3vi6_A 60S ribosomal protein L30; three-layer alpha/beta/ALPA; 1.59A {Homo
sapiens} PDB: 2zkr_6 1ysh_C
Length = 125
Score = 100 bits (251), Expect = 2e-28
Identities = 49/56 (87%), Positives = 53/56 (94%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
RKSEIEYYAMLAKTGVHHY+GNNIELGTACGKY+RVCTL+I D GDSDIIRSMP +
Sbjct: 57 RKSEIEYYAMLAKTGVHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQ 112
>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 = 100 bits (250), Expect = 2e-28
Identities = 6/56 (10%), Positives = 16/56 (28%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
+ +A N+ G G +++ + ++ I S +
Sbjct: 56 VDAWFGTRRTMAAIRTAISHVQNLITGVTKGYRYKMRFVYAHFPINASITNSNTAI 111
>3u5e_c L32, RP73, YL38, 60S ribosomal protein L30; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_f
3izs_f 3o58_Z 3o5h_Z 1t0k_B 3u5i_c 1ck2_A 1cn7_A 1nmu_B*
3jyw_2
Length = 105
Score = 98.7 bits (246), Expect = 6e-28
Identities = 33/53 (62%), Positives = 43/53 (81%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSM 141
RKSE+EYYAML+KT V+++ G N ELGTA GK FRV +SI +AGDSDI+ ++
Sbjct: 52 RKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTL 104
>3cpq_A 50S ribosomal protein L30E; RNA-protein, elongation factor,
ribonucleoprotein, structural genomics, NPPSFA; 1.90A
{Methanocaldococcus jannaschii}
Length = 110
Score = 98.3 bits (245), Expect = 7e-28
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
+ +++YYA L+ V+ + ++ELG CGK F V L + D G S+I+ + +
Sbjct: 51 LEEDVKYYAKLSNIPVYQHKITSLELGAVCGKPFPVAALLVLDEGLSNIMELVEKK 106
>1w41_A 50S ribosomal protein L30E; electrostatic interactions,
thermostability, protein engineering; 1.7A {Thermococcus
celer} SCOP: d.79.3.1 PDB: 3n4y_A 3lfo_A 1w40_A 1go0_A
1go1_A 1h7m_A 1w42_A 1w3e_X 3ra6_A 3ra5_A 3n4z_A 2bo1_A
Length = 101
Score = 97.5 bits (243), Expect = 1e-27
Identities = 21/56 (37%), Positives = 31/56 (55%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G S I+ E
Sbjct: 46 IKEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGASRILALGGKE 101
>4a18_G RPL30; ribosome, eukaryotic initiation factor 6, EIF6, transla
large ribosomal subunit, rRNA; 3.52A {Tetrahymena
thermophila} PDB: 4a19_G 4a1b_G 4a1d_G 4adx_6
Length = 104
Score = 92.1 bits (229), Expect = 2e-25
Identities = 34/52 (65%), Positives = 44/52 (84%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRS 140
RKSEIEYYA LA+ +HH+ G+N+ELGTACGKY R T++I DAGDSDI+++
Sbjct: 52 RKSEIEYYASLAQISIHHFVGSNVELGTACGKYHRCSTMAILDAGDSDILKT 103
>3on1_A BH2414 protein; structural genomics, PSI-2, protein structure
initiative, MI center for structural genomics, MCSG,
unknown function; HET: MSE; 1.65A {Bacillus halodurans}
Length = 101
Score = 61.6 bits (150), Expect = 1e-13
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
K ++ + V GN LG A GK+ RV + + DAG S + ++ E
Sbjct: 48 TKKKLLDKCGSYQIPVKVV-GNRQMLGRAIGKHERVV-IGVKDAGFSRKLAALIDE 101
>3v7q_A Probable ribosomal protein YLXQ; L7AE superfamily, K-turn binding,
K-turn RNA, hypothetical R protein, RNA binding protein;
HET: CIT; 1.55A {Bacillus subtilis}
Length = 101
Score = 58.1 bits (141), Expect = 3e-12
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSM 141
++ K + LG + GK RV +++TD G ++ + S+
Sbjct: 49 TAKKVTDKCNYYKVPYKKV-ESRAVLGRSIGKEARVV-VAVTDQGFANKLISL 99
>2fc3_A 50S ribosomal protein L7AE; alpha-beta-alpha sandwich, ribosome,
RNA binding protein; 1.56A {Aeropyrum pernix} SCOP:
d.79.3.1 PDB: 3pla_C* 3id5_C* 3hax_D* 2hvy_D* 3hay_D*
3nvi_B 3nmu_C 3nvk_E* 3lwr_C 3lwo_C* 3lwq_C* 3lwp_C
3lwv_C 3hjw_C* 2czw_A 1pxw_A
Length = 124
Score = 48.6 bits (116), Expect = 2e-08
Identities = 10/53 (18%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 87 VYRKSEIEYYAMLA-KTGVHH-YTGNNIELGTACGKYFRVCTLSITDAGDSDI 137
V + + +L + + + Y + LG A G +++I + GD++
Sbjct: 54 VDPPEIVMHLPLLCDEKKIPYVYVPSKKRLGEAAGIEVAAASVAIIEPGDAET 106
>1xbi_A 50S ribosomal protein L7AE; alpha-beta-alpha sandwich fold, RNA
binding protein/structural protein complex; HET: EPE;
1.45A {Methanocaldococcus jannaschii} SCOP: d.79.3.1
PDB: 1ra4_A* 1sds_A 3paf_A
Length = 120
Score = 44.9 bits (106), Expect = 5e-07
Identities = 12/66 (18%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 81 VWVLSCVYRKSEIEYYAMLA-KTGVHH-YTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
V + V + + + L + G+ + Y + +LG A G +++I + GD++ +
Sbjct: 49 VIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEEL 108
Query: 139 RSMPSE 144
+ + +
Sbjct: 109 KVLIEK 114
>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 = 38.5 bits (89), Expect = 3e-04
Identities = 22/158 (13%), Positives = 51/158 (32%), Gaps = 38/158 (24%)
Query: 15 RPESITTPATTLSLELPVDVWTSIARISNKVLVLKTIITLSKLFRNQEM---EIHLCLSF 71
RP +++ + L +P + +++ + K + ++ F + L F
Sbjct: 7 RPLTLSHGSLEHVLLVPTASFFIASQLQEQ--FNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 72 LSKMQCPNSVWVLSCVYRKSEIEYYAMLAKTGVHHYT-----GNNI---------ELGTA 117
L +V S V S++ + + + + GN+I E T
Sbjct: 65 LG--------YVSSLV-EPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTT 115
Query: 118 CGK-------YFRVCTLS---ITDAGDSDIIRSMPSEH 145
K Y ++ +S + R++ +
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGN 153
>1vq8_F 50S ribosomal protein L7AE; 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.79.3.1 PDB: 1vq4_F*
1vq5_F* 1vq6_F* 1vq7_F* 1s72_F* 1vq9_F* 1vqk_F* 1vql_F*
1vqm_F* 1vqn_F* 1vqo_F* 1vqp_F* 1yhq_F* 1yi2_F* 1yij_F*
1yit_F* 1yj9_F* 1yjn_F* 1yjw_F* 2otj_F* ...
Length = 120
Score = 35.6 bits (82), Expect = 0.001
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSD 136
+ + + + +LG A G ++TDAG++D
Sbjct: 69 DEKGVPFI----------FVEQQDDLGHAAGLEVGSAAAAVTDAGEAD 106
>1rlg_A 50S ribosomal protein L7AE; protein-RNA, structural protein/RNA
complex; HET: 5BU; 2.70A {Archaeoglobus fulgidus} SCOP:
d.79.3.1
Length = 119
Score = 34.0 bits (78), Expect = 0.004
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 87 VYRKSEIEYYAMLA-KTGVHH-YTGNNIELGTACGKYFRVCTLSITDAGD 134
V + + +L + V + Y + +LG A G + +I + G+
Sbjct: 53 VDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGE 102
>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 = 35.2 bits (80), Expect = 0.005
Identities = 18/111 (16%), Positives = 39/111 (35%), Gaps = 23/111 (20%)
Query: 16 PESITTPATTLSLELPVDVWTSIARISNKV-LVLKTIITLSKLFRNQEM---EIHLCLSF 71
P S P LSL +W + I + V +V+ + S + + + I +
Sbjct: 382 PPSAHIPTILLSL-----IWFDV--IKSDVMVVVNKLHKYSLVEKQPKESTISIPS-IYL 433
Query: 72 LSKMQCPNSVWVLSCVYRKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYF 122
K++ N + +S +++Y + ++ +YF
Sbjct: 434 ELKVKLENEYAL-----HRSIVDHYNIPKTFDSDDLIPPYLD------QYF 473
Score = 29.8 bits (66), Expect = 0.29
Identities = 17/126 (13%), Positives = 33/126 (26%), Gaps = 33/126 (26%)
Query: 35 WTSIARISNKVLVLKTIITLSKLFR-----------NQEMEIHLC----LSFLSKMQCPN 79
W ++ ++ VL+ + L N ++ IH L N
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245
Query: 80 SVWVLSCVYRKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIR 139
+ VL V + + K + T +TD +
Sbjct: 246 CLLVLLNVQNAKAWNAFNLSCKILL---TTRFK---------------QVTDFLSAATTT 287
Query: 140 SMPSEH 145
+ +H
Sbjct: 288 HISLDH 293
>2lfc_A Fumarate reductase, flavoprotein subunit; structural genomics,
northeast structural genomics consortiu PSI-biology; NMR
{Lactobacillus plantarum}
Length = 160
Score = 26.5 bits (59), Expect = 2.7
Identities = 3/13 (23%), Positives = 7/13 (53%)
Query: 95 YYAMLAKTGVHHY 107
+Y + + HH+
Sbjct: 146 FYIIEQRLEHHHH 158
>2lbw_A H/ACA ribonucleoprotein complex subunit 2; L7AE, snoRNP, scaRNP,
RNA binding protein; NMR {Saccharomyces cerevisiae} PDB:
2lbx_A
Length = 121
Score = 25.3 bits (55), Expect = 6.6
Identities = 5/37 (13%), Positives = 11/37 (29%), Gaps = 1/37 (2%)
Query: 101 KTGVHH-YTGNNIELGTACGKYFRVCTLSITDAGDSD 136
V + + + +LG A + I +
Sbjct: 61 DHSVPYIFIPSKQDLGAAGATKRPTSVVFIVPGSNKK 97
>1t3j_A Mitofusin 1; coiled coil antiparallel, dimer, membrane protein;
2.50A {Mus musculus} SCOP: h.4.16.1
Length = 96
Score = 24.6 bits (53), Expect = 6.9
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 28 LELPVDVWT-----SIARISNKVLVLKTIITLSKLFRNQE 62
L VD+ IAR+S ++ L+ + SKL RN+
Sbjct: 41 LCQQVDMTQKHLEEEIARLSKEIDQLEKMQNNSKLLRNKA 80
>2iaf_A Hypothetical protein SDHL; MCSG, PSI2, MAD, structural genomics,
L-serine dehydratase, structure initiative; 2.05A
{Legionella pneumophila} SCOP: d.81.2.1 PDB: 2iqq_A
Length = 151
Score = 24.7 bits (54), Expect = 9.7
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELG 115
++ ++E Y LA TG H T I G
Sbjct: 34 QRVKVELYGSLALTGKGHGTDKAILNG 60
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 0.134 0.413
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,119,363
Number of extensions: 107509
Number of successful extensions: 169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 20
Length of query: 145
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 60
Effective length of database: 4,328,508
Effective search space: 259710480
Effective search space used: 259710480
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 (22.0 bits)
S2: 52 (24.0 bits)