RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029509
(192 letters)
>3bbo_X Ribosomal protein L27; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 198
Score = 240 bits (614), Expect = 6e-82
Identities = 154/200 (77%), Positives = 169/200 (84%), Gaps = 10/200 (5%)
Query: 1 MATA-SMSASLIGSFKGLSLSSSSSSSFLKGDFTVCPK-SVTVSLP---PTSPLPLTIES 55
MA A SMS +LIG+FKGLSLSS+SS FL+GD + PK S TV+LP +P+PLTIES
Sbjct: 1 MAMATSMSLNLIGAFKGLSLSSTSS--FLRGDLSFSPKTSFTVTLPLENLQAPIPLTIES 58
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKGAGSTKNGRDS GQRLGVKI+GDQVAKPGAIIVRQRGTKFH GKNVG+GKDHTIFS
Sbjct: 59 AHKKGAGSTKNGRDSPGQRLGVKIYGDQVAKPGAIIVRQRGTKFHAGKNVGIGKDHTIFS 118
Query: 116 LIDGLVKFEKFGPDRKQISVYPREVQPENPNSYRARKREYFRLQREKKKARKEAY---LA 172
LIDGLVKFEKFGPDRK+ISVYPRE+ PENPNSYRARKRE FRLQREKKKAR+E Y L
Sbjct: 119 LIDGLVKFEKFGPDRKKISVYPREIVPENPNSYRARKRENFRLQREKKKARRENYSYTLP 178
Query: 173 QPQLVLASALDDAADGLPNC 192
P+LVLASA D A+ P C
Sbjct: 179 TPELVLASASVDDAEANPEC 198
>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U* 1sm1_U*
1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0 2zjp_T*
2zjq_T 1nkw_U 3cf5_T* 3dll_T* 3pio_T* 3pip_T* 1pnu_U
1pny_U 1vor_X 1vou_X ...
Length = 91
Score = 162 bits (412), Expect = 1e-52
Identities = 47/88 (53%), Positives = 60/88 (68%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GS+KNGRDS + LGVK FG +V K G I+VRQRGTKF G+ VG+G+DHT+F+
Sbjct: 2 AHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQISVYPREVQPE 143
L DG V F G + IS+ + +
Sbjct: 62 LSDGKVVFINKGKGARFISIEAAQTEVA 89
>3v2d_0 50S ribosomal protein L27; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0 2wdi_0
2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0 2wro_0
2wrr_0 2x9s_0 2x9u_0 2xg0_0 ...
Length = 85
Score = 160 bits (407), Expect = 6e-52
Identities = 47/82 (57%), Positives = 64/82 (78%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GST+NGRDS+ +RLGVK + QV + G I+VRQRGT+F PGKNVG+G+D T+F+
Sbjct: 2 AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQISVYP 137
L+DG+V+F+ G + + V P
Sbjct: 62 LVDGVVEFQDRGRLGRYVHVRP 83
>3r8s_W 50S ribosomal protein L27; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
2qam_W* 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W 2i2v_W
2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W 2qbg_W
2qbi_W* 2qbk_W* 2qov_W 2qox_W 2qoz_W* ...
Length = 76
Score = 138 bits (349), Expect = 3e-43
Identities = 46/75 (61%), Positives = 55/75 (73%), Gaps = 1/75 (1%)
Query: 64 TKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKF 123
T+NGRDS +RLGVK FG + G+IIVRQRGTKFH G NVG G+DHT+F+ DG VKF
Sbjct: 1 TRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKF 60
Query: 124 EKFGP-DRKQISVYP 137
E GP +RK IS+
Sbjct: 61 EVKGPKNRKFISIEA 75
>2ftc_O L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_O
Length = 69
Score = 133 bits (336), Expect = 2e-41
Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 56 AHKKGAGSTKN-GRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIF 114
A KK GS+KN G S G+R G+K G II QR ++HPG +VG+GK+ ++
Sbjct: 1 ASKKSGGSSKNLGGKSSGRRQGIKKMEGHYVHAGNIIATQRHFRWHPGAHVGVGKNKCLY 60
Query: 115 SLIDGLVKF 123
+L +G+V++
Sbjct: 61 ALEEGIVRY 69
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.8 bits (74), Expect = 0.037
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 133 ISVYPREVQ-PENPNSYRARKREYFRLQR--EKKKARKEAYLAQPQLVLASALDD 184
I+ R Q PE+ +R +R+ RLQ K ++ + + + L++
Sbjct: 74 IAQADRLTQEPESIRKWREEQRK--RLQELDAASKVMEQEWREKAK----KDLEE 122
Score = 30.9 bits (69), Expect = 0.18
Identities = 5/48 (10%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 129 DRKQISVYPREVQPENPNSYRARKREYFRLQREKKKARK--EAYLAQP 174
+ + + + + + + ++++ K R +A+ QP
Sbjct: 105 SKVMEQEWREKAKKDLEEWNQRQSE---QVEKNKINNRIADKAFYQQP 149
>3jyw_F 60S ribosomal protein L7(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_F
Length = 213
Score = 30.6 bits (68), Expect = 0.21
Identities = 7/45 (15%), Positives = 8/45 (17%)
Query: 148 YRARKREYFRLQREKKKARKEAYLAQPQLVLASALDDAADGLPNC 192
A A A A LV + P
Sbjct: 24 AAAAAAAAAAAAAAAAAAAAAAAAAAAGLVFVVRIKGINKIPPKP 68
>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 = 31.2 bits (70), Expect = 0.24
Identities = 25/115 (21%), Positives = 33/115 (28%), Gaps = 46/115 (40%)
Query: 24 SSSFLKGDFTVCPKSVTVSLPPTSPL-----PLTIESAHKKGAG-----------STKNG 67
S+ FL P V+ P S L L + K T +G
Sbjct: 417 SNRFL-------P----VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG 465
Query: 68 RDSRG------QRLGVKIFGDQV-----AKPGA--IIVRQRGTKFHPGKNVGLGK 109
D R +R+ I V + A I+ F PG GLG
Sbjct: 466 SDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILD------FGPGGASGLGV 514
Score = 28.1 bits (62), Expect = 2.6
Identities = 21/120 (17%), Positives = 36/120 (30%), Gaps = 52/120 (43%)
Query: 105 VGLGKD--------HTIFSLIDGLVKFEKFGPDRKQISVYPREVQPENPNS-------YR 149
G+G D +++ D K + +G S+ ++ NP + +
Sbjct: 1629 QGMGMDLYKTSKAAQDVWNRADNHFK-DTYG-----FSI--LDIVINNPVNLTIHFGGEK 1680
Query: 150 ARK-RE-YFRLQRE-----KKKARK-----------------EAYL-----AQPQLVLAS 180
++ RE Y + E K K K + L QP L L
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
>2pbk_A KSHV protease; KSHV, KSHV protease, herpesvirus protease, viral
protease, V protein; 1.73A {Human herpesvirus} SCOP:
b.57.1.1 PDB: 1fl1_A 3njq_A*
Length = 228
Score = 29.1 bits (65), Expect = 0.72
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 30 GDFTVCPKSVTVSLPPTSPLPLTIESAHKKGA 61
+ + P VT LP T PLP+TIE H
Sbjct: 19 QELYLDPDQVTDYLPVTEPLPITIE--HLPET 48
>3izc_e 60S ribosomal protein RPL7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_e
3o58_G 3o5h_G 3u5e_F 3u5i_F
Length = 244
Score = 29.0 bits (64), Expect = 0.87
Identities = 10/45 (22%), Positives = 16/45 (35%)
Query: 148 YRARKREYFRLQREKKKARKEAYLAQPQLVLASALDDAADGLPNC 192
Y +R + +R+ K A AQ +LV + P
Sbjct: 55 YETAERNIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKP 99
>1vzv_A Assemblin, varicella-zoster virus protease; hydrolase, serine
protease, viral protease, varicella-zoster coat
protein; 3.00A {Human herpesvirus 3} SCOP: b.57.1.1
Length = 221
Score = 28.7 bits (64), Expect = 0.95
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 30 GDFTVCPKSVTVSLPPTSPLPLTIESAHKKGA 61
G+ + P+ V +LPPTS +P+ I+ H+K
Sbjct: 17 GELNITPEIVRSALPPTSKIPINID--HRKDC 46
>1at3_A Herpes simplex virus type II protease; serine protease, viral
protease, HSV2 protease; HET: DFP; 2.50A {Human
herpesvirus 2} SCOP: b.57.1.1
Length = 247
Score = 28.4 bits (63), Expect = 1.3
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 29 KGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGA 61
G+ + P +V +LPP +PLP+ ++ H+
Sbjct: 35 PGELALDPDTVRAALPPENPLPINVD--HRARC 65
>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 9.00A {Bos
taurus}
Length = 205
Score = 28.3 bits (62), Expect = 1.5
Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 1/77 (1%)
Query: 108 GKDHTIFSLIDGLVKFEKFGPDRKQISVYPREVQPENPNSYRARKREYFRLQREKKKARK 167
G + + ++G V E GP ++ + + P S R + RE R + ++ A
Sbjct: 62 GASEDMGATVNGDVFQEANGPADGYAAIAQADRLTQEPESIR-KWREEQRKRLQELDAAS 120
Query: 168 EAYLAQPQLVLASALDD 184
+ + + L++
Sbjct: 121 KVMEQEWREKAKKDLEE 137
>1z3a_A TRNA-specific adenosine deaminase; tRNA adenosine deaminase, dimer,
zinc, metalloenzyme, structural genomics, PSI, protein
structure initiative; 2.03A {Escherichia coli} SCOP:
c.97.1.2 PDB: 3ocq_A
Length = 168
Score = 27.9 bits (63), Expect = 1.5
Identities = 7/17 (41%), Positives = 15/17 (88%)
Query: 153 REYFRLQREKKKARKEA 169
++FR++R++ KA+K+A
Sbjct: 147 SDFFRMRRQEIKAQKKA 163
>4a17_V RPL7, 60S ribosomal protein L7; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_V 4a1c_V 4a1e_V
Length = 239
Score = 28.2 bits (62), Expect = 1.5
Identities = 7/45 (15%), Positives = 18/45 (40%)
Query: 148 YRARKREYFRLQREKKKARKEAYLAQPQLVLASALDDAADGLPNC 192
Y A +++ +R+ +K A+ ++ A + P+
Sbjct: 52 YEAAEKKIVDEKRKARKTGAFYVPAEAKVAFAIRIRGVNQLHPDV 96
>1o6e_A Capsid protein P40; proteinase, beta-barrel, hydrolase, serine
protease, structu proteomics in europe, spine,
structural genomics; 2.3A {Human herpesvirus 4} SCOP:
b.57.1.1
Length = 235
Score = 27.9 bits (62), Expect = 1.9
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 36 PKSVTVSLPPTSPLPLTIESAHKKGA 61
P +V LP PLPLT+E H A
Sbjct: 29 PLTVKSQLPLKKPLPLTVE--HLPDA 52
>2nx8_A TRNA-specific adenosine deaminase; TAD, hydrolase; 2.00A
{Streptococcus pyogenes serotype M6}
Length = 179
Score = 27.2 bits (61), Expect = 2.4
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 153 REYFRLQREKKKARKEA 169
+ +FR RE+KK K
Sbjct: 154 QTFFRQGRERKKIAKHL 170
>1w9y_A 1-aminocyclopropane-1-carboxylate oxidase 1; oxygenase, 2OG
oxygenase, ACCO, ACC oxidase; 2.1A {Petunia hybrida}
SCOP: b.82.2.1 PDB: 1wa6_X
Length = 319
Score = 27.2 bits (61), Expect = 3.8
Identities = 8/31 (25%), Positives = 10/31 (32%), Gaps = 1/31 (3%)
Query: 142 PENPNSYRARK-REYFRLQREKKKARKEAYL 171
EN Y +Y +L K KE
Sbjct: 271 EENKQVYPKFVFDDYMKLYAGLKFQAKEPRF 301
>2lmc_B DNA-directed RNA polymerase subunit beta; transferase,
transcription; NMR {Escherichia coli k-12}
Length = 84
Score = 25.2 bits (56), Expect = 5.5
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 109 KDHTIFSLIDGLVKFEKFGPDRKQISVYPRE 139
K+ I + I G+V F K ++++ + P +
Sbjct: 22 KEPAILAEISGIVSFGKETKGKRRLVITPVD 52
>3kjd_A Poly [ADP-ribose] polymerase 2; transferase, enzyme-inhibitor
complex, catalytic fragment, S genomics, structural
genomics consortium, SGC; HET: 78P; 1.95A {Homo sapiens}
PDB: 3kcz_A* 1gs0_A
Length = 368
Score = 26.6 bits (58), Expect = 5.8
Identities = 10/59 (16%), Positives = 21/59 (35%)
Query: 120 LVKFEKFGPDRKQISVYPREVQPENPNSYRARKREYFRLQREKKKARKEAYLAQPQLVL 178
L + + K IS Y + + Y + F ++++ +K L L+
Sbjct: 158 LRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLW 216
>3ir4_A Glutaredoxin 2; glutathione, IDP00895, structural genomics, for
structural genomics of infectious diseases, csgid,
oxidoreductase; HET: MSE GSH; 1.20A {Salmonella enterica
subsp} PDB: 1g7o_A
Length = 218
Score = 26.4 bits (58), Expect = 6.0
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 135 VYPREVQPENPNSYRARKREYFRLQREKKKARKEAYLAQPQLVLA 179
+ PR + R+YF ++E + +LA ++
Sbjct: 104 LLPRFAKSAFDEFSTPAARQYFIRKKEASSGSFDNHLAHSAGLIK 148
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: b.40.4.5 b.84.4.2
Length = 209
Score = 26.2 bits (57), Expect = 6.1
Identities = 11/60 (18%), Positives = 18/60 (30%), Gaps = 3/60 (5%)
Query: 87 PGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQISVYPREVQPENPN 146
PG + + PG + IFS + G + +SV P+
Sbjct: 24 PGERLCN--LEEGSPGSGT-YTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPD 80
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 26.5 bits (59), Expect = 7.8
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 109 KDHTIFSLIDGLVKFEKFGPDRKQISVYPRE 139
K+ I + I G+V F K ++++ + P +
Sbjct: 1151 KEPAILAEISGIVSFGKETKGKRRLVITPVD 1181
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
0.315 0.132 0.376
Gapped
Lambda K H
0.267 0.0499 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,791,501
Number of extensions: 163927
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 32
Length of query: 192
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 104
Effective length of database: 4,244,745
Effective search space: 441453480
Effective search space used: 441453480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.1 bits)