RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032363
(142 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 = 182 bits (464), Expect = 5e-60
Identities = 109/138 (78%), Positives = 121/138 (87%), Gaps = 7/138 (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 LIDGLVKFEKFGPDRKQV 133
LIDGLVKFEKFGPDRK++
Sbjct: 119 LIDGLVKFEKFGPDRKKI 136
>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 = 149 bits (379), Expect = 2e-48
Identities = 45/78 (57%), Positives = 56/78 (71%)
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 LIDGLVKFEKFGPDRKQV 133
L DG V F G + +
Sbjct: 62 LSDGKVVFINKGKGARFI 79
>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 = 148 bits (376), Expect = 5e-48
Identities = 46/78 (58%), Positives = 62/78 (79%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GST+NGRDS+ +RLGVK + QV + G I+VRQRGT+F PGKNVG+G+D T+F+
Sbjct: 2 AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQV 133
L+DG+V+F+ G + V
Sbjct: 62 LVDGVVEFQDRGRLGRYV 79
>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 = 128 bits (325), Expect = 2e-40
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
>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 = 127 bits (322), Expect = 6e-40
Identities = 44/71 (61%), Positives = 53/71 (74%), Gaps = 1/71 (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-DRKQV 133
E GP +RK +
Sbjct: 61 EVKGPKNRKFI 71
>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 = 0.097
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
>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 = 29.5 bits (66), Expect = 0.27
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
>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 = 29.1 bits (65), Expect = 0.38
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 = 29.2 bits (65), Expect = 0.40
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
>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 = 28.3 bits (63), Expect = 0.71
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
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xct_B* 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 26.1 bits (58), Expect = 5.0
Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 11/58 (18%)
Query: 60 GAGSTKNGRDSRGQR---LGVKIFGDQVAKPGAII----VRQRGTKFHPGKNVGLGKD 110
GSTK+GRDSR Q L KI + A+ I+ +RQ T F G+G D
Sbjct: 31 AGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAF----GTGIGGD 84
>2bon_A Lipid kinase; DAG kinase, transferase; 1.90A {Escherichia coli}
SCOP: e.52.1.2 PDB: 2jgr_A 2p1r_A
Length = 332
Score = 25.4 bits (56), Expect = 8.3
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 31 DFTVCPKSVTVSLPPTSPL 49
+ P ++ LPP PL
Sbjct: 304 HIEILPAALRCRLPPDCPL 322
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
0.317 0.134 0.385
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,004,467
Number of extensions: 111498
Number of successful extensions: 194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 190
Number of HSP's successfully gapped: 16
Length of query: 142
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 58
Effective length of database: 4,356,429
Effective search space: 252672882
Effective search space used: 252672882
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: 41 (21.6 bits)
S2: 52 (23.8 bits)