RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032476
(140 letters)
>3u5e_V L17A, YL32, 60S ribosomal protein L23-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_M
1s1i_R 3izs_M* 3j16_I 3o5h_U 3o58_U 3u5i_V 2x7n_C 3jyw_R
2zkr_k 3iz5_M 3izr_M 4a17_J 4a1a_J 4a1c_J 4a1e_J
Length = 137
Score = 139 bits (351), Expect = 9e-44
Identities = 102/134 (76%), Positives = 119/134 (88%)
Query: 7 GGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVK 66
G+ G KFR+SLGLPV A +NCADN+GA+NLYII+VKG RLNRLP+A +GDMVMATVK
Sbjct: 4 NGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMATVK 63
Query: 67 KGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECA 126
KGKP+LRKKVMPA++VRQ K WRR+DGVF+YFEDNAGVI NPKGEMKGSAITGP+GKECA
Sbjct: 64 KGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKECA 123
Query: 127 DLWPRIASAANAIV 140
DLWPR+AS + +V
Sbjct: 124 DLWPRVASNSGVVV 137
>1vq8_K 50S ribosomal protein L14P; 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: b.39.1.1 PDB: 1vq4_K*
1vq5_K* 1vq6_K* 1vq7_K* 1s72_K* 1vq9_K* 1vqk_K* 1vql_K*
1vqm_K* 1vqn_K* 1vqo_K* 1vqp_K* 1yhq_K* 1yi2_K* 1yij_K*
1yit_K* 1yj9_K* 1yjn_K* 1yjw_K* 2otj_K* ...
Length = 132
Score = 129 bits (325), Expect = 9e-40
Identities = 60/130 (46%), Positives = 84/130 (64%)
Query: 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70
++ GL + + CADNTGA+ L +ISV G G NRLP A +GD + +V KG P
Sbjct: 3 ALGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTP 62
Query: 71 DLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWP 130
++R++V+ AV+VRQRKP RR DG + FEDNA VIV+ + +G+ + GPI +E A +
Sbjct: 63 EMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREVAQRFG 122
Query: 131 RIASAANAIV 140
+ASAA IV
Sbjct: 123 SVASAATMIV 132
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 121
Score = 108 bits (270), Expect = 1e-31
Identities = 40/118 (33%), Positives = 69/118 (58%), Gaps = 7/118 (5%)
Query: 26 VNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD---LRKKVMPAVIV 82
+N ADN+GA+ L I + G R A +GD+++A +K+ P+ R +V+ AV+V
Sbjct: 8 LNVADNSGARELMCIRIIGASNR----RYARIGDVIVAVIKEAIPNTPLERSEVIRAVVV 63
Query: 83 RQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV 140
R K +R +G+ + ++DNA VI++ +G KG+ I G I +E + +I S A ++
Sbjct: 64 RTCKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFGAIARELRQKFAKIVSLAPEVL 121
>1whi_A Ribosomal protein L14; rRNA-binding; 1.50A {Geobacillus
stearothermophilus} SCOP: b.39.1.1 PDB: 1giy_N 1ml5_n*
1c04_D 1yl3_N 2b66_O 2b9n_O 2b9p_O 487d_M
Length = 122
Score = 102 bits (255), Expect = 2e-29
Identities = 42/121 (34%), Positives = 70/121 (57%), Gaps = 8/121 (6%)
Query: 24 ATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPD---LRKKVMPAV 80
+ + ADN+GA+ + +I V G GR A +GD+V+ATVK P + +V+ AV
Sbjct: 6 SRLKVADNSGAREVLVIKVLGGSGR----RYANIGDVVVATVKDATPGGVVKKGQVVKAV 61
Query: 81 IVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADL-WPRIASAANAI 139
+VR ++ RR DG ++ F++NA VI+ +G+ I GP+ +E D + +I S A +
Sbjct: 62 VVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPEV 121
Query: 140 V 140
+
Sbjct: 122 I 122
>3v2d_O 50S ribosomal protein L14; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2j03_O 2jl6_O 2jl8_O 2v47_O 2v49_O 2wdi_O 2wdj_O 2wdl_O
2wdn_O 2wh2_O 2wh4_O 2wrj_O 2wrl_O 2wro_O 2wrr_O 2x9s_O
2x9u_O 2xg0_O 2xg2_O 2xqe_O ...
Length = 122
Score = 100 bits (251), Expect = 9e-29
Identities = 41/119 (34%), Positives = 67/119 (56%), Gaps = 8/119 (6%)
Query: 26 VNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKK---VMPAVIV 82
+ ADNTGA+ + I V A VGD+++A+VK+ P K V+ AV+V
Sbjct: 8 LEVADNTGARKIMCIRVLKGSNA----KYATVGDVIVASVKEAIPRGAVKEGDVVKAVVV 63
Query: 83 RQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADL-WPRIASAANAIV 140
R +K +R DG + F+DNA VI+N + E +G+ + GP+ +E + + +I S A ++
Sbjct: 64 RTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPEVL 122
>3r8s_K 50S ribosomal protein L14; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3oat_K* 3oas_K* 3ofd_K 3ofc_K 3ofr_K* 3ofz_K* 3og0_K
3ofq_K 3r8t_K 3i1n_K 1p85_I 1p86_I 1vs8_K 1vs6_K 2aw4_K
2awb_K 1vt2_K 2i2v_K 2i2t_K* 2qao_K* ...
Length = 122
Score = 97.8 bits (243), Expect = 2e-27
Identities = 41/121 (33%), Positives = 63/121 (52%), Gaps = 9/121 (7%)
Query: 24 ATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLR---KKVMPAV 80
+N ADN+GA+ + I V G R A VGD++ T+K+ P + V+ AV
Sbjct: 6 TMLNVADNSGARRVMCIKVLGGSHR----RYAGVGDIIKITIKEAIPRGKVKKGDVLKAV 61
Query: 81 IVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEM-KGSAITGPIGKECADL-WPRIASAANA 138
+VR +K RR DG + F+ NA V++N E G+ I GP+ +E + +I S A
Sbjct: 62 VVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPE 121
Query: 139 I 139
+
Sbjct: 122 V 122
>2d9v_A Pleckstrin homology domain-containing protein family B member 1; PH
domain, phret1, structural genomics, NPPSFA; NMR {Mus
musculus}
Length = 130
Score = 31.5 bits (71), Expect = 0.035
Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 6/52 (11%)
Query: 85 RKPWRR------KDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWP 130
+ W+R DG Y+ D + + + +G+EC D+ P
Sbjct: 21 LRRWKRNWFALWLDGTLGYYHDETAQDEEDRVVIHFNVRDIKVGQECQDVQP 72
>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 = 30.8 bits (69), Expect = 0.16
Identities = 18/102 (17%), Positives = 30/102 (29%), Gaps = 38/102 (37%)
Query: 3 KRGR-----------GGS-----AGNKFRMSLGLPVAATVNCADNTGAK----------N 36
RG G S A N R++ A + G + N
Sbjct: 1788 YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN 1847
Query: 37 L----YIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRK 74
+ Y+ + G L L + V+ +K K D+ +
Sbjct: 1848 VENQQYVAA-----GDLRALDTVT---NVLNFIKLQKIDIIE 1881
>3aj4_A Pleckstrin homology domain-containing family B ME; antiparallel
beta sheet, protein transport; HET: SEP EDO; 1.00A {Homo
sapiens} PDB: 3via_A 2dhi_A
Length = 112
Score = 26.4 bits (58), Expect = 2.3
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 18/77 (23%)
Query: 62 MATVKKGKPDLRKKVMPAVIVRQRKPWRR------KDGVFMYFEDNAGVIVNPKGE--MK 113
MA VK G L ++ K W++ DG +Y++D N + + M
Sbjct: 3 MAFVKSGW--LLRQS------TILKRWKKNWFDLWSDGHLIYYDDQTR--QNIEDKVHMP 52
Query: 114 GSAITGPIGKECADLWP 130
I G+EC D P
Sbjct: 53 MDCINIRTGQECRDTQP 69
>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian
clock, PAS domain, transcription, activator, biolo
rhythms, DNA-binding, nucleus; NMR {Homo sapiens}
Length = 121
Score = 25.7 bits (57), Expect = 3.7
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 88 WRRKDGVFMYFEDNAGVIVNPKGE 111
+R KDG F+ + NP +
Sbjct: 81 FRAKDGSFVTLKSQWFSFTNPDTK 104
>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 2b02_A*
2k7s_A 2a24_B
Length = 121
Score = 25.7 bits (57), Expect = 4.3
Identities = 4/23 (17%), Positives = 11/23 (47%)
Query: 88 WRRKDGVFMYFEDNAGVIVNPKG 110
+R K+ +++ ++ NP
Sbjct: 80 FRSKNQEWLWMRTSSFTFQNPYS 102
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A
Length = 117
Score = 25.3 bits (56), Expect = 4.6
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 88 WRRKDGVFMYFEDNAGVIVNPKG 110
K G +++ E VI NP+
Sbjct: 76 MLAKHGGYVWLETQGTVIYNPRN 98
>2b0r_A Possible adenyl cyclase-associated protein; structural genomics
consortium, SGC, unknown function; 2.60A
{Cryptosporidium parvum}
Length = 202
Score = 25.8 bits (56), Expect = 5.8
Identities = 8/75 (10%), Positives = 17/75 (22%), Gaps = 9/75 (12%)
Query: 66 KKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKEC 125
K + Q+ + + A I +G +K
Sbjct: 30 KMKAARQVVTNGSPKVELQKDTYL-----VENHVNCADPITLSEGSIKNKVSVR----CS 80
Query: 126 ADLWPRIASAANAIV 140
+ + N+I
Sbjct: 81 QNSRIIVEQKVNSIF 95
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
0.319 0.136 0.409
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,158,170
Number of extensions: 125558
Number of successful extensions: 260
Number of sequences better than 10.0: 1
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 17
Length of query: 140
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 56
Effective length of database: 4,356,429
Effective search space: 243960024
Effective search space used: 243960024
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 (21.8 bits)
S2: 52 (23.8 bits)