RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8661
(71 letters)
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_D 3u5g_E
Length = 261
Score = 106 bits (265), Expect = 2e-30
Identities = 54/69 (78%), Positives = 60/69 (86%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
+LDKL G +APRPS GPHKLRESLPL++FLRNRLKYAL +EV ILMQR +KVDGKVRT
Sbjct: 19 LLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRT 78
Query: 61 DTNYPAGFM 69
DT YPAGFM
Sbjct: 79 DTTYPAGFM 87
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
Length = 265
Score = 105 bits (264), Expect = 2e-30
Identities = 51/69 (73%), Positives = 59/69 (85%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
MLDKLGG FAP+PS+GPHK RE LPL++ +RNRLKYALT +EV+ ILMQR + VDGKVRT
Sbjct: 19 MLDKLGGAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRT 78
Query: 61 DTNYPAGFM 69
D YPAGFM
Sbjct: 79 DKTYPAGFM 87
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_W
Length = 260
Score = 102 bits (256), Expect = 4e-29
Identities = 41/71 (57%), Positives = 51/71 (71%), Gaps = 2/71 (2%)
Query: 1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKIL--MQRLIKVDGKV 58
ML+KLGG++A RPS GPHKLRESLPL + L+ RL YAL ++V IL ++ + VDGKV
Sbjct: 19 MLNKLGGIWATRPSQGPHKLRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKV 78
Query: 59 RTDTNYPAGFM 69
R D YP G M
Sbjct: 79 RRDKGYPTGLM 89
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}
Length = 213
Score = 84.4 bits (208), Expect = 2e-22
Identities = 18/52 (34%), Positives = 29/52 (55%)
Query: 18 HKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFM 69
H +S+ L+ +R+ LK + +E +IL L+KVDGK + + GFM
Sbjct: 2 HPKDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFM 53
>3tj1_A RNA polymerase I-specific transcription initiatio RRN3; heat
repeat, transcription factor, nucleus; 2.85A
{Saccharomyces cerevisiae}
Length = 649
Score = 28.7 bits (63), Expect = 0.11
Identities = 11/51 (21%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 17 PHKLRESLPLVIFLRNRLKYALTN------QEVLKILMQRLIKVDGKVRTD 61
P+K LV + N LK L ++ +L++++I +D +++ +
Sbjct: 221 PNKNDTRRKLVNYTSNLLK--LRGYCSELGFQIWSLLIEKIISIDVELQNE 269
>4aks_A PATG, thiazoline oxidase/subtilisin-like protease; hydrolase,
patellamide; 2.19A {Prochloron didemni} PDB: 4akt_A
Length = 360
Score = 26.3 bits (58), Expect = 0.70
Identities = 7/39 (17%), Positives = 17/39 (43%)
Query: 26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNY 64
L++ L+ + + + V L++ I D +V +
Sbjct: 304 LLMSLQVQQGKPVDAEAVRTALLKTAIPCDPEVVEEPER 342
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog;
S4 domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 71
Score = 24.2 bits (53), Expect = 2.5
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 20 LRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR 71
LP V+ +L+ A Q + + Q ++V V TD PA F+V
Sbjct: 6 SGRRLPTVLL---KLRMAQHLQAAVAFVEQGHVRVGPDVVTD---PA-FLVT 50
>2djw_A Probable transcriptional regulator, ASNC family; structural
genomics, thermus thermophilus HB8, NPPSFA; 2.40A
{Thermus thermophilus}
Length = 92
Score = 24.1 bits (53), Expect = 2.9
Identities = 6/27 (22%), Positives = 15/27 (55%)
Query: 36 YALTNQEVLKILMQRLIKVDGKVRTDT 62
+E+ ++ Q ++ ++G RT+T
Sbjct: 45 RLKDVEELDDVVTQGILSLEGVERTET 71
>1pp9_A Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_A* 1be3_A* 1l0n_A* 1ntk_A* 1ntm_A*
1ntz_A* 1nu1_A* 1l0l_A* 1ppj_A* 1sqq_A* 1sqv_A* 1sqx_A*
2a06_A* 2fyu_A* 2ybb_A* 1sqb_A* 1sqp_A* 1qcr_A* 1bcc_A*
2bcc_A* ...
Length = 446
Score = 24.5 bits (54), Expect = 3.7
Identities = 6/37 (16%), Positives = 12/37 (32%), Gaps = 3/37 (8%)
Query: 7 GVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEV 43
G + + + ++ RL + T EV
Sbjct: 321 GAHF---VCDHMSIDDMMFVLQGQWMRLCTSATESEV 354
>2cvi_A 75AA long hypothetical regulatory protein ASNC; structural
genomics, unknown function; 1.50A {Pyrococcus
horikoshii} PDB: 2z4p_A 2e1a_A
Length = 83
Score = 23.3 bits (51), Expect = 5.0
Identities = 4/27 (14%), Positives = 13/27 (48%)
Query: 36 YALTNQEVLKILMQRLIKVDGKVRTDT 62
T +++ + + +++ K+ T T
Sbjct: 45 ETDTLKDLDQFITEKIRKMPEIQMTST 71
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
0.325 0.143 0.413
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,059,812
Number of extensions: 48940
Number of successful extensions: 150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 11
Length of query: 71
Length of database: 6,701,793
Length adjustment: 41
Effective length of query: 30
Effective length of database: 5,557,032
Effective search space: 166710960
Effective search space used: 166710960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.6 bits)