RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5605
(152 letters)
>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia
small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP:
a.4.5.84
Length = 150
Score = 174 bits (442), Expect = 4e-57
Identities = 47/122 (38%), Positives = 71/122 (58%)
Query: 13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
+ ++K PEW VK+ + KE P DW+Y R A++ R +Y+ PVG++ + +GGRK
Sbjct: 22 EIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRK 81
Query: 73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
G P F ++ GS+ RKALQ LE +EK GR IT GR +D+IA +++ +
Sbjct: 82 NRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELE 141
Query: 133 EA 134
E
Sbjct: 142 EI 143
>3iz6_S 40S ribosomal protein S19 (S19E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 146
Score = 169 bits (429), Expect = 4e-55
Identities = 68/118 (57%), Positives = 94/118 (79%)
Query: 13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
+SGKM++PEWVDIVK+A+FKEL PYDPDW+YTR A++AR IY+R +GV KI+GGR+
Sbjct: 27 RSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIARKIYLRQGIGVGGFQKIYGGRQ 86
Query: 73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVS 130
RNG P HFC+SSG+++R LQ L+++ II+ GGR ITS GRRD+D++A ++ V+
Sbjct: 87 RNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGRLITSQGRRDLDQVAGRVDVT 144
>3u5c_T 40S ribosomal protein S19-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_S 3o30_M 3o2z_M 3u5g_T 3jyv_T*
Length = 144
Score = 163 bits (415), Expect = 4e-53
Identities = 60/121 (49%), Positives = 84/121 (69%), Gaps = 1/121 (0%)
Query: 13 KSGKMKVPEWVDIVKSAKFKELAPYDPD-WFYTRCAALARHIYMRSPVGVKTVTKIFGGR 71
+ GK++VP +VDIVK++ E+ P D + WFY R A++ARHIYMR VGV + K++GG
Sbjct: 24 RQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGGA 83
Query: 72 KRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131
K GV P +SGS+ RK LQALE++ I+E S GGR+I+ +G+RD+DRIAAQ
Sbjct: 84 KSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQTLEED 143
Query: 132 K 132
+
Sbjct: 144 E 144
>2xzm_T RPS19E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_T
Length = 155
Score = 161 bits (409), Expect = 4e-52
Identities = 45/128 (35%), Positives = 70/128 (54%), Gaps = 5/128 (3%)
Query: 12 SKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGR 71
K+ K+ +PE+ ++ +ELAP D DW Y R AALAR +Y++ G+ T+ IFG
Sbjct: 27 KKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVYLKPHTGISTLKHIFGSN 86
Query: 72 KRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-----GRKITSHGRRDMDRIAAQ 126
K G + G + R AL++LE + II K + R IT G +++RIA Q
Sbjct: 87 KDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMTELNRIATQ 146
Query: 127 IRVSKKEA 134
I + +++A
Sbjct: 147 IAIKQRQA 154
>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 = 36.6 bits (84), Expect = 0.002
Identities = 23/139 (16%), Positives = 42/139 (30%), Gaps = 43/139 (30%)
Query: 42 FYTRCAALARHI------YMRSPVGV----------KTVTKIFGGRK----RNGVCPSHF 81
Y A A+ + + + G +T FGG K R +
Sbjct: 1635 LYKTSKA-AQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENY-SAMI 1692
Query: 82 CRSSGSVARKALQALEQVN-----IIEKSDDGGRKITSHGRRDMDRIAAQIR---VSKKE 133
+ K + +++N +S+ G T Q + K
Sbjct: 1693 FETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQF---------TQPALTLMEK-- 1741
Query: 134 AALQALAAQGITVVPTGAV 152
AA + L ++G+ +P A
Sbjct: 1742 AAFEDLKSKGL--IPADAT 1758
>2yu1_A JMJC domain-containing histone demethylation PROT;
JMJC-domain-containing histone demethylases,
oxidoreductase; HET: AKG; 2.70A {Homo sapiens} PDB:
2yu2_A
Length = 451
Score = 30.7 bits (68), Expect = 0.19
Identities = 6/50 (12%), Positives = 16/50 (32%)
Query: 4 VSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHI 53
V + K +M + +W ++ + + Y+ L +
Sbjct: 108 VDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMV 157
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.4 bits (62), Expect = 0.79
Identities = 8/26 (30%), Positives = 10/26 (38%), Gaps = 7/26 (26%)
Query: 26 VKSAKFK-ELAPYDPDWFYTRCAALA 50
+K K + L Y D ALA
Sbjct: 22 LK--KLQASLKLYADD----SAPALA 41
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein
structure initiati midwest center for structural
genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Length = 382
Score = 28.4 bits (64), Expect = 0.95
Identities = 12/67 (17%), Positives = 20/67 (29%), Gaps = 19/67 (28%)
Query: 81 FCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALA 140
A+ A + I+ G R + G + ++AA L
Sbjct: 114 GVH--ALPEALAVMARPMIAIV-----GSRNASGAGLKFAGQLAAD------------LG 154
Query: 141 AQGITVV 147
A G V+
Sbjct: 155 AAGFVVI 161
>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia
coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A*
3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A
Length = 202
Score = 27.2 bits (61), Expect = 1.9
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 11/65 (16%)
Query: 72 KRNGVCPS------HFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD-----M 120
+ G+ P+ S + A + L+AL + +IE R I + +
Sbjct: 20 SQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLV 79
Query: 121 DRIAA 125
R+AA
Sbjct: 80 GRVAA 84
>3cx5_A Cytochrome B-C1 complex subunit 1, mitochondrial; complex III,
electron transfer complex, cytochrome BC1 complex,
mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ
HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces
cerevisiae} SCOP: d.185.1.1 d.185.1.1 PDB: 1p84_A*
2ibz_A* 1kb9_A* 3cxh_A* 1ezv_A* 1kyo_A*
Length = 431
Score = 26.8 bits (60), Expect = 2.8
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 93 LQALEQVNIIEKSDDGGRKITSHGRR-DMDRIAAQI-RVSK---KEAALQALAAQGITVV 147
Q E N + ++ G ++ G + + +I ++ K A + L Q I +
Sbjct: 349 GQLYESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIA 408
Query: 148 PTGAV 152
TG +
Sbjct: 409 GTGQI 413
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein
structure initiative; 2.20A {Thermoplasma acidophilum
dsm 1728} SCOP: a.4.5.28 b.43.5.2
Length = 230
Score = 26.2 bits (57), Expect = 4.2
Identities = 9/61 (14%), Positives = 17/61 (27%), Gaps = 3/61 (4%)
Query: 85 SGSVARKALQALEQVNIIEKSDDGGR---KITSHGRRDMDRIAAQIRVSKKEAALQALAA 141
S A + + LE+ I ++ IT G + A + +
Sbjct: 40 SQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITG 99
Query: 142 Q 142
Sbjct: 100 T 100
>2kr1_A Ubiquitin protein ligase E3A; UBL conjugation pathway, structural
genomics, PSI-2, structure initiative, northeast
structural genomics consort NESG; NMR {Homo sapiens}
Length = 82
Score = 25.4 bits (55), Expect = 4.3
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 74 NGVCPSHFCRSSGSVARK-----ALQALE 97
N C + FC S + R A++ALE
Sbjct: 41 NEACTNEFCASCPTFLRMDNNAAAIKALE 69
>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4,
UIP4, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: g.44.1.1
Length = 94
Score = 25.2 bits (55), Expect = 4.7
Identities = 7/40 (17%), Positives = 15/40 (37%)
Query: 65 TKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK 104
I G + CP C G + ++ + I+++
Sbjct: 41 LLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQR 80
>3pvs_A Replication-associated recombination protein A; maintenance of
genome stability Pro recombination; 2.50A {Escherichia
coli}
Length = 447
Score = 26.3 bits (59), Expect = 4.9
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 80 HFCRSSGSVARKALQALEQ-VNIIEKSDDGGRKIT 113
AR+AL LE ++ E D G R +
Sbjct: 199 AIAELVNGDARRALNTLEMMADMAEVDDSGKRVLK 233
>1rkq_A Hypothetical protein YIDA; two domain structure with beta-alpha
sandwich. stucture contains A magnesium ION., PSI,
protein structure initiative; 1.40A {Escherichia coli}
SCOP: c.108.1.10
Length = 282
Score = 26.0 bits (58), Expect = 5.1
Identities = 8/28 (28%), Positives = 11/28 (39%), Gaps = 7/28 (25%)
Query: 130 SKKE------AALQALAAQGITVVP-TG 150
A+ A A+G+ VV TG
Sbjct: 19 PDHTISPAVKNAIAAARARGVNVVLTTG 46
>3mpo_A Predicted hydrolase of the HAD superfamily; SGX, PSI, structural
genomics, protein structure initiative; 2.90A
{Lactobacillus brevis}
Length = 279
Score = 26.0 bits (58), Expect = 5.2
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 128 RVSKK-EAALQALAAQGITVVP-TG 150
+++ A+QA AQGI VV TG
Sbjct: 22 ELAQATIDAVQAAKAQGIKVVLCTG 46
>1tuw_A Tetracenomycin polyketide synthesis protein TCMI; dimeric ???
ferredoxin-like fold tetracenomycin C biosynthes unknown
function; 1.90A {Streptomyces glaucescens} SCOP:
d.58.4.8
Length = 109
Score = 25.3 bits (55), Expect = 5.2
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 20 PEWVDIVKSAKFKE-LAPYDPDWFYTRCAALARHIY 54
P + ++ + + + L PY DW + + A Y
Sbjct: 70 PLFQEV--NERVGQYLTPYAQDWEELK-DSKAEVFY 102
>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga
maritima} PDB: 3qg5_A 3tho_A*
Length = 365
Score = 26.0 bits (57), Expect = 6.3
Identities = 5/41 (12%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 94 QALEQV-NIIEKSDDGGRKIT--SHGRRDMDRIAAQIRVSK 131
+ E++ +++++ + + I +H R + ++R++
Sbjct: 319 ENKEKIASVLKELERLNKVIVFITHDREFSEAFDRKLRITG 359
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 26.0 bits (57), Expect = 6.3
Identities = 27/179 (15%), Positives = 52/179 (29%), Gaps = 60/179 (33%)
Query: 6 YIGFRPSKSGKMKVPEWVDIVKSAKFKE--LA-----PYDPDWFYTRCAALARHIYMRSP 58
Y G+ SK+ + V + D+ AK++ L +P+ F + Y +P
Sbjct: 873 YTGWVDSKTKEP-VDDK-DVK--AKYETSILEHSGIRLIEPELF---------NGY--NP 917
Query: 59 VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG---------G 109
+ + ++ +S A + I + + G
Sbjct: 918 EKKEMIQEVIVEE------DLEPFEASKETAEQFKHQHGDKVDIFEIPETGEYSVKLLKG 971
Query: 110 RKITSHGRRDMD-RIAAQI---------RVSKKE-------------AALQALAAQGIT 145
+ D +A QI +S + ++A A GIT
Sbjct: 972 ATLYIPKALRFDRLVAGQIPTGWNAKTYGISDDIISQVDPITLFVLVSVVEAFIASGIT 1030
>2dwc_A PH0318, 433AA long hypothetical phosphoribosylglycinamide
transferase; purine ribonucleotide biosynthesis; HET:
ADP; 1.70A {Pyrococcus horikoshii} PDB: 2czg_A*
Length = 433
Score = 26.1 bits (58), Expect = 6.4
Identities = 6/17 (35%), Positives = 6/17 (35%)
Query: 134 AALQALAAQGITVVPTG 150
AL G VVP
Sbjct: 96 DALFEFEKDGYFVVPNA 112
>3q7c_A Nucleoprotein; deddh exonuclease, 3' exonuclease, hydrolase; 1.50A
{Lassa virus} PDB: 3q7b_A
Length = 243
Score = 25.8 bits (56), Expect = 6.5
Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 14/120 (11%)
Query: 18 KVPEWVDIVKSAKFK-ELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGV 76
W+DI + E+A Y P + H + R P +K + + +G+
Sbjct: 57 NAKTWMDIEGRPEDPVEIALYQPS------SGCYIHFF-REPTDLKQFKQ--DAKYSHGI 107
Query: 77 CPSHFCRSSGSVARKALQALEQ--VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134
+ + + + AL + V + SDD + + S GR+D+ I I +SK ++
Sbjct: 108 DVTDLFATQPGLTSAVIDALPRNMVITCQGSDDIRKLLESQGRKDIKLI--DIALSKTDS 165
>4dw8_A Haloacid dehalogenase-like hydrolase; HAD, putative phosphatase,
enzyme function initiative, EFI, structural genomics;
1.50A {Bacteroides thetaiotaomicron} PDB: 3niw_A 4dwo_A
Length = 279
Score = 25.6 bits (57), Expect = 6.7
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 7/28 (25%)
Query: 130 SKKE------AALQALAAQGITVVP-TG 150
SKKE L + QGI +V +G
Sbjct: 19 SKKEISSRNRETLIRIQEQGIRLVLASG 46
>3now_A UNC-45 protein, SD10334P; armadillo repeat, HSP90, myosin,
tetra-tricopeptide repeat, binding protein required for
myosin function; 2.99A {Drosophila melanogaster}
Length = 810
Score = 25.6 bits (55), Expect = 8.7
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 88 VARKALQALEQVNIIEKSDDG 108
VA + L A E+ IIE+SD+
Sbjct: 772 VATQCLAAAERYRIIERSDNA 792
>2kmv_A Copper-transporting ATPase 1; menkes, nucleotide binding protein,
alternative splicing, ATP-binding, cell membrane,
cytoplasm, disease mutation; NMR {Homo sapiens} PDB:
2kmx_A*
Length = 185
Score = 25.4 bits (55), Expect = 8.7
Identities = 9/56 (16%), Positives = 16/56 (28%), Gaps = 1/56 (1%)
Query: 92 ALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVV 147
+ + I + K+ R M R I + + +G T V
Sbjct: 114 SSSMIIDAQISNALNAQQYKVLIGNREWMIRNGLVIN-NDVNDFMTEHERKGRTAV 168
>3pgv_A Haloacid dehalogenase-like hydrolase; structural genomics, joint
center for structural genomics, J protein structure
initiative; HET: EPE; 2.39A {Klebsiella pneumoniae
subsp}
Length = 285
Score = 25.2 bits (56), Expect = 8.8
Identities = 8/18 (44%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 134 AALQALAAQGITVVP-TG 150
L+ L A+GI V TG
Sbjct: 45 ETLKLLTARGINFVFATG 62
>1nrw_A Hypothetical protein, haloacid dehalogenase-like hydrolase;
structural genomics, PSI, protein structure initiative;
1.70A {Bacillus subtilis} SCOP: c.108.1.10
Length = 288
Score = 25.3 bits (56), Expect = 9.2
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 128 RVSKK-EAALQALAAQGITVVP-TG 150
+VS + E AL+ GI VV TG
Sbjct: 21 QVSLENENALRQAQRDGIEVVVSTG 45
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
0.320 0.133 0.396
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,485,309
Number of extensions: 149500
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 615
Number of HSP's successfully gapped: 72
Length of query: 152
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,328,508
Effective search space: 290010036
Effective search space used: 290010036
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 (21.9 bits)
S2: 53 (24.2 bits)