RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2574
(115 letters)
>3u5c_B RP10A, 40S ribosomal protein S1-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3u5g_B
Length = 255
Score = 148 bits (375), Expect = 2e-48
Identities = 6/75 (8%), Positives = 18/75 (24%)
Query: 1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
M + K+ + ++K + + + + + + A +
Sbjct: 1 MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA 60
Query: 61 TILCQPTGGRARLTE 75
A L
Sbjct: 61 LKGRVVEVCLADLQG 75
>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_6
Length = 81
Score = 140 bits (354), Expect = 4e-45
Identities = 41/73 (56%), Positives = 54/73 (73%)
Query: 3 LAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTI 62
+ +DLL+P EEK+K+K KRL+Q PNSYFMDVKC C I +FS+AQS +IC CS I
Sbjct: 1 MERDLLNPIYEEEKQKNKFKRLIQAPNSYFMDVKCAQCQNIQMIFSNAQSTIICEKCSAI 60
Query: 63 LCQPTGGRARLTE 75
LC+PTGG+ ++
Sbjct: 61 LCKPTGGKVQIQA 73
>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
Length = 86
Score = 133 bits (335), Expect = 3e-42
Identities = 53/77 (68%), Positives = 62/77 (80%), Gaps = 2/77 (2%)
Query: 1 MPLAK--DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAG 58
M L+ DLL+P EK KHK KRLVQ PNS+FMDVKC GC+ ITTVFSH+Q+VV+C G
Sbjct: 1 MVLSNDIDLLNPPAELEKLKHKKKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCPG 60
Query: 59 CSTILCQPTGGRARLTE 75
C T+LCQPTGG+ARLTE
Sbjct: 61 CQTVLCQPTGGKARLTE 77
>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet,
PSI, protein structure initiative; NMR {Archaeoglobus
fulgidus} SCOP: g.41.8.4
Length = 66
Score = 100 bits (250), Expect = 2e-29
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTED 76
+S F+ VKCP C +F H ++V C C + +PTGG+ + +
Sbjct: 2 HSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGKGNIKAE 49
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 34.6 bits (79), Expect = 0.002
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 10/56 (17%)
Query: 10 PSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITT--VFSHAQSVVICAGCSTIL 63
S + + PN + + CP C V ++ V+CA C +L
Sbjct: 5 ESIDKRAGRRG-------PNLN-IVLTCPECKVYPPKIVERFSEGDVVCALCGLVL 52
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation;
NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A
Length = 58
Score = 27.2 bits (60), Expect = 0.42
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 35 VKCPGCYKITTVFSHAQSVVICAGCSTIL 63
V CP V + +IC C ++
Sbjct: 12 VTCPNHPDAILVEDYRAGDMICPECGLVV 40
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation
factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Length = 50
Score = 26.7 bits (59), Expect = 0.50
Identities = 6/30 (20%), Positives = 13/30 (43%)
Query: 34 DVKCPGCYKITTVFSHAQSVVICAGCSTIL 63
CP C ++ + ++CA C ++
Sbjct: 5 QKVCPACESAELIYDPERGEIVCAKCGYVI 34
>2l6l_A DNAJ homolog subfamily C member 24; DPH4, Zn-CSL, J-domain,
chaperone; NMR {Homo sapiens}
Length = 155
Score = 27.5 bits (61), Expect = 0.78
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 30 SYFMDVKCPGCYKITTVFSHAQSVVICAGCS 60
S+++ +C G Y ++ + S++ C CS
Sbjct: 110 SFYLSCRCGGKYSVSKDEAEEVSLISCDTCS 140
>1zso_A Hypothetical protein; structural genomics, PSI, protein structure
initiative, STRU genomics of pathogenic protozoa
consortium, SGPP; 2.17A {Plasmodium falciparum} SCOP:
b.166.1.1
Length = 164
Score = 26.8 bits (59), Expect = 1.3
Identities = 13/104 (12%), Positives = 22/104 (21%), Gaps = 33/104 (31%)
Query: 28 PNSYFMDVKCPGC--------------YKITTVFSHAQSVVICAGC---STILCQPTGGR 70
+ +++ +I A ++ STI T
Sbjct: 31 EYLWIFNIRDSTSSLTRDNIQFRKTDILEIPNSRGTANFMIKWTEYPKYSTINFVNTKNS 90
Query: 71 ARLTEDDTGDSMTV-----RGCALDSGTPTTDTELIRMSHCGGF 109
E + + RG ELI F
Sbjct: 91 CSYEEVNNNEWRDFASFECRGI-----------ELIDFFPSNNF 123
>1w9s_A BH0236 protein, BHCBM6; carbohydrate-binding module, lectin,
beta-glucan, carbohydrate binding, glycoside hydrolase;
1.59A {Bacillus halodurans} SCOP: b.18.1.10 PDB:
1w9t_A* 1w9w_A*
Length = 142
Score = 25.6 bits (56), Expect = 3.9
Identities = 6/38 (15%), Positives = 11/38 (28%)
Query: 56 CAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGT 93
+G T GG + + GD + +
Sbjct: 23 MSGIQTEGTDDDGGGDNIGWINDGDWVKYERVHFERDA 60
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
DNA-binding, DNA- directed RNA polymerase, isopeptide
bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Length = 345
Score = 25.3 bits (54), Expect = 5.1
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 28 PNSYFMDVKCPGC--YKITTVFSHAQSVVICAGCSTIL 63
+ + + CP C Y V ++ V+CA C +L
Sbjct: 15 GPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVL 52
>2g8y_A Malate/L-lactate dehydrogenases; NAD, E.coli, structural GENO PSI,
protein structure initiative, midwest center for struc
genomics, MCSG; HET: NAD 1PE; 2.15A {Escherichia coli}
Length = 385
Score = 25.0 bits (55), Expect = 6.1
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 86 GCALDS-GTPTTDTELIRMSHCGG 108
GC +D G PTT+ +++ S G
Sbjct: 226 GCLIDVNGVPTTNPAVMQESPLGS 249
>1jce_A ROD shape-determining protein MREB; MBL, actin, HSP-70, FTSZ,
structural protein; 2.10A {Thermotoga maritima} SCOP:
c.55.1.1 c.55.1.1 PDB: 1jcf_A 1jcg_A* 2wus_A
Length = 344
Score = 25.1 bits (56), Expect = 6.6
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 69 GRARLTEDDTGDSMTVRGCALDSGTPTTDT 98
G ++++ TV G L +G P T
Sbjct: 211 GNVFPSKENDELETTVSGIDLSTGLPRKLT 240
>1ywh_A Urokinase plasminogen activator surface receptor; UPAR,
three-finger fold, protein-peptide complex, hydrolase;
HET: ALC NAG FUC NDG BMA MAN; 2.70A {Homo sapiens} SCOP:
g.7.1.3 g.7.1.3 g.7.1.3
Length = 313
Score = 24.9 bits (53), Expect = 8.3
Identities = 15/59 (25%), Positives = 19/59 (32%), Gaps = 7/59 (11%)
Query: 35 VKCPGCY--KITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDS 91
+C C S ++ C G TG T + S VRGCA S
Sbjct: 192 RQCYSCKGQSTHGCSSEETFLIDCRGPMNQCLVATG-----THEPKNQSYMVRGCATAS 245
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
0.321 0.135 0.425
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,720,861
Number of extensions: 87564
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 199
Number of HSP's successfully gapped: 22
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
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: 51 (23.5 bits)