RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6291
(79 letters)
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus}
Length = 148
Score = 41.0 bits (97), Expect = 3e-06
Identities = 19/45 (42%), Positives = 33/45 (73%)
Query: 3 VMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLKNVSSQIRQ 47
++K A+ LP++L + +M RLH+FPD+ +PED+LKN+ ++ Q
Sbjct: 103 IVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPEDILKNLVEELPQ 147
>3lmc_A Peptidase, zinc-dependent; structural genomics, PSI-2, protein
structure initiative, no structural genomics
consortium, NESG, MUR16; 2.00A {Methanocorpusculum
labreanum}
Length = 210
Score = 29.4 bits (65), Expect = 0.069
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 24 RLHIFPDQEVPEDLLKNVSSQIRQLRPVP 52
+H+F D VP L + VS ++ + +P
Sbjct: 2 GIHLFWDSRVPVGLSRPVSEELSAVLEMP 30
>3k8k_A Alpha-amylase, SUSG; alpha8/BETA8 barrel, CBM, beta-sandwich,
membrane protein; 2.20A {Bacteroides thetaiotaomicron}
PDB: 3k8m_A* 3k8l_A*
Length = 669
Score = 26.2 bits (58), Expect = 0.99
Identities = 9/57 (15%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 4 MKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSD 60
+ A + + R + RL A HI+ + E+ + + + + D
Sbjct: 347 IADAAKGWIARGVDGLRLDAVKHIYHSETSEEN-PRFLKMFYEDMNAYYKQKGHTDD 402
>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 = 25.8 bits (56), Expect = 1.9
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 12/47 (25%)
Query: 13 PRSLIKFRLMARLHIFP---DQ-EVPEDLLKNVSSQIRQLRPVPRTL 55
P+SL L R P DQ +P S+ R+L+ R L
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIP-------FSE-RKLKFSNRFL 421
>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 = 25.3 bits (54), Expect = 2.0
Identities = 6/18 (33%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 17 IKFRLMARLHIFPDQEVP 34
+K +L A L ++ D P
Sbjct: 22 LK-KLQASLKLYADDSAP 38
>2xap_A Ribonucleoside-diphosphate reductase 1 subunit alpha;
oxidoreductase, DNA replication, allosteric enzyme,
nucleotide-binding; HET: NIY; 2.10A {Escherichia coli}
PDB: 2xo5_A* 2x0x_A 2r1r_A 3r1r_A* 3uus_A* 1r1r_A
2xav_A* 7r1r_A 2xax_A* 6r1r_A 2xaw_A* 5r1r_A 2xo4_A*
2xak_A* 4r1r_A* 2xaz_A* 2xay_A* 1rlr_A 1qfn_B
Length = 761
Score = 24.6 bits (54), Expect = 4.1
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 6/63 (9%)
Query: 20 RLMARLHIF------PDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFP 73
L ARL IF Q P L +V + + L Y+++E + D
Sbjct: 79 YLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHD 138
Query: 74 KDY 76
+D
Sbjct: 139 RDM 141
>3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding, virion, zinc,
core protein, RNA-binding, icosaderal virus; 3.80A
{Rotavirus A} PDB: 3kz4_A 3n09_A
Length = 800
Score = 24.3 bits (52), Expect = 5.2
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 20 RLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPR 53
+ RLHIF VP+D + + ++R L PV
Sbjct: 564 DFLKRLHIFDVARVPDDQMYRLRDRLRLL-PVEV 596
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2,
structure initiative, northeast structural genomics
consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP:
b.40.4.5 b.40.4.16 PDB: 2r7f_A
Length = 469
Score = 24.2 bits (53), Expect = 6.0
Identities = 6/36 (16%), Positives = 13/36 (36%), Gaps = 5/36 (13%)
Query: 24 RLHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYS 59
+P +EV D L + ++ + L +
Sbjct: 291 ATQDYPTREVAGDTLPAMWARRKTLAR-----TRFQ 321
>3pjx_A Cyclic dimeric GMP binding protein; ggdef-EAL tandem domain,
C-DI-GMP receptor, lyase; 2.00A {Pseudomonas
fluorescens} PDB: 3pjw_A 3pju_A* 3pjt_A* 3pfm_A
Length = 430
Score = 24.0 bits (53), Expect = 6.8
Identities = 3/14 (21%), Positives = 6/14 (42%)
Query: 27 IFPDQEVPEDLLKN 40
F + P+ +L
Sbjct: 148 PFAHGDSPQAVLSL 161
>3ax6_A Phosphoribosylaminoimidazole carboxylase, ATPase; structural
genomics, riken structural genomics/proteomics in RSGI,
ATP grAsp, ATP binding; HET: ADP; 2.20A {Thermotoga
maritima}
Length = 380
Score = 23.6 bits (52), Expect = 7.9
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 33 VPEDLLKNVSSQIRQLRPVPRTLASYSDK 61
+ LK + ++ ++ P P TL DK
Sbjct: 73 IDVQTLKKLYNEGYKIHPSPYTLEIIQDK 101
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 24.0 bits (51), Expect = 8.4
Identities = 7/44 (15%), Positives = 17/44 (38%)
Query: 34 PEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKDYI 77
PE +L+ + + Q+ P + + +S I + +
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
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
0.323 0.140 0.408
Gapped
Lambda K H
0.267 0.0838 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,237,725
Number of extensions: 58944
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 175
Number of HSP's successfully gapped: 18
Length of query: 79
Length of database: 6,701,793
Length adjustment: 48
Effective length of query: 31
Effective length of database: 5,361,585
Effective search space: 166209135
Effective search space used: 166209135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.2 bits)