RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11013
(176 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 = 121 bits (303), Expect = 2e-34
Identities = 42/104 (40%), Positives = 65/104 (62%), Gaps = 7/104 (6%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+H+R IRK + EI+ EV S L ++ +KL+P+ I KEIE + I+PL ++ +RKVK+L
Sbjct: 159 SHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLL 218
Query: 133 KKPRFELSKLLELHGEGKGGATIDESGETVDRPEGYEPPVQEAV 176
K+P+F++ L+ LHGEG G E + G++ V E V
Sbjct: 219 KQPKFDVGALMALHGEGSG-------EEKGKKVTGFKDEVLETV 255
>2xzm_4 40S ribosomal protein S3A; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_4
Length = 265
Score = 109 bits (274), Expect = 4e-30
Identities = 33/95 (34%), Positives = 53/95 (55%), Gaps = 1/95 (1%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+ VR IR+K+ I NE K + E L+ + K+IEK+ + I+PL ++ IRKVKVL
Sbjct: 165 SQVRAIRRKINTFITNEAAKLGIAEFSKNLIGEDYTKKIEKETKNIFPLQNITIRKVKVL 224
Query: 133 KKPRFELSKLLELHGEGKGGATI-DESGETVDRPE 166
K+P+ + +K+ EL+ K G G ++
Sbjct: 225 KRPKLDATKIAELYSHEKKGEKATGRDGAPEEQAA 259
>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 = 46.8 bits (110), Expect = 1e-06
Identities = 25/123 (20%), Positives = 48/123 (39%), Gaps = 29/123 (23%)
Query: 32 KNW-----MKLMTTGYLHLSQSLNTFLLGDCGPRGSSLKLVYQ---LFKTHVRQIRKKMV 83
NW KL T + SLN P + + ++ +F I ++
Sbjct: 345 DNWKHVNCDKLTTI----IESSLNVL-----EP--AEYRKMFDRLSVFPPSAH-IPTILL 392
Query: 84 EIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKKPRFELSKLL 143
+I +V+KSD+ VVNKL S+ + ++ + + +++ + +L
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVE--KQPKESTISIPSIYLEL-------KVKLENEY 443
Query: 144 ELH 146
LH
Sbjct: 444 ALH 446
>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 = 44.3 bits (104), Expect = 8e-06
Identities = 19/150 (12%), Positives = 46/150 (30%), Gaps = 40/150 (26%)
Query: 8 HS--E--KMSCVVGALSFNLSSACRTIRKNWMKLMTTGYLHLSQSLNTFLLGDCGPRGSS 63
HS E ++ + +S S + G + PR
Sbjct: 1762 HSLGEYAALASLADVMSI--ESLVEVVFYR-------G----------MTMQVAVPRDEL 1802
Query: 64 LKLVYQLFKTHVRQIRKKMVEIIINEVVKS------DLKEVVNKLLPDS---IAKEIEKK 114
+ Y + + ++ + + VV+ L E+VN + + A ++
Sbjct: 1803 GRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLR-- 1860
Query: 115 CQGIYPLHDVFIRKVKVLKKPRFELSKLLE 144
+ D + +K + ++ +L +
Sbjct: 1861 --AL----DTVTNVLNFIKLQKIDIIELQK 1884
Score = 32.7 bits (74), Expect = 0.051
Identities = 20/86 (23%), Positives = 27/86 (31%), Gaps = 25/86 (29%)
Query: 4 IPTCHSEKMSCVVGA----LSFNL-SSACRTI-RK--NWMKLMTTGYLHLSQSLNTFLLG 55
IP + G+ LS ++ I R W H L
Sbjct: 457 IPVYDTFD-----GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATH-------IL-- 502
Query: 56 DCGPRGSS--LKLVYQLFK-THVRQI 78
D GP G+S L ++ T VR I
Sbjct: 503 DFGPGGASGLGVLTHRNKDGTGVRVI 528
Score = 32.3 bits (73), Expect = 0.082
Identities = 15/107 (14%), Positives = 30/107 (28%), Gaps = 38/107 (35%)
Query: 28 RTIRKNWMKLMTTGYL-------HLSQSLNTFLLGDC--GPRGSSLKLVYQLFKTHVRQI 78
+ IR+N+ ++ + + + +N +G L T Q
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG-------LLSATQFTQP 1734
Query: 79 RKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVF 125
++E E +KS +G+ P F
Sbjct: 1735 ALTLMEKAAFEDLKS----------------------KGLIPADATF 1759
>1wyr_A RHO guanine nucleotide exchange factor 6; CH domain, all-alpha,
NPPSFA, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
Length = 121
Score = 29.5 bits (66), Expect = 0.30
Identities = 10/53 (18%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 95 LKEVVNKLLPDSIAKEIEKKCQGIYPLHD---VFIRKVKVLKKPRFELSKLLE 144
L +++N+L+P S+ ++ Q + F++ L+ F+ L
Sbjct: 45 LCKLINRLMPGSV-EKFCLDPQTEADCINNINDFLKGCATLQVEIFDPDDLYS 96
>3nbi_A RECQ-mediated genome instability protein 1; OB-fold, RPA-like,
protein binding; 2.00A {Homo sapiens}
Length = 216
Score = 29.0 bits (64), Expect = 0.71
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 5/91 (5%)
Query: 81 KMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKKPRFELS 140
+M + + + + +DL+++ + LLPD I + + + G Y L I + + +P + S
Sbjct: 50 QMNKQVFEQWLLTDLRDLEHPLLPDGILEIPKGELNGFYALQ---INSLVDVSQPAY--S 104
Query: 141 KLLELHGEGKGGATIDESGETVDRPEGYEPP 171
++ +L G+ + + +P +P
Sbjct: 105 QIQKLRGKNTTNDLVTAEAQVTPKPWEAKPS 135
>2hmq_A Hemerythrin; oxygen transport; 1.66A {Themiste dyscritum} SCOP:
a.24.4.1 PDB: 2hmz_A 1hmd_A 1hmo_A 1i4y_A 1i4z_A 1hrb_A
Length = 113
Score = 26.3 bits (58), Expect = 3.3
Identities = 17/89 (19%), Positives = 27/89 (30%), Gaps = 14/89 (15%)
Query: 71 FKTHVRQI---RKKMVEIIINEVVKSDLKEVVNKLL---PDSIAKEIEKKCQGIYP---- 120
F+T I K + I + ++D + +N+L E + Y
Sbjct: 14 FRTFYTIIDDEHKTLFNGI-LLLSQADNADHLNELRRCTGKHFLNEQQLMQASQYAGYAE 72
Query: 121 ---LHDVFIRKVKVLKKPRFELSKLLELH 146
HD FI K+ L H
Sbjct: 73 HKKAHDDFIHKLDTWDGDVTYAKNWLVNH 101
>2ftc_K 39S ribosomal protein L19, mitochondrial; mitochondrial ribosome,
large ribosomal subunit, ribosomal R ribosome; 12.10A
{Bos taurus}
Length = 98
Score = 25.6 bits (57), Expect = 4.5
Identities = 8/40 (20%), Positives = 19/40 (47%)
Query: 118 IYPLHDVFIRKVKVLKKPRFELSKLLELHGEGKGGATIDE 157
+ L++ +++++V+K + LL L +T D
Sbjct: 56 CFELYNPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDV 95
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 26.3 bits (59), Expect = 6.1
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 16/50 (32%)
Query: 130 KVLKKPRFELS----KLLELH------GE--GKGGATI----DESGETVD 163
K + KPR + + + G GG + E+G T+
Sbjct: 552 KTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTIS 601
>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 = 26.4 bits (58), Expect = 6.2
Identities = 6/33 (18%), Positives = 12/33 (36%), Gaps = 3/33 (9%)
Query: 12 MSCVVGALS---FNLSSACRTIRKNWMKLMTTG 41
+ VGA + ++ TI ++ G
Sbjct: 1099 IKTPVGACATSVESVDIGVETILSGKARICIVG 1131
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 26.3 bits (59), Expect = 7.1
Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 16/50 (32%)
Query: 130 KVLKKPRFELS----KLLELH------GE--GKGGATI----DESGETVD 163
K + PR ++ K+ ++ E G GG I +G VD
Sbjct: 555 KAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVD 604
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 26.3 bits (59), Expect = 7.6
Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 16/50 (32%)
Query: 130 KVLKKPRFELS----KLLELH------GE--GKGGATI----DESGETVD 163
+ + PR ++S ++ + + GKGG+ I +E+G T++
Sbjct: 545 QAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIE 594
>3ilv_A Glutamine-dependent NAD(+) synthetase; protein structure initiative
II(PSI II), NYSGXRC, structural genomics; 1.79A
{Cytophaga hutchinsonii atcc 33406}
Length = 634
Score = 26.1 bits (58), Expect = 8.4
Identities = 14/99 (14%), Positives = 29/99 (29%), Gaps = 12/99 (12%)
Query: 66 LVYQLFKTHVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVF 125
+ +R K + ++ V K +L P + E+ Y +
Sbjct: 490 FIRSW----LRWAEKNRNQHGLHIVNK---LAPTAELRPSEYTQTDERDL-MPYDVLARI 541
Query: 126 IRKVKVLKKPRFELSKLLELHGEGKGGATIDESGETVDR 164
RK + ++ +G T +E V +
Sbjct: 542 ERKAIKERLSPVQVYTA----LLTEGPYTKNEFKYWVKK 576
>3n1e_A Vacuolar protein sorting-associated protein 54; spinal muscular
atrophy, vesicle trafficking, golgi apparatu tethering
complex, GARP.; 1.70A {Mus musculus} PDB: 3n1b_A
Length = 141
Score = 25.3 bits (55), Expect = 8.7
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 10/78 (12%)
Query: 67 VYQLFKTHVRQIRKKMVEI----IINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYP-- 120
+ + + H+ +I K+V I + K ++K V +I K++ K + I+
Sbjct: 13 ITKDYHDHIAEISAKLVAIMDSLFDKLLSKYEVKAPVPSPCFRNICKQMTKMHEAIFDLL 72
Query: 121 ----LHDVFIRKVKVLKK 134
+F+R K
Sbjct: 73 PEEQTQMLFLRINASYKL 90
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
0.318 0.136 0.394
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,614,949
Number of extensions: 146916
Number of successful extensions: 380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 374
Number of HSP's successfully gapped: 24
Length of query: 176
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 89
Effective length of database: 4,272,666
Effective search space: 380267274
Effective search space used: 380267274
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.4 bits)