RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8360
(152 letters)
>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide;
transcription; NMR {Homo sapiens} SCOP: a.143.1.2
Length = 127
Score = 113 bits (284), Expect = 2e-33
Identities = 65/94 (69%), Positives = 72/94 (76%), Gaps = 4/94 (4%)
Query: 58 ILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIA 117
IL + ++ + + +YERARVLGTRALQIAMCAPVMVELEGETDPL IA
Sbjct: 38 ILPSGERPQANQKRITTPYMT----KYERARVLGTRALQIAMCAPVMVELEGETDPLLIA 93
Query: 118 MKELKARKIPIIIRRYLPDNSYEDWGIDELKIID 151
MKELKARKIPIIIRRYLPD SYEDWG+DEL I D
Sbjct: 94 MKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127
>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD
polypeptide; transcription, mRNA, multiprotein complex;
HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP:
a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F
1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F*
1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F
1y77_F* ...
Length = 155
Score = 112 bits (280), Expect = 2e-32
Identities = 54/109 (49%), Positives = 69/109 (63%)
Query: 41 GDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMC 100
G + G E +K K K+ +YERAR+LGTRALQI+M
Sbjct: 45 GKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMN 104
Query: 101 APVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI 149
APV V+LEGETDPL+IAMKEL +KIP++IRRYLPD S+EDW ++EL +
Sbjct: 105 APVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV 153
>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 142
Score = 109 bits (274), Expect = 9e-32
Identities = 51/82 (62%), Positives = 62/82 (75%)
Query: 66 KSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARK 125
K K + +YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL +K
Sbjct: 60 SGKAVAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKK 119
Query: 126 IPIIIRRYLPDNSYEDWGIDEL 147
IP+++RRYLPD SYEDW + EL
Sbjct: 120 IPLLVRRYLPDGSYEDWSVAEL 141
>4ayb_K DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_I
4b1o_K 4b1p_I 2waq_K 2wb1_I 2pmz_K 3hkz_K
Length = 95
Score = 102 bits (257), Expect = 8e-30
Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 2/66 (3%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYE 140
RYE ARV+ RALQ+AM AP ++++ TD + IA +E K +PI IRR LP+
Sbjct: 29 RYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKII 88
Query: 141 DWGIDE 146
+ +
Sbjct: 89 LLSLRK 94
>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 = 44.7 bits (105), Expect = 3e-06
Identities = 24/168 (14%), Positives = 47/168 (27%), Gaps = 77/168 (45%)
Query: 6 SNTDLCCTYGSWLGW----AF-------TLLLD-----ENAPTPSKANKWMGDLNLILGI 49
+ T ++G A+ ++L D E P+P M L I
Sbjct: 294 VSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSP------M------LSI 341
Query: 50 KGERALVLILNHYMKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAM---------C 100
++ Q+ + + + + ++I++
Sbjct: 342 SNL--------------TQEQV-------QDYVNKTNSHLPAGKQVEISLVNGAKNLVVS 380
Query: 101 APVMVELEGETDPLQIAMKELKA-------------RKIPIIIRRYLP 135
P L G L + +++ KA RK R+LP
Sbjct: 381 GPPQ-SLYG----LNLTLRKAKAPSGLDQSRIPFSERK-LKFSNRFLP 422
Score = 32.7 bits (74), Expect = 0.042
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 25/62 (40%)
Query: 70 QIKNNNKLNIKQIRYERARVLG--TRALQIAMCAPVMVELEGETDPLQIAMKELKARKIP 127
+I N N N +Q V RAL D + + +K +KI
Sbjct: 1842 EIVNYNVEN-QQY------VAAGDLRAL----------------DTVTNVLNFIKLQKID 1878
Query: 128 II 129
II
Sbjct: 1879 II 1880
>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 = 31.1 bits (69), Expect = 0.080
Identities = 6/22 (27%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 117 AMKELKARKIPIIIRRYLPDNS 138
A+K+L+A ++ Y D++
Sbjct: 21 ALKKLQAS-----LKLYADDSA 37
>3kdw_A Putative sugar binding protein; structural genomics, joint C
structural genomics, JCSG, protein structure
initiative; HET: MSE; 1.70A {Bacteroides vulgatus atcc
8482} PDB: 3g6i_A*
Length = 221
Score = 29.4 bits (65), Expect = 0.34
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 35 KANKWMGDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNIKQIR 83
++ K + L L + +I N Y K+ N I +K +
Sbjct: 39 RSQKIVDKLELTDTVAAREVTTIIANRYFKL---NDIYETRDAKVKLAK 84
>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold,
ATPase, parallel dimer; 2.80A {Thermus thermophilus}
Length = 997
Score = 29.0 bits (65), Expect = 0.64
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 107 LEGETDPLQIAMKELKARKIPIIIRRYLPDNSY-EDWGIDELK 148
L G+ + ++ A + + + +L + EDW ++ LK
Sbjct: 774 LLGKDEEVKEAAIGMVEETVASLAENFLNPEVHPEDWDLEGLK 816
>1y79_1 Peptidyl-dipeptidase DCP; hinge bending, carboxypeptidase,
neurolysin, ACE, hydrolase; HET: TRP; 2.00A {Escherichia
coli}
Length = 680
Score = 27.2 bits (61), Expect = 2.8
Identities = 6/26 (23%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 69 NQIKNNNKLNIKQI---RYERARVLG 91
N+ + I+++ R ++A +LG
Sbjct: 251 KNDANDTRAIIQRLVEIRAQQATLLG 276
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 26.1 bits (57), Expect = 6.7
Identities = 7/60 (11%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 63 MKVKSKNQIKNNNKLNIKQIRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELK 122
+ + +I + ++ E ++ + + + P + + G+T P+ ++ L+
Sbjct: 18 SHMFKREEIIEMANKDFEKAWIETKDLIKAKKINES--YPRIKPVFGKTHPVNDTIENLR 75
>3u1w_A Hypothetical periplasmic protein; BLIP-like, structural genomics,
joint center for structural JCSG, protein structure
initiative; 2.00A {Parabacteroides distasonis}
Length = 253
Score = 25.3 bits (55), Expect = 8.5
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 120 ELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR 152
++ ++P + + Y +W +D+ I+R
Sbjct: 63 DISFAQLPAAVSTAFKQSFYSNWTVDDTYAINR 95
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 0.137 0.417
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,392,501
Number of extensions: 134714
Number of successful extensions: 270
Number of sequences better than 10.0: 1
Number of HSP's gapped: 268
Number of HSP's successfully gapped: 21
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 (21.8 bits)
S2: 53 (24.4 bits)