RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy548
(84 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 = 102 bits (255), Expect = 4e-30
Identities = 63/69 (91%), Positives = 65/69 (94%)
Query: 15 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 74
+YERARVLGTRALQIAMCAPVMVELEGETDPL IAMKELKARKIPIIIRRYLPD SYEDW
Sbjct: 59 KYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDW 118
Query: 75 GIDELKIID 83
G+DEL I D
Sbjct: 119 GVDELIITD 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 = 102 bits (254), Expect = 9e-30
Identities = 48/67 (71%), Positives = 60/67 (89%)
Query: 15 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 74
+YERAR+LGTRALQI+M APV V+LEGETDPL+IAMKEL +KIP++IRRYLPD S+EDW
Sbjct: 87 KYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDW 146
Query: 75 GIDELKI 81
++EL +
Sbjct: 147 SVEELIV 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 = 99.4 bits (247), Expect = 7e-29
Identities = 49/65 (75%), Positives = 59/65 (90%)
Query: 15 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 74
+YERAR+LGTRALQI+M APV+V+LEGETDPLQIAMKEL +KIP+++RRYLPD SYEDW
Sbjct: 77 KYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDW 136
Query: 75 GIDEL 79
+ EL
Sbjct: 137 SVAEL 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 = 94.1 bits (234), Expect = 3e-27
Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 2/66 (3%)
Query: 15 RYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYE 72
RYE ARV+ RALQ+AM AP ++++ TD + IA +E K +PI IRR LP+
Sbjct: 29 RYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKII 88
Query: 73 DWGIDE 78
+ +
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 = 30.8 bits (69), Expect = 0.030
Identities = 9/37 (24%), Positives = 13/37 (35%), Gaps = 11/37 (29%)
Query: 28 QIAMCAPVMVELEGETDPLQIA---MKELKARKIPII 61
Q A G+ L + +K +KI II
Sbjct: 1852 QYV-AA-------GDLRALDTVTNVLNFIKLQKIDII 1880
Score = 27.7 bits (61), Expect = 0.39
Identities = 16/95 (16%), Positives = 32/95 (33%), Gaps = 37/95 (38%)
Query: 4 SPSFIITI-------VIKRYER--ARVLGTRALQIAM---------CAPVMVELEGETDP 45
PS +++I V + + + + ++I++ P L G
Sbjct: 334 VPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQ-SLYG---- 388
Query: 46 LQIAMKELKA-------------RKIPIIIRRYLP 67
L + +++ KA RK R+LP
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPFSERK-LKFSNRFLP 422
Score = 25.4 bits (55), Expect = 3.1
Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 26/76 (34%)
Query: 12 VIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPI-----IIRRYL 66
+IK Y AR++ R + L A+ E A+ + I Y
Sbjct: 122 LIKNYITARIMAKRPFD-----------KKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF 170
Query: 67 PDNSYEDWGIDELKII 82
+EL+ +
Sbjct: 171 ----------EELRDL 176
>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 = 30.3 bits (67), Expect = 0.043
Identities = 6/22 (27%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 49 AMKELKARKIPIIIRRYLPDNS 70
A+K+L+A ++ Y D++
Sbjct: 21 ALKKLQAS-----LKLYADDSA 37
>1a8d_A Tetanus neurotoxin; clostridial, ganglioside binding region; 1.57A
{Clostridium tetani} SCOP: b.29.1.6 b.42.4.2 PDB: 1af9_A
1fv3_A* 1fv2_A* 3hmy_A* 3hn1_A* 1d0h_A* 1dfq_A* 1dll_A*
1yxw_A* 1yyn_A* 1diw_A*
Length = 452
Score = 27.7 bits (60), Expect = 0.40
Identities = 5/26 (19%), Positives = 13/26 (50%)
Query: 59 PIIIRRYLPDNSYEDWGIDELKIIDR 84
I ++ +N+ + ID+ +I +
Sbjct: 206 NITLKLDRCNNNNQYVSIDKFRIFCK 231
>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold,
ATPase, parallel dimer; 2.80A {Thermus thermophilus}
Length = 997
Score = 27.5 bits (61), Expect = 0.45
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 39 LEGETDPLQIAMKELKARKIPIIIRRYLPDNSY-EDWGIDELK 80
L G+ + ++ A + + + +L + EDW ++ LK
Sbjct: 774 LLGKDEEVKEAAIGMVEETVASLAENFLNPEVHPEDWDLEGLK 816
>2f06_A Conserved hypothetical protein; structural genomics hypothetical
protein, PSI, protein struc initiative; HET: MSE HIS;
2.10A {Bacteroides thetaiotaomicron} SCOP: d.58.18.11
d.58.18.11
Length = 144
Score = 24.9 bits (54), Expect = 2.7
Identities = 8/55 (14%), Positives = 16/55 (29%)
Query: 6 SFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPI 60
+ IV + + L + + V + L + L A + I
Sbjct: 46 GILRGIVSDPDKAYKALKDNHFAVNITDVVGISCPNVPGALAKVLGFLSAEGVFI 100
>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 = 2.9
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 52 ELKARKIPIIIRRYLPDNSYEDWGIDELKIIDR 84
++ ++P + + Y +W +D+ I+R
Sbjct: 63 DISFAQLPAAVSTAFKQSFYSNWTVDDTYAINR 95
>3pff_A ATP-citrate synthase; phosphohistidine, organic acid, ATP-grAsp,
lyase, transferas; HET: TLA ADP; 2.30A {Homo sapiens}
Length = 829
Score = 24.0 bits (52), Expect = 8.9
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 29 IAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRR 64
IA V +G ++ LK ++ I +RR
Sbjct: 344 IANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRR 379
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
0.326 0.143 0.414
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: 1,434,358
Number of extensions: 78099
Number of successful extensions: 266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 18
Length of query: 84
Length of database: 6,701,793
Length adjustment: 52
Effective length of query: 32
Effective length of database: 5,249,901
Effective search space: 167996832
Effective search space used: 167996832
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.6 bits)