RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4748
(136 letters)
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon,
hyperthermophilic, extremophIle; NMR {Thermococcus
celer} SCOP: g.41.3.1
Length = 57
Score = 54.1 bits (130), Expect = 3e-11
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 92 KTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
+ ++ P + C +C NDT + +Q R+ DE TIF+ CTKC
Sbjct: 5 EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKC 49
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 113
Score = 55.5 bits (133), Expect = 4e-11
Identities = 20/127 (15%), Positives = 36/127 (28%), Gaps = 27/127 (21%)
Query: 12 EFCSKCGTIL-PLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVF 70
++C +C +L P D V C+ E
Sbjct: 5 QYCIECNNMLYPREDKVDRVLRLACRN-CDYSEI------------------------AA 39
Query: 71 EEIKAEYTIHFNTVEKEK-QKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTI 129
+ + + VE D + P +++C RC+ + R D T+
Sbjct: 40 TSKVYRHELQSSNVENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTL 99
Query: 130 FFTCTKC 136
+ C C
Sbjct: 100 IYVCVHC 106
>3qt1_I DNA-directed RNA polymerases I, II, and III subun;
transferase-transcription complex, RNA polymerase II,
transc elongation; 4.30A {Saccharomyces cerevisiae}
Length = 133
Score = 55.6 bits (133), Expect = 5e-11
Identities = 27/127 (21%), Positives = 45/127 (35%), Gaps = 27/127 (21%)
Query: 12 EFCSKCGTIL-PLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVF 70
FC C +L P D + + + C+T E+
Sbjct: 25 RFCRDCNNMLYPREDKENNRLLFECRTC-SYVEE------------------------AG 59
Query: 71 EEIKAEYTIHFNTVEKEKQ-KDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTI 129
+ + + N E +D P +R+C +C++ + LQ+RSADE T
Sbjct: 60 SPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTT 119
Query: 130 FFTCTKC 136
F+ C C
Sbjct: 120 FYKCVNC 126
>1tfi_A Transcriptional elongation factor SII; transcription regulation;
NMR {Homo sapiens} SCOP: g.41.3.1
Length = 50
Score = 46.3 bits (110), Expect = 3e-08
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 104 KCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
C +C +Y +Q RSADE T F C +C
Sbjct: 11 TCGKCKKKNCTYTQVQTRSADEPMTTFVVCNEC 43
>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1
PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I
1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I*
1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...
Length = 122
Score = 48.0 bits (113), Expect = 4e-08
Identities = 19/133 (14%), Positives = 36/133 (27%), Gaps = 39/133 (29%)
Query: 12 EFCSKCGTIL-PLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVF 70
FC C +L P D + + + C+T
Sbjct: 5 RFCRDCNNMLYPREDKENNRLLFECRT-------------------------------CS 33
Query: 71 EEIKAEYTIHFNTVEKEKQKDKTEIADGP-------IVERKCKRCNNDTMSYATLQLRSA 123
+A + + + + +R+C +C++ + Q R
Sbjct: 34 YVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRK 93
Query: 124 DEGQTIFFTCTKC 136
D +FF C C
Sbjct: 94 DTSMVLFFVCLSC 106
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA,
transcription, arrest, BACKTRACKING cleavage,
transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A
{Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S*
1enw_A
Length = 178
Score = 47.9 bits (113), Expect = 6e-08
Identities = 15/50 (30%), Positives = 17/50 (34%)
Query: 87 EKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
I C +C +SY LQ RSA T F TC C
Sbjct: 122 LYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEAC 171
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA
cleavage, proofreading, BACKTRACKING, gene expression,
multiprotein complex; 3.80A {Saccharomyces cerevisiae}
SCOP: i.8.1.1 PDB: 1eo0_A
Length = 309
Score = 45.5 bits (106), Expect = 8e-07
Identities = 19/66 (28%), Positives = 24/66 (36%), Gaps = 2/66 (3%)
Query: 71 EEIKAEYTIHFNTVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIF 130
+K + Q E + C +C +SY LQ RSADE T F
Sbjct: 239 APLKQKIEEIAKQNLYNAQGATIERSVTDRFT--CGKCKEKKVSYYQLQTRSADEPLTTF 296
Query: 131 FTCTKC 136
TC C
Sbjct: 297 CTCEAC 302
>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 = 29.2 bits (65), Expect = 0.39
Identities = 19/112 (16%), Positives = 37/112 (33%), Gaps = 20/112 (17%)
Query: 41 TQEQQPL----LLGPDILFLKRF-----KGHFNLFL-AVFEEIKAEY----TIHFNTVEK 86
+ +P L+G + ++ G F+ L E + Y IH +
Sbjct: 49 AADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL 108
Query: 87 EKQKDKTEIADGPIVE-----RKCKRCNNDTMSYATLQLRSADEGQTIFFTC 133
++ D T + +++ R + D S + L R+ EG
Sbjct: 109 LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL-FRAVGEGNAQLVAI 159
Score = 27.7 bits (61), Expect = 1.7
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 16/37 (43%)
Query: 41 TQEQQPLLLGPDILFLKRFKGHFNLF-LAVFEEIKAE 76
TQ QP L L A FE++K++
Sbjct: 1729 TQFTQPALT---------------LMEKAAFEDLKSK 1750
>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 = 27.7 bits (61), Expect = 1.2
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 14 CSKCGTILP--LFDF-KGDVKCYVC 35
C +C P + F +GDV C +C
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALC 48
Score = 26.9 bits (59), Expect = 1.9
Identities = 7/54 (12%), Positives = 15/54 (27%), Gaps = 11/54 (20%)
Query: 83 TVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
+++K + + + C C + EG + C C
Sbjct: 6 SIDKRAGRRGPNLN----IVLTCPECKVYP----PKIVERFSEGDVV---CALC 48
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 27.5 bits (61), Expect = 1.5
Identities = 6/25 (24%), Positives = 8/25 (32%)
Query: 14 CSKCGTILPLFDFKGDVKCYVCKTS 38
C +CG I K C +
Sbjct: 1064 CDQCGYIGWYDKNKNKYVCPIHGDK 1088
>3pg6_A E3 ubiquitin-protein ligase DTX3L; DNA-damage, metal-binding,
nucleus, phosphorylation, chromatin regulator, UBL
conjugation pathway, zinc-finger; HET: CIT; 1.70A {Homo
sapiens}
Length = 159
Score = 26.8 bits (59), Expect = 2.0
Identities = 7/24 (29%), Positives = 8/24 (33%), Gaps = 1/24 (4%)
Query: 24 FDFKGDVKCYVCKTSYGTQE-QQP 46
TSYG Q+ QP
Sbjct: 7 HHHHSSGLVPRGSTSYGIQKGNQP 30
>3pfq_A PKC-B, PKC-beta, protein kinase C beta type; phosphorylation,
transferase; HET: TPO SEP ANP; 4.00A {Rattus norvegicus}
PDB: 1tbn_A 1tbo_A 2e73_A
Length = 674
Score = 26.9 bits (59), Expect = 2.7
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 4 EGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTS 38
+ + FC CG++L +KC C +
Sbjct: 106 KIHTYSSPTFCDHCGSLLYGL-IHQGMKCDTCMMN 139
>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}
Length = 530
Score = 25.7 bits (56), Expect = 6.4
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 67 LAVFEEIKAEYTIHFNTVEKEKQKDKTEIADGPIV 101
L ++EE+K T + K E+ DG I+
Sbjct: 178 LILYEEVKPNLTERIQDYDVSLDKALDELMDGDII 212
>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 = 25.2 bits (54), Expect = 9.5
Identities = 17/96 (17%), Positives = 31/96 (32%), Gaps = 18/96 (18%)
Query: 24 FDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHF-- 81
F F ++ + S +L + LK +K + +E + + F
Sbjct: 500 FRF---LEQKIRHDSTAWNASGSIL--NTLQQLKFYKPYICDNDPKYERLVNAI-LDFLP 553
Query: 82 ---NTVEKEKQKDKTEIA----DGPIVE---RKCKR 107
+ K D IA D I E ++ +R
Sbjct: 554 KIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
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 0.138 0.425
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,975,720
Number of extensions: 103074
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 290
Number of HSP's successfully gapped: 30
Length of query: 136
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 52
Effective length of database: 4,356,429
Effective search space: 226534308
Effective search space used: 226534308
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: 52 (24.0 bits)