RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8689
(72 letters)
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon,
hyperthermophilic, extremophIle; NMR {Thermococcus
celer} SCOP: g.41.3.1
Length = 57
Score = 77.2 bits (190), Expect = 3e-21
Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 22 AWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
+ + TT+ CPKC + AY+ ++QTR+ DEP T FYKC CG WR
Sbjct: 7 DLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS 55
>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 = 72.5 bits (177), Expect = 1e-18
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 5 RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
L+ E V A+ + ++++CP+C A F Q +R D MT Y C +
Sbjct: 47 ELQSSNVENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVH- 105
Query: 65 KCGFRWRE 72
CGF + E
Sbjct: 106 -CGFAFEE 112
>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 = 72.9 bits (178), Expect = 1e-18
Identities = 29/68 (42%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 5 RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
L E V+ + + ++ +CPKC F Q+Q RSADEPMTTFYKC N
Sbjct: 67 ELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVN- 125
Query: 65 KCGFRWRE 72
CG RW+E
Sbjct: 126 -CGHRWKE 132
>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 = 67.5 bits (164), Expect = 3e-16
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 6 LKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIK 65
+ + + A E T C KC+ + + Q+QTRSA P+TTF C
Sbjct: 113 KIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEA-- 170
Query: 66 CGFRWR 71
CG RW+
Sbjct: 171 CGNRWK 176
>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 = 67.9 bits (164), Expect = 1e-15
Identities = 23/51 (45%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 21 AAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
A E T C KC+ + + Q+QTRSADEP+TTF C CG RW+
Sbjct: 259 ATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEA--CGNRWK 307
>1tfi_A Transcriptional elongation factor SII; transcription regulation;
NMR {Homo sapiens} SCOP: g.41.3.1
Length = 50
Score = 62.8 bits (153), Expect = 1e-15
Identities = 22/44 (50%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
T C KC+ + Q+QTRSADEPMTTF C CG RW+
Sbjct: 7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE--CGNRWK 48
>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 = 61.8 bits (149), Expect = 2e-14
Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 2/68 (2%)
Query: 5 RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
L E V+ + + ++ +CPKC F Q Q R D M F+ C +
Sbjct: 47 ELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS- 105
Query: 65 KCGFRWRE 72
C +
Sbjct: 106 -CSHIFTS 112
>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron
transfer, DIIR center, oxidoreductase; 1.40A
{Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1
PDB: 1yv1_A 1yux_A
Length = 202
Score = 28.2 bits (62), Expect = 0.16
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 26 VDTTEEKCPKCEHPRAYF 43
EKCP C P+ F
Sbjct: 182 KGEDFEKCPICFRPKDTF 199
>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 = 28.3 bits (63), Expect = 0.19
Identities = 8/41 (19%), Positives = 12/41 (29%), Gaps = 17/41 (41%)
Query: 15 HVMGGAAAWE-----------------NVDTTEEKCPKCEH 38
H G A AW N D ++ + E+
Sbjct: 1384 HPKGAAGAWMMNGALQILNSGIIPGNRNADNVDKILEQFEY 1424
>3e7j_A Heparinase II protein; alpha and beta lyase, alpha6/alpha6
incomplete toroid, sugar protein, lyase; HET: NAG GCU
GCD; 2.10A {Pedobacter heparinus} PDB: 3e80_A* 2fut_A*
2fuq_A*
Length = 749
Score = 28.1 bits (61), Expect = 0.23
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 5/44 (11%)
Query: 22 AWENVDTTEEKCPKCEHPRAYFMQ-----IQTRSADEPMTTFYK 60
W++VD P HPR Y + ++ R D + +
Sbjct: 9 VWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWA 52
>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix
bundle, rubre like, electron transport; 1.63A
{Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB:
1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A
1ryt_A
Length = 191
Score = 27.8 bits (61), Expect = 0.23
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 31 EKCPKCEHPRAYFMQI 46
E CP C HP+A+F +
Sbjct: 172 ELCPACAHPKAHFELL 187
>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress,
oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A
3pza_A 3qvd_A 1nnq_A 2hr5_A
Length = 170
Score = 27.4 bits (60), Expect = 0.32
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 31 EKCPKCEHPRAYFMQIQ 47
E CP C P+ F+ +
Sbjct: 154 EYCPVCGAPKEKFVVFE 170
>2qkd_A Zinc finger protein ZPR1; helical hairpins, beta helix,
anti-parrallel beta sheet, double straded anti-parallel
beta helix, metal binding protein; 2.00A {Mus musculus}
Length = 404
Score = 25.0 bits (54), Expect = 2.5
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 3/50 (6%)
Query: 24 ENVDTTEEKCPKCEHPRAYFMQ-IQTRSADEPMTTFYKCCNIKCGFRWRE 72
V CP+C P M+ +Q E + C N CG R E
Sbjct: 214 NEVLQFNTNCPECNAPAQTNMKLVQIPHFKEVIIMATNCEN--CGHRTNE 261
>2qgp_A HNH endonuclease; Q39X46, GMR87, X-RAY, NESG, structural
genomics, PSI-2, protein structure initiative; 2.60A
{Geobacter metallireducens gs-15}
Length = 112
Score = 24.3 bits (53), Expect = 3.0
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 3 CGRLKIKPKE--IDHVM----GGAAAWENV 26
CG P+E +DH++ GG + NV
Sbjct: 41 CGE-IFPPEELTMDHLVPVVRGGKSTRGNV 69
>3ilv_A Glutamine-dependent NAD(+) synthetase; protein structure initiative
II(PSI II), NYSGXRC, structural genomics; 1.79A
{Cytophaga hutchinsonii atcc 33406}
Length = 634
Score = 24.5 bits (54), Expect = 3.6
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 11 KEIDHVMGGAAAWENVDTTEE 31
I++V+ WE D T +
Sbjct: 414 ATIENVIERPLTWEKDDITLQ 434
>1zlg_A Anosmin 1; insulin-like growth factor receptor Cys-rich fold, WHEY
acidic protein fold, fibronectin type III fold, hormone-
growth factor complex; NMR {Homo sapiens}
Length = 680
Score = 24.5 bits (52), Expect = 4.3
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 32 KCPKCEHPRAYFMQ-IQTRSADEPMTTFYKCCNIKCG 67
CP E + +++ D + KCC+ CG
Sbjct: 110 DCPAPEKASGFAAACVESCEVDNECSGVKKCCSNGCG 146
>1tz7_A 4-alpha-glucanotransferase; (beta, alpha)8- barrel; 2.15A {Aquifex
aeolicus} SCOP: c.1.8.1
Length = 505
Score = 24.2 bits (53), Expect = 5.0
Identities = 6/12 (50%), Positives = 7/12 (58%)
Query: 13 IDHVMGGAAAWE 24
+DH G A WE
Sbjct: 305 LDHFRGFEAYWE 316
>1esw_A Amylomaltase; (beta,alpha)8-barrel, glucanotransferase,
alpha-amylase FAMI acarbose, transferase; HET: ACR;
1.90A {Thermus aquaticus} SCOP: c.1.8.1 PDB: 1cwy_A*
1fp8_A 1fp9_A 2owc_A* 2oww_A* 2owx_A* 2x1i_A*
Length = 500
Score = 23.4 bits (51), Expect = 7.7
Identities = 7/13 (53%), Positives = 7/13 (53%)
Query: 12 EIDHVMGGAAAWE 24
IDH G A WE
Sbjct: 291 RIDHFRGFEAYWE 303
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
0.324 0.136 0.473
Gapped
Lambda K H
0.267 0.0492 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,134,147
Number of extensions: 48389
Number of successful extensions: 178
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 21
Length of query: 72
Length of database: 6,701,793
Length adjustment: 42
Effective length of query: 30
Effective length of database: 5,529,111
Effective search space: 165873330
Effective search space used: 165873330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.0 bits)