RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6966
(155 letters)
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 41.6 bits (97), Expect = 5e-05
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
++ VLGIEA R ++ KE+ V+ G Y
Sbjct: 1332 FIDIMEVLGIEAGRAALYKEVYNVIASDGSY 1362
Score = 27.8 bits (61), Expect = 2.0
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 15/63 (23%)
Query: 3 PLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGP--PH 60
P P P S YS TS ++SP+ P+ P+ P+S S P P
Sbjct: 1607 PTSPSYSPTSPSYSPTS-------------PSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1653
Query: 61 WTP 63
++P
Sbjct: 1654 YSP 1656
Score = 26.6 bits (58), Expect = 4.0
Identities = 26/101 (25%), Positives = 35/101 (34%), Gaps = 14/101 (13%)
Query: 1 MLPLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPH 60
P P S +S TS P P A+SP+ P+ P+ P+S S P
Sbjct: 1528 EAPTSPGFGVSSPGFSPTS-PTYSP-----TSPAYSPTSPSYSPTSPSYSPTSPSYSP-- 1579
Query: 61 WTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGP 101
P SP + S P+ T+ SY P
Sbjct: 1580 ----TSPSYSPTSPSYSPTSPS--YSPTSPSYSPTSPSYSP 1614
Score = 26.6 bits (58), Expect = 4.7
Identities = 23/69 (33%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 3 PLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWT 62
P P P S YS TS P P + + S S SP +P S TS P ++
Sbjct: 1565 PTSPSYSPTSPSYSPTS-PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS---PSYS 1620
Query: 63 PYIRPDPSP 71
P P SP
Sbjct: 1621 P-TSPSYSP 1628
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 39.7 bits (92), Expect = 2e-04
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
+E +LGIEA R ++ KE+ V++F G Y
Sbjct: 1338 FVEILQILGIEATRSALLKELRNVIEFDGSY 1368
Score = 29.7 bits (66), Expect = 0.43
Identities = 24/80 (30%), Positives = 29/80 (36%), Gaps = 2/80 (2%)
Query: 3 PLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWT 62
P P P S YS TS P P + + S S SP +P S TS +
Sbjct: 1636 PTSPSYSPTSPSYSPTS-PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1694
Query: 63 PYIRPDPSPFILPLTGVSHP 82
P P SP P + P
Sbjct: 1695 PSYSP-TSPSYSPTSPSYSP 1713
Score = 25.8 bits (56), Expect = 8.1
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 3 PLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWT 62
P +P S YS TS P P T+ ++SP+ SP +P S+TS +
Sbjct: 1566 STSPAYMPSSPSYSPTS-PSYSP-TSP----SYSPTS--PSYSPTSPSYSATSPSYSPTS 1617
Query: 63 PYIRPDPSPF 72
P P +
Sbjct: 1618 PSYSPTSPSY 1627
Score = 25.8 bits (56), Expect = 9.2
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 10/93 (10%)
Query: 11 PSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSS--TSKGPPHWTPYIRPD 68
P+SP ++P P + ++SP+ P+ P+ P+S S P ++P P
Sbjct: 1601 PTSPSYSATSPSYSPTS-----PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP-TSPS 1654
Query: 69 PSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGP 101
SP + S P+ T+ SY P
Sbjct: 1655 YSPTSPSYSPTSPS--YSPTSPSYSPTSPSYSP 1685
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 37.4 bits (86), Expect = 0.001
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
+ E V GIEA R+ + +E++ VL GL
Sbjct: 277 IREIEEVFGIEAAREIIIREISKVLAEQGLD 307
>1tz7_A 4-alpha-glucanotransferase; (beta, alpha)8- barrel; 2.15A
{Aquifex aeolicus} SCOP: c.1.8.1
Length = 505
Score = 31.1 bits (71), Expect = 0.12
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 1 MLPLHPLILP-PSSPYSCTST 20
+LPL+P L +SPYS S
Sbjct: 63 VLPLNPTSLEAGNSPYSSNSL 83
>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication,
ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus;
2.60A {Saccharomyces cerevisiae}
Length = 371
Score = 30.7 bits (68), Expect = 0.17
Identities = 14/78 (17%), Positives = 23/78 (29%), Gaps = 2/78 (2%)
Query: 11 PSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPS 70
P +P ++ ++ + S P P P SS+S P I S
Sbjct: 14 EGPPTVQQQSPSVIRQSPTQRRKTSTTSSTSRAPPPTNPDASSSSSSFAV--PTIHFKES 71
Query: 71 PFILPLTGVSHPLDLHPS 88
PF + +
Sbjct: 72 PFYKIQRLIPELVMNVEV 89
Score = 25.3 bits (54), Expect = 9.8
Identities = 8/76 (10%), Positives = 18/76 (23%), Gaps = 2/76 (2%)
Query: 36 SPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGT 95
S + + + P + + P + P +P +
Sbjct: 1 SLTPLSAITVRSMEGPPTVQQQSPSVIRQSPTQRRKTSTTSSTSRAPPPTNPDASSS--S 58
Query: 96 TGSYGPEGTWIHDPLY 111
+ P + P Y
Sbjct: 59 SSFAVPTIHFKESPFY 74
>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 = 30.4 bits (68), Expect = 0.27
Identities = 24/147 (16%), Positives = 34/147 (23%), Gaps = 64/147 (43%)
Query: 9 LPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSP---PTPHPSSTSKG-------- 57
LP +SP+ + L L + LI + + P T G
Sbjct: 421 LPVASPF---HSHL-LVPASDLINKDLVKNNVSFNAKDIQIPVYD---TFDGSDLRVLSG 473
Query: 58 -------------PPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGP--- 101
P W +H LD P G G
Sbjct: 474 SISERIVDCIIRLPVKWE----------TTTQFKATHILDFGP------GGASGLGVLTH 517
Query: 102 ---EGTWIH-----------DPLYGLR 114
+GT + D YG +
Sbjct: 518 RNKDGTGVRVIVAGTLDINPDDDYGFK 544
>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin,
armadillo repeat, nuclear receptor LIGA binding domain,
protein binding; HET: P6L; 2.76A {Homo sapiens}
Length = 352
Score = 28.8 bits (64), Expect = 0.75
Identities = 20/110 (18%), Positives = 34/110 (30%), Gaps = 9/110 (8%)
Query: 2 LPLHPLILPPS----SPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKG 57
LPL+ LPP+ SP+ + + +P L P P ++S
Sbjct: 34 LPLNHAALPPTDYDRSPFVTSPISMTMPPHGSLQGYQTYGHFPSRAIKSEYPDPYTSS-- 91
Query: 58 PPHWTPYIRPDPSPFILPLTG---VSHPLDLHPSVLLLEGTTGSYGPEGT 104
P Y D P + + L P ++ +Y +
Sbjct: 92 PESIMGYSYMDSYQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQ 141
>3kb9_A EPI-isozizaene synthase; terpenoid cyclase, alpha-helical fold,
farnesyl diphosphate, metal-binding, lyase, magnesium;
HET: BTM; 1.60A {Streptomyces coelicolor} PDB: 3kbk_A
3lgk_A 3lg5_A*
Length = 382
Score = 28.6 bits (63), Expect = 0.91
Identities = 13/53 (24%), Positives = 17/53 (32%), Gaps = 5/53 (9%)
Query: 35 HSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHP 87
HS + P T+ TP P LP+ + P LHP
Sbjct: 10 HSSGLVPRGSHMVHAFPHGTTA-----TPTAIAVPPSLRLPVIEAAFPRQLHP 57
>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 = 28.4 bits (64), Expect = 0.94
Identities = 8/20 (40%), Positives = 9/20 (45%), Gaps = 1/20 (5%)
Query: 1 MLPLHPLILPPSSPYSCTST 20
+LPL P SPY S
Sbjct: 46 VLPLGPT-GYGDSPYQSFSA 64
>3bbn_J Ribosomal protein S10; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} SCOP:
i.1.1.1
Length = 197
Score = 27.8 bits (61), Expect = 1.4
Identities = 15/77 (19%), Positives = 22/77 (28%), Gaps = 7/77 (9%)
Query: 2 LPLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHW 61
+ PL L SS + L + S S +R S +P SS+S
Sbjct: 9 IVFSPLALSNSSSFPNKPQVSNLSLHS-------SLSNLRRTLSHSSPSSSSSSNVRVFA 61
Query: 62 TPYIRPDPSPFILPLTG 78
P +
Sbjct: 62 APEVLESQETGPESYVE 78
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 27.2 bits (61), Expect = 2.1
Identities = 9/45 (20%), Positives = 15/45 (33%)
Query: 11 PSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTS 55
P P + P +T ++ P+ P P H S +
Sbjct: 2 PQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAA 46
>2kl7_A Fibulin-4; secreted, calcium, disease mutation, disulfide bond,
EGF- like domain, glycoprotein, polymorphism,
structural genomics, PSI-2; NMR {Homo sapiens}
Length = 71
Score = 25.8 bits (56), Expect = 2.2
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 5/42 (11%)
Query: 22 LILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTP 63
L LPR+ +I + H P PP P + PP + P
Sbjct: 27 LCLPRSAAVINDLHGEG-----PPPPVPPAQHPNPCPPGYEP 63
>1x1n_A 4-alpha-glucanotransferase; disproportionating enzyme,
amylomaltase, D-enzyme; 1.80A {Solanum tuberosum} SCOP:
c.1.8.1
Length = 524
Score = 26.7 bits (59), Expect = 3.5
Identities = 8/23 (34%), Positives = 9/23 (39%), Gaps = 3/23 (13%)
Query: 1 MLPLHPL---ILPPSSPYSCTST 20
+LPL P SPYS
Sbjct: 67 VLPLVPPGKRGNEDGSPYSGQDA 89
>4dql_A Bifunctional P-450/NADPH-P450 reductase; rossmann fold, redox, FAD
and NADP+ binding, oxidoreductase; HET: FAD NAP 1PE PG4;
2.15A {Bacillus megaterium} PDB: 4dqk_A*
Length = 393
Score = 26.4 bits (59), Expect = 4.1
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 2 LPLHPLI--LPPSSP--YSCTSTPLILPRTTHL---ILNAHSPSGIRSY 43
+ I LP P YS +S+P + + + +++ + SG Y
Sbjct: 157 MKFSEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEY 205
>2j89_A Methionine sulfoxide reductase A; MSRA, poplar, oxidoreductase;
1.7A {Populus trichocarpa}
Length = 261
Score = 26.2 bits (58), Expect = 4.3
Identities = 19/93 (20%), Positives = 27/93 (29%), Gaps = 1/93 (1%)
Query: 4 LHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTP 63
L L SS + T+TPL+L L +A S + P + PP
Sbjct: 2 LQTLSTHLSSTSTSTTTPLLLLSKPFLSPSAKSQLSHSKPFNFPRTLKPISYYKPPMANI 61
Query: 64 YIRPDP-SPFILPLTGVSHPLDLHPSVLLLEGT 95
+ + P T L G
Sbjct: 62 LSKLGFGTRSPDPSTMDPTIPQGPDDDLPAPGQ 94
>2ab1_A Hypothetical protein; HS.95870, DUF498, structural genomics,
protein structure INI PSI, center for eukaryotic
structural genomics, CESG; 2.59A {Homo sapiens} SCOP:
c.103.1.1 PDB: 2q4q_A
Length = 122
Score = 25.6 bits (56), Expect = 5.3
Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 37 PSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVL 90
P G R++ T S P + ++ G+S L + S +
Sbjct: 30 PGGSRTWDWRETGTEHSPGVQPADVKEVVEKGVQTLVI-GRGMSEALKVPSSTV 82
>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding,
isopeptide BO ligase, nucleotide-binding, UBL
conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A
2kx0_A
Length = 96
Score = 24.7 bits (54), Expect = 6.8
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 27 TTHLILNAHSPSGIRSYPSPPTPHPSSTSK 56
T HL+L + +R P HP S ++
Sbjct: 67 TLHLVLRLRGYADLREDPDRQDHHPGSGAQ 96
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 25.8 bits (56), Expect = 7.0
Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 2/79 (2%)
Query: 32 LNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLL 91
+ H + + +S+ P P P + P G+ P LH +
Sbjct: 1 MAHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGP--GIGSPGQLHSPIST 58
Query: 92 LEGTTGSYGPEGTWIHDPL 110
L GP + I P+
Sbjct: 59 LSSPINGMGPPFSVISSPM 77
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION,
membrane protein; HET: ATP; 2.10A {Rattus norvegicus}
SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 25.6 bits (55), Expect = 8.1
Identities = 8/54 (14%), Positives = 14/54 (25%)
Query: 36 SPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSV 89
P + TP ++ S + +P G L +V
Sbjct: 32 PPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFSSLSNAV 85
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 0.140 0.450
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,493,722
Number of extensions: 143794
Number of successful extensions: 460
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 52
Length of query: 155
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 69
Effective length of database: 4,300,587
Effective search space: 296740503
Effective search space used: 296740503
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 (21.6 bits)
S2: 53 (24.1 bits)