RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11904
(199 letters)
>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 = 30.4 bits (68), Expect = 0.30
Identities = 14/77 (18%), Positives = 23/77 (29%), Gaps = 25/77 (32%)
Query: 77 SRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQV------GSHYCQACA 130
+R +I+ R G N + +C C+ ++ G C C
Sbjct: 3 TRESIDKRAGRRGPNLNIV-------------LTCPECKVYPPKIVERFSEGDVVCALCG 49
Query: 131 YKKGEHLVLVTAD--PE 145
+ LV D E
Sbjct: 50 LVLSDKLV----DTRSE 62
>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 = 0.40
Identities = 40/248 (16%), Positives = 75/248 (30%), Gaps = 94/248 (37%)
Query: 10 LNNGDRITSVRISFRHMVYE---DA--------------LTILSYASPYEVQIETEKEIY 52
G++ +R ++ M++E D T ++ S + T+
Sbjct: 1675 HFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQ---- 1730
Query: 53 F----IMVCSKCE----KKLGKVITPDNWKSG-SRNTIESGGRRIGENKALTASKARFNP 103
F + + K K G +I D +G S +GE AL AS A
Sbjct: 1731 FTQPALTLMEKAAFEDLKSKG-LIPADATFAGHS----------LGEYAAL-ASLADVMS 1778
Query: 104 YTQKFES-CKICRQKVHQVGSHYCQACAYKKGEH----LVLVTADPEK------------ 146
ES ++ V G A + E ++ +P +
Sbjct: 1779 ----IESLVEV----VFYRGM--TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQY 1828
Query: 147 -GDKFALISGEHL----------VLVTADPEKGDKFAFDN-----HAFKEGTPIIRTLED 190
++ +G + V A GD A D + K ++ ++
Sbjct: 1829 VVERVGKRTGWLVEIVNYNVENQQYVAA----GDLRALDTVTNVLNFIK-----LQKIDI 1879
Query: 191 DKLKVSVP 198
+L+ S+
Sbjct: 1880 IELQKSLS 1887
>2eeh_A PDZ domain-containing protein 7; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 100
Score = 28.1 bits (63), Expect = 0.82
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 5 AETWALNNGDRITSV-RISFRHMVYEDALTIL 35
AE L GD+IT V +S A+ +L
Sbjct: 49 AERAGLCVGDKITEVNGLSLESTTMGSAVKVL 80
>1uf1_A KIAA1526 protein; PDZ domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
protein binding; NMR {Homo sapiens} SCOP: b.36.1.1
Length = 128
Score = 27.9 bits (62), Expect = 1.2
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 5 AETWALNNGDRITSV-RISFRHMVYEDALTIL 35
AE L GD+I V SF ++++++A+ +L
Sbjct: 59 AEGSGLKVGDQILEVNGRSFLNILHDEAVRLL 90
>2y94_A 5'-AMP-activated protein kinase catalytic subunit; transferase,
nucleotide-binding, staurosporine-binding,
serine/threonine-protein kinase; HET: TPO STU AMP;
3.24A {Rattus norvegicus}
Length = 476
Score = 27.4 bits (61), Expect = 3.6
Identities = 6/15 (40%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
Y+V I T +I+ +M
Sbjct: 82 YQV-ISTPSDIFMVM 95
>3r6d_A NAD-dependent epimerase/dehydratase; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG,
veillo parvula; HET: MLZ; 1.25A {Veillonella parvula dsm
2008} PDB: 3r14_A*
Length = 221
Score = 26.9 bits (59), Expect = 3.7
Identities = 5/45 (11%), Positives = 12/45 (26%)
Query: 120 QVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTAD 164
Q+ H+ L + +I E + ++
Sbjct: 16 QIAQXLTATLLTYTDMHITLYGRQLKTRIPPEIIDHERVTVIEGS 60
>3h4j_B AMPK kdaid, SNF1-like protein kinase SSP2; ATP-binding,
nucleotide-binding, phosphoprotei
serine/threonine-protein kinase, transferase; 2.80A
{Schizosaccharomyces pombe}
Length = 336
Score = 26.9 bits (60), Expect = 4.2
Identities = 5/15 (33%), Positives = 9/15 (60%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
Y+V I T +I ++
Sbjct: 75 YDV-ITTPTDIVMVI 88
>3fe3_A MAP/microtubule affinity-regulating kinase 3; serine/threonine
protein kinase, MARK;PAR-1, UBA domai TAK1;P78;MARK3,
ATP-binding; 1.90A {Homo sapiens} PDB: 2qnj_A 1y8g_A*
1zmw_A 1zmu_A 1zmv_A 2wzj_A 2r0i_A 2hak_A 3iec_A
Length = 328
Score = 26.9 bits (60), Expect = 4.5
Identities = 10/15 (66%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
+EV IETEK +Y IM
Sbjct: 80 FEV-IETEKTLYLIM 93
>2h6d_A 5'-AMP-activated protein kinase catalytic subunit alpha-2;
ATP-binding, cholesterol biosynthesis, fatty acid
biosynthesis;kinase, lipid synthesis; 1.85A {Homo
sapiens} PDB: 3aqv_A* 2yza_A*
Length = 276
Score = 26.8 bits (60), Expect = 4.6
Identities = 5/15 (33%), Positives = 9/15 (60%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
Y+V I T + + +M
Sbjct: 77 YQV-ISTPTDFFMVM 90
>2eue_A Carbon catabolite derepressing protein kinase; kinase domain;
2.20A {Saccharomyces cerevisiae} PDB: 3fam_A 3hyh_A
3dae_A 2fh9_A 3mn3_A
Length = 275
Score = 26.8 bits (60), Expect = 5.1
Identities = 5/15 (33%), Positives = 11/15 (73%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
Y+V I+++ EI ++
Sbjct: 79 YDV-IKSKDEIIMVI 92
>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU
PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1
g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A
2opf_A* 1q3b_A*
Length = 262
Score = 26.3 bits (59), Expect = 5.7
Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 81 IESGG--RRIGENKALTASKARFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 129
+ G + AL RF + + E C+ C + + ++C C
Sbjct: 209 YATRGQVDENKHHGAL----FRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGC 260
>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET:
VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A*
1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A
1pjj_A*
Length = 271
Score = 26.3 bits (59), Expect = 6.9
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 5/35 (14%)
Query: 100 RFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 129
Y + E C C + KV G+H+C C
Sbjct: 234 ELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVC 268
>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair,
sequence context; HET: DNA 08Q; 1.60A {Geobacillus
stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A*
3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A*
2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A*
3sar_A* 3sav_A* ...
Length = 273
Score = 26.3 bits (59), Expect = 7.5
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 104 YTQKFESCKIC-----RQKVHQVGSHYCQAC 129
Y ++ CK C + V G+HYC C
Sbjct: 241 YGRQGNPCKRCGTPIEKTVVAGRGTHYCPRC 271
>3tki_A Serine/threonine-protein kinase CHK1; cell checkpoint,
transferase-transferase inhib complex; HET: S25; 1.60A
{Homo sapiens} PDB: 2qhm_A* 2r0u_A* 3tkh_A* 2qhn_A*
2hy0_A* 2hog_A* 2hxq_A* 2hxl_A* 3f9n_A*
Length = 323
Score = 26.1 bits (58), Expect = 7.6
Identities = 2/15 (13%), Positives = 3/15 (20%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
Y Y +
Sbjct: 71 YGH-RREGNIQYLFL 84
>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 = 26.4 bits (57), Expect = 7.6
Identities = 21/115 (18%), Positives = 33/115 (28%), Gaps = 25/115 (21%)
Query: 10 LNNGDRITSVRISFRHMVYEDALTILSYASPYEVQIETEKEI--YFIMVCSKCEKKLGKV 67
L +R + YE+ L +L VQ + F + C K L +
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLVLL-----NVQ---NAKAWNAFNLSC----KIL--L 270
Query: 68 ITPD----NWKSGSRNT-IESGGRRIG----ENKALTASKARFNPYTQKFESCKI 113
T ++ S + T I + E K+L P E
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325
Score = 26.4 bits (57), Expect = 9.8
Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 16/63 (25%)
Query: 23 FRHMVYEDALTILSYASPYEVQIETEKEIY----FIMVCSKCEKKLGKVITPDNWKSGSR 78
+ H+ + L E ++ + ++ F+ E+K+ T N
Sbjct: 474 YSHIGHH-----LKNIEHPE-RMTLFRMVFLDFRFL------EQKIRHDSTAWNASGSIL 521
Query: 79 NTI 81
NT+
Sbjct: 522 NTL 524
>3d00_A Tungsten formylmethanofuran dehydrogenase subunit; FWDE/GAPDH
domain-like fold, structural genomics, joint CENT
structural genomics; HET: MSE; 1.90A {Syntrophus
aciditrophicus}
Length = 191
Score = 25.7 bits (56), Expect = 8.1
Identities = 8/35 (22%), Positives = 11/35 (31%), Gaps = 2/35 (5%)
Query: 98 KARFNPYTQKFES--CKICRQKVHQVGSHYCQACA 130
K F K + C CR+ C +C
Sbjct: 151 KPGFLEKKHKGKIVLCPQCREAYPAQDGELCLSCQ 185
>2pml_X PFPK7, Ser/Thr protein kinase; phosphorylati transferase,
transferase; HET: ANP; 2.60A {Plasmodium falciparum}
PDB: 2pmn_X* 2pmo_X*
Length = 348
Score = 26.2 bits (58), Expect = 8.2
Identities = 4/15 (26%), Positives = 6/15 (40%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
+ I E+Y I
Sbjct: 109 EGI-ITNYDEVYIIY 122
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns
helix, riken STR genomics/proteomics initiative, RSGI,
structural genomics; 1.90A {Thermus thermophilus} SCOP:
a.156.1.2 b.113.1.1 g.39.1.8
Length = 266
Score = 25.9 bits (58), Expect = 8.6
Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 5/26 (19%)
Query: 109 ESCKIC-----RQKVHQVGSHYCQAC 129
C C R+ V G+H+C C
Sbjct: 236 LPCPACGRPVERRVVAGRGTHFCPTC 261
>2yex_A Serine/threonine-protein kinase CHK1; transferase, cell cycle;
HET: YEX; 1.30A {Homo sapiens} PDB: 2x8e_A* 2ydk_A*
2ydj_A* 2yer_A* 2ydi_A* 1nvq_A* 1nvr_A* 1nvs_A* 2wmq_A*
2wmr_A* 2wms_A* 2wmt_A* 2wmu_A* 2wmv_A* 2wmw_A* 2wmx_A*
2x8d_A* 2x8i_A* 2xey_A* 2xez_A* ...
Length = 276
Score = 26.0 bits (58), Expect = 9.1
Identities = 2/15 (13%), Positives = 3/15 (20%), Gaps = 1/15 (6%)
Query: 41 YEVQIETEKEIYFIM 55
Y Y +
Sbjct: 71 YGH-RREGNIQYLFL 84
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 0.133 0.402
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,069,423
Number of extensions: 174599
Number of successful extensions: 535
Number of sequences better than 10.0: 1
Number of HSP's gapped: 534
Number of HSP's successfully gapped: 27
Length of query: 199
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,216,824
Effective search space: 463850640
Effective search space used: 463850640
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 (21.7 bits)
S2: 55 (24.9 bits)