RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8691
(211 letters)
>2yud_A YTH domain-containing protein 1; structure genomics, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 180
Score = 121 bits (305), Expect = 3e-35
Identities = 83/176 (47%), Positives = 103/176 (58%), Gaps = 41/176 (23%)
Query: 28 PEKPTIRTYDYITKINYLFRDARFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRE 87
D +K+ Y+ +DARFF+IKSNN ENV +AK+
Sbjct: 5 SSGVRAVRKDQTSKLKYVLQDARFFLIKSNNHENVSLAKA-------------------- 44
Query: 88 SRDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRESRNVLLIFSVRESGKFSGF 147
GVWSTLP NE+KLN A+R +R+V+LIFSVRESGKF GF
Sbjct: 45 ---------------------KGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGF 83
Query: 148 ARLASEADHGVSPVKWVLPPGLSGKVLNGVFKIDWVSRKELPFTSTLHLYNSWNEG 203
ARL+SE+ HG SP+ WVLP G+S K+L GVFKIDW+ R+ELPFT + HL N WNE
Sbjct: 84 ARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEH 139
>2yu6_A YTH domain-containing protein 2; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 141
Score = 105 bits (263), Expect = 3e-29
Identities = 48/156 (30%), Positives = 71/156 (45%), Gaps = 48/156 (30%)
Query: 48 DARFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFK 107
R+F++KS+N N++I++
Sbjct: 7 GVRYFIMKSSNLRNLEISQQ---------------------------------------- 26
Query: 108 VYGVWSTLPQNEQKLNQAYRESRNVLLIFSVRESGKFSGFARLASEADHGVSPVKWVLPP 167
G+WST P NE+KLN+A+ ES V L+FSV+ SG F GF+R++SE S
Sbjct: 27 -KGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQGFSRMSSEIGREKSQDWGSAGL 85
Query: 168 GLSGKVLNGVFKIDWVSRKELPFTSTLHLYNSWNEG 203
G GVFK++W+ ++ LPF HL N WN+
Sbjct: 86 G-------GVFKVEWIRKESLPFQFAHHLLNPWNDN 114
>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 = 40.6 bits (94), Expect = 2e-04
Identities = 24/112 (21%), Positives = 39/112 (34%), Gaps = 34/112 (30%)
Query: 21 AEKVTARPEKPTIRTYDYITKINYLFRDARFFVIKSNNSENVDIAKSQGVWSTLPQNEQK 80
+ +P++ T YI + + L+ D + F K N V Q K
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA-KYN------------VSR--LQPYLK 139
Query: 81 LNQAYRESRD-----------------VLLIFSNYYVSNELNFKVYGVWSTL 115
L QA E R L + +Y V +++FK++ W L
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLNL 189
Score = 28.3 bits (62), Expect = 2.5
Identities = 24/140 (17%), Positives = 47/140 (33%), Gaps = 24/140 (17%)
Query: 80 KLNQAYRESRDVLLIFSNYYVSNELNFKVYGV----WSTLPQNEQK--LNQAYRESRNVL 133
+ + + +D+L +F + +V N F V S L + E + S +
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDN---FDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 134 LIFSVRESGK--FSGFARLASEADHG--VSPVKWV-LPPGLSGKVL----------NGVF 178
L +++ + F ++ +SP+K P + ++ N VF
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 179 KIDWVSRKELPFTSTLHLYN 198
VSR + L
Sbjct: 127 AKYNVSRLQPYLKLRQALLE 146
>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain,
TGF-beta, epigenetics, methylation, K9ME3, K14AC,
transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB:
3u5m_A* 3u5o_A* 3u5p_A*
Length = 207
Score = 30.2 bits (67), Expect = 0.31
Identities = 14/48 (29%), Positives = 20/48 (41%)
Query: 89 RDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRESRNVLLIF 136
DV LIF N NE+ V T N + ++ + + V L F
Sbjct: 146 ADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYF 193
>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 = 28.0 bits (61), Expect = 1.4
Identities = 5/21 (23%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 14 EVKKARSAEKVTARPEK-PTI 33
+KK +++ K+ A + P +
Sbjct: 21 ALKKLQASLKLYA-DDSAPAL 40
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 27.6 bits (62), Expect = 2.6
Identities = 16/112 (14%), Positives = 36/112 (32%), Gaps = 26/112 (23%)
Query: 80 KLNQAYRESRDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRESRNVLLIFSVR 139
KL + + N L+F + E +L + + ++ + V
Sbjct: 84 KLEKPKGRDSKKVRAARTLLAKN-LSFNI---------TEDELKEVFEDALEIR---LVS 130
Query: 140 ESGKFSGFA----RLASEADHGVSPVKWVLPPGLSGKVLNG-VFKIDWVSRK 186
+ GK G A + ++A+ + G ++G + + K
Sbjct: 131 QDGKSKGIAYIEFKSEADAEKNLE--------EKQGAEIDGRSVSLYYTGEK 174
>1t71_A Phosphatase, conserved HYPO; crystal, X-RAY crystallography,
structural GENO berkeley structural genomics center,
BSGC, PSI; 2.10A {Mycoplasma pneumoniae M129} SCOP:
d.159.1.9
Length = 281
Score = 27.0 bits (60), Expect = 5.0
Identities = 9/41 (21%), Positives = 13/41 (31%)
Query: 2 VSLCNIMVSLCVEVKKARSAEKVTARPEKPTIRTYDYITKI 42
L + + V KK E + + P DY I
Sbjct: 241 AQLNGVFFEVDVNTKKVIKTEAIRIVEDDPRYLKQDYFNLI 281
>4g65_A TRK system potassium uptake protein TRKA; structural genomics,
center for structural genomics of infec diseases, csgid,
niaid; HET: MSE; 2.09A {Vibrio vulnificus}
Length = 461
Score = 26.8 bits (60), Expect = 5.5
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 7/48 (14%)
Query: 6 NIMVSLCVEVKKARSAEKVTARPEKPTIRTYDYITKINYLFRDARFFV 53
N+ C + AR IR+ Y+ + LF+ V
Sbjct: 82 NMAA--CQVAFTLFNTPNRIAR-----IRSPQYLAQKEALFKSGAIPV 122
>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger,
bromodomain, SUMO, acetylation, alternative splicing,
metal-binding, nucleus; NMR {Homo sapiens}
Length = 189
Score = 26.4 bits (57), Expect = 6.3
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 78 EQKLNQAYRES----RDVLLIFSNYYVSNE 103
++KL+ Y +DV +F + E
Sbjct: 125 QEKLSPPYSSPQEFAQDVGRMFKQFNKLTE 154
>2vuv_A Codakine; sugar-binding protein, C-type, lectin, mannose,
invertebrate; HET: CIT; 1.3A {Codakia orbicularis} PDB:
2vuz_A*
Length = 129
Score = 25.3 bits (56), Expect = 9.9
Identities = 11/56 (19%), Positives = 16/56 (28%), Gaps = 21/56 (37%)
Query: 168 GLSGKVLNGVFKIDWVSRKELPFTSTLHLYNSWNEGE-------------WYNSWN 210
L G+ + G ++ W S Y W E + SWN
Sbjct: 65 WLGGQKVGGAWQ--WSSS------GAAFDYLRWGPNEPNNSGGNEDCLHYNWLSWN 112
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
0.317 0.132 0.399
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,136,907
Number of extensions: 166916
Number of successful extensions: 328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 327
Number of HSP's successfully gapped: 17
Length of query: 211
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 122
Effective length of database: 4,216,824
Effective search space: 514452528
Effective search space used: 514452528
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)