RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4833
(141 letters)
>2nsm_A Carboxypeptidase N catalytic chain; caroxypeptidase, zinc
peptidase, transthyretin-like domain, processing,
peptide modification, hydrolase; HET: NAG; 2.10A {Homo
sapiens}
Length = 439
Score = 35.4 bits (81), Expect = 0.004
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 4/74 (5%)
Query: 11 VRGQVLSVQGLGITGIRVSVDKDSGRFGFTLTRGGGWFDMLVNGGGAVTLQFQRSPYRPQ 70
++G VL + +SV T G +F +L+ G V+ Y P+
Sbjct: 323 IKGMVLDQNYNNLANAVISV--SGINHDVTSGDHGDYFRLLLPGIYTVS--ATAPGYDPE 378
Query: 71 TRTVFIPWNQIVVL 84
T TV + + ++
Sbjct: 379 TVTVTVGPAEPTLV 392
>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 = 35.4 bits (81), Expect = 0.004
Identities = 31/157 (19%), Positives = 47/157 (29%), Gaps = 53/157 (33%)
Query: 16 LSVQGLGITGIRVSVDKDSGRFGFTLTRGGGWFDMLVNG-------GGAVTLQ------- 61
LS+ L ++ V+K + L G LVNG G +L
Sbjct: 339 LSISNLTQEQVQDYVNKTNSH----LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLR 394
Query: 62 --------FQ-RSPYR---PQTRTVFIPWNQIVVLP---PVKMQLSDASDIFREVASGVT 106
Q R P+ + F+P V P + L ASD+ +
Sbjct: 395 KAKAPSGLDQSRIPFSERKLKFSNRFLP----VASPFHSHL---LVPASDLINKDLVKNN 447
Query: 107 ----------PSYAPKGNSDLQHYGPRSSNKTVRHCE 133
P Y SDL+ S + + R +
Sbjct: 448 VSFNAKDIQIPVYDTFDGSDLRVL---SGSISERIVD 481
>1uwy_A Carboxypeptidase M; metallopeptidase, GPI-anchor, metalloprotease,
zinc, lipoprotein, hydrolase, structural proteomics in
europe, spine; HET: NAG; 3.0A {Homo sapiens} SCOP:
b.3.2.1 c.56.5.1
Length = 426
Score = 34.2 bits (78), Expect = 0.008
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 2/67 (2%)
Query: 11 VRGQVLSVQGLGITGIRVSVDKDSGRFGFTLTRGGGWFDMLVNGGGAVTLQFQRSPYRPQ 70
V+GQV G + + V V + + G ++ +L+ G + + P
Sbjct: 298 VKGQVFDQNGNPLPNVIVEVQDRKHICPYRTNKYGEYYLLLLPGSYIIN--VTVPGHDPH 355
Query: 71 TRTVFIP 77
V IP
Sbjct: 356 ITKVIIP 362
>1h8l_A Carboxypeptidase GP180 residues 503-882; hydrolase, zinc-dependent
protease; HET: NAG BMA NDG GEM; 2.6A {Lophonetta
specularioides} SCOP: b.3.2.1 c.56.5.1 PDB: 1qmu_A*
Length = 380
Score = 31.4 bits (71), Expect = 0.086
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 7/76 (9%)
Query: 11 VRGQVL-SVQGLGITGIRVSVDKDSGRF-GFTLTRGGGWFDMLVNGGGAVTLQFQRSPYR 68
+ G VL + G GI +SV T + G ++ +LV G + Y
Sbjct: 303 IWGFVLDATDGRGILNATISVA---DINHPVTTYKDGDYWRLLVQG--TYKVTASARGYD 357
Query: 69 PQTRTVFIPWNQIVVL 84
P T+TV + V +
Sbjct: 358 PVTKTVEVDSKGGVQV 373
>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 = 28.8 bits (63), Expect = 0.47
Identities = 5/23 (21%), Positives = 9/23 (39%), Gaps = 5/23 (21%)
Query: 112 KGNSDLQHYGPRSS-----NKTV 129
K + L+ Y S+ T+
Sbjct: 24 KLQASLKLYADDSAPALAIKATM 46
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 26.4 bits (59), Expect = 1.4
Identities = 8/43 (18%), Positives = 18/43 (41%), Gaps = 10/43 (23%)
Query: 1 MTDDELRVAVVRGQVLSVQGLG-ITGIRVSVDKDSGR---FGF 39
TD++L + + G+ I I+ ++ +G+ F
Sbjct: 13 TTDEDLT------EAVHSLGVNDILEIKFFENRANGQSKGFAL 49
>3mn8_A LP15968P; catalytic domain of alpha/beta-hydrolase fold,
C-terminal, A transthyretin-like domain, hydrolase; HET:
NAG GEM; 2.70A {Drosophila melanogaster}
Length = 435
Score = 27.6 bits (61), Expect = 1.5
Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 5/100 (5%)
Query: 11 VRGQVLSVQGLGITGIRVSVDKDSGRFGFTLTRGGGWFDMLVNGGGAVTLQ-FQRSPYRP 69
++G V G I V V + ++ G ++ +L G +V F P
Sbjct: 339 IKGLVTDASGFPIADANVYVAGLEEK-PMRTSKRGEYWRLLTPGLYSVHASAFGYQTSAP 397
Query: 70 QTRTVFIPWNQIVVLPPVKMQLSDASDIFREVASGVTPSY 109
Q V + + + +L+ F ++S +P Y
Sbjct: 398 QQVRVTNDNQEALR---LDFKLAPVETNFDGISSFYSPYY 434
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 26.2 bits (58), Expect = 2.2
Identities = 7/41 (17%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 1 MTDDELRVAVVR-GQVLSVQGLGITGIRVSVDKDSGRF-GF 39
+T + + + G + + + G I + D+++G+ G
Sbjct: 19 VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 59
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 1 MTDDELRVAVVRGQVLSVQGLGITGIRVSVDKDSGR---FGF 39
++DD+++ V G I ++ D +G+ +GF
Sbjct: 137 LSDDDIK------SVFEAFG-KIKSATLARDPTTGKHKGYGF 171
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 25.7 bits (57), Expect = 2.7
Identities = 6/13 (46%), Positives = 7/13 (53%)
Query: 27 RVSVDKDSGRFGF 39
V +DKD G F
Sbjct: 37 SVVMDKDKGVFAI 49
>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 = 26.7 bits (58), Expect = 2.9
Identities = 10/69 (14%), Positives = 21/69 (30%), Gaps = 5/69 (7%)
Query: 72 RTVFIPWNQIVVLPPVKMQLSDASDIFREVASGVTPSYAPKGNSDLQHYGPRSSNKTVRH 131
R WN + QL ++ P Y N + + P+ +
Sbjct: 508 RHDSTAWNASGSILNTLQQL----KFYKPYICDNDPKYERLVN-AILDFLPKIEENLICS 562
Query: 132 CESSLFQVS 140
+ L +++
Sbjct: 563 KYTDLLRIA 571
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 25.7 bits (57), Expect = 3.5
Identities = 7/42 (16%), Positives = 18/42 (42%), Gaps = 10/42 (23%)
Query: 1 MTDDELRVAVVRGQVLSVQGLGITGIRVSVDKDSGR---FGF 39
T++++ + S G + +++ D +GR + F
Sbjct: 14 QTEEQIL------DLCSNVG-PVINLKMMFDPQTGRSKGYAF 48
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 25.7 bits (57), Expect = 3.5
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 3/24 (12%)
Query: 19 QGLGITGIRVSVDKDSGR---FGF 39
+ L I +R+ DKD+ + F +
Sbjct: 37 KDLSIRSVRLVRDKDTDKFKGFCY 60
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 25.7 bits (57), Expect = 3.6
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 12/43 (27%)
Query: 1 MTDDELRVAVVR-GQVLSVQGLGITGIRVSVDKDSGR---FGF 39
+T+D LR G++ S+ ++ +D ++GR +GF
Sbjct: 38 ITEDMLRGIFEPFGRIESI--------QLMMDSETGRSKGYGF 72
>1xrk_A Bleomycin resistance protein; arm exchange, ligand binding
protein, thermostable mutant, antibiotic inhibitor;
HET: BLM; 1.50A {Streptoalloteichus hindustanus} SCOP:
d.32.1.2 PDB: 2zhp_A* 1byl_A
Length = 124
Score = 25.6 bits (56), Expect = 3.7
Identities = 7/50 (14%), Positives = 15/50 (30%)
Query: 35 GRFGFTLTRGGGWFDMLVNGGGAVTLQFQRSPYRPQTRTVFIPWNQIVVL 84
R GF+ F +V + + + P ++ + L
Sbjct: 25 DRLGFSRVFVEDDFAGVVRDDVTLFISAVQDQVVPDNTQAWVWVRGLDEL 74
>2la6_A RNA-binding protein FUS; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative, RNA recognition; NMR {Homo
sapiens}
Length = 99
Score = 25.3 bits (56), Expect = 4.9
Identities = 7/41 (17%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 1 MTDDELRVAVVR-GQVLSVQGLGITGIRVSVDKDSGRF-GF 39
+T + + + G + + + G I + D+++G+ G
Sbjct: 25 VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
>2iv2_X Formate dehydrogenase H; oxidoreductase, 4Fe-4S, anaerobic,
complete proteome, direct protein sequencing, Fe4S4,
iron, iron sulfur cluster; HET: 2MD MGD; 2.27A
{Escherichia coli} SCOP: b.52.2.2 c.81.1.1 PDB: 1fdi_A*
1fdo_A* 1aa6_A*
Length = 715
Score = 26.0 bits (58), Expect = 5.6
Identities = 4/22 (18%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 89 MQLSDASDIFREVASGVTPSYA 110
M ++ +I+ E+ + P +
Sbjct: 493 MHYNNTQEIWDELRH-LCPDFY 513
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 24.4 bits (54), Expect = 6.5
Identities = 11/43 (25%), Positives = 15/43 (34%), Gaps = 12/43 (27%)
Query: 1 MTDDELRVAVVR-GQVLSVQGLGITGIRVSVDKDSGR---FGF 39
+ D+ LR A LS V D +G +GF
Sbjct: 13 VDDETLRNAFKDFPSYLSG--------HVMWDMQTGSSRGYGF 47
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 102
Score = 24.5 bits (54), Expect = 9.3
Identities = 8/42 (19%), Positives = 17/42 (40%), Gaps = 13/42 (30%)
Query: 1 MTDDELRVAVVRGQVLSVQGLGITGIRVSVDKDSGR---FGF 39
T++ L+ + + R+ D+++G FGF
Sbjct: 27 TTEETLKESF--DGSVRA--------RIVTDRETGSSKGFGF 58
>3m2o_A Glyoxalase/bleomycin resistance protein; unknown function,
structural genomics, putative glyoxylase/B resistance
protein; HET: PG4; 1.35A {Rhodopseudomonas palustris}
PDB: 3vcx_A*
Length = 164
Score = 24.8 bits (54), Expect = 9.4
Identities = 10/89 (11%), Positives = 22/89 (24%), Gaps = 8/89 (8%)
Query: 37 FGFTLTRGGGWFDMLVNGGGAVTLQFQRSPYRPQTRTVFIPWNQIVVLPPVKMQLSDASD 96
FGF W+ L + ++L ++ D
Sbjct: 47 FGFRPLFEADWYVHLQSAEDPAVNLAILDGQHSTIPAAGRGQVSGLILN---FEVDDPDR 103
Query: 97 IFRE-VASGVTPSYAPKGNSDLQHYGPRS 124
+ +G+ + + +G R
Sbjct: 104 EYARLQQAGLPILLTLR----DEDFGQRH 128
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
0.319 0.136 0.408
Gapped
Lambda K H
0.267 0.0477 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,127,119
Number of extensions: 118603
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 329
Number of HSP's successfully gapped: 36
Length of query: 141
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 57
Effective length of database: 4,356,429
Effective search space: 248316453
Effective search space used: 248316453
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 (21.8 bits)
S2: 52 (24.4 bits)