RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15354
(218 letters)
>2ejs_A Autocrine motility factor receptor, isoform 2; CUE, ubiquitin
ligase complex, ubiquitin-conjugating enzyme, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 58
Score = 45.2 bits (107), Expect = 3e-07
Identities = 11/42 (26%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 118 DSRMYAEAQRIREIFPNIPLNAIVRELGRSHGNAELTISRLI 159
+S++ A A +I+E+FP +P + ++++L + + E+T ++
Sbjct: 10 NSQLNAMAHQIQEMFPQVPYHLVLQDLQLT-RSVEITTDNIL 50
>2ekf_A Ancient ubiquitous protein 1; CUE, ubiquitin ligase complex,
ubiquitin-conjugating enzyme, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 61
Score = 43.7 bits (103), Expect = 1e-06
Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 112 SGARRYDSRMYAEAQRIREIFPNIPLNAIVRELGRSHGNAELTISRLI 159
+ D ++ AQR++E+ P++PL I R+L ++ G +LTI+ L+
Sbjct: 4 GSSGSPDVQLATLAQRVKEVLPHVPLGVIQRDLAKT-GCVDLTITNLL 50
>4g3o_A E3 ubiquitin-protein ligase AMFR; all-helical structure, BAG6;
1.60A {Homo sapiens}
Length = 58
Score = 43.0 bits (101), Expect = 2e-06
Identities = 11/54 (20%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 106 ALATQNSGARRYDSRMYAEAQRIREIFPNIPLNAIVRELGRSHGNAELTISRLI 159
++ + S + ++ A A +I+E+FP +P + ++++L + + E+T ++
Sbjct: 2 SMGYRGSENLYFQGQLNAMAHQIQEMFPQVPYHLVLQDLQLT-RSVEITTDNIL 54
>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 = 44.3 bits (104), Expect = 2e-05
Identities = 24/126 (19%), Positives = 47/126 (37%), Gaps = 30/126 (23%)
Query: 8 LGLINLGRN---TRFSRSTFLSKLKSFLCRTEAPI------VLFPEEETTNGKKGLLKFL 58
+ L+N +N + +S L L L + +AP + F E + K +FL
Sbjct: 368 ISLVNGAKNLVVSGPPQS--LYGLNLTLRKAKAPSGLDQSRIPFSERK----LKFSNRFL 421
Query: 59 PV--------MKRAQNETDEDLMSRIEACIACEGRLSPTLCTP------SEKYELEKRLV 104
PV + A + ++DL+ + A + ++ P T + +R+V
Sbjct: 422 PVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQI-PVYDTFDGSDLRVLSGSISERIV 480
Query: 105 RALATQ 110
+
Sbjct: 481 DCIIRL 486
Score = 36.6 bits (84), Expect = 0.005
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 17/78 (21%)
Query: 137 LNAI-VRELGRSHGNAELTISRLIADSSFQNLSFNSS---SSFNQS-PSPSSPSTPQFNA 191
++A R L SHG+ E + L+ +SF F +S FN+ P P+
Sbjct: 1 MDAYSTRPLTLSHGSLEHVL--LVPTASF----FIASQLQEQFNKILPEPTE------GF 48
Query: 192 SPHNRMSAFAEKKAQFIA 209
+ + + AE +F+
Sbjct: 49 AADDEPTTPAELVGKFLG 66
>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 = 36.4 bits (83), Expect = 0.006
Identities = 31/245 (12%), Positives = 67/245 (27%), Gaps = 64/245 (26%)
Query: 21 RSTFLSKLKSFLCRT--EAPIVLFPEEETTNGKKGLLKFLPVMKRAQNETDEDLMSRIEA 78
+ L+ L+ R + + +FP + LL + + D+M +
Sbjct: 359 IESSLNVLEPAEYRKMFDR-LSVFPPS--AHIPTILLSLI-----WFDVIKSDVMVVVNK 410
Query: 79 CI--------ACEGRLS-PTL-----CTPSEKYELEKRLVRALATQNSGARRYDS----- 119
E +S P++ +Y L + +V + +DS
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP----KTFDSDDLIP 466
Query: 120 ---RMY---------AEAQRIREI--FPNIPLNA--IVRELGRSHGNAELTISRLIADSS 163
Y + + F + L+ + +++ R A ++
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI-RHDSTAWNASGSILNT-- 523
Query: 164 FQNLSFNSSSSFNQSPSPSSPST------PQFNA----SPHNRM--SAFAEKKAQFIAEA 211
Q L F + P P+ S + + A + EA
Sbjct: 524 LQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEA 583
Query: 212 RRRAA 216
++
Sbjct: 584 HKQVQ 588
>1wgl_A TOLL-interacting protein; CUE domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI, immune
system; NMR {Homo sapiens} SCOP: a.5.2.4
Length = 59
Score = 30.5 bits (68), Expect = 0.051
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 123 AEAQRIREIFPNIPLNAIVRELGRSHGNAELTISRLI 159
+ + I+++FPN+ I L GN + I+ L+
Sbjct: 11 EDLKAIQDMFPNMDQEVIRSVLEAQRGNKDAAINSLL 47
>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 = 31.8 bits (71), Expect = 0.073
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 22/49 (44%)
Query: 95 EKYELEKRLVRALATQNSGARRYDSRMYA--EAQRIREIFPNIPLNAIV 141
EK L K+L +L ++YA A P + + A +
Sbjct: 18 EKQAL-KKLQASL------------KLYADDSA-------PALAIKATM 46
>2dae_A KIAA0733 protein; mitogen-activated protein kinase kinase kinase 7
interacting protein 2, MAP3K7IP2, CUE domain, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 29.8 bits (66), Expect = 0.16
Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 126 QRIREIFPNIPLNAIVRELGRSHGNAELTISRLIADSSFQNLSFNSSSSFNQSPSPSSPS 185
+R+ FP +P + R + +++ N + + L +S+ + L +F+ S PS
Sbjct: 15 HDLRQKFPEVPEVVVSRCMLQNNNNLDACCAVLSQEST-RYLYGEGDLNFSDDSGISGPS 73
Query: 186 T 186
+
Sbjct: 74 S 74
>3h0u_A Putative enoyl-COA hydratase; structural genomics, isomerase,
PSI-2, protein structure initiative; 1.50A {Streptomyces
avermitilis}
Length = 289
Score = 29.1 bits (66), Expect = 1.0
Identities = 1/18 (5%), Positives = 4/18 (22%)
Query: 197 MSAFAEKKAQFIAEARRR 214
+ ++ Q
Sbjct: 252 TAELFKQGFQTRGATELD 269
>1hq1_A Signal recognition particle protein; protein-RNA complex, double
helix, tetraloop, internal loop, SRP,
ribonucleoprotein; HET: CCC; 1.52A {Escherichia coli}
SCOP: a.36.1.1 PDB: 3lqx_A* 2pxb_A 2pxd_A 2pxe_A 2pxf_A
2pxk_A 2pxl_A 2pxp_A 2pxq_A 2pxt_A 2pxu_A 2pxv_A
Length = 105
Score = 27.9 bits (63), Expect = 1.1
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 50 GKKGLLKFLP----VMKRAQNETDEDLMSRIEACI 80
G L+ LP + +++ D+ ++ R+EA I
Sbjct: 19 GMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAII 53
>2di0_A Activating signal cointegrator 1 complex subunit 2; ASCC2, CUE
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: a.5.2.4
Length = 71
Score = 26.8 bits (59), Expect = 1.6
Identities = 6/37 (16%), Positives = 19/37 (51%)
Query: 126 QRIREIFPNIPLNAIVRELGRSHGNAELTISRLIADS 162
+++++ P++ I+ L H + E I+ ++ +
Sbjct: 18 SQVKDLLPDLGEGFILACLEYYHYDPEQVINNILEER 54
>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA
binding protein, hydrolase, gtpas; HET: GCP; 3.94A
{Escherichia coli} PDB: 2j28_9
Length = 433
Score = 28.3 bits (64), Expect = 2.4
Identities = 8/33 (24%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 52 KGLLKFLP----VMKRAQNETDEDLMSRIEACI 80
L+ LP + +++ D+ ++ R+EA I
Sbjct: 348 ASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAII 380
>2dhy_A CUE domain-containing protein 1; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 67
Score = 26.2 bits (57), Expect = 2.4
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 110 QNSGARRYDSRMYAEA-QRIREIFPNIPLNAIVRELGRSHGNAELTISRLIADSS 163
AR+ + +A + +FPN+ + I L + G + TI +L+ +
Sbjct: 6 SGRPARQVRRLEFNQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQMNL 60
>2jqe_A SRP54, signal recognition 54 kDa protein; AF54, structure,
solution, signaling protein; NMR {Archaeoglobus
fulgidus}
Length = 119
Score = 26.7 bits (60), Expect = 3.3
Identities = 4/36 (11%), Positives = 11/36 (30%), Gaps = 5/36 (13%)
Query: 50 GKKGLLKFLPVM-----KRAQNETDEDLMSRIEACI 80
+ + + LP E ++ M + +
Sbjct: 27 PVRKIFEMLPFGLGLKVDNDVMEMTQEKMKKFRVIM 62
>1l6w_A Fructose-6-phosphate aldolase 1; alpha-beta barrel, domain
swapping, lyase; 1.93A {Escherichia coli} SCOP: c.1.10.1
Length = 220
Score = 27.2 bits (61), Expect = 3.8
Identities = 5/15 (33%), Positives = 9/15 (60%)
Query: 121 MYAEAQRIREIFPNI 135
M +A ++R I +I
Sbjct: 68 MVNDALKLRSIIADI 82
>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
signaling protein; NMR {Mus musculus} SCOP: a.4.5.47
Length = 84
Score = 25.9 bits (57), Expect = 3.9
Identities = 7/36 (19%), Positives = 14/36 (38%)
Query: 126 QRIREIFPNIPLNAIVRELGRSHGNAELTISRLIAD 161
+++ NI + L AE S++I +
Sbjct: 22 LSASKLYNNITFEELGALLEIPAAKAEKIASQMITE 57
>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M
domain, RNA-binding, signal sequence-binding,
helix-turn-helix, protein targeting; 3.20A {Thermus
aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB:
2iy3_A
Length = 425
Score = 27.5 bits (62), Expect = 4.2
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 52 KGLLKFLPVMKRAQNETDEDLMSRIEACI 80
+L LP + + DE + R+EA +
Sbjct: 339 SEILGLLPGVPQGLK-VDEKAIKRLEAIV 366
>3qqw_A Putative citrate lyase; TIM beta/alpha-barrel, structural genomics,
joint center for structural genomics, JCSG, protein
structure initiative; HET: MSE; 2.44A {Ralstonia
eutropha}
Length = 332
Score = 26.9 bits (60), Expect = 5.5
Identities = 7/44 (15%), Positives = 14/44 (31%), Gaps = 8/44 (18%)
Query: 92 TPSEKYELE--KRLVRALATQNSGARRYDSRM-----YAEAQRI 128
P E+E ++ A + G +Y + Y +
Sbjct: 268 RPDFT-EVEDAAGILVAAQDADWGPIQYKGELHDRATYRYFWEV 310
>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding,
signal recognition particle, GTP-binding, RNA-binding;
2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B
Length = 432
Score = 26.3 bits (59), Expect = 8.0
Identities = 6/33 (18%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 52 KGLLKFLP----VMKRAQNETDEDLMSRIEACI 80
K +L +P M + + E + + + I
Sbjct: 344 KKILSMIPGFGGAMPKELSHLTEAKIKKYKVII 376
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 26.4 bits (59), Expect = 8.4
Identities = 4/33 (12%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 52 KGLLKFLP----VMKRAQNETDEDLMSRIEACI 80
K +L+ +P + E+ + + + +
Sbjct: 347 KQILRMIPGLGYSLPDDVISIGEERLKKFKVIM 379
>3r4i_A Citrate lyase; TIM beta/alpha-barrel, structural genomics, joint
center for structural genomics, JCSG, protein structure
initiative; 2.24A {Burkholderia xenovorans}
Length = 339
Score = 26.1 bits (58), Expect = 9.0
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 8/44 (18%)
Query: 92 TPSEKYELE--KRLVRALATQNSGARRYDSRM-----YAEAQRI 128
P ++ E+ ++ A + G RY + Y +
Sbjct: 267 APRDE-EITTATEILLAAQSAQWGPTRYHDTLHDRASYRYYWSV 309
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 0.130 0.365
Gapped
Lambda K H
0.267 0.0571 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,142,915
Number of extensions: 176923
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 458
Number of HSP's successfully gapped: 26
Length of query: 218
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,188,903
Effective search space: 536179584
Effective search space used: 536179584
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 (25.3 bits)