RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy986
(71 letters)
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains,
type I domains, fragIle X mental retardation protein,
RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A
Length = 144
Score = 57.3 bits (138), Expect = 1e-12
Identities = 42/62 (67%), Positives = 52/62 (83%), Gaps = 2/62 (3%)
Query: 1 MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
LE++E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IE +NE P+EEG VPF
Sbjct: 63 FLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPF 120
Query: 61 MV 62
+
Sbjct: 121 VF 122
Score = 37.7 bits (87), Expect = 4e-05
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
E V +L+G IG +G IQ+ GV + ++ D
Sbjct: 6 EQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCT 46
>1we8_A Tudor and KH domain containing protein; structural genomics,
riken structural genomics/proteomics initiative, RSGI,
RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1
Length = 104
Score = 46.0 bits (109), Expect = 2e-08
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
E L VP+ VG++IG+ G I+ I SG ++ + ++E L R
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASG-AKITCDKESEGTLLLSR 62
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif, immune system; 2.00A
{Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A
Length = 76
Score = 43.4 bits (103), Expect = 9e-08
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
+ VP NLVG ++GK G+ + E + +G R++I E P
Sbjct: 7 MAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFLP 46
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 42.7 bits (101), Expect = 2e-07
Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
+ + + +P G VIGK G I+++ +++G V++ + D + +
Sbjct: 14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAG-VKMILIQDGSQNTNVDK 61
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold,
RNA-binding motif, protein/RNA structure, RNA binding
protein/RNA complex; 2.40A {Homo sapiens} SCOP:
d.51.1.1
Length = 87
Score = 42.3 bits (100), Expect = 3e-07
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
+ VP NLVG ++GK G+ + E + +G R++I E P
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFLP 46
>1x4m_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
SCOP: d.51.1.1
Length = 94
Score = 42.0 bits (99), Expect = 5e-07
Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
+ + + +P + G VIGK G I+++ +++G V++ + D +
Sbjct: 15 AVQEIMIPASKAGLVIGKGGETIKQLQERAG-VKMVMIQDGPQNTGADK 62
>1x4n_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
SCOP: d.51.1.1 PDB: 2opu_A
Length = 92
Score = 41.6 bits (98), Expect = 7e-07
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
E +VP +VG +IG+ G I I +SG +++I D+ P
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESG-CKIQIAPDSGGLP 58
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 41.7 bits (98), Expect = 8e-07
Identities = 16/41 (39%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
+ VPR+ VG VIG++G +I++I + +G VR++ + D+ P
Sbjct: 15 VPVPRHSVGVVIGRSGEMIKKIQNDAG-VRIQFKQDDGTGP 54
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 41.4 bits (97), Expect = 1e-06
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
E + +P + G VIG+ G ++ I ++G V+I P
Sbjct: 7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTG-AFVEISRQLPPNGD 51
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 40.7 bits (96), Expect = 1e-06
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
+ +P++L G +IGK G+ I++I +SG +KI+ E
Sbjct: 11 VTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKIDEPLEGSE 50
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA
binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} SCOP:
d.51.1.1 PDB: 1khm_A
Length = 89
Score = 40.4 bits (95), Expect = 2e-06
Identities = 14/38 (36%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46
+ +P++L G +IGK G+ I++I +SG +KI+ E
Sbjct: 18 VTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKIDEPLE 54
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA
binding protein, KH domain, KSRP, posttranscriptional
regulation, mRNA decay; NMR {Homo sapiens}
Length = 164
Score = 41.7 bits (98), Expect = 2e-06
Identities = 16/44 (36%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
+ VPR+ VG VIG++G +I++I + +G VR++ + D+ P
Sbjct: 92 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAG-VRIQFKQDDGTGP 134
Score = 39.4 bits (92), Expect = 1e-05
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
+ +P G VIGK G I+++ +++G V++ + D + +
Sbjct: 6 IMIPAGKAGLVIGKGGETIKQLQERAG-VKMILIQDGSQNTNVDK 49
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA
binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1
Length = 82
Score = 40.3 bits (95), Expect = 2e-06
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
L +P NL+G +IG+ G I EI SG ++KI E
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIRQMSG-AQIKIANPVEGSS 49
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
DNA-binding, nucleus, phosph ribonucleoprotein,
RNA-binding, RNA binding protein; NMR {Homo sapiens}
Length = 160
Score = 41.3 bits (97), Expect = 2e-06
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
L VP + G +IGK G I+EI + +G +V++ GD P T
Sbjct: 93 LVVPASQCGSLIGKGGCKIKEIRESTG-AQVQVAGDMLPNST 133
Score = 34.0 bits (78), Expect = 0.001
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
L + VG +IGK G ++++ ++SG R+ I N P+
Sbjct: 9 LLMHGKEVGSIIGKKGESVKKMREESG-ARINISEGNCPE 47
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain,
cell projection, cytoplasm, nucleus, phosphoprotein,
translation regulation; 2.75A {Homo sapiens}
Length = 163
Score = 40.9 bits (96), Expect = 3e-06
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
++VP + G+VIGK G+ + E+ + + V + D P
Sbjct: 89 IRVPASAAGRVIGKGGKTVNELQNLTA-AEVVVPRDQTPDEN 129
Score = 36.7 bits (85), Expect = 1e-04
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
+ +P VG +IGK G+ I+++ + +KI P
Sbjct: 7 VFIPAQAVGAIIGKKGQHIKQLSRFAS-ASIKIAPPETPDSK 47
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 39.2 bits (92), Expect = 3e-06
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
L +P +L+G +IG+ G I EI SG ++KI E
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQMSG-AQIKIANPVEGST 48
>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 38.6 bits (90), Expect = 1e-05
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
+E + +P L +IG GR+I+ I+++ G V + +
Sbjct: 15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGS 60
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein complex; HET: 5BU;
1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 38.7 bits (90), Expect = 2e-05
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
+ VP + G +IGK G ++ I+++SG V++ +
Sbjct: 108 IIVPNSTAGLIIGKGGATVKAIMEQSG-AWVQLSQKPDG 145
Score = 38.3 bits (89), Expect = 4e-05
Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLP 52
+ +P G +IGK G+ I ++ ++G +K+ + P
Sbjct: 10 VLIPSYAAGSIIGKGGQTIVQLQKETG-ATIKLSKSKDFYPGTT 52
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 37.4 bits (87), Expect = 3e-05
Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
++ +P+ VIGKNG +Q++ K+ +++I ++P
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTA-TKIQIPRPDDPSNQ 61
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET:
DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1
Length = 174
Score = 38.3 bits (89), Expect = 3e-05
Identities = 16/41 (39%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
+ +PR VG VIG+NG +I++I + +G VR++ + D+ P
Sbjct: 7 VPIPRFAVGIVIGRNGEMIKKIQNDAG-VRIQFKPDDGTTP 46
Score = 37.5 bits (87), Expect = 6e-05
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
VP G +IGK G I+ I +SG R++++ + P
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSG-ARIELQRNPPPNA 147
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding
protein-DNA complex; 1.70A {Homo sapiens} SCOP:
d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*
Length = 73
Score = 36.1 bits (84), Expect = 6e-05
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
L + VG +IGK G ++++ ++SG R+ I N P
Sbjct: 9 LLMHGKEVGSIIGKKGESVKKMREESG-ARINISEGNCP 46
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo
sapiens} SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 35.4 bits (82), Expect = 1e-04
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
+ + +IGK+G I I D+ V V+I D+E
Sbjct: 3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYK-VSVRIPPDSEKS 47
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 104
Score = 35.9 bits (83), Expect = 1e-04
Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
++VP +L VIG+ G I++++D+ V + +
Sbjct: 18 TIEVEVPFDLHRYVIGQKGSGIRKMMDEFE-VNIHVPAPELQS 59
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 97
Score = 34.8 bits (80), Expect = 3e-04
Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
+ S+ V K+IG+ G +I +I + V ++ ++
Sbjct: 18 KLSVTVDPKYHPKIIGRKGAVITQIRLEHD-VNIQFPDKDDGNQP 61
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 35.6 bits (83), Expect = 4e-04
Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
E++QVP + K +G G ++++ ++G V + +
Sbjct: 569 ETVQVPLSKRAKFVGPGGYNLKKLQAETG-VTISQVDE 605
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 34.0 bits (78), Expect = 6e-04
Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
E + + + ++IG G+ I++I+D+ V ++ P P
Sbjct: 19 EDVPLDHRVHARIIGARGKAIRKIMDEFK-VDIRFPQSGAPDPNC 62
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 35.2 bits (82), Expect = 6e-04
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 7/47 (14%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNE 46
E++ +P + + +VIG G++I+EIV +G VK+ +
Sbjct: 572 ETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDG 618
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 34.4 bits (80), Expect = 9e-04
Identities = 10/38 (26%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
++++ + + VIGK G +I+ + +++G ++IE D
Sbjct: 562 HTIKINPDKIKDVIGKGGSVIRALTEETG-TTIEIEDD 598
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 83
Score = 33.4 bits (76), Expect = 0.001
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
+ ++VP +VG V+G G I+ I ++ V D EP +
Sbjct: 9 QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAV 56
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 33.7 bits (78), Expect = 0.002
Identities = 11/38 (28%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
++++P + +G+VIG ++I +I + +G + IE D
Sbjct: 600 ITVKIPVDKIGEVIGPKRQMINQIQEDTG-AEITIEDD 636
>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform
B'; KH domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.51.1.1
Length = 91
Score = 31.2 bits (70), Expect = 0.006
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN 45
E V +L+G IG +G IQ+ GV ++++ D
Sbjct: 17 EEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDT 55
Score = 24.7 bits (53), Expect = 2.2
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 1 MLEYSEESLQVPR 13
LE+ E+ +QVP
Sbjct: 74 FLEFVEDFIQVPS 86
>1tua_A Hypothetical protein APE0754; structural genomics, protein
structure initiative, MCSG, four layers alpha-beta
sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1
d.51.1.1
Length = 191
Score = 31.5 bits (71), Expect = 0.009
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVL 63
++V +G VIG G + EI+ ++G + ++ +N P EG P ++
Sbjct: 8 VKVKPERLGAVIGPRGEVKAEIMRRTG-TVITVDTENSMVIVEPEAEGIPPVNLM 61
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA
processing factor, RNA binding protein; 2.30A
{Pyrococcus horikoshii} PDB: 3aev_B
Length = 219
Score = 30.8 bits (69), Expect = 0.020
Identities = 13/58 (22%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVL 63
EE +++P++ + +IGK G+ +EI ++ ++ I+ + +E + P V
Sbjct: 35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTK-TKITIDSETGEVWITSTKETEDPLAVW 91
Score = 23.9 bits (51), Expect = 4.8
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 11 VPRNLVGKVIGKNGRIIQEIVDKSGV 36
+ G++IG+ GR Q I + SG
Sbjct: 135 ALPRVRGRIIGRKGRTRQIIEEMSGA 160
>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 102
Score = 29.9 bits (67), Expect = 0.023
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46
S+ P L +IGK G+ + +I + V ++ +
Sbjct: 29 SSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGED 68
>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal
NUS domain, structural genomics, NPPSFA; 2.00A
{Aeropyrum pernix} PDB: 2cy1_A
Length = 144
Score = 25.4 bits (56), Expect = 1.4
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 11 VPRNLVGKVIGKNGRIIQEIVDKSG 35
V G+ IG+ GR+I+ + + G
Sbjct: 42 VSEGEAGRAIGRGGRLIKLLREALG 66
>1xub_A Phenazine biosynthesis protein PHZF; biosynthetic protein; 1.30A
{Pseudomonas fluorescens} SCOP: d.21.1.2 d.21.1.2 PDB:
1u1w_A* 1u1v_A* 1u1x_A* 1xua_A* 1t6k_A
Length = 298
Score = 25.7 bits (57), Expect = 1.4
Identities = 8/46 (17%), Positives = 13/46 (28%), Gaps = 9/46 (19%)
Query: 21 GKNGRIIQEIVDKSGVVRVKIEGDNE-------PQPTLPREEGQVP 59
N R+ E + G + ++E N QP
Sbjct: 107 TDNHRLYLET--QMGTIAFELERQNGSVIAASMDQPIPTWTALGRD 150
>1ym5_A YHI9, hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region;
PHZF enzyme superfamily, double hot-DOG, structural
genomics; 2.05A {Saccharomyces cerevisiae}
Length = 300
Score = 25.3 bits (56), Expect = 1.5
Identities = 6/23 (26%), Positives = 9/23 (39%), Gaps = 2/23 (8%)
Query: 22 KNGRIIQEIVDKSGVVRVKIEGD 44
++QE K G V + I
Sbjct: 99 TATSLVQEC--KIGAVPITINEG 119
>1qya_A ORFB, hypothetical protein YDDE; putative phenazine biosynthesis
protein, epimerase, antibiot biosynthesis protein,
structural genomics; 2.00A {Escherichia coli} SCOP:
d.21.1.2 d.21.1.2 PDB: 1sdj_A 1qy9_A
Length = 307
Score = 25.3 bits (56), Expect = 1.6
Identities = 12/40 (30%), Positives = 14/40 (35%), Gaps = 8/40 (20%)
Query: 22 KNGRIIQEIVDKSGVVRVKIEGDNE------PQPTLPREE 55
N I Q +G RV IE N+ Q T E
Sbjct: 100 GNCTIWQTS--LAGKHRVTIEKHNDDYRISLEQGTPGFEP 137
>3edn_A Phenazine biosynthesis protein, PHZF family; diaminopimelate
epimerase-like fold, alpha and beta protein class,
structural genomics; HET: MSE; 1.50A {Bacillus
anthracis}
Length = 299
Score = 24.6 bits (54), Expect = 3.1
Identities = 4/32 (12%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 20 IGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
+ + + E K+G++ ++I + + +
Sbjct: 90 LEEKASLTIET--KAGILPIQIGVNENGETFI 119
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 24.6 bits (54), Expect = 3.4
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 17 GKVIGKNGRIIQEIVDKSG 35
G VIGK+G ++EI + G
Sbjct: 114 GLVIGKHGATLREITKQIG 132
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 24.6 bits (54), Expect = 3.4
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 17 GKVIGKNGRIIQEIVDKSG 35
G VIGK G +EIV +G
Sbjct: 110 GLVIGKYGSTSREIVKNTG 128
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 24.6 bits (54), Expect = 3.6
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 17 GKVIGKNGRIIQEIVDKSG 35
G VIGKNG ++ I K
Sbjct: 119 GLVIGKNGETLRLITQKVK 137
>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural
genomics, NPPSFA, nationa on protein structural and
functional analyses; HET: SSA; 3.00A {Aquifex aeolicus}
Length = 425
Score = 24.4 bits (54), Expect = 3.6
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 7 ESLQVPRNLVGKVIG---KNGRIIQEIVDKSGVVRVKIE 42
E+L+ RN + K IG + G+ EI ++ ++ +I+
Sbjct: 47 EALRSERNKLSKEIGKLKREGKDTTEIQNRVKELKEEID 85
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA
recognition, complex E, KH domain, QUA2 homology; NMR
{Homo sapiens} SCOP: d.51.1.1
Length = 131
Score = 24.1 bits (52), Expect = 3.9
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43
N VG +IG G ++ I + ++ I G
Sbjct: 22 NFVGLLIGPRGNTLKNIEKECN-AKIMIRG 50
>2hxv_A Diaminohydroxyphosphoribosylaminopyrimidine deami
amino-6-(5-phosphoribosylamino)uracil...;
oxidoreductase, structural genomics; HET: NDP; 1.80A
{Thermotoga maritima} SCOP: c.71.1.2 c.97.1.2
Length = 360
Score = 24.4 bits (54), Expect = 3.9
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 15 LVGKVIGKNGRIIQE 29
VG V+ K+GRII E
Sbjct: 37 PVGAVVVKDGRIIAE 51
>3cp0_A Membrane protein implicated in regulation of MEMB protease
activity; beta barrel, structural genomics, PSI-2;
1.65A {Corynebacterium glutamicum atcc 13032}
Length = 82
Score = 23.6 bits (51), Expect = 4.7
Identities = 5/26 (19%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 19 VIGKNGRIIQEIVDKSGVVRVKIEGD 44
++G +++++ SG +V+++G
Sbjct: 24 LVGHRAEVLEDVGATSG--QVRLDGS 47
>3s6b_A Methionine aminopeptidase; malaria, proteolysis, "PITA bread" fold,
structur genomics, structural genomics consortium, SGC,
hydrolase; 1.95A {Plasmodium falciparum}
Length = 368
Score = 23.8 bits (52), Expect = 5.0
Identities = 8/24 (33%), Positives = 9/24 (37%), Gaps = 2/24 (8%)
Query: 17 GKVIGKNGRIIQEIVDKSG--VVR 38
G G +I V K VVR
Sbjct: 242 GMFYKNIGTLIDAYVSKKNFSVVR 265
>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis,
CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA
synthetase family; 2.00A {Candida albicans} PDB:
3qo7_A* 3qo8_A* 3qo5_A
Length = 485
Score = 23.7 bits (52), Expect = 5.6
Identities = 7/44 (15%), Positives = 17/44 (38%), Gaps = 3/44 (6%)
Query: 2 LEYSEESLQVPRNLVGKVIG---KNGRIIQEIVDKSGVVRVKIE 42
L + + N V K IG K ++++ + + + +
Sbjct: 45 LRFDLDEHNKKLNSVQKEIGKRFKAKEDAKDLIAEKEKLSNEKK 88
>3pka_A Methionine aminopeptidase; hydrolase-hydrolase inhibitor complex;
HET: Y02; 1.25A {Mycobacterium tuberculosis} PDB:
3pkb_A* 3pkc_A* 3pkd_A* 3pke_A* 3iu7_A* 3iu8_A* 3iu9_A*
1y1n_A 1yj3_A
Length = 285
Score = 23.6 bits (52), Expect = 5.9
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 17 GKVIGKNGRIIQEIVDKSG--VVR 38
G+ + GR+I+ ++ G VVR
Sbjct: 177 GRALSVIGRVIESYANRFGYNVVR 200
>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; HET: SSA; 2.60A
{Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A*
2zr3_A
Length = 455
Score = 23.7 bits (52), Expect = 6.2
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 7 ESLQVPRNLVGKVIG---KNGRIIQEIVDKSGVVRVKIE 42
L+ RN + IG K G + E++ KS + +I
Sbjct: 48 NRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIG 86
>2b3z_A Riboflavin biosynthesis protein RIBD; alpha/beta/alpha, deaminase
domain and reductase domain, hydrolase, oxidoreductase;
2.41A {Bacillus subtilis} SCOP: c.71.1.2 c.97.1.2 PDB:
2d5n_A* 3ex8_A*
Length = 373
Score = 23.6 bits (52), Expect = 7.5
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 15 LVGKVIGKNGRII 27
LVG V+ K+G+I+
Sbjct: 37 LVGAVVVKDGQIV 49
>2b3h_A Methionine aminopeptidase 1; hydrolase, metalloprotease, pitab;
HET: GOL; 1.10A {Homo sapiens} PDB: 2b3k_A 2b3l_A
2gz5_A* 2nq6_A* 2nq7_A* 2g6p_A*
Length = 329
Score = 23.4 bits (51), Expect = 7.8
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 17 GKVIGKNGRIIQEIVDKSG--VVR 38
G + G IIQ+ +G VVR
Sbjct: 211 GVRYRELGNIIQKHAQANGFSVVR 234
>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus
thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A*
1set_A* 1sry_A
Length = 421
Score = 23.2 bits (51), Expect = 9.2
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 7 ESLQVPRNLVGKVIGK-NGRIIQEIVDKSGVVRVKIE 42
+ +Q RN V K + K + ++ + + + +
Sbjct: 45 QEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAK 81
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
0.314 0.137 0.376
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,059,814
Number of extensions: 52711
Number of successful extensions: 257
Number of sequences better than 10.0: 1
Number of HSP's gapped: 257
Number of HSP's successfully gapped: 72
Length of query: 71
Length of database: 6,701,793
Length adjustment: 41
Effective length of query: 30
Effective length of database: 5,557,032
Effective search space: 166710960
Effective search space used: 166710960
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: 42 (21.9 bits)
S2: 51 (23.2 bits)