RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3
[Candidatus Liberibacter asiaticus str. psy62]
(227 letters)
>3ofo_C 30S ribosomal protein S3; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 2gyb_C
2gy9_C* 3fih_C* 2wwl_C 3ofp_C
Length = 206
Score = 264 bits (676), Expect = 1e-71
Identities = 110/207 (53%), Positives = 150/207 (72%), Gaps = 1/207 (0%)
Query: 2 GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTH 61
GQK++P RLG+ WNS WFA E+ L D K+R+YL L +A V++I+IER
Sbjct: 1 GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA 60
Query: 62 KNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIA 121
K+ R+ +++ARPG++IGKKG D+EK+RK ++++ +++ EV KPE++A L+A SI
Sbjct: 61 KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSIT 120
Query: 122 QQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAH 181
QLERRV+FRRAMKRAVQ+AMR GA G+KV SGRL GAE++RTE Y EGRVPL TLRA
Sbjct: 121 SQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD 180
Query: 182 IDYGTAVAETAYGSCGIKVYVSLRDEV 208
IDY T+ A T YG G+KV++ + E+
Sbjct: 181 IDYNTSEAHTTYGVIGVKVWI-FKGEI 206
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C
3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C
2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ...
Length = 233
Score = 234 bits (597), Expect = 1e-62
Identities = 112/219 (51%), Positives = 154/219 (70%), Gaps = 1/219 (0%)
Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
MGQK++P RLG+ WNS WFA E+ L D K+R+YL L +A V++I+IER
Sbjct: 1 MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP 60
Query: 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120
K+ R+ +++ARPG++IGKKG D+EK+RK ++++ +++ EV KPE++A L+A SI
Sbjct: 61 AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI 120
Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180
QLERRV+FRRAMKRAVQ+AMR GA G+KV SGRL GAE++RTE Y EGRVPL TLRA
Sbjct: 121 TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA 180
Query: 181 HIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAE 219
IDY T+ A T YG G+KV++ + E+ + + E
Sbjct: 181 DIDYNTSEAHTTYGVIGVKVWI-FKGEILGGMAAVEQPE 218
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 217 bits (554), Expect = 1e-57
Identities = 73/218 (33%), Positives = 129/218 (59%), Gaps = 11/218 (5%)
Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQ--------AGV 52
MGQKINP+ FRLG + S WF++ Y L ED KIR+ ++ ++++ G+
Sbjct: 1 MGQKINPLGFRLGTTQSHYSLWFSQPKNYAEGLQEDQKIRDCIKNYVQKNTKTSSGVEGI 60
Query: 53 AKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSN---MTNSEIHLSVNEVPKP 109
A+I I++ ++I++ P L+I + +E ++ + N ++++++ + KP
Sbjct: 61 ARIEIQKRIDLIQVIIHMGFPKLLIENRPQGVEDLKINVQKELNCVNRKLNIAITRIAKP 120
Query: 110 EINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYL 169
+ ++A+ IA QL+ RV FR+AMK+A++ + G+++ +GR++G E++R E
Sbjct: 121 YGDPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTKGIQIQIAGRIDGKEIARIEWIR 180
Query: 170 EGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDE 207
EGRVPLQT+RA IDY T YG GIK+++ + +E
Sbjct: 181 EGRVPLQTIRAKIDYCAYTVRTIYGVLGIKIWIFMGEE 218
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C*
1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F*
1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C
1xmo_C* 1xmq_C* 1xnq_C* ...
Length = 239
Score = 216 bits (552), Expect = 3e-57
Identities = 102/225 (45%), Positives = 143/225 (63%)
Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
MG KI+PI FRLG+ W SRW+A +Y LL ED +IR L+ L AG+A++ IER
Sbjct: 1 MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA 60
Query: 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120
N + V+ A+PG++IG+ G I +R++L+ +T + L+V EV P ++A L+AQ +
Sbjct: 61 ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV 120
Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180
A+Q+ERR RRA+K+AVQ M GA G KVI SGR+ GAE +RTE +GRVPL TLRA
Sbjct: 121 AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA 180
Query: 181 HIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEK 225
+IDYG A+A T YG G+K Y+ L + + + E+
Sbjct: 181 NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEER 225
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 1s1h_C
Length = 243
Score = 170 bits (432), Expect = 2e-43
Identities = 39/193 (20%), Positives = 83/193 (43%), Gaps = 6/193 (3%)
Query: 20 SRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGK 79
+ ++ ++ A ++ E+L L + G + + + T II+ + R ++G+
Sbjct: 2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61
Query: 80 KGTDIEKIRK---KLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKR 136
KG I ++ K + L +V + A A+S+ +L + RRA
Sbjct: 62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYG 121
Query: 137 AVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPL--QTLRAHIDYGTAVAETAYG 194
++ M GA G +V+ SG+L + +++ +++G + + ++D G
Sbjct: 122 VLRFIMESGAKGCEVVVSGKL-RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180
Query: 195 SCGIKVYVSLRDE 207
GIKV + L +
Sbjct: 181 VLGIKVKIMLPWD 193
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
ribosome; NMR {Homo sapiens} SCOP: d.52.3.1
Length = 92
Score = 72.4 bits (178), Expect = 7e-14
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 38 KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS---NM 94
++ E+L L + G + + + T II+ + R ++G+KG I ++ +
Sbjct: 11 ELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGF 70
Query: 95 TNSEIHLSVNEV 106
+ L +V
Sbjct: 71 PEGSVELYAEKV 82
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 37.6 bits (87), Expect = 0.002
Identities = 46/270 (17%), Positives = 81/270 (30%), Gaps = 121/270 (44%)
Query: 8 ILFRLGVNCTWNSRWFARGSEYGALLHED-----------LKIREYLQCHLKQAGVAKIL 56
+LF +GV C + S ++L + L I +L Q V
Sbjct: 302 VLFFIGVRC---YEAYPNTSLPPSILEDSLENNEGVPSPMLSIS-----NLTQEQVQDY- 352
Query: 57 IERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS-VNE----V---PK 108
+ +T N + P ++ +S VN V P
Sbjct: 353 VNKT--NSHL------P---------------------AGKQVEISLVNGAKNLVVSGP- 382
Query: 109 PE----INATLIAQSIAQQLER-RVVFRRAMKRAVQSAMRF------------------- 144
P+ +N TL L++ R+ F +R ++ + RF
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFS---ERKLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 145 ----GADGVKVIASGRL--------NGAELSR----------TECYLEGRV--PLQT-LR 179
+ V + + +G++L R +C + V T +
Sbjct: 440 NKDLVKNNVS-FNAKDIQIPVYDTFDGSDL-RVLSGSISERIVDCIIRLPVKWETTTQFK 497
Query: 180 A-HI-DYGTAVAETAYGSCGIKVYVS-LRD 206
A HI D+G G+ G+ V +D
Sbjct: 498 ATHILDFGPG------GASGLGVLTHRNKD 521
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 35.8 bits (82), Expect = 0.007
Identities = 22/111 (19%), Positives = 45/111 (40%), Gaps = 13/111 (11%)
Query: 48 KQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVP 107
K++ ++ + + +I+ + +PGL+IGK G + +I K +I V
Sbjct: 90 KESVISSYYFD--PDSGEVIIEAEKPGLVIGKHGATLREITK--------QIGWIPKVVR 139
Query: 108 KPEINATLIA---QSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASG 155
P I + + + + L+ R + + R + V+V A G
Sbjct: 140 TPPIKSRTVKNIREFMRNNLKERKEILKTVGRKIHRECTSKDQWVRVTALG 190
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/proteomics
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus HB8} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 34.1 bits (77), Expect = 0.024
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 9/55 (16%)
Query: 58 ERTHKNCRI--IVYSARPG---LIIGKKGTDIEKI----RKKLSNMTNSEIHLSV 103
ER + I I+Y RP ++IG+ G I++I RK+L + +++L +
Sbjct: 222 ERENGVLYIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYLDL 276
>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 = 33.4 bits (75), Expect = 0.040
Identities = 19/149 (12%), Positives = 39/149 (26%), Gaps = 4/149 (2%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQL 124
+ + G++IG+ G I+KI+ I ++ PE A + Q
Sbjct: 6 DVPIPRFAVGIVIGRNGEMIKKIQND----AGVRIQFKPDDGTTPERIAQITGPPDRAQH 61
Query: 125 ERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDY 184
++ + G G VP I
Sbjct: 62 AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121
Query: 185 GTAVAETAYGSCGIKVYVSLRDEVSDSDS 213
G ++ G ++ + + +
Sbjct: 122 GGETIKSISQQSGARIELQRNPPPNADPN 150
Score = 27.3 bits (59), Expect = 3.0
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 4/73 (5%)
Query: 44 QCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSV 103
+ + G + + IV + + GLIIGK G I+ I + + I L
Sbjct: 86 RGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSIS----QQSGARIELQR 141
Query: 104 NEVPKPEINATLI 116
N P + N L
Sbjct: 142 NPPPNADPNMKLF 154
>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 = 32.8 bits (74), Expect = 0.067
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 48 KQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKK 90
K+A + I + +++ + +PGL+IGK G + I +K
Sbjct: 95 KEAEITNIAFD--PSVGEVLIEAKKPGLVIGKNGETLRLITQK 135
>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 = 32.7 bits (73), Expect = 0.070
Identities = 6/26 (23%), Positives = 16/26 (61%), Gaps = 7/26 (26%)
Query: 131 RRAMKRAVQSAMRFGAD------GVK 150
++A+K+ +Q++++ AD +K
Sbjct: 19 KQALKK-LQASLKLYADDSAPALAIK 43
Score = 28.8 bits (63), Expect = 1.00
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 85 EK-IRKKLSNMTNSEIHLSVNE-VPKPEINATL 115
EK KKL + + L ++ P I AT+
Sbjct: 18 EKQALKKL----QASLKLYADDSAPALAIKATM 46
Score = 27.7 bits (60), Expect = 2.3
Identities = 8/43 (18%), Positives = 14/43 (32%), Gaps = 25/43 (58%)
Query: 175 LQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPA 217
L+ L+A +K+Y +D + PA
Sbjct: 22 LKKLQA----------------SLKLY---------ADDSAPA 39
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein/RNA complex; HET:
5BU; 1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 32.3 bits (72), Expect = 0.087
Identities = 27/151 (17%), Positives = 53/151 (35%), Gaps = 7/151 (4%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQL 124
++++ S G IIGK G I +++K+ T + I LS ++ P + +
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKE----TGATIKLSKSKDFYPGTTERVCLIQGTIEA 64
Query: 125 ERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDY 184
V A K + V ++ + + + VP T I
Sbjct: 65 LNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKII---VPNSTAGLIIGK 121
Query: 185 GTAVAETAYGSCGIKVYVSLRDEVSDSDSTI 215
G A + G V +S + + + + +
Sbjct: 122 GGATVKAIMEQSGAWVQLSQKPDGINLQNRV 152
>2q1s_A Putative nucleotide sugar epimerase/ dehydratase; rossman fold,
protein-NADH complex, sugar binding protein; HET: NAI;
1.50A {Bordetella bronchiseptica} PDB: 2pzj_A* 2q1t_A*
2q1u_A*
Length = 377
Score = 31.1 bits (69), Expect = 0.24
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 52 VAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKL 91
+A + E T N + RP GK+ EK R++L
Sbjct: 296 LATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARREL 335
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
cytoplasm, DNA-binding, nucleus, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Homo sapiens}
Length = 160
Score = 29.8 bits (66), Expect = 0.48
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNM 94
R++++ G IIGKKG ++K+R++
Sbjct: 8 RLLMHGKEVGSIIGKKGESVKKMREESGAR 37
Score = 28.2 bits (62), Expect = 1.6
Identities = 19/111 (17%), Positives = 43/111 (38%), Gaps = 9/111 (8%)
Query: 2 GQKINPILFRLGVNCTW-----NSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKIL 56
G+ + + G R A+ I + L+ + +
Sbjct: 24 GESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDISSSMTNSTA 83
Query: 57 IERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVP 107
R R++V +++ G +IGK G I++IR+ T +++ ++ + +P
Sbjct: 84 ASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRES----TGAQVQVAGDMLP 130
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like,
hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8
d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X
Length = 301
Score = 30.0 bits (67), Expect = 0.53
Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 15/78 (19%)
Query: 39 IREYLQCHLKQ------AGVAKILIERTHKNCRI--IVYSARPG---LIIGKKGTDIEKI 87
IRE L L + + I ++ R G ++IG KG I+ I
Sbjct: 198 IREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTI 257
Query: 88 ----RKKLSNMTNSEIHL 101
RK + M + +HL
Sbjct: 258 GIEARKDMQEMFEAPVHL 275
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA,
30S ribosome assembly, GTP-binding; HET: GNP; 1.90A
{Aquifex aeolicus}
Length = 308
Score = 29.4 bits (65), Expect = 0.75
Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 74 GLIIGKKGTDIEKI----RKKLSNMTNSEIHLSV 103
+IIGKKG +++I R++L + ++L +
Sbjct: 253 PIIIGKKGQRLKEIGKRARQELELILGRPVYLEL 286
>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 = 28.2 bits (62), Expect = 1.4
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKK 90
++ + + G IIGKKG I+++ +
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRF 31
>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 = 28.4 bits (62), Expect = 1.5
Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110
I++ + + GL+IGK G I++++++ ++ L +
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQER----AGVKMILIQDGSQNTN 46
>3m2p_A UDP-N-acetylglucosamine 4-epimerase; SGXNY, 11155J, isomerase,
structural genomics, PSI-2, protein structure
initiative; HET: UDP; 2.95A {Bacillus cereus}
Length = 311
Score = 27.3 bits (60), Expect = 2.7
Identities = 7/40 (17%), Positives = 13/40 (32%)
Query: 52 VAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKL 91
VA + ++V + I D K ++ L
Sbjct: 235 VANTINNAFGNKDNLLVKNPNANEGIHSSYMDSSKAKELL 274
>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 = 27.1 bits (60), Expect = 3.0
Identities = 19/82 (23%), Positives = 28/82 (34%), Gaps = 11/82 (13%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP-------EINATLIA 117
I V G I+GK G + + ++ T + I +S P I + A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQEL----TGARIQISKKGEFLPGTRNRRVTITGSPAA 61
Query: 118 QSIAQQLERRVVFRRAMKRAVQ 139
AQ L + V RA
Sbjct: 62 TQAAQYLISQRVTYEQGVRASN 83
>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type
IV secretion, hydrolase/protein binding complex; 2.40A
{Helicobacter pylori 26695}
Length = 152
Score = 27.0 bits (60), Expect = 3.8
Identities = 10/69 (14%), Positives = 26/69 (37%), Gaps = 3/69 (4%)
Query: 38 KIREYLQCHLKQAGV-AKILIERTHKNCRIIVY--SARPGLIIGKKGTDIEKIRKKLSNM 94
+I++ L+ + ++ +++ L+IG+KG + + L N
Sbjct: 6 EIKQELKDLFSHLPYKINKVEVSLYEPGVLLIDIDGEDSALLIGEKGYRYKALSYLLFNW 65
Query: 95 TNSEIHLSV 103
+ S+
Sbjct: 66 IHPTYGYSI 74
>2cxc_A NUSA; transcription termination, RNA binding protein, KH domain,
structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1}
PDB: 2cy1_A
Length = 144
Score = 26.9 bits (59), Expect = 4.5
Identities = 11/56 (19%), Positives = 18/56 (32%)
Query: 34 HEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK 89
DL+ + + K I V G IGK G ++++ R
Sbjct: 75 SSDLERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARL 130
Score = 26.1 bits (57), Expect = 7.7
Identities = 8/42 (19%), Positives = 18/42 (42%)
Query: 50 AGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKL 91
+ +++ + +V G IG+ G I+ +R+ L
Sbjct: 24 VTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLIKLLREAL 65
>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 = 26.7 bits (59), Expect = 4.9
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110
++ + G IIGK G I++IR + + + I + +
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHE----SGASIKIDEPLEGSED 58
>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
Length = 73
Score = 26.3 bits (58), Expect = 5.5
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111
R++++ G IIGKKG ++K+R++ + + I++S P+ I
Sbjct: 8 RLLMHGKEVGSIIGKKGESVKKMREE----SGARINISEGNCPERII 50
>3n0r_A Response regulator; sigma factor, receiver, two-component SI
transduction, signaling protein; HET: MSE GOL; 1.25A
{Caulobacter vibrioides}
Length = 286
Score = 26.1 bits (57), Expect = 6.1
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 32 LLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLII-------GKKGTD- 83
++ ++ I ++ +++ G I T V PGL++ G G D
Sbjct: 165 IIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLADIQLADGSSGIDA 224
Query: 84 IEKIRKK 90
++ I +
Sbjct: 225 VKDILGR 231
>2bry_A NEDD9 interacting protein with calponin homology and LIM domains;
transport, coiled coil, cytoskeleton, FAD, flavoprotein,
metal-binding, zinc; HET: FAD; 1.45A {Mus musculus} PDB:
2c4c_A* 2bra_A*
Length = 497
Score = 26.0 bits (56), Expect = 6.6
Identities = 16/130 (12%), Positives = 32/130 (24%), Gaps = 11/130 (8%)
Query: 42 YLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHL 101
L G +L+E+ K R V P I + +K +
Sbjct: 106 RAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFC-------TG 158
Query: 102 SVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAE 161
+++ + ++ L+ A L + + G +
Sbjct: 159 TLDHISIRQLQLLLLKV--ALLLGVEIHWGVKFTGLQPPPR--KGSGWRAQLQPNPPAQL 214
Query: 162 LSRTECYLEG 171
S L
Sbjct: 215 ASYEFDVLIS 224
>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 = 25.9 bits (57), Expect = 8.4
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111
+ + +IGK G ++ + K T ++I + + P +I
Sbjct: 20 TVAIPKEHHRFVIGKNGEKLQDLELK----TATKIQIPRPDDPSNQI 62
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH
domains, type I KH domains, fragIle X mental
retardation protein, RNA binding protein; 1.90A {Homo
sapiens} PDB: 2fmr_A
Length = 144
Score = 25.9 bits (56), Expect = 8.5
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 74 GLIIGKKGTDIEKIRKK 90
GL IG G +I++ RK
Sbjct: 16 GLAIGTHGANIQQARKV 32
>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding,
ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3
PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A
Length = 105
Score = 25.7 bits (56), Expect = 8.7
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIR 88
ED ++ + +Q + + + +AK L R K CR ++ + T+ E
Sbjct: 11 EDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWTEEEDRI 66
>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 = 25.6 bits (56), Expect = 9.2
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110
V G IIG+ G I +I+++ + +I ++ + PE
Sbjct: 18 EYKVPDGMVGFIIGRGGEQISRIQQE----SGCKIQIAPDSGGLPE 59
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.320 0.134 0.387
Gapped
Lambda K H
0.267 0.0583 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,935,151
Number of extensions: 87659
Number of successful extensions: 369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 53
Length of query: 227
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 138
Effective length of database: 3,535,514
Effective search space: 487900932
Effective search space used: 487900932
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: 55 (25.3 bits)