RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3
[Candidatus Liberibacter asiaticus str. psy62]
(227 letters)
>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 ... (C:1-109)
Length = 109
Score = 139 bits (351), Expect = 4e-34
Identities = 48/109 (44%), Positives = 74/109 (67%)
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 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109
K+ R+ +++ARPG++IGKKG D+EK+RK ++++ +++ EV KP
Sbjct: 61 AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKP 109
>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* ... (C:1-109)
Length = 109
Score = 134 bits (340), Expect = 6e-33
Identities = 47/109 (43%), Positives = 69/109 (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 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109
N + V+ A+PG++IG+ G I +R++L+ +T + L+V EV P
Sbjct: 61 ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNP 109
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(C:1-121)
Length = 121
Score = 127 bits (320), Expect = 1e-30
Identities = 35/120 (29%), Positives = 66/120 (55%), Gaps = 11/120 (9%)
Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQ--------AGV 52
MGQKINP+ FRLG + S WF++ Y L ED KIR+ ++ ++++ G+
Sbjct: 1 MGQKINPLGFRLGTTQSHYSLWFSQPKNYAEGLQEDQKIRDCIKNYVQKNTKTSSGVEGI 60
Query: 53 AKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK---KLSNMTNSEIHLSVNEVPKP 109
A+I I++ ++I++ P L+I + +E ++ K N N ++++++ + KP
Sbjct: 61 ARIEIQKRIDLIQVIIHMGFPKLLIENRPQGVEDLKINVQKELNCVNRKLNIAITRIAKP 120
>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 ... (C:110-233)
Length = 124
Score = 120 bits (302), Expect = 2e-28
Identities = 63/116 (54%), Positives = 79/116 (68%)
Query: 110 EINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYL 169
E++A L+A SI QLERRV+FRRAMKRAVQ+AMR GA G+KV SGRL GAE++RTE Y
Sbjct: 1 ELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYR 60
Query: 170 EGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEK 225
EGRVPL TLRA IDY T+ A T YG G+KV++ + + + + K
Sbjct: 61 EGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPK 116
>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* ... (C:110-239)
Length = 130
Score = 118 bits (298), Expect = 5e-28
Identities = 55/116 (47%), Positives = 74/116 (63%)
Query: 110 EINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYL 169
++A L+AQ +A+Q+ERR RRA+K+AVQ M GA G KVI SGR+ GAE +RTE
Sbjct: 1 NLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAA 60
Query: 170 EGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEK 225
+GRVPL TLRA+IDYG A+A T YG G+K Y+ L + + + E+
Sbjct: 61 QGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEER 116
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(C:122-218)
Length = 97
Score = 114 bits (287), Expect = 1e-26
Identities = 40/96 (41%), Positives = 64/96 (66%)
Query: 112 NATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEG 171
+ ++A+ IA QL+ RV FR+AMK+A++ + G+++ +GR++G E++R E EG
Sbjct: 2 DPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTKGIQIQIAGRIDGKEIARIEWIREG 61
Query: 172 RVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDE 207
RVPLQT+RA IDY T YG GIK+++ + +E
Sbjct: 62 RVPLQTIRAKIDYCAYTVRTIYGVLGIKIWIFMGEE 97
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
ribosome; NMR {Homo sapiens} (A:)
Length = 92
Score = 108 bits (273), Expect = 5e-25
Identities = 17/96 (17%), Positives = 36/96 (37%), Gaps = 11/96 (11%)
Query: 33 LHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92
++ E+L L + G + + + T II+ + R ++G+KG I ++ +
Sbjct: 6 SGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQ 65
Query: 93 NMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRV 128
PE + L A+ +A +
Sbjct: 66 -----------KRFGFPEGSVELYAEKVATRGSGPS 90
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} PDB: 1s1h_C (c:1-94)
Length = 94
Score = 106 bits (267), Expect = 2e-24
Identities = 18/102 (17%), Positives = 41/102 (40%), Gaps = 11/102 (10%)
Query: 20 SRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGK 79
+ ++ ++ A ++ E+L L + G + + + T II+ + R ++G+
Sbjct: 2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61
Query: 80 KGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIA 121
KG I ++ + PE + L A+ +A
Sbjct: 62 KGRRIRELTAVVQ-----------KRFGFPEGSVELYAEKVA 92
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} PDB: 1s1h_C (c:95-243)
Length = 149
Score = 99.3 bits (247), Expect = 4e-22
Identities = 25/118 (21%), Positives = 50/118 (42%), Gaps = 3/118 (2%)
Query: 111 INATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLE 170
+ A A+S+ +L + RRA ++ M GA G +V+ SG+L G + +++ +++
Sbjct: 2 LCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRG-QRAKSMKFVD 60
Query: 171 GRVPL--QTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKD 226
G + + ++D G GIKV + L + + V +
Sbjct: 61 GLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVE 118
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding,
RAS-like, hydrolase; 2.40A {Escherichia coli}
(A:182-284)
Length = 103
Score = 46.2 bits (110), Expect = 3e-06
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 13/86 (15%)
Query: 29 YGALLHEDLKIREYLQCHLKQAGVAKILIERTHKN------CRIIVYSARP---GLIIGK 79
+ E ++ + + + IER N ++ R ++IG
Sbjct: 9 QRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGN 68
Query: 80 KGTDIEKI----RKKLSNMTNSEIHL 101
KG I+ I RK + M + +HL
Sbjct: 69 KGAKIKTIGIEARKDMQEMFEAPVHL 94
>2qs8_A XAA-Pro dipeptidase; amidohydrolase, TIM barrel, protein
structure initiative, PSI-2, NYSGXRC, structural
genomics; 2.33A {Alteromonas macleodii} (A:159-277)
Length = 119
Score = 32.5 bits (74), Expect = 0.047
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 8/66 (12%)
Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAV 188
+ AV+ + GADG+K+ +G + S + + A + YG V
Sbjct: 19 EVYAAVRQRYKDGADGIKITVTGGVLSVAKSGQNPQF----TQEEVDAVVSAAKDYGXWV 74
Query: 189 AETAYG 194
A A+G
Sbjct: 75 AVHAHG 80
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006)
Length = 120
Score = 32.4 bits (74), Expect = 0.058
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 4/23 (17%)
Query: 119 SIAQQLERRVVFRR--AMKRAVQ 139
SI +E VVF R M+ AV
Sbjct: 7 SIESLVE--VVFYRGMTMQVAVP 27
>3be7_A Zn-dependent arginine carboxypeptidase; unknown source,
amidohydrolase, sargasso SEA, structural genomics,
protein structure initiative, PSI; HET: ARG; 2.30A
{Unidentified} (A:137-268)
Length = 132
Score = 31.9 bits (72), Expect = 0.074
Identities = 15/70 (21%), Positives = 28/70 (40%)
Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETA 192
++ V+ ++GAD +K A+G + + ++G VA A
Sbjct: 31 EARKMVRKNRKYGADLIKFCATGGVMSRNTDVNAKQFTLEEMKAIVDEAHNHGMKVAAHA 90
Query: 193 YGSCGIKVYV 202
+G GIK +
Sbjct: 91 HGLIGIKAAI 100
>3feq_A Putative amidohydrolase; unknown source, sargasso SEA,
structural genomics, protein structure initiative, PSI;
2.63A {Unidentified} (A:134-273)
Length = 140
Score = 31.2 bits (70), Expect = 0.12
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAV 188
++ AV+ ++ GA +K++ASG + S T+ + +RA +D T V
Sbjct: 40 GVRLAVREEIQKGATQIKIMASGGV----ASPTDPIANTQYSEDEIRAIVDEAEAANTYV 95
Query: 189 AETAYGSCGIKVYV 202
AY I V
Sbjct: 96 MAHAYTGRAIARAV 109
>2p9b_A Possible prolidase; protein structure initiative II, PSI-2,
amidohydrolase, structural genomics; 1.70A
{Bifidobacterium longum NCC2705} (A:165-339)
Length = 175
Score = 30.8 bits (69), Expect = 0.16
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 133 AMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAV 188
+ AV ++ G + +K+ A+G + A+ + ++ RA D YG V
Sbjct: 22 EARTAVAQNLKAGVNAIKIAATGGVTDAQEIGEAGSP--QXSVEQXRAICDEAHQYGVIV 79
Query: 189 AETAYGSCGIKVYV 202
A G++ +
Sbjct: 80 GAHAQSPEGVRRSL 93
>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* (A:)
Length = 178
Score = 28.9 bits (63), Expect = 0.63
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKK 90
++++ S G IIGK G I +++K+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKE 34
>2ghs_A AGR_C_1268P; 15155668, calcium-binding protein, regucalcin,
structural genomics, joint center for structural
genomics, JCSG; 1.55A {Agrobacterium tumefaciens str}
(A:)
Length = 326
Score = 28.9 bits (62), Expect = 0.67
Identities = 3/30 (10%), Positives = 7/30 (23%), Gaps = 4/30 (13%)
Query: 176 QTLRAHIDYGTAVAETAYG----SCGIKVY 201
+ H + A + S +
Sbjct: 4 DKIHHHHHHXNAPLSHSRPXXQPSEDKSLA 33
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH
domain, cell projection, cytoplasm, nucleus,
phosphoprotein, translation regulation; 2.75A {Homo
sapiens} (A:)
Length = 163
Score = 28.0 bits (61), Expect = 1.1
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKL 91
++ + + G IIGKKG I+++ +
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFA 32
>2gys_A Cytokine receptor common beta chain; dimer of interlocking
chains of fibronectin-III domains, four fibronectin-III
domains PER chain; HET: NAG FUC BMA NDG; 2.70A {Homo
sapiens} (A:1-98)
Length = 98
Score = 27.9 bits (62), Expect = 1.3
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 170 EGRVPLQTLRAHIDYGTAV----AETA 192
E +PLQTLR + DY + + A+T
Sbjct: 1 EETIPLQTLRCYNDYTSHITCRWADTQ 27
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain,
RNA binding protein; NMR {Homo sapiens} (A:)
Length = 107
Score = 27.6 bits (61), Expect = 1.6
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109
+ + + GL+IG+ G +++ I ++ T + + +S P
Sbjct: 10 TFSIPTHKCGLVIGRGGENVKAINQQ----TGAFVEISRQLPPNG 50
>2cxc_A NUSA; transcription termination, RNA binding protein, KH
domain, structural genomics, NPPSFA; 2.00A {Aeropyrum
pernix K1} PDB: 2cy1_A (A:1-75)
Length = 75
Score = 27.3 bits (61), Expect = 1.7
Identities = 9/55 (16%), Positives = 18/55 (32%), Gaps = 4/55 (7%)
Query: 47 LKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHL 101
+ + +++ + +V G IG+ G I K L I +
Sbjct: 21 ITGVTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLI----KLLREALGKNIEV 71
>1wf3_A GTP-binding protein; GTPase, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, hydrolase; HET: GNP; 1.88A {Thermus
thermophilus HB8} (A:180-301)
Length = 122
Score = 27.3 bits (61), Expect = 1.8
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 16/54 (29%)
Query: 53 AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101
A + +ER + K ++IG+ G I++I RK+L + +++L
Sbjct: 53 AILYVERPSQK-----------AIVIGEGGRKIKEIGQATRKQLEALLGKKVYL 95
>1j4w_A FUSE binding protein; single-stranded DNA binding protein;
HET: DNA; NMR {Homo sapiens} (A:89-174)
Length = 86
Score = 27.1 bits (60), Expect = 1.8
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 58 ERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109
+ IV + + GLIIGK G I+ I ++ + + I L N P
Sbjct: 12 PGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQ----SGARIELQRNPPPNA 59
>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} (A:191-294)
Length = 104
Score = 27.0 bits (60), Expect = 2.2
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 16/54 (29%)
Query: 53 AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101
+I+++R K +IIGKKG +++I R++L + ++L
Sbjct: 52 GEIIVDRENLK-----------PIIIGKKGQRLKEIGKRARQELELILGRPVYL 94
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif; 2.00A {Homo sapiens}
(A:)
Length = 76
Score = 26.3 bits (58), Expect = 3.7
Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109
+ V G I+GK G + + ++ T + I +S P
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQEL----TGARIQISKKGEFLP 46
>1b9u_A Protein (ATP synthase); membrane protein; HET: GMA; NMR
{Synthetic} (A:)
Length = 34
Score = 25.8 bits (57), Expect = 4.7
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 111 INATLIAQSIA 121
+NAT++ Q+IA
Sbjct: 3 LNATILGQAIA 13
>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} (A:)
Length = 94
Score = 25.9 bits (57), Expect = 4.7
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
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} (A:)
Length = 83
Score = 25.9 bits (57), Expect = 5.2
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102
++ V GL++G KG I++I+++ T++ I
Sbjct: 13 QVRVPYRVVGLVVGPKGATIKRIQQR----THTYIVTP 46
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo
sapiens} (A:)
Length = 71
Score = 25.9 bits (57), Expect = 5.3
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 4/47 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111
I + +IGK G +I +I+ + + + I
Sbjct: 8 EINIDHKFHRHLIGKSGANINRIKD----QYKVSVRIPPDSEKSNLI 50
>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} (A:)
Length = 104
Score = 25.6 bits (56), Expect = 5.3
Identities = 18/102 (17%), Positives = 32/102 (31%), Gaps = 16/102 (15%)
Query: 54 KILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI-- 111
+ L + V +IG+KG+ I K+ + IH+ E+ I
Sbjct: 9 EALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDE----FEVNIHVPAPELQSDIIAI 64
Query: 112 --------NATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFG 145
A ++L+ R R+ +S G
Sbjct: 65 TGLAANLDRAKAGLLERVKELQAEQEDRA--LRSFKSGPSSG 104
>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 (A:1-64)
Length = 64
Score = 25.8 bits (57), Expect = 5.7
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKK 90
+ IV GL IG G +I++ RK
Sbjct: 7 QFIVREDLXGLAIGTHGANIQQARKV 32
>1hn0_A Chondroitin ABC lyase I; chondroitinase ABC I, chonroitin
digestion, mechanism; 1.90A {Proteus vulgaris}
(A:277-434)
Length = 158
Score = 25.6 bits (56), Expect = 5.8
Identities = 5/22 (22%), Positives = 7/22 (31%)
Query: 23 FARGSEYGALLHEDLKIREYLQ 44
F +GS H R +
Sbjct: 102 FVKGSALVTTHHWGYSSRWWYI 123
>2egx_A Putative acetylglutamate kinase; structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.92A {Thermus thermophilus HB8}
(A:)
Length = 269
Score = 25.3 bits (54), Expect = 6.3
Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 2/58 (3%)
Query: 107 PKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVK--VIASGRLNGAEL 162
P I + E + + MKR V A+ GVK V A GR+
Sbjct: 201 PDEASLVREIPVERIEDPEYLALAQGRMKRKVMGAVEAVKGGVKRVVFADGRVENPIR 258
>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural
genomics, unknown function, NPPSFA; NMR {Mus musculus}
(A:)
Length = 60
Score = 25.4 bits (56), Expect = 6.6
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65
ED ++R ++ +A RT + C+
Sbjct: 15 EDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQ 47
>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} (A:)
Length = 95
Score = 25.2 bits (55), Expect = 6.9
Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 4/47 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEI 111
+ + IIG +G I KI + +I + P P
Sbjct: 20 DVPLDHRVHARIIGARGKAIRKIMDE----FKVDIRFPQSGAPDPNC 62
>3gku_A Probable RNA-binding protein; APC21302, structural
genomics, PSI-2, protein structure initiative; 2.95A
{Clostridium symbiosum atcc 14940} (A:61-140)
Length = 80
Score = 25.4 bits (56), Expect = 7.1
Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 38 KIREYLQCHLKQAGV---AKILIERTHKNCRIIVYSARPGLIIGKKG 81
K E+L+ + T K + + G++IGK+G
Sbjct: 5 KAIEFLEQVFDAXNXAVDISVEYNETEKEXNVNLKGDDXGILIGKRG 51
>2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV,
GRAM-positive bacteria, quinolone target, DNA binding,
DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae}
PDB: 3foe_A* 3fof_A* (A:207-341,A:477-496)
Length = 155
Score = 25.2 bits (55), Expect = 7.3
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 8/57 (14%)
Query: 48 KQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVN 104
K AG+A++ E RI I KK + E + L T+ +I+ + N
Sbjct: 74 KVAGIAEVRDESDRDGLRI--------AIELKKDANTELVLNYLFKYTDLQINYNFN 122
>1d8w_A L-rhamnose isomerase; beta-alpha-8-barrels, aldose-ketose
isomerization, hydride shift; 1.60A {Escherichia coli}
(A:)
Length = 426
Score = 25.2 bits (54), Expect = 7.5
Identities = 6/76 (7%), Positives = 12/76 (15%), Gaps = 5/76 (6%)
Query: 125 ERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDY 184
R + K + + + FG L + +
Sbjct: 160 SIRQFWIDHCKASRRVSAYFGEQLGTPSVXNIWIPD-----GXKDITVDRLAPRQRLLAA 214
Query: 185 GTAVAETAYGSCGIKV 200
V
Sbjct: 215 LDEVISEKLNPAHHID 230
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR
{Homo sapiens} (A:)
Length = 85
Score = 25.2 bits (55), Expect = 7.8
Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPK 108
I++ + + GL+IGK G I++++++ ++ L +
Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQER----AGVKMILIQDGSQN 56
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain,
RNA binding protein; 2.10A {Homo sapiens} (A:)
Length = 82
Score = 25.2 bits (55), Expect = 7.9
Identities = 10/38 (26%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102
+ + + G IIG++G +I +IR+ M+ ++I ++
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQ----MSGAQIKIA 42
>2cxc_A NUSA; transcription termination, RNA binding protein, KH
domain, structural genomics, NPPSFA; 2.00A {Aeropyrum
pernix K1} PDB: 2cy1_A (A:76-144)
Length = 69
Score = 25.0 bits (55), Expect = 7.9
Identities = 10/53 (18%), Positives = 19/53 (35%), Gaps = 2/53 (3%)
Query: 39 IREYLQCHLKQAGVAKILI--ERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK 89
+ ++ + I + K I V G IGK G ++++ R
Sbjct: 3 LERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARL 55
>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} (A:)
Length = 97
Score = 25.2 bits (55), Expect = 8.0
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 4/46 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110
+ V IIG+KG I +IR + + I +
Sbjct: 20 SVTVDPKYHPKIIGRKGAVITQIRLE----HDVNIQFPDKDDGNQP 61
>1gvd_A MYB proto-oncogene protein; transcription, transcription
regulation, C-MYB, DNA binding, ION binding, nuclear
protein; 1.45A {Mus musculus} (A:)
Length = 52
Score = 25.1 bits (55), Expect = 8.5
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65
ED ++ + +Q + + + +AK L R K CR
Sbjct: 10 EDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCR 42
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2;
RNA binding protein, KH domain, KSRP,
posttranscriptional regulation, mRNA decay; NMR {Homo
sapiens} (A:1-81)
Length = 81
Score = 25.1 bits (55), Expect = 8.6
Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPK 108
I++ + + GL+IGK G I++++++ ++ L +
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQER----AGVKMILIQDGSQN 44
>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding
protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A
(A:1-51)
Length = 51
Score = 25.0 bits (55), Expect = 8.9
Identities = 8/33 (24%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65
EDLK+++ + + +++++I R + CR
Sbjct: 8 EDLKLQQLVMRYGAKDWIRISQLMITRNPRQCR 40
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded
DNA binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} (A:)
Length = 89
Score = 24.8 bits (54), Expect = 9.5
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102
++ + G IIGK G I++IR + + I +
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRH----ESGASIKID 50
>1hh2_P NUSA, N utilization substance protein A; transcription
regulation, termination; 2.1A {Thermotoga maritima}
(P:277-344)
Length = 68
Score = 25.0 bits (55), Expect = 9.6
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 39 IREYLQCHLKQAGVAKILI-ERTHKNCRIIVYSARPGLIIGKKGTDIEKIRK 89
++ + L A V ++ I ++ +K R++V + L IGK G + K
Sbjct: 3 PKQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAK 54
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian,
alpha-beta fold, DNA binding protein; 0.95A {Homo
sapiens} (A:)
Length = 82
Score = 24.8 bits (54), Expect = 9.6
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS 102
++ + G IIGK G I++IR + + I +
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRH----ESGASIKID 43
>1guu_A C-MYB, MYB proto-oncogene protein; transcription,
transcription regulation, DNA binding, ION bindi
proto-oncogene, nuclear protein, activator; 1.6A {Mus
musculus} (A:)
Length = 52
Score = 24.7 bits (54), Expect = 9.9
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 35 EDLKIREYLQCH--LKQAGVAKILIERTHKNCR 65
ED K+++ ++ + +A L RT C+
Sbjct: 10 EDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQ 42
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.320 0.134 0.387
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,698,725
Number of extensions: 73591
Number of successful extensions: 287
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 78
Length of query: 227
Length of database: 4,956,049
Length adjustment: 85
Effective length of query: 142
Effective length of database: 2,082,624
Effective search space: 295732608
Effective search space used: 295732608
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: 53 (24.3 bits)