RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2143
(149 letters)
>3iz6_R 40S ribosomal protein S15 (S19P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
2zkq_s 1s1h_S 3jyv_S*
Length = 154
Score = 166 bits (423), Expect = 4e-54
Identities = 80/111 (72%), Positives = 92/111 (82%)
Query: 39 NFSTVEETQKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIKRKPMALV 98
Q KKRTFRK+++RGVDLD LLDM T+ L++L RARRRF RG+KRKPMAL+
Sbjct: 7 ETEVAAGAQPKKRTFRKYSYRGVDLDALLDMSTDDLVQLFPARARRRFQRGLKRKPMALI 66
Query: 99 KKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVEIK 149
KKLRKAKK+AP EKPE V+THLRNMIIVPEM+GS+VGVYNGKTFNQVEIK
Sbjct: 67 KKLRKAKKDAPAGEKPEPVRTHLRNMIIVPEMIGSIVGVYNGKTFNQVEIK 117
>3u5c_P 40S ribosomal protein S15; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_R 3o30_I 3o2z_I 3u5g_P 1s1h_S 3jyv_S*
Length = 142
Score = 165 bits (419), Expect = 1e-53
Identities = 64/106 (60%), Positives = 80/106 (75%)
Query: 44 EETQKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIKRKPMALVKKLRK 103
+ KKR F+ ++RGVDL++LL+M TE ++L R RRRFARG+ KP +KKLR
Sbjct: 3 QAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRA 62
Query: 104 AKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVEIK 149
AK AP NEKP V+TH+RNMIIVPEM+GSVVG+YNGK FNQVEI+
Sbjct: 63 AKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIR 108
>2xzm_S RPS15E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_S 3j0o_S 3j0l_S 3j0p_S 3j0q_S
Length = 144
Score = 150 bits (381), Expect = 6e-48
Identities = 48/112 (42%), Positives = 69/112 (61%), Gaps = 9/112 (8%)
Query: 47 QKKKRTFRKFTFRGVDLDQLLDMP---------TEQLMELMHCRARRRFARGIKRKPMAL 97
K++ +KFTFRG L++L + +++L L + RRR RGI K
Sbjct: 2 ADNKKSIKKFTFRGKGLEELTALASGSNSEKLISDELAALFDAKTRRRVKRGISEKYAKF 61
Query: 98 VKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTFNQVEIK 149
V K+R++K++ P EKP VKTH R+MI++PE+VG +VGVYNGK F VE+K
Sbjct: 62 VNKVRRSKEKCPAGEKPVPVKTHYRSMIVIPELVGGIVGVYNGKEFVNVEVK 113
>3bbn_S Ribosomal protein S19; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 92
Score = 43.3 bits (103), Expect = 1e-06
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 87 ARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
R +K+ P LRK +K EK E++ T R I+P M+G + ++NG+
Sbjct: 2 TRSLKKNPFVANHLLRKIEKLNKKAEK-EIIVTWSRASTIIPTMIGHTIAIHNGREH 57
>3i1m_S 30S ribosomal protein S19; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_S* 3e1a_L 3e1c_L 1vs5_S 3i1o_S
3i1q_S 3i1s_S 3i1z_S 3i21_S 3izv_W* 3izw_W* 3kc4_S
3or9_S 3ora_S 3sfs_S* 3uoq_S* 2qal_S* 1p6g_S 1p87_S
2aw7_S ...
Length = 92
Score = 43.3 bits (103), Expect = 1e-06
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 87 ARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
R +K+ P + L+K +K +K + ++T R I P M+G + V+NG+
Sbjct: 2 PRSLKKGPFIDLHLLKKVEKAVESGDK-KPLRTWSRRSTIFPNMIGLTIAVHNGRQH 57
>3a1p_B 30S ribosomal protein S19; RIMM N-terminal domain, PRC-barrel
domain, beta barrels, ribosome, 30S ribosomal subunit,
ribosome biogenesis; 2.30A {Thermus thermophilus} PDB:
1fka_S 1gix_V* 1hnw_S* 1hnx_S* 1hnz_S* 1hr0_S 1ibk_S*
1ibl_S* 1ibm_S 1jgo_V* 1jgp_V* 1jgq_V* 1ml5_V* 1xmo_S*
1xmq_S* 1xnq_S* 1xnr_S* 1yl4_V 2b64_S* 2b9m_S* ...
Length = 93
Score = 42.9 bits (102), Expect = 1e-06
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 87 ARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
R +K+ L K + EK ++KT R IVPEMVG + VYNGK
Sbjct: 2 PRSLKKGVFVDDHLLEKVLELNAKGEK-RLIKTWSRRSTIVPEMVGHTIAVYNGKQH 57
>3r8n_S 30S ribosomal protein S19; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_S 3fih_S* 2wwl_S 3oar_S
3oaq_S 3ofb_S 3ofa_S 3ofp_S 3ofx_S 3ofy_S 3ofo_S 3r8o_S
4a2i_S 2gy9_S 2gyb_S
Length = 79
Score = 42.5 bits (101), Expect = 2e-06
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 88 RGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNGKTF 143
R +K+ P + L+K +K +K + ++T R I P M+G + V+NG+
Sbjct: 1 RSLKKGPFIDLHLLKKVEKAVESGDK-KPLRTWSRRSTIFPNMIGLTIAVHNGRQH 55
>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 = 39.1 bits (90), Expect = 3e-04
Identities = 23/122 (18%), Positives = 39/122 (31%), Gaps = 32/122 (26%)
Query: 27 DIYNDRGEYRTRNFSTVEETQKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRAR--- 83
+ E + F VEE + F + P+ + R R
Sbjct: 69 WTLLSKQEEMVQKF--VEEVLRINYKFLMSPIKTEQRQ-----PSMMTRMYIEQRDRLYN 121
Query: 84 --RRFARG-IKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVPEMVGSVVGVYNG 140
+ FA+ + R KLR+A E P + +++ ++GS G
Sbjct: 122 DNQVFAKYNVSRLQP--YLKLRQALLELRPAKN-----------VLIDGVLGS------G 162
Query: 141 KT 142
KT
Sbjct: 163 KT 164
Score = 35.2 bits (80), Expect = 0.006
Identities = 17/128 (13%), Positives = 34/128 (26%), Gaps = 19/128 (14%)
Query: 16 RC-FLGTVNRNTDIYNDRGEYRTRNFSTVEE----TQKKKRT-FRKFTFRGVDLDQLLDM 69
C L T R + + T + S T + ++ K+ L
Sbjct: 265 SCKILLT-TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL--DCRPQDL--- 318
Query: 70 PTE------QLMELMHCRARRRFARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRN 123
P E + + ++ R A KL + + +P +
Sbjct: 319 PREVLTTNPRRLSIIAESIRDGLAT-WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Query: 124 MIIVPEMV 131
+ + P
Sbjct: 378 LSVFPPSA 385
>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 = 33.1 bits (75), Expect = 0.030
Identities = 17/94 (18%), Positives = 29/94 (30%), Gaps = 33/94 (35%)
Query: 59 RGVDLDQLLDM--------PTEQLMEL-MHCRARRRF--ARGIKRKPMAL---VKKLRKA 104
+ +Q+ D P + +E+ + + + G P +L LRKA
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVEISLVN-GAKNLVVS-G---PPQSLYGLNLTLRKA 396
Query: 105 KKEAPPN----------EKPEVVKTHLRNMIIVP 128
K AP K + L + P
Sbjct: 397 K--APSGLDQSRIPFSERKLKFSNRFLP--VASP 426
Score = 30.4 bits (68), Expect = 0.23
Identities = 35/223 (15%), Positives = 65/223 (29%), Gaps = 90/223 (40%)
Query: 2 TESSLSSKSSAVVPRCFL-----GTVN------RNTDIYNDRGEYRT-------RNFSTV 43
+ S+L + G + R D+Y Y + T+
Sbjct: 141 SNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELR--DLYQT---YHVLVGDLIKFSAETL 195
Query: 44 EETQKKKRTFRKFTFRGVDLDQLLD-----------------MPTEQLMELMH----CRA 82
E + K +G+++ + L+ P +++L H +
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL 255
Query: 83 --------RRRF------ARGIKRKPMALV-----------KKLRKAKK----------E 107
R ++G+ A+ +RKA E
Sbjct: 256 LGFTPGELRSYLKGATGHSQGL---VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYE 312
Query: 108 APPNE--KPEVVKTHLRNMIIVPE-MVGSVVGVYNGKTFNQVE 147
A PN P +++ L N VP M+ S+ + T QV+
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPML-SISNL----TQEQVQ 350
Score = 30.0 bits (67), Expect = 0.28
Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 31/89 (34%)
Query: 69 MPTEQLMELMHCRARRRFARGIKRKPMALVKKLRKAKKEAPPNEKPEVVKTHLRNMIIVP 128
M E L+E++ F RG + A P + E+ +++ + I P
Sbjct: 1777 MSIESLVEVV-------FYRG-------------MTMQVAVPRD--ELGRSNYGMIAINP 1814
Query: 129 ---------EMVGSVVGVYNGKTFNQVEI 148
E + VV +T VEI
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVEI 1843
>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 = 28.4 bits (62), Expect = 0.69
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 98 VKKLRKAKKEAPPNEKP 114
+KKL+ + K + P
Sbjct: 22 LKKLQASLKLYADDSAP 38
>3ue3_A Septum formation, penicillin binding protein 3, peptidoglycan
synthetase; transpeptidase, transferase; 2.30A
{Acinetobacter}
Length = 554
Score = 28.4 bits (64), Expect = 0.83
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 63 LDQLLDMPTEQLMELMHCRARRRFARGIKRK-PMALVKKLRKAK 105
L ++ M + L + M RAR R+ ++R+ P + +
Sbjct: 85 LADVVGMDRKTLKKHMTDRARSRYLV-LQREVPPQQADLILQHN 127
>3tad_C Liprin-beta-1; protein binding; 2.90A {Mus musculus}
Length = 265
Score = 28.3 bits (62), Expect = 1.1
Identities = 19/133 (14%), Positives = 40/133 (30%), Gaps = 9/133 (6%)
Query: 1 MTESSLSS----KSSAVVPRCFLGTVNRNTDIYNDRGEYRTRNFSTVEETQKKKRTFRKF 56
++ L K S + L ++ + G+ + + + +F
Sbjct: 52 ASQQDLEKELGIKHSLHRKKLQLALQALGSEEETNYGKLDFNWVTRWLDDIGLPQYKTQF 111
Query: 57 TFRGVDLDQLLDMPTEQLMEL-----MHCRARRRFARGIKRKPMALVKKLRKAKKEAPPN 111
VD L M + L+ L +H + +R + ++ R+ E
Sbjct: 112 DEGRVDGRMLHYMTVDDLLSLKVVSVLHHLSIKRAIQVLRINNFEPNCLRRRPSDENSIT 171
Query: 112 EKPEVVKTHLRNM 124
T+ R M
Sbjct: 172 PSEVQQWTNHRVM 184
>2f3n_A SH3 and multiple ankyrin repeat domains 3; postsynaptic density,
SAM domain, shank, scaffolding protein, structural
protein; 2.10A {Rattus norvegicus} SCOP: a.60.1.2 PDB:
2f44_A
Length = 76
Score = 26.2 bits (58), Expect = 1.5
Identities = 7/40 (17%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 55 KFTFRGVDLDQLLDMPTEQLMEL--MHCRARRRFARGIKR 92
+F ++ L + E +EL R R +++
Sbjct: 25 RFEDHEIEGAHLPALTKEDFVELGVTRVGHRENIERALRQ 64
>1pqw_A Polyketide synthase; rossmann fold, dimer, structural genomics,
PSI, protein STRU initiative; 2.66A {Mycobacterium
tuberculosis} SCOP: c.2.1.1
Length = 198
Score = 27.2 bits (61), Expect = 1.7
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 51 RTFRK-FTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGI 90
K +F VDLD L + + +L+ + A G
Sbjct: 150 AALAKSASFSVVDLDLNLKLQPARYRQLLQ-HILQHVADGK 189
>3pbt_A Penicillin-binding protein 3; PBP3, hydrolase-antibiotic complex;
HET: UE1; 1.64A {Pseudomonas aeruginosa} PDB: 3pbn_A*
3pbo_A* 3pbr_A* 3pbs_A* 3pbq_A* 3oc2_A 3ocl_A* 3ocn_A*
Length = 538
Score = 27.6 bits (62), Expect = 1.7
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 63 LDQLLDMPTEQLMELMHCRARRRFARGIKRK-PMALVKKLRKAK 105
L L T+ + + A R F + R + + K
Sbjct: 58 LAAALGQDTKLFADRIEQNAEREFIY-LVRGLTPEQGEGVIALK 100
>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP
phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium
tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A*
1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A*
1w2h_A*
Length = 214
Score = 27.3 bits (61), Expect = 1.8
Identities = 11/57 (19%), Positives = 17/57 (29%), Gaps = 7/57 (12%)
Query: 62 DLDQLLDMPTEQLMELMHCRARRRFARGIKR--KPMALVKKLRK-----AKKEAPPN 111
D LL + E E RA+R R + L ++ A +
Sbjct: 134 DWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAAQGWGGR 190
>2ke7_A Ankyrin repeat and sterIle alpha motif domain- containing protein
1B; SAM domain, alternative splicing, ANK repeat, cell
junction, cell membrane; NMR {Homo sapiens}
Length = 103
Score = 26.4 bits (58), Expect = 2.2
Identities = 11/73 (15%), Positives = 21/73 (28%), Gaps = 16/73 (21%)
Query: 50 KRTFRKFTFRGVDLDQLLDMPTEQLMELMHCRARRRFARGIK-----RKPMALVKKLRKA 104
+ F V M + L+E+ GI ++ + ++ L K
Sbjct: 38 ENHLMANGFDNVQFMGSNVMEDQDLLEI-----------GILNSGHRQRILQAIQLLPKM 86
Query: 105 KKEAPPNEKPEVV 117
+ P V
Sbjct: 87 RPIGHDGYHPTSV 99
>2gle_A Neurabin-1; SAM domain, scaffold, protein protein interaction,
protein binding; NMR {Rattus norvegicus}
Length = 74
Score = 25.8 bits (57), Expect = 2.6
Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 55 KFTFRGVDLDQLLDMPTEQLMEL--MHCRARRRFARGIKR 92
+F+ + + +QLL + +L L + R + +K
Sbjct: 27 EFSAQNISGEQLLQLDGNKLKALGMTSSQDRALVKKKLKE 66
>2xki_A Neural hemoglobin; oxygen storage, metal-binding; HET: HEM SO4;
1.30A {Cerebratulus lacteus} PDB: 1kr7_A* 1v07_A*
2xkg_A* 2xkh_A* 2vyz_A* 2vyy_A*
Length = 110
Score = 26.2 bits (57), Expect = 3.1
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 54 RKFTFRGVDLDQLLD 68
KF F+GV L L
Sbjct: 24 NKFGFKGVALGSLKG 38
>2i6l_A Mitogen-activated protein kinase 6; MAPK6, ERK3, extracellular
signal regulated kinase 3, serine phosphorylation,
threonine phosphorylation; 2.25A {Homo sapiens}
Length = 320
Score = 26.5 bits (59), Expect = 4.0
Identities = 10/62 (16%), Positives = 20/62 (32%), Gaps = 7/62 (11%)
Query: 54 RKFTFRGVD-LDQL------LDMPTEQLMELMHCRARRRFARGIKRKPMALVKKLRKAKK 106
K F G L+Q+ + + E+ + + + L + L +
Sbjct: 221 GKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISR 280
Query: 107 EA 108
EA
Sbjct: 281 EA 282
>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding,
DNA-binding nucleotide-binding, transcription,
transcription regulation; HET: CMP; 1.66A {Escherichia
coli}
Length = 260
Score = 25.4 bits (56), Expect = 9.1
Identities = 9/80 (11%), Positives = 19/80 (23%), Gaps = 10/80 (12%)
Query: 10 SSAVVPRCFLGTVNRNTDIYNDRGEYRTRNFSTVEETQKKKRTFRKFTFRGVDLDQLLDM 69
SS +VPR G+ + T ++ ++ K
Sbjct: 8 SSGLVPR---GSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSMVL-------GKPQ 57
Query: 70 PTEQLMELMHCRARRRFARG 89
L + ++
Sbjct: 58 TDPTLEWFLSHCHIHKYPSK 77
>3se5_A Cell filamentation protein FIC-related protein; ampylation,
adenylylation, transferase; HET: ANP P6G; 1.70A
{Neisseria meningitidis}
Length = 164
Score = 25.1 bits (54), Expect = 9.6
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 6/53 (11%)
Query: 27 DIYNDRGEYRTRNFSTVEETQKKKRTFRKFTFRGVDLDQLLDMPTEQLMELMH 79
+Y+ G+ R N S K F + L ++ MP E++
Sbjct: 49 GLYDFAGQIREDNIS------KGGFRFANAMYLKEALVKIEQMPERTFEEIIA 95
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 0.133 0.375
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,208,660
Number of extensions: 125752
Number of successful extensions: 336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 334
Number of HSP's successfully gapped: 32
Length of query: 149
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 64
Effective length of database: 4,328,508
Effective search space: 277024512
Effective search space used: 277024512
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 (24.1 bits)