RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4063
(205 letters)
>1whi_A Ribosomal protein L14; rRNA-binding; 1.50A {Geobacillus
stearothermophilus} SCOP: b.39.1.1 PDB: 1giy_N 1ml5_n*
1c04_D 1yl3_N 2b66_O 2b9n_O 2b9p_O 487d_M
Length = 122
Score = 59.3 bits (143), Expect = 8e-12
Identities = 27/114 (23%), Positives = 43/114 (37%), Gaps = 23/114 (20%)
Query: 35 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGIIV 92
I+ +RL+V DN + VI + + IGD V+ +K G++
Sbjct: 2 IQQESRLKVADNSG--------AREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVK 53
Query: 93 GVK-------------KHQKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 133
+ + + D N V+I D +P GTRI P+ LR
Sbjct: 54 KGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELR 107
>3v2d_O 50S ribosomal protein L14; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2j03_O 2jl6_O 2jl8_O 2v47_O 2v49_O 2wdi_O 2wdj_O 2wdl_O
2wdn_O 2wh2_O 2wh4_O 2wrj_O 2wrl_O 2wro_O 2wrr_O 2x9s_O
2x9u_O 2xg0_O 2xg2_O 2xqe_O ...
Length = 122
Score = 56.6 bits (136), Expect = 6e-11
Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 23/114 (20%)
Query: 35 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAI--YNQTHIGTIGDKVLVAIKGEKKKGIIV 92
I+ T L V DN + I + + T+GD ++ ++K +G +
Sbjct: 2 IQPQTYLEVADNTGA--------RKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVK 53
Query: 93 GVKKHQKPHIP-------------KTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 133
+ + + D N V+I++ P GTR+ P+ LR
Sbjct: 54 EGDVVKAVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELR 107
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 121
Score = 54.7 bits (131), Expect = 3e-10
Identities = 29/114 (25%), Positives = 38/114 (33%), Gaps = 23/114 (20%)
Query: 35 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGIIV 92
I+ T L V DN + I I ++ IGD ++ IK +
Sbjct: 2 IQPQTHLNVADNSGA--------RELMCIRIIGASNRRYARIGDVIVAVIKEAIPNTPLE 53
Query: 93 G-------------VKKHQKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 133
K I + D N V+ID G P GTRI I LR
Sbjct: 54 RSEVIRAVVVRTCKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFGAIARELR 107
>3r8s_K 50S ribosomal protein L14; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3oat_K* 3oas_K* 3ofd_K 3ofc_K 3ofr_K* 3ofz_K* 3og0_K
3ofq_K 3r8t_K 3i1n_K 1p85_I 1p86_I 1vs8_K 1vs6_K 2aw4_K
2awb_K 1vt2_K 2i2v_K 2i2t_K* 2qao_K* ...
Length = 122
Score = 54.3 bits (130), Expect = 5e-10
Identities = 25/115 (21%), Positives = 43/115 (37%), Gaps = 24/115 (20%)
Query: 35 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGIIV 92
I+ T L V DN + I + +H +GD + + IK +G +
Sbjct: 2 IQEQTMLNVADNSGA--------RRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVK 53
Query: 93 GVK-------------KHQKPHIPKTDTNNVVLIDDSG-TPLGTRIHVPIPSMLR 133
+ + + D N VL++++ P+GTRI P+ LR
Sbjct: 54 KGDVLKAVVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELR 108
>1vq8_K 50S ribosomal protein L14P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: b.39.1.1 PDB: 1vq4_K*
1vq5_K* 1vq6_K* 1vq7_K* 1s72_K* 1vq9_K* 1vqk_K* 1vql_K*
1vqm_K* 1vqn_K* 1vqo_K* 1vqp_K* 1yhq_K* 1yi2_K* 1yij_K*
1yit_K* 1yj9_K* 1yjn_K* 1yjw_K* 2otj_K* ...
Length = 132
Score = 53.2 bits (127), Expect = 1e-09
Identities = 22/115 (19%), Positives = 48/115 (41%), Gaps = 24/115 (20%)
Query: 35 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIY------NQTHIGTIGDKVLVAIKG---E 85
++ + + DN + +VI+++ N+ +GDK+ V++ E
Sbjct: 12 LEKGSLITCADNTG--------ARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTPE 63
Query: 86 KKKGIIVGVKKHQKPHIP-------KTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 133
++ ++ V Q+ I K + N V++D++ P GT + PI +
Sbjct: 64 MRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREVA 118
>3u5e_V L17A, YL32, 60S ribosomal protein L23-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_M
1s1i_R 3izs_M* 3j16_I 3o5h_U 3o58_U 3u5i_V 2x7n_C 3jyw_R
2zkr_k 3iz5_M 3izr_M 4a17_J 4a1a_J 4a1c_J 4a1e_J
Length = 137
Score = 53.2 bits (127), Expect = 2e-09
Identities = 18/115 (15%), Positives = 37/115 (32%), Gaps = 24/115 (20%)
Query: 35 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIY------NQTHIGTIGDKVLVAIK----- 83
+ + + DN + +IA+ N+ ++GD V+ +K
Sbjct: 17 LPVGAIMNCADNSG--------ARNLYIIAVKGSGSRLNRLPAASLGDMVMATVKKGKPE 68
Query: 84 --GEKKKGIIVGVKKHQKP---HIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 133
+ I+V K + + N V+ + G G+ I P+
Sbjct: 69 LRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKECA 123
>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 = 34.3 bits (78), Expect = 0.026
Identities = 36/223 (16%), Positives = 63/223 (28%), Gaps = 93/223 (41%)
Query: 9 HPSYQTTPSALKLCSDLYHTTPCLHHIKLLTRLRVVDNCEIGRQAMAEGKP-PRVIAIYN 67
+P+ PS L+ D+ E EG P P
Sbjct: 314 YPNTSLPPSILE------------------------DSLENN-----EGVPSP------- 337
Query: 68 QTHIGTIGDKVLVAIKGEKKKGIIVGVKKHQKPHIPKTDTNNVVLIDDSGTPLGTRIHV- 126
+++I ++ + V K H+P + L++ G + V
Sbjct: 338 -----------MLSISNLTQEQVQDYVNKTNS-HLPAGKQVEISLVN------GAKNLVV 379
Query: 127 --PIPSM--LRTILKEKTLSKGADYTNTLNSINNISMNVAKLLKFSRC-----SPLHFSP 177
P S+ L L++ G D + S + LKFS SP H S
Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS--------ERKLKFSNRFLPVASPFH-SH 430
Query: 178 ------------------SYSHSSFRLQ-HATGTSSNPQEADK 201
S++ ++ + T S+ +
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSG 473
Score = 30.8 bits (69), Expect = 0.31
Identities = 20/106 (18%), Positives = 34/106 (32%), Gaps = 45/106 (42%)
Query: 2 EYYEWKDHPSYQTTPSALKLC-------SDLYHTTPCLHHIKLLTRLR------VVDNCE 48
EY +AL L ++++ R V E
Sbjct: 1766 EY-------------AAL-ASLADVMSIESL---------VEVV-FYRGMTMQVAVPRDE 1801
Query: 49 IGRQ--AMAEGKPPRVIAIYNQTHIGTIGDKVLVAIKGEKKKGIIV 92
+GR M P RV A ++Q + + ++V K+ G +V
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEALQYVVERV------GKRTGWLV 1841
>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 = 30.6 bits (68), Expect = 0.40
Identities = 22/223 (9%), Positives = 55/223 (24%), Gaps = 61/223 (27%)
Query: 6 WKDHPSYQTTPSALKLCSDLYHTTPCLHHIKLLTRLRVVDNCEIGRQA----MAEGKPPR 61
W + + + + L++ L + + + + +
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245
Query: 62 VIAI----YNQTHIGT--IGDKVLVAIKGEKKKGIIVGVKKHQKPHIPKTDTNNVVLIDD 115
+ + N + K+L+ T T + D
Sbjct: 246 CLLVLLNVQNAKAWNAFNLSCKILL------------------------T-TRFKQVTDF 280
Query: 116 SGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINNISMNVAKL-LKFSRCSPLH 174
T H+ + T+ ++ S Y + L + +P
Sbjct: 281 LSA--ATTTHISLDHHSMTLTPDEVKSLLLKYLD---------CRPQDLPREVLTTNPRR 329
Query: 175 FS---------PS----YSHSSF-RLQHATGTSSNPQEADKFQ 203
S + + H + +L +S N E +++
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Score = 27.9 bits (61), Expect = 2.8
Identities = 15/83 (18%), Positives = 26/83 (31%), Gaps = 16/83 (19%)
Query: 6 WKDHPSYQTTPSALKLCS------DLYHTTPCLHHIKLLTRL----------RVVDNCEI 49
W D KL +T + I L ++ +VD+ I
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNI 455
Query: 50 GRQAMAEGKPPRVIAIYNQTHIG 72
+ ++ P + Y +HIG
Sbjct: 456 PKTFDSDDLIPPYLDQYFYSHIG 478
Score = 27.9 bits (61), Expect = 3.3
Identities = 24/193 (12%), Positives = 58/193 (30%), Gaps = 61/193 (31%)
Query: 59 PPRVIAIYNQTHIGTIGDKV---------LVAIKGEKKKGIIVGVKKHQKPHIPKTDTNN 109
P V+ N + I + + + +K II +P + +
Sbjct: 319 PREVLTT-NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Query: 110 VVLIDDSGTPLGTRIHVPIPSML-------------RTILKE---KTLSK--GADYTNTL 151
+ + S IP++L ++ + +L + + T ++
Sbjct: 378 LSVFPPS---------AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428
Query: 152 NSI---------NNISMNVAKLL---KFSRCSPL-HFSP------SYSHSSFRLQHATGT 192
SI N +++ ++ + P YSH L++
Sbjct: 429 PSIYLELKVKLENEYALH-RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI--- 484
Query: 193 SSNPQEADKFQVL 205
+P+ F+++
Sbjct: 485 -EHPERMTLFRMV 496
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 28.7 bits (65), Expect = 1.5
Identities = 9/77 (11%), Positives = 22/77 (28%), Gaps = 17/77 (22%)
Query: 75 GDKVLVAIKGEKKK--GIIVGVKKHQKPHIP----KTDTNNVVLIDDSGTPLGTRIHVPI 128
GD+++ I EK++ + + + ++ D + I
Sbjct: 57 GDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHP------LLKDAI 110
Query: 129 PSMLRTILKEKTLSKGA 145
P + L+
Sbjct: 111 P-----CRAARGLNHEF 122
>1aoz_A Ascorbate oxidase; oxidoreductase(oxygen acceptor); HET: NAG; 1.90A
{Cucurbita pepo var} SCOP: b.6.1.3 b.6.1.3 b.6.1.3 PDB:
1aso_A* 1asp_A* 1asq_A*
Length = 552
Score = 27.3 bits (61), Expect = 4.2
Identities = 10/63 (15%), Positives = 18/63 (28%), Gaps = 4/63 (6%)
Query: 98 QKPHIPK-TDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEKTLSKGADYTNTLNSINN 156
P P D + T P+ R L ++ +IN+
Sbjct: 310 PPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFL---LNTQNVINGYVKWAIND 366
Query: 157 ISM 159
+S+
Sbjct: 367 VSL 369
>1ufb_A TT1696 protein; structural genomics, riken structural
genomics/proteomics initiative, RSGI, unknown function;
1.90A {Thermus thermophilus} SCOP: a.24.16.3
Length = 127
Score = 26.4 bits (57), Expect = 4.5
Identities = 9/41 (21%), Positives = 12/41 (29%)
Query: 1 MEYYEWKDHPSYQTTPSALKLCSDLYHTTPCLHHIKLLTRL 41
+ Y W + Q +ALK H I L
Sbjct: 24 LGDYAWACFAAQQAAEAALKGLHLARGQVAWGHSILDLLAD 64
>3u7q_A Nitrogenase molybdenum-iron protein alpha chain; multiple rossmann
fold domains, reductase, nitrogen fixing,
oxidoreductase; HET: HCA ICS 1CL CLF; 1.00A {Azotobacter
vinelandii} PDB: 1g21_A* 1g20_A* 1fp4_A* 1m1n_A* 1l5h_A*
1m1y_A* 1m34_A* 1n2c_A* 2afh_A* 2afi_A* 2afk_A* 2min_A*
3min_A* 3k1a_A* 1h1l_A* 1qgu_A* 1qh1_A* 1qh8_A*
Length = 492
Score = 27.1 bits (60), Expect = 4.7
Identities = 7/43 (16%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 51 RQAMAEGKPPRVIAIYNQTHIGTIGDKVL-VAIKGEKKKGIIV 92
+ + I++ ++ IG IGD + V+ + +
Sbjct: 136 DEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTI 178
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 0.133 0.395
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,099,558
Number of extensions: 177720
Number of successful extensions: 401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 395
Number of HSP's successfully gapped: 24
Length of query: 205
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 116
Effective length of database: 4,216,824
Effective search space: 489151584
Effective search space used: 489151584
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 (24.9 bits)