RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4541
(309 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 = 2e-11
Identities = 31/139 (22%), Positives = 52/139 (37%), Gaps = 33/139 (23%)
Query: 186 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGIIV 243
I+ +RL+V DN + VI + + IGD V+ +K G++
Sbjct: 2 IQQESRLKVADNSG--------AREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVK 53
Query: 244 GVK-------------KHQKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEK 290
+ + + D N V+I D +P GTRI P+ LR
Sbjct: 54 KGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELR------ 107
Query: 291 TLSKGADYTKLLAIATTFI 309
D+ K++++A I
Sbjct: 108 ----DKDFMKIISLAPEVI 122
Score = 29.6 bits (66), Expect = 0.59
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 34 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKG 88
I+ +RL+V DN + VI + + IGD V+ +K G
Sbjct: 2 IQQESRLKVADNS--------GAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGG 50
Score = 29.6 bits (66), Expect = 0.59
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 110 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKG 164
I+ +RL+V DN + VI + + IGD V+ +K G
Sbjct: 2 IQQESRLKVADNS--------GAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGG 50
>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 = 55.4 bits (133), Expect = 6e-10
Identities = 25/139 (17%), Positives = 50/139 (35%), Gaps = 33/139 (23%)
Query: 186 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAI--YNQTHIGTIGDKVLVAIKGEKKKGIIV 243
I+ T L V DN + I + + T+GD ++ ++K +G +
Sbjct: 2 IQPQTYLEVADNTGA--------RKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVK 53
Query: 244 GVKKHQKPHIP-------------KTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEK 290
+ + + D N V+I++ P GTR+ P+ LR
Sbjct: 54 EGDVVKAVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELR------ 107
Query: 291 TLSKGADYTKLLAIATTFI 309
+ K++++A +
Sbjct: 108 ----EKGFMKIVSLAPEVL 122
Score = 26.5 bits (58), Expect = 6.7
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 34 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAI--YNQTHIGTIGDKVLVAIKGEKKKG 88
I+ T L V DN + I + + T+GD ++ ++K +G
Sbjct: 2 IQPQTYLEVADNTGA--------RKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRG 50
Score = 26.5 bits (58), Expect = 6.7
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 110 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAI--YNQTHIGTIGDKVLVAIKGEKKKG 164
I+ T L V DN + I + + T+GD ++ ++K +G
Sbjct: 2 IQPQTYLEVADNTGA--------RKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRG 50
>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 = 53.9 bits (129), Expect = 2e-09
Identities = 27/136 (19%), Positives = 50/136 (36%), Gaps = 34/136 (25%)
Query: 186 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGIIV 243
I+ T L V DN + I + +H +GD + + IK +G +
Sbjct: 2 IQEQTMLNVADNSGA--------RRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVK 53
Query: 244 GVK-------------KHQKPHIPKTDTNNVVLIDDSG-TPLGTRIHVPIPSMLRTILKE 289
+ + + D N VL++++ P+GTRI P+ LR
Sbjct: 54 KGDVLKAVVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELR----- 108
Query: 290 KTLSKGADYTKLLAIA 305
+ K++++A
Sbjct: 109 -----SEKFMKIISLA 119
Score = 27.3 bits (60), Expect = 3.3
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 10/80 (12%)
Query: 34 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGETP 91
I+ T L V DN + I + +H +GD + + IK +G+
Sbjct: 2 IQEQTMLNVADNSGA--------RRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVK 53
Query: 92 SALKLCSDLYHTTPCLHHIK 111
L + + T +
Sbjct: 54 KGDVLKAVVVRTKKGVRRPD 73
Score = 27.3 bits (60), Expect = 3.3
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 10/80 (12%)
Query: 110 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGETP 167
I+ T L V DN + I + +H +GD + + IK +G+
Sbjct: 2 IQEQTMLNVADNSGA--------RRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVK 53
Query: 168 SALKLCSDLYHTTPCLHHIK 187
L + + T +
Sbjct: 54 KGDVLKAVVVRTKKGVRRPD 73
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 121
Score = 52.3 bits (125), Expect = 5e-09
Identities = 32/139 (23%), Positives = 48/139 (34%), Gaps = 34/139 (24%)
Query: 186 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKGIIV 243
I+ T L V DN + I I ++ IGD ++ IK +
Sbjct: 2 IQPQTHLNVADNSGA--------RELMCIRIIGASNRRYARIGDVIVAVIKEAIPNTPLE 53
Query: 244 G-------------VKKHQKPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKEK 290
K I + D N V+ID G P GTRI I LR +K
Sbjct: 54 RSEVIRAVVVRTCKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFGAIARELR----QK 109
Query: 291 TLSKGADYTKLLAIATTFI 309
+ K++++A +
Sbjct: 110 -------FAKIVSLAPEVL 121
Score = 26.9 bits (59), Expect = 4.2
Identities = 13/57 (22%), Positives = 19/57 (33%), Gaps = 10/57 (17%)
Query: 34 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKG 88
I+ T L V DN + I I ++ IGD ++ IK
Sbjct: 2 IQPQTHLNVADNSGA--------RELMCIRIIGASNRRYARIGDVIVAVIKEAIPNT 50
Score = 26.9 bits (59), Expect = 4.2
Identities = 13/57 (22%), Positives = 19/57 (33%), Gaps = 10/57 (17%)
Query: 110 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTH--IGTIGDKVLVAIKGEKKKG 164
I+ T L V DN + I I ++ IGD ++ IK
Sbjct: 2 IQPQTHLNVADNSGA--------RELMCIRIIGASNRRYARIGDVIVAVIKEAIPNT 50
>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 = 51.3 bits (122), Expect = 2e-08
Identities = 18/140 (12%), Positives = 44/140 (31%), Gaps = 35/140 (25%)
Query: 186 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIY------NQTHIGTIGDKVLVAIK----- 234
+ + + DN + +IA+ N+ ++GD V+ +K
Sbjct: 17 LPVGAIMNCADNSG--------ARNLYIIAVKGSGSRLNRLPAASLGDMVMATVKKGKPE 68
Query: 235 --GEKKKGIIVGVKKHQKP---HIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKE 289
+ I+V K + + N V+ + G G+ I P+ +
Sbjct: 69 LRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKECADL--- 125
Query: 290 KTLSKGADYTKLLAIATTFI 309
+ ++ + + +
Sbjct: 126 --------WPRVASNSGVVV 137
>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 = 50.9 bits (121), Expect = 2e-08
Identities = 24/140 (17%), Positives = 56/140 (40%), Gaps = 35/140 (25%)
Query: 186 IKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIY------NQTHIGTIGDKVLVAIKG---E 236
++ + + DN + +VI+++ N+ +GDK+ V++ E
Sbjct: 12 LEKGSLITCADNTG--------ARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTPE 63
Query: 237 KKKGIIVGVKKHQKPHIP-------KTDTNNVVLIDDSGTPLGTRIHVPIPSMLRTILKE 289
++ ++ V Q+ I K + N V++D++ P GT + PI + +
Sbjct: 64 MRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREVA----Q 119
Query: 290 KTLSKGADYTKLLAIATTFI 309
+ + + + AT +
Sbjct: 120 R-------FGSVASAATMIV 132
>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 = 37.7 bits (87), Expect = 0.004
Identities = 27/144 (18%), Positives = 43/144 (29%), Gaps = 62/144 (43%)
Query: 34 IKLLTRLR------VVDNCEIGRQ--AMAEGKPPRVIAIYNQTHIGTIGDKVLVAIKGEK 85
++++ R V E+GR M P RV A ++Q + + ++V K
Sbjct: 1783 VEVV-FYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV------GK 1835
Query: 86 KKGETPSALKLCSDLYHTTPCLHHIKLLTRLRVV-DNCEIGRQAMAEGKPPRVIAIYNQT 144
+ G L +V N E +Q V A
Sbjct: 1836 RTGW------LVE-------------------IVNYNVE-NQQY--------VAA----- 1856
Query: 145 HIGTIGD-----KVLVAIKGEKKK 163
G + VL IK +K
Sbjct: 1857 --GDLRALDTVTNVLNFIKLQKID 1878
Score = 32.7 bits (74), Expect = 0.18
Identities = 22/111 (19%), Positives = 36/111 (32%), Gaps = 45/111 (40%)
Query: 161 KKKGETP-------------SALKLC-------SDLYHTTPCLHHIKLLTRLR------V 194
K KG P +AL L ++++ R
Sbjct: 1748 KSKGLIPADATFAGHSLGEYAAL-ASLADVMSIESL---------VEVV-FYRGMTMQVA 1796
Query: 195 VDNCEIGRQ--AMAEGKPPRVIAIYNQTHIGTIGDKVLVAIKGEKKKGIIV 243
V E+GR M P RV A ++Q + + ++V K+ G +V
Sbjct: 1797 VPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV------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 = 36.0 bits (82), Expect = 0.018
Identities = 34/316 (10%), Positives = 84/316 (26%), Gaps = 85/316 (26%)
Query: 19 KLCSDLYHTTPCLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQTHIGTIGDKVL 78
+L +D +++ +RL+ RQA+ E +P + + I G +
Sbjct: 118 RLYNDNQVFAK--YNV---SRLQPYLKL---RQALLELRPAKNVLIDGV---LGSGKTWV 166
Query: 79 VA------------------IK-GEKKKGETPSALKLCSDLYHTTPCLHHIKLLTRLRVV 119
+ E + L++ L + + +
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPE--TVLEMLQKLLYQIDPNWTSRSDHSSNIK 224
Query: 120 DNCEIGRQA----MAEGKPPRVIAI----YNQTHIGT--IGDKVLV---------AIKGE 160
+ + + + N + K+L+ +
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAA 284
Query: 161 KKKGETPSALKLCSDLYHTTPCLHHIKLLTRLRVVDNCEIGRQAMAEGKPPRVIAIYNQT 220
+ L H + L ++ + L +C + P V+ N
Sbjct: 285 TTTHIS---------LDHHSMTLTPDEVKSLLLKYLDCRP------QDLPREVLTT-NPR 328
Query: 221 HIGTIGDKV---------LVAIKGEKKKGIIVGVKKHQKPHIPKTDTNNVVLIDDSGTPL 271
+ I + + + +K II +P + + + + S
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS---- 384
Query: 272 GTRIHVPIPSMLRTIL 287
IP++L +++
Sbjct: 385 -----AHIPTILLSLI 395
Score = 33.3 bits (75), Expect = 0.10
Identities = 23/163 (14%), Positives = 52/163 (31%), Gaps = 28/163 (17%)
Query: 84 EKKKGETPSALKLCSDLYHTTPC----LHHIKLLTRLRVVDNCEIGRQAMAEGKPP-RVI 138
E P L + ++ H+ ++++ + AE + +
Sbjct: 321 EVLTT-NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS-LNVLEPAEYRKMFDRL 378
Query: 139 AIYNQ-THIGTIGDKVLVAIKGEKKKGETPSALKLCS-------DLYHTTPCLHHIKLLT 190
+++ HI T +L I + K + + +T + I L
Sbjct: 379 SVFPPSAHIPT---ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLEL 435
Query: 191 RL----------RVVDNCEIGRQAMAEGKPPRVIAIYNQTHIG 223
++ +VD+ I + ++ P + Y +HIG
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG 478
Score = 32.9 bits (74), Expect = 0.14
Identities = 30/221 (13%), Positives = 67/221 (30%), Gaps = 44/221 (19%)
Query: 15 PSALKLCSDLYHTTPC----LHHIKLLTRLRVVDNCEIGRQAMAEGKPP-RVIAIYNQ-T 68
P L + ++ H+ ++++ + AE + ++++
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS-LNVLEPAEYRKMFDRLSVFPPSA 385
Query: 69 HIGTIGDKVLVAIKGEKKKGETPSALKLCS-------DLYHTTPCLHHIKLLTRL----- 116
HI T +L I + K + + +T + I L ++
Sbjct: 386 HIPT---ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 117 -----RVVDNCEIGRQAMAEGKPPRVIAIYNQTHIGTIGDKVLVAIKGEKKKGETPSAL- 170
+VD+ I + ++ P + Y +HIG L I+ ++
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG----HHLKNIEHPERMTLFRMVFL 498
Query: 171 -------KLCSDLYHTTPCLHHIKLLTRLR-----VVDNCE 199
K+ D + L +L+ + DN
Sbjct: 499 DFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDP 539
Score = 31.7 bits (71), Expect = 0.36
Identities = 21/139 (15%), Positives = 41/139 (29%), Gaps = 36/139 (25%)
Query: 8 KSLLSRTPSALKLCSDLYHTTPCLHHIKLLTRL----------RVVDNCEIGRQAMAEGK 57
SL+ + P + I L ++ +VD+ I + ++
Sbjct: 414 YSLVEKQP-----KESTIS----IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDL 464
Query: 58 PPRVIAIYNQTHIGTIGDKVLVAIKGEKKKGETPSAL--------KLCSDLYHTTPCLHH 109
P + Y +HIG L I+ ++ K+ D
Sbjct: 465 IPPYLDQYFYSHIG----HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSI 520
Query: 110 IKLLTRLR-----VVDNCE 123
+ L +L+ + DN
Sbjct: 521 LNTLQQLKFYKPYICDNDP 539
>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 = 27.9 bits (63), Expect = 5.7
Identities = 9/77 (11%), Positives = 22/77 (28%), Gaps = 17/77 (22%)
Query: 226 GDKVLVAIKGEKKK--GIIVGVKKHQKPHIP----KTDTNNVVLIDDSGTPLGTRIHVPI 279
GD+++ I EK++ + + + ++ D + I
Sbjct: 57 GDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHP------LLKDAI 110
Query: 280 PSMLRTILKEKTLSKGA 296
P + L+
Sbjct: 111 P-----CRAARGLNHEF 122
>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 = 26.8 bits (58), Expect = 5.9
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 6/27 (22%)
Query: 5 KNVKSLLSRTPSALKLCSDLYHTTPCL 31
+ +K L ++LKL +D + P L
Sbjct: 20 QALKKL----QASLKLYAD--DSAPAL 40
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
0.320 0.137 0.405
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: 4,784,664
Number of extensions: 300137
Number of successful extensions: 553
Number of sequences better than 10.0: 1
Number of HSP's gapped: 546
Number of HSP's successfully gapped: 37
Length of query: 309
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 216
Effective length of database: 4,105,140
Effective search space: 886710240
Effective search space used: 886710240
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: 57 (25.6 bits)