RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6264
(120 letters)
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus}
Length = 148
Score = 98.8 bits (247), Expect = 6e-28
Identities = 40/87 (45%), Positives = 59/87 (67%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+RHIA G +W+++ Y HTGYPGG A QLH DP ++K A+ LP++L +
Sbjct: 61 NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT 120
Query: 62 LMARLHIFPDQEVPEDLLKNVSSQIRQ 88
+M RLH+FPD+ +PED+LKN+ ++ Q
Sbjct: 121 MMERLHLFPDEYIPEDILKNLVEELPQ 147
>3v2d_N 50S ribosomal protein L13; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N
2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 2wrj_N 2wrl_N
2wro_N 2wrr_N 2x9s_N 2x9u_N ...
Length = 140
Score = 58.7 bits (143), Expect = 2e-12
Identities = 20/74 (27%), Positives = 39/74 (52%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ I + G + +++ Y ++GYPGG+ ++ P V++ AV+ LP+ + R
Sbjct: 56 NADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRR 115
Query: 62 LMARLHIFPDQEVP 75
L RL ++ + P
Sbjct: 116 LFKRLKVYAGPDHP 129
>3r8s_J 50S ribosomal protein L13; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H
1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J
2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ...
Length = 142
Score = 58.3 bits (142), Expect = 3e-12
Identities = 18/74 (24%), Positives = 37/74 (50%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ +A+ G + + Y+HHTG+ GG+ ++ P V++ AV+ LP+ +
Sbjct: 58 NADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRA 117
Query: 62 LMARLHIFPDQEVP 75
+ +L ++ E
Sbjct: 118 MFRKLKVYAGNEHN 131
>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H*
1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 3pio_G*
3pip_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K
Length = 174
Score = 58.4 bits (142), Expect = 5e-12
Identities = 20/74 (27%), Positives = 34/74 (45%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ +AL G + + Y +TGY GG+ A + P V++ AV LP+
Sbjct: 84 NAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRA 143
Query: 62 LMARLHIFPDQEVP 75
+ RL ++ + P
Sbjct: 144 MHTRLKVYAGETHP 157
>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A
{Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N
Length = 163
Score = 58.0 bits (141), Expect = 6e-12
Identities = 20/74 (27%), Positives = 39/74 (52%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ I + G + +++ Y ++GYPGG+ ++ P V++ AV+ LP+ + R
Sbjct: 79 NADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRR 138
Query: 62 LMARLHIFPDQEVP 75
L RL ++ + P
Sbjct: 139 LFKRLKVYAGPDHP 152
>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 250
Score = 58.3 bits (141), Expect = 1e-11
Identities = 21/74 (28%), Positives = 37/74 (50%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ +A+ G + ++ Y H+G PGG+ QL + P +++ AVR LP+ +
Sbjct: 157 NADKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQLQKRIPERIIEHAVRGMLPKGRLGRY 216
Query: 62 LMARLHIFPDQEVP 75
L L ++ E P
Sbjct: 217 LFNHLKVYKGAEHP 230
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 47.5 bits (113), Expect = 5e-08
Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 1/75 (1%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
+ + + G ++ + +H H P+ + KA+R + + +
Sbjct: 31 RAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGK 90
Query: 62 -LMARLHIFPDQEVP 75
+ RL +F P
Sbjct: 91 AALERLKVFEGIPPP 105
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 45.7 bits (109), Expect = 2e-07
Identities = 8/75 (10%), Positives = 23/75 (30%), Gaps = 1/75 (1%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ + G + + ++ + ++++ +R LP + R
Sbjct: 32 NAEKAVITGNREVIFSKYKQRTGLRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWKTDRGR 91
Query: 62 -LMARLHIFPDQEVP 75
RL ++
Sbjct: 92 KAFRRLKVYVGIPKE 106
>3izc_K 60S ribosomal protein RPL16 (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_K
3o58_P 3o5h_P 3u5e_O 3u5i_O
Length = 199
Score = 46.1 bits (109), Expect = 2e-07
Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 1/80 (1%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
+ + + G ++ + +H H P+ + KA+R + + +
Sbjct: 37 RAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGK 96
Query: 62 -LMARLHIFPDQEVPEDLLK 80
+ RL +F P D K
Sbjct: 97 AALERLKVFEGIPPPYDKKK 116
>4a17_I RPL13A, 60S ribosomal protein L13A; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_I 4a1c_I 4a1e_I
Length = 198
Score = 44.5 bits (105), Expect = 1e-06
Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 1/75 (1%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
+ I + G ++ R F H P+ + +AVR LP K
Sbjct: 36 RTEAINISGSLFRNRVKFSEFLNKWMNHNPRRGVQHFRAPSRIFWRAVRGMLPHKTPKGA 95
Query: 62 -LMARLHIFPDQEVP 75
+ RL IF P
Sbjct: 96 AALERLKIFEGIPTP 110
>1vq8_J 50S ribosomal protein L13P; 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: c.21.1.1 PDB: 1giy_M
1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I*
1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K*
1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
Length = 145
Score = 43.4 bits (103), Expect = 1e-06
Identities = 13/91 (14%), Positives = 28/91 (30%), Gaps = 5/91 (5%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ + G E + + G + P + K+ +R LP + R
Sbjct: 40 NAERAVITGREEQIVEKYEKRVDIGN----DNGYFYPKRPDGIFKRTIRGMLPHKKQRGR 95
Query: 62 -LMARLHIFPDQEVPEDLLKNVSSQIRQLRP 91
+ ++ ED + + +L
Sbjct: 96 EAFESVRVYLGNPYDEDGEVLDGTSLDRLSN 126
>3iz5_K 60S ribosomal protein L13A (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_K
Length = 206
Score = 43.8 bits (103), Expect = 2e-06
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 1/75 (1%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELP-RSLIKF 60
I + G +++ + + +H P ++ + +R +P ++
Sbjct: 42 RCEEICMSGGLVRQKMKYLRFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTARGE 101
Query: 61 RLMARLHIFPDQEVP 75
+ARL + P
Sbjct: 102 AALARLKAYEGVPPP 116
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 37.3 bits (86), Expect = 4e-04
Identities = 11/75 (14%), Positives = 24/75 (32%), Gaps = 1/75 (1%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
I + G ++ + + + P+ + + VR LP + +
Sbjct: 37 RCEGINISGNFYRNKLNYLAFLRKRMNTNPSRGPYDFRAPSRIFWRTVRGMLPHKTKRGQ 96
Query: 62 -LMARLHIFPDQEVP 75
+ RL +F P
Sbjct: 97 AALDRLKVFDGIPPP 111
>3lmc_A Peptidase, zinc-dependent; structural genomics, PSI-2, protein
structure initiative, no structural genomics
consortium, NESG, MUR16; 2.00A {Methanocorpusculum
labreanum}
Length = 210
Score = 29.8 bits (66), Expect = 0.17
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 65 RLHIFPDQEVPEDLLKNVSSQIRQLRPVP 93
+H+F D VP L + VS ++ + +P
Sbjct: 2 GIHLFWDSRVPVGLSRPVSEELSAVLEMP 30
>3tew_A Protective antigen; protein transport, toxin; HET: MXE; 1.45A
{Bacillus anthracis} PDB: 3tex_A 3tey_A 3q8b_A 3q8a_A
1t6b_X 1acc_A 3q8e_A 3q8c_A 3tez_A 3mhz_A* 3q8f_A*
3kwv_A 3hvd_A 1tzo_A 1tzn_A 3etb_J 3ino_A
Length = 715
Score = 27.2 bits (59), Expect = 1.7
Identities = 4/33 (12%), Positives = 11/33 (33%)
Query: 18 YFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVR 50
Y G+ + L W + ++ ++
Sbjct: 120 YQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQ 152
>3u0r_A Apoptosis inhibitor 5; heat repeat, armadillo repeat, lysine
acetylation; 2.50A {Homo sapiens} PDB: 3v6a_A
Length = 507
Score = 26.8 bits (58), Expect = 1.8
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 1/77 (1%)
Query: 36 LHEIDPTLVMKKAVRWELPRSLIKFRLMARLHIFP-DQEVPEDLLKNVSSQIRQLRPVPR 94
++ P L L L +L+A + F D E E L+ + ++ + P+P
Sbjct: 266 CEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPP 325
Query: 95 TLASYSDKEVDEFPKIN 111
A + +E PK+
Sbjct: 326 EEAENGENAGNEEPKLQ 342
>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 = 26.1 bits (56), Expect = 3.1
Identities = 6/18 (33%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 58 IKFRLMARLHIFPDQEVP 75
+K +L A L ++ D P
Sbjct: 22 LK-KLQASLKLYADDSAP 38
>3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding, virion, zinc,
core protein, RNA-binding, icosaderal virus; 3.80A
{Rotavirus A} PDB: 3kz4_A 3n09_A
Length = 800
Score = 25.9 bits (56), Expect = 4.5
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 61 RLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPR 94
+ RLHIF VP+D + + ++R L PV
Sbjct: 564 DFLKRLHIFDVARVPDDQMYRLRDRLRLL-PVEV 596
>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 = 25.6 bits (55), Expect = 5.4
Identities = 14/98 (14%), Positives = 30/98 (30%), Gaps = 18/98 (18%)
Query: 23 GYPG-GVSWTLAWQ-LHEIDPTLVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLK 80
G G G +W +A M + W + + + PE +L+
Sbjct: 157 GVLGSGKTW-VALDVCLSYKVQCKMDFKIFW------LNLK---------NCNSPETVLE 200
Query: 81 NVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKDYI 118
+ + Q+ P + + +S I + +
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
>3k8k_A Alpha-amylase, SUSG; alpha8/BETA8 barrel, CBM, beta-sandwich,
membrane protein; 2.20A {Bacteroides thetaiotaomicron}
PDB: 3k8m_A* 3k8l_A*
Length = 669
Score = 25.5 bits (56), Expect = 6.1
Identities = 9/57 (15%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 45 MKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSD 101
+ A + + R + RL A HI+ + E+ + + + + D
Sbjct: 347 IADAAKGWIARGVDGLRLDAVKHIYHSETSEEN-PRFLKMFYEDMNAYYKQKGHTDD 402
>1oao_C CODH, carbon monoxide dehydrogenase/acetyl-COA synthase alpha;
oxidoreductase-transferase complex, electron transfer,
oxidoreductase; 1.90A {Moorella thermoacetica} SCOP:
e.26.1.3 PDB: 2z8y_M 3i01_M 3i04_M 1mjg_M 1ru3_A 3git_A
3s2x_A
Length = 729
Score = 24.8 bits (54), Expect = 9.0
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 22 TGYPGGVSWTLAWQLHEIDPT 42
G G VSW A +EI+
Sbjct: 525 VGLCGAVSWLDAKASYEINHA 545
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
0.322 0.138 0.443
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,050,107
Number of extensions: 110189
Number of successful extensions: 236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 235
Number of HSP's successfully gapped: 33
Length of query: 120
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,412,271
Effective search space: 167666298
Effective search space used: 167666298
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 (21.9 bits)
S2: 51 (23.5 bits)