RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1551
(190 letters)
>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R
1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R*
1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U*
1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ...
Length = 88
Score = 41.2 bits (97), Expect = 1e-05
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 112 PCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLI 171
E+ + N+++L++F+S G+IL +TG+ K+ L I +A+ GL+
Sbjct: 21 KVKATLGEFDLRDYRNVEVLKRFLSE-TGKILPRRRTGLSGKEQRILAKTIKRARILGLL 79
Query: 172 TF 173
F
Sbjct: 80 PF 81
>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R
3i1z_R 3i21_R 3izv_V* 3izw_V* 3kc4_R 3or9_R 3ora_R
3sfs_R* 3uoq_R* 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R
2i2u_R ...
Length = 75
Score = 40.7 bits (96), Expect = 1e-05
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 112 PCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLI 171
C + I +I L+ +I+ +G+I+ TG K +L AI +A+ L+
Sbjct: 10 FCRFTAEGVQEIDYKDIATLKNYITE-SGKIVPSRITGTRAKYQRQLARAIKRARYLSLL 68
Query: 172 TF 173
+
Sbjct: 69 PY 70
>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 103
Score = 40.8 bits (96), Expect = 2e-05
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 112 PCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLI 171
PI + I N+ L+ +FIS G+ILS + KQ + AI QA+ L
Sbjct: 19 LPPIQSGDR--IDYRNMSLISRFISE-QGKILSRRVNRLTLKQQRLITSAIKQARILSL- 74
Query: 172 TFDLPF 177
LPF
Sbjct: 75 ---LPF 77
>3r8n_R 30S ribosomal protein S18; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_R 3fih_R* 3iy8_R 2wwl_R
3oar_R 3oaq_R 3ofb_R 3ofa_R 3ofp_R 3ofx_R 3ofy_R 3ofo_R
3r8o_R 4a2i_R
Length = 55
Score = 35.9 bits (84), Expect = 5e-04
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 127 NIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDLPF 177
+I L+ +I+ +G+I+ TG K +L AI +A+ L LP+
Sbjct: 6 DIATLKNYITE-SGKIVPSRITGTRAKYQRQLARAIKRARYLSL----LPY 51
>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 = 34.8 bits (79), Expect = 0.013
Identities = 24/216 (11%), Positives = 50/216 (23%), Gaps = 68/216 (31%)
Query: 9 VIPESEVWDVWIPPQRQFSLSRICCEEEGTEE-------------NKDEKP--------- 46
V P IP LS I + ++ K K
Sbjct: 380 VFPP----SAHIPTIL---LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY 432
Query: 47 VDPAKDRRNPVPVEISI--RYLASEAYQKCYGDEPVWKYYRRNHKG--MFAPKKTRKTC- 101
++ N + SI Y + + P Y +H G + + +
Sbjct: 433 LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 102 ----------IRSGIIATGNPCPICRD------------EYLI-IHPYN---IKLLEQFI 135
+ I Y+ P + + F+
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552
Query: 136 SPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLI 171
+ ++ ++ LL A+++ +
Sbjct: 553 PKIEENLICS--------KYTDLLRIALMAEDEAIF 580
Score = 30.6 bits (68), Expect = 0.35
Identities = 27/220 (12%), Positives = 64/220 (29%), Gaps = 56/220 (25%)
Query: 2 KEME--TAPVIPESEVWDVWIPPQRQFSLSRI--CCEEEGTE------ENKDEKP----V 47
K+++ ++ + E+ + + R+ + E E +
Sbjct: 36 KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95
Query: 48 DPAKDRRNPVPVEISIRYLASEAYQKCYGDEPVW-KYYRRNHKGMFAPKKTRKTCIRS-- 104
P K + P ++ Y E + Y D V+ KY + P + +
Sbjct: 96 SPIKTEQRQ-PSMMTRMY--IEQRDRLYNDNQVFAKYNVSRLQ----PYLKLRQALLELR 148
Query: 105 --------GIIATGNPC---PICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQ- 152
G++ +G +C K+ + + +I ++ C
Sbjct: 149 PAKNVLIDGVLGSGKTWVALDVCLSY---------KVQCKM----DFKIF-WLNLKNCNS 194
Query: 153 -----KQHLKLLVAITQAKNKGL-ITFDLPFREYNYKDYF 186
+ KLL I + ++ R ++ +
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Score = 30.2 bits (67), Expect = 0.46
Identities = 20/156 (12%), Positives = 52/156 (33%), Gaps = 42/156 (26%)
Query: 58 PVEISIRYLASEAYQKCYGDEPV-WKYYRR-NHKGMFAPKKTRKTCIRSGIIATGNPCPI 115
P +S + +E+ + D W ++ N + ++ + P
Sbjct: 327 PRRLS---IIAESIR----DGLATWDNWKHVNCDKL---TTIIESSLNVL-----EP-AE 370
Query: 116 CRDEY--LIIHPYNIKLLEQFISPVNGEILSY---------MKTGVCQKQ---------- 154
R + L + P + + +S + +++ K + +KQ
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 155 -HLKLLVAIT--QAKNKGLITFDLPFREYNYKDYFP 187
+L+L V + A ++ ++ + ++ D P
Sbjct: 431 IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
>2w2d_B Bontoxilysin-A, botulinum neurotoxin A heavy chain;
metalloprotease, membrane domain, protein engineering,
neuro metal-binding; 2.59A {Clostridium botulinum}
Length = 431
Score = 29.8 bits (66), Expect = 0.54
Identities = 23/78 (29%), Positives = 32/78 (41%), Gaps = 12/78 (15%)
Query: 111 NPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVC----QKQHLKLLVAITQAK 166
N C + +I PY +K LE F + + +L Y+ Q LK V
Sbjct: 343 NQCSVSYLMNSMI-PYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKV------ 395
Query: 167 NKGLITFDLPFREYNYKD 184
N L T D+PF+ Y D
Sbjct: 396 NNTLST-DIPFQLSKYVD 412
>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin
ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB:
2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A
2ldr_A*
Length = 389
Score = 29.7 bits (66), Expect = 0.62
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 99 KTCIRSGIIATGNPCPICR-----DEYLIIHPYN 127
+C+ S + G CP CR E +++ P++
Sbjct: 356 TSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPFD 389
>2nyy_A Botulinum neurotoxin type A; neurotoxin, FAB, protein antibody
complex, toxin- system complex; 2.61A {Clostridium
botulinum} PDB: 2nz9_A 3bta_A 3v0a_A* 3v0b_A 3v0c_A
3zus_A 3zur_A
Length = 1295
Score = 29.1 bits (64), Expect = 0.99
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 16/80 (20%)
Query: 111 NPCPICRDEYLI--IHPYNIKLLEQFISPVNGEILSYMK----TGVCQKQHLKLLVAITQ 164
N C + YL+ + PY +K LE F + + +L Y+ T + Q LK V T
Sbjct: 788 NQCSVS---YLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKVNNT- 843
Query: 165 AKNKGLITFDLPFREYNYKD 184
++ D+PF+ Y D
Sbjct: 844 ------LSTDIPFQLSKYVD 857
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
toprim, walker B ATP binding motif; 2.50A {Deinococcus
radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Length = 228
Score = 27.2 bits (61), Expect = 2.6
Identities = 5/21 (23%), Positives = 6/21 (28%)
Query: 99 KTCIRSGIIATGNPCPICRDE 119
C I C +C D
Sbjct: 55 HVCPICFNITDAEKCDVCADP 75
>3p8b_A DNA-directed RNA polymerase, subunit E''; transcription elongation
factor, RNA polymerase, transferase transcription
complex; 1.80A {Pyrococcus furiosus}
Length = 81
Score = 25.2 bits (55), Expect = 5.2
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 83 YYRRNHKGMFAPKKTRKT---CIRSGIIATGNPCPIC 116
++ +H P+ + + C I + + CP+C
Sbjct: 5 HHHHHHSSGLVPRGSHMSEKACRHCHYITSEDRCPVC 41
>3ewm_A Uncharacterized sugar kinase PH1459; carbohydrate kinase, PFKB
family, PSI-II, NYSGXRC, structural genomics, protein
structure initiative; 1.90A {Pyrococcus horikoshii} PDB:
3ih0_A* 3gbu_A*
Length = 313
Score = 26.8 bits (60), Expect = 5.3
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 161 AITQAKNKGLITFDLPFREYNYKD 184
I + K LI FD+ R ++
Sbjct: 147 VIKKIKGSSLIAFDVNLRLDLWRG 170
>1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane
protein, oxidoreductase; HET: HEM HEO; 3.50A
{Escherichia coli} SCOP: b.6.1.2 f.17.2.1
Length = 315
Score = 26.8 bits (59), Expect = 5.4
Identities = 7/36 (19%), Positives = 12/36 (33%), Gaps = 2/36 (5%)
Query: 80 VWKYYRRNHKGMFAPKKTRKTCIRSGIIATGNPCPI 115
WKY N ++P + + + P I
Sbjct: 66 AWKYRASNKDAKYSPNWSHSNKVE--AVVWTVPILI 99
>3p0k_A Sulfhydryl oxidase; 4-helix bundle, 5-helix bundle, flavin adenine
dinucleotide, oxidoreductase, viral protein; HET: FAD;
1.47A {Autographa californica nucleopolyhedro} PDB:
3qzy_A*
Length = 266
Score = 26.5 bits (58), Expect = 5.6
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 113 CPICRDEYLIIHPYNIKLLE 132
C +CRD Y+ + + I +E
Sbjct: 156 CAMCRDHYMNVKGFIIYHIE 175
>3v0a_B NTNH; botulinum neurotoxin, toxin, neurotoxin associated protein,
progenitor toxin complex, VHH bound interlocked complex;
HET: MES; 2.70A {Clostridium botulinum} PDB: 3v0b_B
Length = 1196
Score = 26.4 bits (57), Expect = 8.1
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 7/74 (9%)
Query: 111 NPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGL 170
N IC E I P I +EQ I+ +N + +++ + KL Q N+ +
Sbjct: 752 NNAAICVFESNIY-PKFISFMEQCINNINIKTKEFIQKCTNINEDEKL-----QLINQNV 805
Query: 171 ITFDLPFREYNYKD 184
L F N ++
Sbjct: 806 FN-SLDFEFLNIQN 818
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 25.8 bits (56), Expect = 8.8
Identities = 12/64 (18%), Positives = 18/64 (28%), Gaps = 18/64 (28%)
Query: 91 MFAPKKTRKTCIRSGI-IATGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTG 149
M + K R G + CP C+ +P I G++
Sbjct: 1 MMTRESIDKRAGRRGPNLNIVLTCPECKV-----YPPKI-----VERFSEGDV------- 43
Query: 150 VCQK 153
VC
Sbjct: 44 VCAL 47
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 0.138 0.433
Gapped
Lambda K H
0.267 0.0485 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,009,630
Number of extensions: 167391
Number of successful extensions: 445
Number of sequences better than 10.0: 1
Number of HSP's gapped: 444
Number of HSP's successfully gapped: 38
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
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: 54 (25.2 bits)