RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 025294
(255 letters)
>3r8n_K 30S ribosomal protein S11; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_K 3fih_K* 3iy8_K 2wwl_K
3oar_K 3oaq_K 3ofb_K 3ofa_K 3ofp_K 3ofx_K 3ofy_K 3ofo_K
3r8o_K 4a2i_K 3i1m_K 1vs7_K* 3e1a_C 3e1c_C 1vs5_K 3i1o_K
...
Length = 117
Score = 97.3 bits (243), Expect = 6e-26
Identities = 44/120 (36%), Positives = 59/120 (49%), Gaps = 13/120 (10%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI NNT VT+TD +GN A++G +G K + +AA+ AE + G+
Sbjct: 9 AHIHASFNNTIVTITDRQGNALGWATAGGS-GFRGSRKSTPFAAQVAAERCADAVKEYGI 67
Query: 198 KSVVVRVKGFTYFKKKRQ-AIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
K++ V VKG R+ I + GF I I D T PHNGCR PKKRR+
Sbjct: 68 KNLEVMVKGPGP---GRESTIRALNAAGFR-------ITNITDVTPIPHNGCRPPKKRRV 117
>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 140
Score = 97.4 bits (243), Expect = 1e-25
Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 11/119 (9%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
+H++ NNT VTVTD +G AS+G +G + + +AA+ A + R G+
Sbjct: 32 IHVQASFNNTIVTVTDVRGRVVSWASAGTC-GFRGTKRGTPFAAQTAAGNAIRTVVEQGM 90
Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
+ V +KG + A+ + R G + ++ D T PHNGCR PKKRR+
Sbjct: 91 QRAEVMIKGPG--LGRDAALRAIRRSGI-------LLSFVRDVTPMPHNGCRPPKKRRV 140
>3u5c_O RP59A, 40S ribosomal protein S14-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_K 3o30_H 3o2z_H 3u5g_O 1s1h_K
3jyv_K*
Length = 137
Score = 95.5 bits (238), Expect = 5e-25
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 16/125 (12%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGG-PKMSRYAAEATAEHVGRLARNMG 196
I N+TFV VTD G + I +G + ++K + S YAA A+ V + +G
Sbjct: 17 ARIYASFNDTFVHVTDLSGKETIARVTGGM-KVKADRDESSPYAAMLAAQDVAAKCKEVG 75
Query: 197 LKSVVVRVKGFTYFKKK-----RQ-AIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRL 249
+ +V V+++ + K Q A+ + R G I IED T P + R
Sbjct: 76 ITAVHVKIRATGGTRTKTPGPGGQAALRALARSGL-------RIGRIEDVTPVPSDSTRK 128
Query: 250 PKKRR 254
RR
Sbjct: 129 KGGRR 133
>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.55.4.1
PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K* 1hr0_K 1ibk_K*
1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N* 1jgq_N* 1ml5_N*
1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K* 1xmq_K* 1xnq_K*
...
Length = 129
Score = 95.0 bits (237), Expect = 5e-25
Identities = 42/118 (35%), Positives = 55/118 (46%), Gaps = 11/118 (9%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
+I NNT VT+TD GN +S G + KG K + YAA+ A + A G+
Sbjct: 19 AYIHASYNNTIVTITDPDGNPITWSSGGVI-GYKGSRKGTPYAAQLAALDAAKKAMAYGM 77
Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254
+SV V V+G + QAI + G + I D T PHNGCR KK R
Sbjct: 78 QSVDVIVRGTG--AGREQAIRALQASGLQ-------VKSIVDDTPVPHNGCRPKKKFR 126
>2xzm_K RPS14E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_K 3j0o_K 3j0l_K 2zkq_k 3iz6_K 3jyv_K*
Length = 151
Score = 89.1 bits (221), Expect = 2e-22
Identities = 31/125 (24%), Positives = 53/125 (42%), Gaps = 16/125 (12%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSR-YAAEATAEHVGRLARNMG 196
HI N+TF+ VTD G + + +G + ++K + S YAA A V + +
Sbjct: 31 CHIMATWNDTFIHVTDLSGRETLVRVTGGM-KVKADREESSPYAAMQAAIDVVNRCKELK 89
Query: 197 LKSVVVRVKGFTYFKKK-----RQ-AIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRL 249
+ ++ ++++ + K Q A+ + R G I IED T P + R
Sbjct: 90 INALHIKLRAKGGVETKQPGPGAQSALRALARSGMK-------IGRIEDVTPIPTDSTRR 142
Query: 250 PKKRR 254
RR
Sbjct: 143 EGGRR 147
>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 = 33.5 bits (76), Expect = 0.066
Identities = 35/187 (18%), Positives = 57/187 (30%), Gaps = 76/187 (40%)
Query: 2 LSFSSLRKATSLLRYNGAFNRPLSADFAG-----Y-----------FEN-----EKRHFC 40
+ ++ L+ G P A FAG Y E+ R
Sbjct: 1739 MEKAAFE----DLKSKGLI--PADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMT 1792
Query: 41 SSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRSS 100
V R E GRS N GM A++ + A+ E
Sbjct: 1793 MQVAVPRDELGRS------NYGM--IAINPGRVAAS---------------FSQEA---- 1825
Query: 101 RPMDFVRGIVEEDEKRFTGPSQFGQFPR---YNVEHSSEFV---HIK-LMRNNTFVTVTD 153
++ +VE K + G YNVE + ++V ++ L +T V +
Sbjct: 1826 -----LQYVVERVGK------RTGWLVEIVNYNVE-NQQYVAAGDLRAL---DTVTNVLN 1870
Query: 154 SKGNKRI 160
++I
Sbjct: 1871 FIKLQKI 1877
Score = 26.9 bits (59), Expect = 8.7
Identities = 15/95 (15%), Positives = 28/95 (29%), Gaps = 43/95 (45%)
Query: 5 SSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMN 64
++L K L++ Y AR + R + +
Sbjct: 114 TTLVKTKELIKN--------------YIT------------ARIMAKRPFDKKSNS---- 143
Query: 65 LCAV--SVEQNVAAPYAL-GFRNFIHSTGQGDDET 96
A+ +V + A A+ G GQG+ +
Sbjct: 144 --ALFRAVGEGNAQLVAIFG--------GQGNTDD 168
>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 = 29.4 bits (65), Expect = 1.3
Identities = 19/119 (15%), Positives = 40/119 (33%), Gaps = 25/119 (21%)
Query: 56 RVLGNL---GMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEE 112
R+ L + VE+ + Y F+ S + E + S +E+
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINY-----KFLMSPIK--TEQRQPSMMTRM---YIEQ 115
Query: 113 DEKRFTGPSQFGQFPRYNVEHSSEFVHIK--L--MRNNTFVTVTDSKGNKRIGASSGCL 167
++ + F +YNV ++ ++ L +R V + G G + +
Sbjct: 116 RDRLYNDNQVF---AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG---SGKT--WV 166
>3uyj_A Lysine-specific demethylase 8; jellyroll-like all beta fold,
nuclear, oxidored; HET: AKG; 2.35A {Homo sapiens} PDB:
4aap_A*
Length = 248
Score = 27.0 bits (60), Expect = 6.0
Identities = 9/52 (17%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 191 LARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGF---ANSRDQNPIVYIEDT 239
+ G ++V V V ++ Q +M+ E F + + Y+
Sbjct: 58 IQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNE-FISKYIVNEPRDVGYLAQH 108
>3p96_A Phosphoserine phosphatase SERB; ssgcid, structural genomics,
structural genomics center for infectious disease,
hydrolas; 2.05A {Mycobacterium avium}
Length = 415
Score = 26.7 bits (59), Expect = 7.5
Identities = 12/66 (18%), Positives = 20/66 (30%), Gaps = 6/66 (9%)
Query: 161 GASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSF 220
G + + E+ G ++ A R +G VV GF + +
Sbjct: 242 GLPATVIDEVAGQLELMPGARTTLRT-----LRRLGYACGVVS-GGFRRIIEPLAEELML 295
Query: 221 REGFAN 226
AN
Sbjct: 296 DYVAAN 301
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 0.135 0.400
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,852,478
Number of extensions: 223500
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 10
Length of query: 255
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 164
Effective length of database: 4,160,982
Effective search space: 682401048
Effective search space used: 682401048
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: 56 (25.5 bits)