RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13112
(302 letters)
>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 = 45.0 bits (106), Expect = 2e-05
Identities = 55/318 (17%), Positives = 101/318 (31%), Gaps = 104/318 (32%)
Query: 4 PLRLE--SRDYVL----SFHFFETRLRDDISFQ----ERSQGSAKCDLMPTPRSPRE--- 50
PL L S ++VL + F ++L++ F E ++G A D P +P E
Sbjct: 8 PLTLSHGSLEHVLLVPTASFFIASQLQEQ--FNKILPEPTEGFAADD---EPTTPAELVG 62
Query: 51 -------REARPHAQPRKAP------GSAQRDRKQGS-----AKRDPMHNPTKPQER--V 90
P + + +G+ A + N T + +
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 91 ARPYMQPRVANTRNEVRYFPKFTVMYAHDPD--KICKTGD--IVLI-----------EEL 135
+ Y+ R+ R + + + G+ +V I EEL
Sbjct: 123 IKNYITARIMAKRPFDK---------KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEEL 173
Query: 136 PQKL-TTLITHKVNKVVYP--LGDITDPITG--KKVVGLRVDLGKYFPK-FTVM-YAHDP 188
+ L T Y +GD+ +++ +D K F + ++ + +P
Sbjct: 174 -RDLYQT----------YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP 222
Query: 189 DKICKTGD----------IVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVV--G 236
T D LI + Q ++T K+ + G++ + G G
Sbjct: 223 S---NTPDKDYLLSIPISCPLI-GVIQLAHYVVTAKLLG--FTPGELRSYLKGATGHSQG 276
Query: 237 LRTAVLTA------DFYK 248
L TAV A F+
Sbjct: 277 LVTAVAIAETDSWESFFV 294
Score = 32.7 bits (74), Expect = 0.16
Identities = 42/288 (14%), Positives = 82/288 (28%), Gaps = 81/288 (28%)
Query: 34 QGSAK----CDLMPTPRSPRE--REARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQ 87
QGS + DL T ++ ++ A H + G + D + +H +
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWNRADNHF--KDTYGFSILDIVINNPVNLTIHFGGEKG 1681
Query: 88 ERVARPYM-----QPRVANTRNEVRYFPKFT-----VMYAHDPDKICKTG---------D 128
+R+ Y + E + F + + + + T +
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTE-KIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 129 IVLIEELPQKLTTLITHKVNKVV--YPLG------------DITDPITGKKVVGLRVDLG 174
E+L K LI + + LG I + +VV R G
Sbjct: 1741 KAAFEDLKSK--GLI--PADATFAGHSLGEYAALASLADVMSIESLV---EVVFYR---G 1790
Query: 175 KYF----PKFTV------MYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD 224
P+ + M A +P ++ + +E Q + + + +V +
Sbjct: 1791 MTMQVAVPRDELGRSNYGMIAINPGRVAASFS----QEALQYVVERVGKRTGWLVEIVNY 1846
Query: 225 ITDP----ITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAP 268
+ G L T +F K +K D +
Sbjct: 1847 NVENQQYVAAGDL-RALDTVTNVLNFIKL----------QKIDIIELQ 1883
>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 = 40.2 bits (93), Expect = 6e-04
Identities = 49/318 (15%), Positives = 80/318 (25%), Gaps = 118/318 (37%)
Query: 18 FFETRLRDDISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKR 77
F E LR + F LM SP + E R QP + +R
Sbjct: 82 FVEEVLRINYKF-----------LM----SPIKTEQR---QP-------SMMTRMYIEQR 116
Query: 78 DPMHNPTKPQERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQ 137
D ++ N+ + F K+ V +L Q
Sbjct: 117 DRLY----------------------NDNQVFAKYNVSRLQ------------PYLKLRQ 142
Query: 138 KLTTLITHKVNKVVY-PLGDITDPITGKKVVGL------RVDLGKYFPKF--TVMYAHDP 188
L L K N ++ LG +GK V L +V F F + + P
Sbjct: 143 ALLELRPAK-NVLIDGVLG------SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 189 DKI---------------CKTGD-----IVLIEELPQKLTTLITHKVNKVVYP-----LG 223
+ + D + I + +L L+ K Y L
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK----PYENCLLVLL 251
Query: 224 DITDPITGKKV-VGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHR 282
++ + + + + T K T
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRF----------KQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 283 ES---YIRYHEFDDDDQP 297
E ++Y + D P
Sbjct: 302 EVKSLLLKYLDCRPQDLP 319
Score = 29.1 bits (64), Expect = 2.1
Identities = 33/219 (15%), Positives = 67/219 (30%), Gaps = 68/219 (31%)
Query: 102 TRNEVR-YFPKFTVMYAHD-PDKICKTG--DIVLIEELPQ---------------KLTTL 142
T +EV+ K+ D P ++ T + +I E + KLTT+
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 143 ITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPD--KI-CKTGDIV- 198
I +N + +P + K F + +V P I ++
Sbjct: 359 IESSLNVL--------EP----------AEYRKMFDRLSVF----PPSAHIPTILLSLIW 396
Query: 199 --LIEELPQKLTT------LITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKEL 250
+I+ + L+ + + + I + K ++ +
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVK-------LENEYALHRSI 449
Query: 251 YELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
+ Y N + FD D+ + S+I +H
Sbjct: 450 VDHY--NIPKTFDSDDLIPP--YLDQYFY----SHIGHH 480
>3r8n_Q 30S ribosomal protein S17; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_Q 3fih_Q* 3iy8_Q 2wwl_Q
3oar_Q 3oaq_Q 3ofb_Q 3ofa_Q 3ofp_Q 3ofx_Q 3ofy_Q 3ofo_Q
3r8o_Q 4a2i_Q 3i1m_Q 1vs7_Q* 3e1a_J 3e1c_J 1vs5_Q 3i1o_Q
...
Length = 80
Score = 36.0 bits (84), Expect = 0.001
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK+ + T ++ HD + C GD+V I E
Sbjct: 32 GKFIKRTTKLHVHDENNECGIGDVVEIRE 60
Score = 32.1 bits (74), Expect = 0.028
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 106 VRYFPKFTVMYAHDPDKICKTGDIVLIEE 134
++ K + HD + C GD+V I E
Sbjct: 35 IKRTTKL---HVHDENNECGIGDVVEIRE 60
>1qd7_I S17 ribosomal protein; 30S ribosomal subunit, low resolution model,
ribosome; 5.50A {Thermus thermophilus} SCOP: i.1.1.3
PDB: 1eg0_G 1rip_A
Length = 89
Score = 36.1 bits (84), Expect = 0.002
Identities = 12/29 (41%), Positives = 12/29 (41%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK AHD K GDIV I E
Sbjct: 32 GKRVKYSKKYKAHDEHNEAKVGDIVKIME 60
Score = 32.6 bits (75), Expect = 0.029
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 106 VRYFPKFTVMYAHDPDKICKTGDIVLIEE 134
V+Y K+ AHD K GDIV I E
Sbjct: 35 VKYSKKY---KAHDEHNEAKVGDIVKIME 60
>3bbn_Q Ribosomal protein S17; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 142
Score = 36.3 bits (84), Expect = 0.004
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
+ AHDPD K GD+V +E+
Sbjct: 90 KRRVRMKKKYQAHDPDNQFKVGDVVRLEK 118
Score = 32.9 bits (75), Expect = 0.046
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 106 VRYFPKFTVMYAHDPDKICKTGDIVLIEE 134
VR K+ AHDPD K GD+V +E+
Sbjct: 93 VRMKKKY---QAHDPDNQFKVGDVVRLEK 118
>2vqe_Q 30S ribosomal protein S17; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: b.40.4.5 PDB: 1gix_T*
1hnw_Q* 1hnx_Q* 1hnz_Q* 1hr0_Q 1ibk_Q* 1ibl_Q* 1ibm_Q
1jgo_T* 1jgp_T* 1jgq_T* 1ml5_T* 1xmo_Q* 1xmq_Q* 1xnq_Q*
1xnr_Q* 1yl4_T 2b64_Q* 2b9m_Q* 2b9o_Q* ...
Length = 105
Score = 33.8 bits (78), Expect = 0.012
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK + AHDP++ K GD+V I E
Sbjct: 32 YGKVIKRSKKYLAHDPEEKYKLGDVVEIIE 61
Score = 31.1 bits (71), Expect = 0.11
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 106 VRYFPKFTVMYAHDPDKICKTGDIVLIEE 134
++ K+ AHDP++ K GD+V I E
Sbjct: 36 IKRSKKY---LAHDPEEKYKLGDVVEIIE 61
>3u5c_L RP41, S18, YS12, 40S ribosomal protein S11-A; translation,
ribosome, ribosomal, ribosomal R ribosomal protein,
eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_P 3o30_F 3o2z_F 3u5g_L 3jyv_Q*
1s1h_Q
Length = 156
Score = 33.6 bits (77), Expect = 0.034
Identities = 17/93 (18%), Positives = 28/93 (30%), Gaps = 9/93 (9%)
Query: 43 PTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARPYMQPRVANT 102
TP++ E P S + G+ MH + R Y+
Sbjct: 43 KTPKTAIEGSYIDKKCPFTGLVSIRGKILTGTVVSTKMHRTIV----IRRAYLHY----I 94
Query: 103 RNEVRYFPKFTVMYAHDPDKI-CKTGDIVLIEE 134
RY + + H + GDIV + +
Sbjct: 95 PKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQ 127
Score = 31.7 bits (72), Expect = 0.15
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 174 GKYFPKFTVMYAHDPDKI-CKTGDIVLIEE 202
+Y + + H + GDIV + +
Sbjct: 98 NRYEKRHKNVPVHVSPAFRVQVGDIVTVGQ 127
>2zkq_q 40S ribosomal protein S11E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 3jyv_Q* 1s1h_Q
Length = 158
Score = 32.1 bits (73), Expect = 0.098
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 174 GKYFPKFTVMYAHDPDKI--CKTGDIVLIEE 202
++ + M H + GDIV + E
Sbjct: 100 NRFEKRHKNMSVHLSPCFRDVQIGDIVTVGE 130
Score = 31.3 bits (71), Expect = 0.19
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 14/75 (18%)
Query: 74 SAKRDPMHNPTKPQER-----VARPYMQPRVANTRNEVRYFPKF-------TVMYAHDPD 121
K+ P + R V + MQ + R+ + Y K+ M H
Sbjct: 56 IDKKCPFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSP 115
Query: 122 KI--CKTGDIVLIEE 134
+ GDIV + E
Sbjct: 116 CFRDVQIGDIVTVGE 130
>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_Q
Length = 157
Score = 31.8 bits (72), Expect = 0.15
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 174 GKYFPKFTVMYAHDPDKI-CKTGDIVLIEE 202
+Y + + H K GDI++ +
Sbjct: 97 NRYEKRHRNIPVHISPCFSVKEGDILVAGQ 126
Score = 30.2 bits (68), Expect = 0.40
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 107 RYFPKFTVMYAHDPDKI-CKTGDIVLIEE 134
RY + + H K GDI++ +
Sbjct: 98 RYEKRHRNIPVHISPCFSVKEGDILVAGQ 126
>3iz6_P 40S ribosomal protein S11 (S17P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 161
Score = 31.0 bits (70), Expect = 0.25
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 174 GKYFPKFTVMYAHDPDKI-CKTGDIVLIEE 202
+Y + + + AH K GD V+I +
Sbjct: 99 QRYEKRHSNIPAHVSPCFRVKEGDHVIIGQ 128
Score = 29.9 bits (67), Expect = 0.54
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 13/74 (17%)
Query: 74 SAKRDPMHNPTKPQER-----VARPYMQPRVANTRNEVRYFPKF-------TVMYAHDPD 121
K+ P + R M + RN + + K+ + + AH
Sbjct: 55 IDKKCPFTGTVSIRGRIIAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHVSP 114
Query: 122 KI-CKTGDIVLIEE 134
K GD V+I +
Sbjct: 115 CFRVKEGDHVIIGQ 128
>2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target
base partner, 5-methylpyr 2(1H)-ONE, base flipping; HET:
5PY 6MA NEA; 1.61A {Thermus aquaticus} SCOP: c.66.1.27
d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A* 2ih5_A* 2jg3_A*
2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A* 1g38_A*
Length = 421
Score = 28.5 bits (63), Expect = 3.3
Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 3/87 (3%)
Query: 206 KLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYE--LYGKNPQR-KF 262
+ T T K+ PLGD+ + + L G+N +
Sbjct: 244 RFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWV 303
Query: 263 DYKKAPRRGWQEDKKDFTHRESYIRYH 289
DY+K W ++ R+ Y H
Sbjct: 304 DYEKNHSGLWMPKERAKELRDFYATPH 330
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 0.417
Gapped
Lambda K H
0.267 0.0524 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,780,685
Number of extensions: 284838
Number of successful extensions: 438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 429
Number of HSP's successfully gapped: 29
Length of query: 302
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 209
Effective length of database: 4,105,140
Effective search space: 857974260
Effective search space used: 857974260
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 (21.7 bits)
S2: 57 (26.2 bits)