RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12657
(260 letters)
>2ftc_K 39S ribosomal protein L19, mitochondrial; mitochondrial ribosome,
large ribosomal subunit, ribosomal R ribosome; 12.10A
{Bos taurus}
Length = 98
Score = 101 bits (255), Expect = 6e-28
Identities = 50/88 (56%), Positives = 66/88 (75%)
Query: 10 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLY 69
IP F+VGSIL VT+AD + K +F+GICIQ+ GL F+LRNV++ G+EI ++LY
Sbjct: 1 IPEFYVGSILRVTTADPYASGKISQFLGICIQRSGRGLGATFILRNVIEGQGVEICFELY 60
Query: 70 DPTIHNITVLRLEKRLDDDLLYLRDALP 97
+P + I V++LEKRLDD LLYLRDALP
Sbjct: 61 NPRVQEIQVVKLEKRLDDSLLYLRDALP 88
>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 = 56.4 bits (135), Expect = 3e-09
Identities = 35/206 (16%), Positives = 68/206 (33%), Gaps = 44/206 (21%)
Query: 79 LRLEKRLDDDLLYLRD-ALPNVVD--NLG---------IEIAYDMYDPTIHNITVLRLEK 126
L K ++ LL L + + NL ++ + T +I++
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 127 RLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPINDIKVKLKPRPWVGRWERKGYKGI 186
L D ++ L +Y P +L P ++ I ++ W+ +
Sbjct: 297 TLTPD--EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL--ATWDNWKHVNC 352
Query: 187 DDVDQHITEKMKGQKKKLE--EPWEKYDLMKEYRR--------TIPE--------EEQEE 228
D + I + L EP E + + R IP + +
Sbjct: 353 DKLTTII-------ESSLNVLEPAEYRKM---FDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 229 IFSEVFSELHQLSLSNKKLKKSRVYV 254
V ++LH+ SL K+ K+S + +
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISI 428
Score = 47.9 bits (113), Expect = 2e-06
Identities = 38/279 (13%), Positives = 82/279 (29%), Gaps = 80/279 (28%)
Query: 30 NKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDLYDPTIHN-------ITVLRLE 82
+KFV ++ Y L + Y ++N V RL+
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQR-QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135
Query: 83 K--RLDDDLLYLRDALPNVVDNLGIEIAYDMYDPTIHNI-----TVL--------RLEKR 127
+L LL LR A NV+ I + T + +++ +
Sbjct: 136 PYLKLRQALLELRPA-KNVL---------------IDGVLGSGKTWVALDVCLSYKVQCK 179
Query: 128 LDDDLLYL--------RDALPQYSTFPFDMEPEY--LLDGA---PVPINDIKVKLKPRPW 174
+D + +L L + ++P + D + + I+ I+ +L+
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR---- 235
Query: 175 VGRWERKGYKG----IDDV-DQHITEKMKGQKK------------KLEEPWEKYDLMKEY 217
+ K Y+ + +V + K L + + +
Sbjct: 236 -RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294
Query: 218 RRTIPEEEQEEIFSEVFSELHQLSLSNKKLKKSRVYVKP 256
T+ +E + + + L + L + + P
Sbjct: 295 SMTLTPDEVKSLLLKY------LDCRPQDLPREVLTTNP 327
Score = 43.3 bits (101), Expect = 6e-05
Identities = 44/293 (15%), Positives = 92/293 (31%), Gaps = 79/293 (26%)
Query: 2 IKRRSVIDIPSFFVGS-ILSVTSADKH--DPNKTRKFVGICIQKRYCGLRHEFVLRNVVD 58
++ + +F + IL +T+ K D I + L + V ++
Sbjct: 253 VQNAKAWN--AFNLSCKIL-LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309
Query: 59 NLGIEIAYDLYDP----TIHNITVLRLEKRLDDDLL-------YLRDALPNVVDNLGIEI 107
L DL P T + + + + + D L D L + IE
Sbjct: 310 YLDCRPQ-DL--PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI-----IES 361
Query: 108 AYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDME-PEYLL-----DGAPVP 161
+ ++ +P + +++ D L S FP P LL D
Sbjct: 362 SLNVLEPAEY--------RKMFDRL----------SVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 162 INDIKVKLKPRPWVGRWERKGYKGIDDVDQHITEKMKGQK---KKLEEPWEKYDLMKEYR 218
+ + KL V + ++ I + + K++ + + + + Y++ K +
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI---VDHYNIPKTFD 460
Query: 219 ---------------------RTIPEEEQEEIFSEVFSELHQLSLSNKKLKKS 250
+ I E+ +F VF + L +K++
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE---QKIRHD 510
>3bbo_R Ribosomal protein L19; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 233
Score = 49.3 bits (117), Expect = 2e-07
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 9 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 66
+P G I+ + + NK R + GI I ++ G+ +R ++ +G+EI +
Sbjct: 139 PVPGIRTGDIVQIRL--EVPENKRRLSVYKGIVISRQNAGIHTTIRIRRIIAGVGVEIVF 196
Query: 67 DLYDPTIHNITVLRLEKRLDDDLLYLRD 94
LY P I I V+ K L YLRD
Sbjct: 197 PLYSPNIKEIKVVSHRKVRKARLYYLRD 224
>3r8s_P 50S ribosomal protein L19; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_N 1p86_N 2awb_P 2gya_N 2gyc_N 2aw4_P 2i2v_P 2j28_P
2i2t_P* 2qao_P* 2qba_P* 2qbc_P* 2qbe_P 2qbg_P 2qbi_P*
2qbk_P* 2qov_P 2qox_P 2qoz_P* 2qp1_P* ...
Length = 114
Score = 42.9 bits (102), Expect = 7e-06
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 9 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 66
D+PSF G + V + +K R F G+ I R GL F +R + + G+E +
Sbjct: 15 DVPSFRPGDTVEVKVWVV-EGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVF 73
Query: 67 DLYDPTIHNITVLRLEKRLDDDLLYLRD 94
+ P + +I+V R L YLR+
Sbjct: 74 QTHSPVVDSISVKRRGAVRKAKLYYLRE 101
>2zjr_M 50S ribosomal protein L19; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.34.5.6 PDB: 1nwx_N* 1nwy_N* 1sm1_N*
1xbp_N* 2zjp_M* 2zjq_M 1nkw_N 3cf5_M* 3dll_M* 3pio_M*
3pip_M* 1pnu_N 1pny_N 1vor_Q 1vou_Q 1vow_Q 1voy_Q 1vp0_Q
Length = 166
Score = 43.6 bits (103), Expect = 1e-05
Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 3/95 (3%)
Query: 2 IKRRSVIDIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDN 59
I++ +P F G + V + + + N+TR F G+ I G R F +R +
Sbjct: 16 IEQDHTRQLPDFRPGDTVRVDTKVR-EGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFG 74
Query: 60 LGIEIAYDLYDPTIHNITVLRLEKRLDDDLLYLRD 94
G+E + P ++ +T++ K L YLR+
Sbjct: 75 EGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRE 109
>3v2d_T 50S ribosomal protein L19; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_S 2hgj_S 2hgu_S 2j03_T 2jl6_T 2jl8_T 2v47_T 2v49_T
2wdi_T 2wdj_T 2wdl_T 2wdn_T 2wh2_T 2wh4_T 2wrj_T 2wrl_T
2wro_T 2wrr_T 2x9s_T 2x9u_T ...
Length = 146
Score = 42.4 bits (100), Expect = 2e-05
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 9 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 66
D+P F G + V+ K + N+TR F GI I+ R G F +R V +G+E +
Sbjct: 18 DLPEFRPGDTVRVSYKVK-EGNRTRIQDFEGIVIRIRRNGFNTTFTVRKVSYGVGVERIF 76
Query: 67 DLYDPTIHNITVLRLEKRLDDDLLYLRD 94
L+ P I I +++ + L ++R+
Sbjct: 77 PLHSPLIQKIDIVQRGRARRAKLYFIRN 104
>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 = 33.0 bits (74), Expect = 0.048
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 83 KRLDDDL-LYLRDALPNVVDNLGIE 106
K+L L LY D+ P + +E
Sbjct: 23 KKLQASLKLYADDSAPALAIKATME 47
Score = 28.4 bits (62), Expect = 1.6
Identities = 7/16 (43%), Positives = 9/16 (56%), Gaps = 1/16 (6%)
Query: 126 KRLDDDL-LYLRDALP 140
K+L L LY D+ P
Sbjct: 23 KKLQASLKLYADDSAP 38
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.3 bits (70), Expect = 0.18
Identities = 8/62 (12%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 177 RWERKGYKGIDDVDQHITEKMKGQ-KKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFS 235
R + D + + ++ + + KK LEE ++ E + + + + +
Sbjct: 97 RLQEL-----DAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDA 151
Query: 236 EL 237
++
Sbjct: 152 DI 153
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics,
riken structural genomics/proteomics initiative, RSGI;
NMR {Mus musculus} SCOP: a.21.1.1
Length = 108
Score = 29.2 bits (65), Expect = 0.49
Identities = 11/44 (25%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 191 QHITEKMKGQ-KKKLEEPWEKYDL-MKEYRRTIPEEEQEEIFSE 232
+ +++K K KK ++ + Y++ + + ++PEEEQ+ + E
Sbjct: 53 KLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGE 96
>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 = 30.8 bits (69), Expect = 0.52
Identities = 17/102 (16%), Positives = 29/102 (28%), Gaps = 18/102 (17%)
Query: 91 YLRDALPNVVDNL-GIEIAYDMYD---PTIHNIT--VLRLEKRLDDDLLYLRDALPQYST 144
L A + +L ++++ D P LR L + +
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLR---VLSGSI--SERIVDCIIR 485
Query: 145 FPFDME------PEYLLDGAPVPINDIKVKLKPRPWVGRWER 180
P E ++LD P + + L R G R
Sbjct: 486 LPVKWETTTQFKATHILDFGPGGASGL-GVLTHRNKDGTGVR 526
>3mwp_A Nucleoprotein; structural genomics, scottish structural PROT
facility, SSPF, nuclear protein; 1.79A {Lassa virus
josiah} PDB: 3mwt_A 3mx2_A* 3mx5_A* 3r3l_A 3t5q_A 3t5n_A
Length = 577
Score = 30.3 bits (68), Expect = 0.61
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 78 VLRLEKRLDDDLLYLRDALPNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYL 135
++R E+R D+DL LRD L V+NL + + ++LR+ DDLL L
Sbjct: 61 LMRKERRDDNDLKRLRD-LNQAVNNL-------VELKSTQQKSILRVGTLTSDDLLIL 110
>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome
segregation, cell adhesion, kleisin, MIT cell cycle;
HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP:
c.37.1.12
Length = 430
Score = 30.0 bits (68), Expect = 0.72
Identities = 19/106 (17%), Positives = 34/106 (32%), Gaps = 2/106 (1%)
Query: 152 EYLLDGAPVPINDIKVKLKPRPWVGRWERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKY 211
Y +DG V D + L+ + + DV+Q + + EE
Sbjct: 118 SYKIDGKTVSYKDYSIFLE-NENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSI 176
Query: 212 DLMKEYRRTIPEEEQ-EEIFSEVFSELHQLSLSNKKLKKSRVYVKP 256
KEY + E+ + +E ++ K K + V
Sbjct: 177 QYKKEYEELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLF 222
>1gpu_A Transketolase; transferase(ketone residues); HET: THD; 1.86A
{Saccharomyces cerevisiae} SCOP: c.36.1.6 c.36.1.10
c.48.1.1 PDB: 1ngs_A* 1trk_A* 1ay0_A* 1tkb_A* 1tka_A*
1tkc_A*
Length = 680
Score = 29.8 bits (68), Expect = 0.92
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 187 DDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQE 227
+V H + + + W K L EY++ PE E
Sbjct: 291 QEVYDHYQKTILKPGVEANNKWNK--LFSEYQKKFPELGAE 329
>3m49_A Transketolase; alpha-beta-alpha sandwich, csgid, transferase,
structural genomics, center for structural genomics of
infectious diseases; HET: MSE TDP PG5 TRS BTB; 2.00A
{Bacillus anthracis} PDB: 3hyl_A*
Length = 690
Score = 29.4 bits (67), Expect = 1.5
Identities = 7/41 (17%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 187 DDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQE 227
++V ++ + ++ + + W ++ EY + PE E
Sbjct: 315 EEVYENFRKTVQDVGETAQAEWNT--MLGEYAQAYPELANE 353
>3qa8_A MGC80376 protein; kinase ubiquitin-like domain, phosphorylation,
kinase domain ubiquitin-like domain, kinase, substrate
binding; 3.60A {Xenopus laevis} PDB: 3qad_A* 3rzf_A*
Length = 676
Score = 27.3 bits (60), Expect = 6.8
Identities = 19/95 (20%), Positives = 29/95 (30%), Gaps = 2/95 (2%)
Query: 164 DIKVKLKPRPWVGRWERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMKEY--RRTI 221
KV+ K + ++ + G E W + LM R T
Sbjct: 233 HGKVREKSNEHIVVYDDLTGAVKFSSVLPTPNHLSGILAGKLERWLQCMLMWHQRQRGTD 292
Query: 222 PEEEQEEIFSEVFSELHQLSLSNKKLKKSRVYVKP 256
P+ F + S L LS + RV+ P
Sbjct: 293 PQNPNVGCFQALDSILSLKLLSVMNMVSGRVHTYP 327
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 0.141 0.418
Gapped
Lambda K H
0.267 0.0403 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,314,048
Number of extensions: 279771
Number of successful extensions: 672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 33
Length of query: 260
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 168
Effective length of database: 4,133,061
Effective search space: 694354248
Effective search space used: 694354248
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: 56 (26.2 bits)