RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12656
(291 letters)
>2ftc_K 39S ribosomal protein L19, mitochondrial; mitochondrial ribosome,
large ribosomal subunit, ribosomal R ribosome; 12.10A
{Bos taurus}
Length = 98
Score = 112 bits (283), Expect = 8e-32
Identities = 54/98 (55%), Positives = 74/98 (75%)
Query: 84 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMY 143
IP F+VGSIL VT+AD + K +F+GICIQ+ GL F+LRNV++ G+EI +++Y
Sbjct: 1 IPEFYVGSILRVTTADPYASGKISQFLGICIQRSGRGLGATFILRNVIEGQGVEICFELY 60
Query: 144 DPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDME 181
+P + I V++LEKRLDD LLYLRDALP+YSTF +M+
Sbjct: 61 NPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDVNMK 98
>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 = 58.7 bits (141), Expect = 8e-10
Identities = 41/305 (13%), Positives = 88/305 (28%), Gaps = 89/305 (29%)
Query: 5 ISRVHRSTRLNSLTILRNLSKNSPLQFENAENGEKKLSIPQENRFMYQEFLPDPELKFRN 64
+ + + L +L+ L + + + + + + + R
Sbjct: 189 LKNCNSPETV--LEMLQKLLYQIDPNWTSRSDHSSNIKLRIH----------SIQAELRR 236
Query: 65 QVREK-LERS----DMIKRRSVIDIPSFFVGS-ILSVTSADKHDPNKTRKFVGICIQKRY 118
++ K E ++ + +F + IL +T+ K
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWN--AFNLSCKIL-LTTRFK------------------ 275
Query: 119 CGLRHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPF 178
V D L +I++ L D ++ L +Y
Sbjct: 276 ----------QVTDFLSAATTT--------HISLDHHSMTLTPD--EVKSLLLKYLDCRP 315
Query: 179 DMEPEYLLDGAPVPINDIKVKLKPRPWVGRWERKGYKGIDDVDQHITEKMKGQKKKLE-- 236
P +L P ++ I ++ W+ + D + I + L
Sbjct: 316 QDLPREVLTTNPRRLSIIAESIRDGL--ATWDNWKHVNCDKLTTII-------ESSLNVL 366
Query: 237 EPWEKYDLMKEYRR--------TIPE--------EEQEEIFSEVFSELHQLSLSNKKLKK 280
EP E + + R IP + + V ++LH+ SL K+ K+
Sbjct: 367 EPAEYRKM---FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Query: 281 SRVYV 285
S + +
Sbjct: 424 STISI 428
Score = 43.3 bits (101), Expect = 7e-05
Identities = 42/328 (12%), Positives = 90/328 (27%), Gaps = 99/328 (30%)
Query: 46 ENRFMYQEFLPDPELKFRNQVR----EKLERSDMIKRRSVIDI---PSFFVGSILSVTSA 98
E+++ Y++ L E F + + + +S ++ + + I G++ +
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKS-ILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 99 DKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMYDPTIHN-------IT 151
+KFV ++ Y L + Y ++N
Sbjct: 72 LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR-QPSMMTRMYIEQRDRLYNDNQVFAKYN 130
Query: 152 VLRLEK--RLDDDLLYLR--------------------DALPQYST---FPFDM------ 180
V RL+ +L LL LR D Y F +
Sbjct: 131 VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLK 190
Query: 181 ---EPEYLLD---------------------GAPVPINDIKVKLKPRPWVGRWERKGYKG 216
PE +L+ + I+ I+ +L+ + K Y+
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR-----RLLKSKPYEN 245
Query: 217 ----IDDV-DQHITEKMKGQKK------------KLEEPWEKYDLMKEYRRTIPEEEQEE 259
+ +V + K L + + + T+ +E +
Sbjct: 246 CLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 260 IFSEVFSELHQLSLSNKKLKKSRVYVKP 287
+ + L + L + + P
Sbjct: 306 LLLKY------LDCRPQDLPREVLTTNP 327
Score = 28.7 bits (63), Expect = 3.0
Identities = 33/280 (11%), Positives = 78/280 (27%), Gaps = 103/280 (36%)
Query: 17 LTIL-RNLSKNSPLQFENAENGEKKLSIPQENRFMYQEFLPDPELKFRNQVREKLERSDM 75
L+++ ++ K+ N K S+ ++ +P L+ + ++ +
Sbjct: 392 LSLIWFDVIKSDV---MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA---- 444
Query: 76 IKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLG 135
RS++D D + +D
Sbjct: 445 -LHRSIVD----------HYNIPKTFDSDDLIP--------------------PYLDQYF 473
Query: 136 IE-IAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPIN 194
I + H + E+ + LD
Sbjct: 474 YSHIGH-------HLKNIEHPER--------------------MTLFRMVFLD-----FR 501
Query: 195 DIKVKLK--PRPWVGRWER-------KGYKGIDDVDQHITEKMKGQKKKLEEPWEKYD-L 244
++ K++ W K YK +I + +P KY+ L
Sbjct: 502 FLEQKIRHDSTAWNASGSILNTLQQLKFYK------PYICDN---------DP--KYERL 544
Query: 245 MKEYRRTIPEEEQEEIFSEVFSELHQLSLSNKKLKKSRVY 284
+ +P+ E+ I S+ +++L +++L + ++
Sbjct: 545 VNAILDFLPKIEENLICSK-YTDLLRIALMA---EDEAIF 580
>3bbo_R Ribosomal protein L19; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 233
Score = 50.8 bits (121), Expect = 1e-07
Identities = 29/151 (19%), Positives = 62/151 (41%)
Query: 18 TILRNLSKNSPLQFENAENGEKKLSIPQENRFMYQEFLPDPELKFRNQVREKLERSDMIK 77
++R+ +++S + + +P E+ +E P + + L + +
Sbjct: 74 FVVRSEAEDSSDAPAESVAVVAEEELPVESEAEAEERPPRQQRVKLGDIMGILNKKAVHA 133
Query: 78 RRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 137
+ +P G I+ + + + + GI I ++ G+ +R ++ +G+E
Sbjct: 134 AEELRPVPGIRTGDIVQIRLEVPENKRRLSVYKGIVISRQNAGIHTTIRIRRIIAGVGVE 193
Query: 138 IAYDMYDPTIHNITVLRLEKRLDDDLLYLRD 168
I + +Y P I I V+ K L YLRD
Sbjct: 194 IVFPLYSPNIKEIKVVSHRKVRKARLYYLRD 224
>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 = 44.0 bits (104), Expect = 8e-06
Identities = 25/106 (23%), Positives = 48/106 (45%), Gaps = 6/106 (5%)
Query: 68 EKLERSDMIK---RRSVIDIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLR 122
K+ R ++++ + +P F G + V + + + N+TR F G+ I G R
Sbjct: 5 IKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVR-EGNRTRSQAFEGVVIAINGSGSR 63
Query: 123 HEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRD 168
F +R + G+E + P ++ +T++ K L YLR+
Sbjct: 64 KSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRE 109
>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 = 1e-05
Identities = 29/107 (27%), Positives = 50/107 (46%), Gaps = 8/107 (7%)
Query: 64 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGL 121
+ + ++LE+ M + D+PSF G + V + +K R F G+ I R GL
Sbjct: 1 SNIIKQLEQEQMKQ-----DVPSFRPGDTVEVKVWVV-EGSKKRLQAFEGVVIAIRNRGL 54
Query: 122 RHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRD 168
F +R + + G+E + + P + +I+V R L YLR+
Sbjct: 55 HSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLRE 101
>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 = 41.2 bits (97), Expect = 7e-05
Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 8/108 (7%)
Query: 63 RNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCG 120
R + + +E + D+P F G + V+ K + N+TR F GI I+ R G
Sbjct: 3 RGALIKLVESRYVRT-----DLPEFRPGDTVRVSYKVK-EGNRTRIQDFEGIVIRIRRNG 56
Query: 121 LRHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRD 168
F +R V +G+E + ++ P I I +++ + L ++R+
Sbjct: 57 FNTTFTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAKLYFIRN 104
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.53
Identities = 8/62 (12%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 208 RWERKGYKGIDDVDQHITEKMKGQ-KKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFS 266
R + D + + ++ + + KK LEE ++ E + + + + +
Sbjct: 97 RLQEL-----DAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDA 151
Query: 267 EL 268
++
Sbjct: 152 DI 153
>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 = 30.1 bits (69), Expect = 0.89
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 218 DDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQE 258
+V H + + + W K L EY++ PE E
Sbjct: 291 QEVYDHYQKTILKPGVEANNKWNK--LFSEYQKKFPELGAE 329
>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 = 29.7 bits (67), Expect = 1.2
Identities = 19/106 (17%), Positives = 34/106 (32%), Gaps = 2/106 (1%)
Query: 183 EYLLDGAPVPINDIKVKLKPRPWVGRWERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKY 242
Y +DG V D + L+ + + DV+Q + + EE
Sbjct: 118 SYKIDGKTVSYKDYSIFLE-NENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSI 176
Query: 243 DLMKEYRRTIPEEEQ-EEIFSEVFSELHQLSLSNKKLKKSRVYVKP 287
KEY + E+ + +E ++ K K + V
Sbjct: 177 QYKKEYEELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLF 222
>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 = 1.4
Identities = 7/41 (17%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 218 DDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQE 258
++V ++ + ++ + + W ++ EY + PE E
Sbjct: 315 EEVYENFRKTVQDVGETAQAEWNT--MLGEYAQAYPELANE 353
>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 = 28.4 bits (62), Expect = 1.8
Identities = 7/16 (43%), Positives = 9/16 (56%), Gaps = 1/16 (6%)
Query: 157 KRLDDDL-LYLRDALP 171
K+L L LY D+ P
Sbjct: 23 KKLQASLKLYADDSAP 38
>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 = 27.2 bits (60), Expect = 2.5
Identities = 11/44 (25%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 222 QHITEKMKGQ-KKKLEEPWEKYDL-MKEYRRTIPEEEQEEIFSE 263
+ +++K K KK ++ + Y++ + + ++PEEEQ+ + E
Sbjct: 53 KLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGE 96
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
0.318 0.137 0.402
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: 4,558,811
Number of extensions: 285274
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 29
Length of query: 291
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 198
Effective length of database: 4,105,140
Effective search space: 812817720
Effective search space used: 812817720
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 (26.6 bits)