RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1265
(384 letters)
>3r8s_R 50S ribosomal protein L21; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1vs8_R 1vs6_R 2aw4_R 2awb_R 1vt2_R 2i2v_R 2j28_R 2i2t_R*
2qao_R* 2qba_R* 2qbc_R* 2qbe_R 2qbg_R 2qbi_R* 2qbk_R*
2qov_R 2qox_R 2qoz_R* 2qp1_R* 2rdo_R ...
Length = 103
Score = 66.8 bits (164), Expect = 4e-14
Identities = 20/109 (18%), Positives = 46/109 (42%), Gaps = 12/109 (11%)
Query: 210 FAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLV 269
+A+ G+Q +V+ + ++ A G+ ++F +VL++ + +G P + G
Sbjct: 2 YAVFQSGGKQHRVSEGQTVRLEKLDIAT--GETVEFAEVLMIANGEEVKIGVPFV-DG-G 57
Query: 270 NVTGTIIEKDLSHTR----TNFRKIPRKRHTRFRFFRTQLTMIRINEIE 314
+ ++ H R + RK + + + R T ++I I
Sbjct: 58 VIKAEVVA----HGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGIS 102
>3bbo_T Ribosomal protein L21; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 257
Score = 67.8 bits (165), Expect = 4e-13
Identities = 31/105 (29%), Positives = 44/105 (41%), Gaps = 3/105 (2%)
Query: 210 FAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLV 269
FA++ + RQ V P I A DKI KVLLVG T +G P++
Sbjct: 125 FAVVVIGSRQYIVIPGRWIYTQRLKGAT-VNDKIVLNKVLLVGTKASTYIGTPIV-TN-A 181
Query: 270 NVTGTIIEKDLSHTRTNFRKIPRKRHTRFRFFRTQLTMIRINEIE 314
V + E+ L F+ +K + R R +T I+I I
Sbjct: 182 AVHAVVEEQLLDDKVIVFKYKKKKNYRRNIGHRQPITRIKITGIT 226
>3v2d_V 50S ribosomal protein L21; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_P 2hgj_U 2hgq_U 2hgu_U 1vsa_P 2j03_V 2jl6_V 2jl8_V
2v47_V 2v49_V 2wdi_V 2wdj_V 2wdl_V 2wdn_V 2wh2_V 2wh4_V
2wrj_V 2wrl_V 2wro_V 2wrr_V ...
Length = 101
Score = 62.9 bits (154), Expect = 1e-12
Identities = 27/109 (24%), Positives = 48/109 (44%), Gaps = 14/109 (12%)
Query: 210 FAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLV 269
FAI+ G+Q +V P + V+ P G ++ +LL G + T+VG P++ G
Sbjct: 2 FAIVKTGGKQYRVEPGLKLRVEKLDAEP--GATVELPVLLLGG--EKTVVGTPVV-EG-A 55
Query: 270 NVTGTIIEKDLSHTR----TNFRKIPRKRHTRFRFFRTQLTMIRINEIE 314
+V ++ H R + + ++ R + R T + I EI
Sbjct: 56 SVVAEVLG----HGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR 100
>2zjr_O 50S ribosomal protein L21; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.155.1.1 PDB: 1nwx_P* 1nwy_P* 1pnu_P
1pny_P 1sm1_P* 1vor_S 1vou_S 1vow_S 1voy_S 1vp0_S
1xbp_P* 1yl3_2 2b66_V 2b9n_V 2b9p_V 2zjp_O* 2zjq_O
1nkw_P 3cf5_O* 3dll_O* ...
Length = 100
Score = 60.6 bits (148), Expect = 6e-12
Identities = 26/109 (23%), Positives = 43/109 (39%), Gaps = 15/109 (13%)
Query: 210 FAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGADFTLVGRPLLTPGLV 269
FAII G+Q +V+ D+I V+S GDK++ + + + G V
Sbjct: 2 FAIIQTGGKQYRVSEGDVIRVESLQGEA--GDKVELKALFVGGE---QTVFGEDA-GK-Y 54
Query: 270 NVTGTIIEKDLSHTR----TNFRKIPRKRHTRFRFFRTQLTMIRINEIE 314
V ++E H R + ++ R R T I+I I+
Sbjct: 55 TVQAEVVE----HGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGIQ 99
>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 = 55.4 bits (133), Expect = 2e-08
Identities = 54/298 (18%), Positives = 95/298 (31%), Gaps = 96/298 (32%)
Query: 2 SILDTSYWHGSHALECKRNIQTEPTYLRRVTIHCLVPRGLIEGTVATEVLSFRNRKGERI 61
+ ++ G E N P+ L + EG + +LS N
Sbjct: 298 KAITVLFFIGVRCYEAYPNTSLPPSILEDS-----LENN--EGV-PSPMLSISN------ 343
Query: 62 GQETASRSEKDTSYWRGSHALECKRNIHYIQTEPTYL---RRVTIHCLV--PRGL-IEGP 115
++ + ++ Y+ ++L ++V I LV + L + GP
Sbjct: 344 ----LTQEQ-----------VQD-----YVNKTNSHLPAGKQVEI-SLVNGAKNLVVSGP 382
Query: 116 VAT-EVLSFRNRKGEDRTGDSQ---PFRERTLSVQDK----GTPYIRPDLDVKVVALTSP 167
+ L+ RK + +G Q PF ER L ++ +P+ S
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPF------------HSH 430
Query: 168 LLLPSSSEF-----TKGTEIVSTKLSSVPVYLNLVNNQIERNEQGRLFAIIHVLGRQTKV 222
LL+P+S + + +PVY + + R G +I +
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDI-QIPVY-DTFDGSDLRVLSG---SISERI------ 479
Query: 223 TPNDIIIVDSNSFAPLNGDKIKFEK---VLLVGGADFTLVGRPLLTPGLVNVTGTIIE 277
D II P+ + K +L DF G P GL +T +
Sbjct: 480 --VDCIIRL-----PVKWETTTQFKATHIL-----DF---G-PGGASGLGVLTHRNKD 521
Score = 40.4 bits (94), Expect = 0.001
Identities = 74/359 (20%), Positives = 107/359 (29%), Gaps = 112/359 (31%)
Query: 24 EPTYLRRVTIHCLVPR--GLIEGTVATEVLSFRNRKGERIGQETASRSEKDTSYWRGSHA 81
E YL IH L + + T+ +N RI + + +++ +R
Sbjct: 92 ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR--AV 149
Query: 82 LECKRNIHYI---Q--TEPTY---LRRV--TIHCLVPRGLIEGPVATEVLSFRNRKGEDR 131
E + I Q T+ Y LR + T H LV LI+ + E LS R
Sbjct: 150 GEGNAQLVAIFGGQGNTD-DYFEELRDLYQTYHVLV-GDLIK--FSAETLSELIR----T 201
Query: 132 TGDSQPFRERTLSVQD-KGTPYIRPDLDVKVVALTS-PL-----------------LLPS 172
T D++ + L++ + P PD D + S PL P
Sbjct: 202 TLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPG 261
Query: 173 ------SSEFTKGTEIVSTKL----SSVPVYLNLVNNQIERNEQGRLFAIIHVLG-RQTK 221
+V+ S + V I LF I G R +
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT-----VLFFI----GVRCYE 312
Query: 222 VTPN----DIIIVDSNSFAPLNGDKIKFEKV----LLVGGADFTLVGRPL------LTPG 267
PN I+ DS N E V L + V + L G
Sbjct: 313 AYPNTSLPPSILEDSLE----NN-----EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAG 363
Query: 268 ------LVN------VTGTIIEKDLSHTRTNFRK-----------IP-RKRHTRF--RF 300
LVN V+G + L RK IP +R +F RF
Sbjct: 364 KQVEISLVNGAKNLVVSGPP--QSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF 420
Score = 40.0 bits (93), Expect = 0.001
Identities = 38/250 (15%), Positives = 78/250 (31%), Gaps = 91/250 (36%)
Query: 154 RPDLDVKVVALTSPLLLPSSS---------EFTKGTEIVSTKL------SSVP----VYL 194
RP L + +L LL+P++S +F K + ++ +L
Sbjct: 7 RP-LTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFL 65
Query: 195 NLVNNQIERNEQGRLFAIIHVLGRQTKVTPNDIIIVDSNSFAPLNGDKIKFEKVLLVGGA 254
V++ +E ++ G+ ++++ L +FE L G
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLC---------------------LT----EFENCYL-EGN 99
Query: 255 DF-TLVGRPLLTPGLVNVTGTIIEKDLSHTRTNFR-----KIPRKRHTRFRFFRTQLTMI 308
D L + L+ T + K + K P + + FR +
Sbjct: 100 DIHALAAK------LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRA----V 149
Query: 309 RINEIEIIEKV--GQRKDVEGTQRLINLC---LQTQYNLILENQGKTY-------MASLA 356
+++ + GQ G + L+ Y +TY + A
Sbjct: 150 GEGNAQLV-AIFGGQ-----GN---TDDYFEELRDLY--------QTYHVLVGDLIKFSA 192
Query: 357 QHLPVLVTSS 366
+ L L+ ++
Sbjct: 193 ETLSELIRTT 202
>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 = 29.8 bits (66), Expect = 1.9
Identities = 19/114 (16%), Positives = 36/114 (31%), Gaps = 29/114 (25%)
Query: 278 KD-LSHTRTNFRKIPRKRHTRFRFFRTQLTMIRINEIEIIEKVGQRKDVEGTQRLINL-- 334
KD LS F + + ++ L+ I+ I + + V GT RL
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQ-DMPKSILSKEEIDHI-----IMSKDAVSGTLRLFWTLL 72
Query: 335 -------------CLQTQYNLILENQGKTYMASLAQHLPVLVTSSY-RRKNSLW 374
L+ Y ++ P ++T Y +++ L+
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ------PSMMTRMYIEQRDRLY 120
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA
synthetase, tyrrs, ligase, tyrosine, RNA-binding,
ATP-binding; 2.9A {Mycobacterium tuberculosis}
Length = 432
Score = 28.0 bits (63), Expect = 6.0
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 149 GTPYIRPDLDVKVVALTSPLLLPSS-SEFTKGTE 181
G +R L V ALT PL+ + ++F K T
Sbjct: 204 GVRLVRQKLGATVHALTVPLVTAADGTKFGKSTG 237
>3ckj_A Putative uncharacterized protein; mycobacteria, unknown function;
HET: CIT; 1.80A {Mycobacterium paratuberculosis} PDB:
3ckn_A* 3cko_A* 3ckq_A* 3ckv_A* 3e26_A 3e25_A
Length = 329
Score = 27.7 bits (61), Expect = 7.2
Identities = 6/32 (18%), Positives = 17/32 (53%)
Query: 203 RNEQGRLFAIIHVLGRQTKVTPNDIIIVDSNS 234
+E+ + ++I + +++I++DS S
Sbjct: 57 LDEEDTIGSVIDSISPLVDGLVDELIVLDSGS 88
>1ps9_A 2,4-dienoyl-COA reductase; iron-sulfur, TIM barrel, flavodoxin,
flavin, electron transfer, hydride transfer,
oxidoreductase; HET: FAD FMN NAP MDE; 2.20A {Escherichia
coli} SCOP: c.1.4.1 c.3.1.1 c.4.1.1
Length = 671
Score = 27.3 bits (61), Expect = 9.3
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 246 EKVLLVGGADFTLVGRPLLT-PGLVN 270
+ +L G AD + RP L L++
Sbjct: 296 DDILSRGDADMVSMARPFLADAELLS 321
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 0.136 0.396
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,575,548
Number of extensions: 329684
Number of successful extensions: 639
Number of sequences better than 10.0: 1
Number of HSP's gapped: 628
Number of HSP's successfully gapped: 20
Length of query: 384
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 289
Effective length of database: 4,049,298
Effective search space: 1170247122
Effective search space used: 1170247122
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: 58 (25.9 bits)