RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14031
(280 letters)
>1lsh_B Lipovitellin (LV-2); vitellogenin, lipoprotein, plasma apolipoprote
apolipoprotein B, APOB; HET: PLD UPL; 1.90A
{Ichthyomyzon unicuspis} SCOP: f.7.1.1
Length = 319
Score = 35.6 bits (81), Expect = 0.013
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 10/67 (14%)
Query: 6 GVCTVFGDPHYRTFDGKFY--SFQGSCKYQLTADCTG-GAFSIRVTNDARDTKTSSWTKT 62
C + TF+G F+ SC + L +C+ F + + D+ +
Sbjct: 259 SACELNEQ-SLTTFNGAFFNYDMPESCYHVLAQECSSRPPFIVLIKLDSER------RIS 311
Query: 63 VSIRIGD 69
+ +++ D
Sbjct: 312 LELQLDD 318
>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 = 34.4 bits (78), Expect = 0.045
Identities = 33/234 (14%), Positives = 60/234 (25%), Gaps = 75/234 (32%)
Query: 28 GSCKYQLTADCTGGAFSIRVTNDARDTKTSS----WTKTVSIRIGDMKVNLGEKLRVKID 83
GS K + D V + W + + + + +KL +ID
Sbjct: 160 GSGKTWVALD---------VCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID 210
Query: 84 G---QRVALPYDLPSKVIVTKTAESVLVETAIGIKVL------WDGNSFLEVSAPAKF-- 132
R ++ ++ + L+++ L + ++ F
Sbjct: 211 PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW------NAFNL 264
Query: 133 --KILDRLCGLCGNFNGISSDDLTTKRGRVVTDANKFGASWRVGGRKACSRPNTENSVGL 190
KIL LTT R + VTD + +S+ L
Sbjct: 265 SCKIL-----------------LTT-RFKQVTDF--------LSAATTTHISLDHHSMTL 298
Query: 191 G------------GVRCNHRLPQRKYRDKKCKPLRSDVFSA-CHARLNHLMYFK 231
R LP+ P R + + L +K
Sbjct: 299 TPDEVKSLLLKYLDCRPQ-DLPREV---LTTNPRRLSIIAESIRDGLATWDNWK 348
Score = 28.7 bits (63), Expect = 3.1
Identities = 32/213 (15%), Positives = 58/213 (27%), Gaps = 69/213 (32%)
Query: 50 DARDTKTSSWTKTVSIRIGDMKVNLGEKLRVK--------IDG---QRVALPYDLPSKVI 98
D T S + + +RI ++ L L+ K + + ++L K++
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269
Query: 99 VT----KTAESVLVETAIGIKVLWDGNSFLEVSAPAKFKILDRLCGLCGNFNGISSDDLT 154
+T + + + T I + + D + L + DL
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTP----------DEVKSLLLKYLDCRPQDLP 319
Query: 155 TKRGRVVTDANK-----FGASWRVGGRKACSRPNT-ENSVGLGGVRCNHRLPQRKYRDKK 208
R V N S R G T +N ++
Sbjct: 320 ----REVLTTNPRRLSIIAESIRDG-------LATWDN-----------------WKHVN 351
Query: 209 CKPLRSDVFSACHARLNHL------MYFKSCLV 235
C L + + + LN L F V
Sbjct: 352 CDKL-TTIIESS---LNVLEPAEYRKMFDRLSV 380
>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 = 0.099
Identities = 41/248 (16%), Positives = 67/248 (27%), Gaps = 90/248 (36%)
Query: 25 SFQGSCKYQLTADCTGGAFSI--RVTNDARDTKTSSWTKTVSIRIGD-----MKVNLG-- 75
SF + F I R +T S+ + M L
Sbjct: 291 SF-----FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPM---LSIS 342
Query: 76 ----EKLRVKIDGQRVALPYD------L---PSKVIVTKTAESV--LVETAIGIKVLWD- 119
E+++ ++ LP L ++V+ +S+ L T K
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGL 402
Query: 120 --------------GNSFLEVSAP--------AKFKILDRLCGLCGNFNGISSDDLT--- 154
N FL V++P A I L + N + ++ D+
Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDL--VKNNVS-FNAKDIQIPV 459
Query: 155 --TKRG---RVVTD-------------------ANKFGASWRV----GGRKACSRPNTEN 186
T G RV++ +F A+ + GG N
Sbjct: 460 YDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519
Query: 187 SVGLGGVR 194
G GVR
Sbjct: 520 KDGT-GVR 526
Score = 33.1 bits (75), Expect = 0.11
Identities = 46/281 (16%), Positives = 65/281 (23%), Gaps = 132/281 (46%)
Query: 105 SVLVETAIGI--KVLWDGNSFL--------------EVSAP----AKF------------ 132
+LV TA L + F E + P KF
Sbjct: 19 VLLVPTASFFIASQLQE--QFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSK 76
Query: 133 -----KILDRLCG------LCGN--------FNGISSDDLTTKRGRVVTDANKFGASWRV 173
++L+ L GN + L K ++ N A +
Sbjct: 77 VGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLV-KTKELIK--NYITAR-IM 132
Query: 174 GGRKACSRPN-------TENSVGL----GGVRCNHRLPQ---RKY----RD--KKCKPLR 213
R + N E + L GG Q Y RD + L
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGG--------QGNTDDYFEELRDLYQTYHVLV 184
Query: 214 SDVFSACHARLNHLM------------------------------YFKSCLVDMCECPL- 242
D+ L+ L+ Y S + CPL
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI---SCPLI 241
Query: 243 ---KNCHCESFTAYARECSRLGVQLGDWRK----LTGCHSG 276
+ H Y LG G+ R TG G
Sbjct: 242 GVIQLAH------YVVTAKLLGFTPGELRSYLKGATGHSQG 276
Score = 32.3 bits (73), Expect = 0.18
Identities = 36/221 (16%), Positives = 60/221 (27%), Gaps = 79/221 (35%)
Query: 16 YRTFDGKFYSFQGSCKYQLTADCTGGAFSIR--VTNDARDTKTSSWTKTVSIRIGDMKVN 73
Y+T + + + D G FSI V N+ ++I G K
Sbjct: 1636 YKTSKAAQDVWNRADNH--FKDTYG--FSILDIVINN---------PVNLTIHFGGEK-- 1680
Query: 74 LGEKLR---------VKIDGQRVALP-------------YDLPSKVIVTKT-----AESV 106
G+++R +DG+ + ++ + T A
Sbjct: 1681 -GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL-SATQFTQPA-LT 1737
Query: 107 LVETAIGIKVLWD-----------GNSFL-EVSAPAKFKILDRLCGLCGNFNGISSDD-- 152
L+E A + L G+S L E +A L L +S +
Sbjct: 1738 LMEKAA-FEDLKSKGLIPADATFAGHS-LGEYAA---------LASLAD---VMSIESLV 1783
Query: 153 -LTTKRGRVVTDANKFGASWRVGGRKACSRPNTENSVGLGG 192
+ RG + A R P V
Sbjct: 1784 EVVFYRGMTMQVAVPRDELGRSNYGMIAINP---GRVAASF 1821
Score = 28.5 bits (63), Expect = 3.6
Identities = 17/114 (14%), Positives = 35/114 (30%), Gaps = 28/114 (24%)
Query: 99 VTKTAESVLVETAIGIKVLWDGNSFLEVSAPAKFKILDRL--CGLCGN--FNGISSDDLT 154
T ++ ++ AI W+ SF K + L G+ + S
Sbjct: 270 ATGHSQGLVTAVAIAETDSWE--SFFVSVR----KAITVLFFIGVRCYEAYPNTSLPP-- 321
Query: 155 TKRGRVVTDANKFG---ASW--RVGGRKACSRPNTENSVGLGGVRCNHRLPQRK 203
++ D+ + S + ++ ++ V + N LP K
Sbjct: 322 ----SILEDSLENNEGVPSPMLSISN---LTQEQVQDYVN----KTNSHLPAGK 364
>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription;
2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A
Length = 214
Score = 29.4 bits (66), Expect = 1.2
Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 7/94 (7%)
Query: 13 DPHYRTFDGKFYSFQGSCKYQLTADCTGGAFSIRVTNDARDTKTSSWTKTVSIRIGDM-- 70
PH T K K L G + + +D + ++ + +++G
Sbjct: 122 CPHGGTIPAKGELLVEKHKLTLEEAKEKGDYILARVHD--NFDLLTYLERNGLQVGKTIR 179
Query: 71 ---KVNLGEKLRVKIDGQRVALPYDLPSKVIVTK 101
+ +++DGQ + L + ++ V K
Sbjct: 180 FLGYDDFSHLYSLEVDGQEIQLAQPIAQQIYVEK 213
>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix,
metal ION, ACT DNA-binding, ferrous iron, transcription;
1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A
1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A
1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A
1xcv_A 1f5t_A ...
Length = 226
Score = 28.3 bits (63), Expect = 2.7
Identities = 7/45 (15%), Positives = 19/45 (42%), Gaps = 9/45 (20%)
Query: 66 RIGDMKVNLGEKLRV---------KIDGQRVALPYDLPSKVIVTK 101
++ D + +G ++ + +G+ V L DL + + +
Sbjct: 181 QLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEE 225
>1rp0_A ARA6, thiazole biosynthetic enzyme; protein ligand complex,
biosynthetic protein; HET: AHZ HTO; 1.60A {Arabidopsis
thaliana} SCOP: c.3.1.6
Length = 284
Score = 28.1 bits (62), Expect = 3.0
Identities = 25/100 (25%), Positives = 44/100 (44%), Gaps = 9/100 (9%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRVALPYDLPSKVIVTKTAESVLVETAIGIKVLWDGNSFLE 125
+ +++V + E+ V G L L S +IV K A L E + + ++++
Sbjct: 60 KNPNVQVAIIEQ-SVSP-GGGAWLGGQLFSAMIVRKPAHLFLDEIGVAYD---EQDTYVV 114
Query: 126 VSAPAKF--KILDRLCGLCG--NFNGISSDDLTTKRGRVV 161
V A F I+ +L FN ++++DL K RV
Sbjct: 115 VKHAALFTSTIMSKLLARPNVKLFNAVAAEDLIVKGNRVG 154
>2oqr_A Sensory transduction protein REGX3; response regulator,
winged-helix-turn-helix, DNA-binding, 3D swapping, two
component system; 2.03A {Mycobacterium tuberculosis
H37RV}
Length = 230
Score = 27.8 bits (63), Expect = 3.0
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 52 RDTKTSSWTKTVSIRIGDMKVNLGEKLRVKIDGQRVALP---YDL 93
R S + G +++++ E+ V ++G + LP +DL
Sbjct: 121 RGGDDDSEMSDGVLESGPVRMDV-ERHVVSVNGDTITLPLKEFDL 164
>3v2d_H 50S ribosomal protein L6; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_F 2hgj_H 2hgq_H 2hgu_H 1vsa_F 2j03_H 2jl6_H 2jl8_H
2v47_H 2v49_H 2wdi_H 2wdj_H 2wdl_H 2wdn_H 2wh2_H 2wh4_H
2wrj_H 2wrl_H 2wro_H 2wrr_H ...
Length = 180
Score = 27.8 bits (63), Expect = 3.2
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRVA-------LPYDLPSKVIVTKTAESVLVE 109
RIG + + + + + V++ RV L + ++ V V VE
Sbjct: 3 RIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVE 53
>1rl6_A Protein (ribosomal protein L6); RNA-binding protein, gentamicin
resistance, alpha/beta protein; 2.00A {Geobacillus
stearothermophilus} SCOP: d.141.1.1 d.141.1.1 PDB:
1giy_H 1ml5_h* 1c04_B 1yl3_H 2b66_H 2b9n_H 2b9p_H 1eg0_J
487d_J
Length = 177
Score = 27.5 bits (62), Expect = 3.7
Identities = 8/51 (15%), Positives = 17/51 (33%), Gaps = 7/51 (13%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRVA-------LPYDLPSKVIVTKTAESVLVE 109
R+G + + + V ++G V L + +T + V
Sbjct: 2 RVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVT 52
>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A
{Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB:
3nns_A*
Length = 220
Score = 27.8 bits (63), Expect = 3.7
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 65 IRIGDMKVNLGEKLRVKIDGQRVALP---YDL 93
GD+K++ V + G+R+ LP +++
Sbjct: 123 YDFGDLKIDA-TGFTVFLKGKRIHLPKKEFEI 153
>2zjr_E 50S ribosomal protein L6; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.141.1.1 d.141.1.1 PDB: 1nwx_E*
1xbp_E* 2zjp_E* 2zjq_E 1nwy_E 3cf5_E* 3dll_E* 3pio_E*
3pip_E* 1pnu_E 1pny_E 1vor_H 1vou_H 1vow_H 1voy_H 1vp0_H
Length = 185
Score = 27.5 bits (62), Expect = 4.1
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 7/51 (13%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRVA-------LPYDLPSKVIVTKTAESVLVE 109
RIG + + + V L +++ V + + +LVE
Sbjct: 3 RIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVE 53
>1nkw_E 50S ribosomal protein L6; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1sm1_E*
Length = 212
Score = 27.2 bits (61), Expect = 4.7
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 7/51 (13%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRVA-------LPYDLPSKVIVTKTAESVLVE 109
RIG + + + V L +++ V + + +LVE
Sbjct: 30 RIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVE 80
>2gwr_A DNA-binding response regulator MTRA; two-component regulatory
system, transcription regulation, phosphorylation, OMPR
family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A
Length = 238
Score = 27.1 bits (61), Expect = 5.1
Identities = 7/32 (21%), Positives = 20/32 (62%), Gaps = 4/32 (12%)
Query: 65 IRIGDMKVNLGEKLRVKIDGQRVALP---YDL 93
+ I D+++++ +V +G++++L +DL
Sbjct: 131 LSIADVEIDV-PAHKVTRNGEQISLTPLEFDL 161
>3r8s_G 50S ribosomal protein L6; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_E
1p86_E 2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G* 2qao_G*
2qba_G* 2qbc_G* 2qbe_G 2qbg_G 2qbi_G* 2qbk_G* 2qov_G
2qox_G 2qoz_G* 2qp1_G* 2rdo_G 2vhm_G ...
Length = 176
Score = 26.7 bits (60), Expect = 7.5
Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 7/51 (13%)
Query: 66 RIGDMKVNLGEKLRVKIDGQRVA-------LPYDLPSKVIVTKTAESVLVE 109
R+ V + + VKI+GQ + L L V V ++
Sbjct: 2 RVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFG 52
>3ocr_A Class II aldolase/adducin domain protein; PSI-2, midwest center for
structural genomics, protein struc initiative, MCSG,
lyase; 1.95A {Pseudomonas syringae PV}
Length = 273
Score = 26.5 bits (59), Expect = 8.5
Identities = 5/31 (16%), Positives = 12/31 (38%)
Query: 23 FYSFQGSCKYQLTADCTGGAFSIRVTNDARD 53
++ + +C Q+ A G A + +
Sbjct: 206 LHALEYACNIQIAAQSAGNAELVFPPREVIA 236
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
0.322 0.137 0.441
Gapped
Lambda K H
0.267 0.0843 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,320,969
Number of extensions: 247730
Number of successful extensions: 537
Number of sequences better than 10.0: 1
Number of HSP's gapped: 537
Number of HSP's successfully gapped: 28
Length of query: 280
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 188
Effective length of database: 4,133,061
Effective search space: 777015468
Effective search space used: 777015468
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 (21.9 bits)
S2: 57 (25.5 bits)