BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 029796
(187 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 265
Score = 309 bits (791), Expect = 7e-85, Method: Compositional matrix adjust.
Identities = 145/164 (88%), Positives = 159/164 (96%)
Query: 13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
DV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88 DVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147
Query: 73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
RYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207
Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
IH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE
Sbjct: 208 IHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEE 251
>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 261
Score = 224 bits (572), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 104/164 (63%), Positives = 131/164 (79%)
Query: 13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
DV+++ TNENFRL+YD KGRF +H + DEEA +KL KV+ VQ G+KG+PY+ T+DGRTI
Sbjct: 88 DVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTI 147
Query: 73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
RYPDP IK NDT+K+DL KITDFIKFD G +V VTGGRN GR+G I ++E+H G F+
Sbjct: 148 RYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDL 207
Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
+HI+D+L + F TRL NVF IG+ KP++SLPKGKGIKLSI EE
Sbjct: 208 VHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEE 251
>pdb|2XZM|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 260
Score = 191 bits (485), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 92/170 (54%), Positives = 122/170 (71%)
Query: 7 FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
+ T L DVV I KT+++FR+LYDTKGRF L SL EEAK+KL KV + G IPYI T
Sbjct: 84 YPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVT 143
Query: 67 YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
+D RTIR+P+P IK DT+K DL NKI +F + GN+ + G N GRVGII++ EKH
Sbjct: 144 HDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKH 203
Query: 127 KGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
+GSF+ H++DA G+ FATRLGN+F +G+G K W+ LP G G++ +I+EE
Sbjct: 204 QGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRETILEE 253
>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 273
Score = 159 bits (403), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 81/165 (49%), Positives = 110/165 (66%), Gaps = 1/165 (0%)
Query: 13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
DVV IPKT + FR+LYD KGRF L + + E+ K+ KV +V G IP T+DG I
Sbjct: 85 DVVEIPKTGDRFRILYDVKGRFALVRVSEAESSIKMMKVVNVYTGTGRIPVAVTHDGHRI 144
Query: 73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
RYPDP DT+ D++E K+ D IK G +VMVTGG NRGR+G I + E+H G+F+
Sbjct: 145 RYPDPRTSRGDTLVYDVKEKKVLDLIKIGNGKVVMVTGGANRGRIGEIVSIERHPGAFDI 204
Query: 133 IHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEE 176
++DA GHEFATR N+F IGK S V+LPK +G+++++I+E
Sbjct: 205 ARLKDASGHEFATRATNIFVIGKDMSSVPVTLPKQQGLRINVIQE 249
>pdb|3KBG|A Chain A, Crystal Structure Of The 30s Ribosomal Protein S4e From
Thermoplasma Acidophilum. Northeast Structural Genomics
Consortium Target Tar28
Length = 213
Score = 67.0 bits (162), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 49/160 (30%), Positives = 74/160 (46%), Gaps = 7/160 (4%)
Query: 7 FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
F DV+ I E++R++Y+ +G L E A KL KVRS + T
Sbjct: 48 FAVGFXDVIEI--NGESYRVVYNDQGALVLXKETKERASXKLLKVRSKVIAPGNRIQLGT 105
Query: 67 YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
+DGRT D IK D + + + + KI++ IK GN +T G + + G I E
Sbjct: 106 HDGRTFITDDKSIKVGDVLAVSVPDXKISEIIKXQPGNKAYITAGSHVNQTGTISKIEAK 165
Query: 127 KGSFET-IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 165
+GS +H Q+ F+T +VF IG +V P+
Sbjct: 166 EGSSANLVHFQEG----FSTIKDHVFXIGSSKFSFVLSPE 201
>pdb|3J20|E Chain E, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 243
Score = 64.7 bits (156), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 49/165 (29%), Positives = 85/165 (51%), Gaps = 7/165 (4%)
Query: 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYI 64
+ F + DVVSIP+T E++R+L + G+ LH + ++EA K ++R+ + + +
Sbjct: 81 YKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQL 140
Query: 65 NTYDGR----TIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVG-I 119
N +DG +I D + T+ + + E +I + + F+ G V VT G+N R G I
Sbjct: 141 NFHDGTNHIVSIAEKDNYFTSY-TVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRI 199
Query: 120 IKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 164
++ + G + + I+D G F T F +G KP +SLP
Sbjct: 200 VEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGT-DKPKISLP 243
>pdb|3UAJ|H Chain H, Crystal Structure Of The Envelope Glycoprotein
Ectodomain From Dengue Virus Serotype 4 In Complex With
The Fab Fragment Of The Chimpanzee Monoclonal Antibody
5h2
pdb|3UAJ|C Chain C, Crystal Structure Of The Envelope Glycoprotein
Ectodomain From Dengue Virus Serotype 4 In Complex With
The Fab Fragment Of The Chimpanzee Monoclonal Antibody
5h2
pdb|3UC0|H Chain H, Crystal Structure Of Domain I Of The Envelope
Glycoprotein Ectodomain From Dengue Virus Serotype 4 In
Complex With The Fab Fragment Of The Chimpanzee
Monoclonal Antibody 5h2
pdb|3UC0|I Chain I, Crystal Structure Of Domain I Of The Envelope
Glycoprotein Ectodomain From Dengue Virus Serotype 4 In
Complex With The Fab Fragment Of The Chimpanzee
Monoclonal Antibody 5h2
Length = 236
Score = 26.6 bits (57), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 55 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 95
Q KG+ +I R Y +P +K+ TI +D +N+I+
Sbjct: 39 QSPGKGLEWIGYAHSRVSAYYNPSLKSRVTISVDTSKNQIS 79
>pdb|1N9L|A Chain A, Crystal Structure Of The Phot-lov1 Domain From
Chlamydomonas Reinhardtii In The Dark State.
pdb|1N9N|A Chain A, Crystal Structure Of The Phot-Lov1 Domain From
Chlamydomonas Reinhardtii In Illuminated State. Data
Set Of A Single Crystal.
pdb|1N9O|A Chain A, Crystal Structure Of The Phot-Lov1 Domain From
Chlamydomonas Reinhardtii In Illuminated State.
Composite Data Set
Length = 109
Score = 26.6 bits (57), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 36 LHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD 76
+ +RD K + C VR + + + G P+ N I+ PD
Sbjct: 54 VQKIRDAIKKGEACSVRLLNYRKDGTPFWNLLTVTPIKTPD 94
>pdb|2RF8|A Chain A, Crystal Structure Of The Mutant C2a Conjugated Bile Acid
Hydrolase From Clostridium Perfringens
pdb|2RF8|B Chain B, Crystal Structure Of The Mutant C2a Conjugated Bile Acid
Hydrolase From Clostridium Perfringens
Length = 329
Score = 26.6 bits (57), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 38 SLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD 76
S R E K L + S +KGI Y NTY+ I D
Sbjct: 265 STRTVEEKSDLTQYTSCMCLEKGIYYYNTYENNQINAID 303
>pdb|2RG2|A Chain A, Crystal Structure Of Variant R18l Of Conjugated Bile Acid
Hydrolase From Clostridium Perfringens
Length = 328
Score = 26.6 bits (57), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 38 SLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD 76
S R E K L + S +KGI Y NTY+ I D
Sbjct: 264 STRTVEEKSDLTQYTSCMCLEKGIYYYNTYENNQINAID 302
>pdb|2BJF|A Chain A, Crystal Structure Of Conjugated Bile Acid Hydrolase From
Clostridium Perfringens In Complex With Reaction
Products Taurine And Deoxycholate
pdb|2BJG|A Chain A, Crystal Structure Of Conjugated Bile Acid Hydrolase From
Clostridium Perfringens In Complex With Reaction
Products Taurine And Deoxycholate
pdb|2BJG|B Chain B, Crystal Structure Of Conjugated Bile Acid Hydrolase From
Clostridium Perfringens In Complex With Reaction
Products Taurine And Deoxycholate
Length = 329
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 38 SLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD 76
S R E K L + S +KGI Y NTY+ I D
Sbjct: 265 STRTVEEKSDLTQYTSCMCLEKGIYYYNTYENNQINAID 303
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.142 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,460,093
Number of Sequences: 62578
Number of extensions: 227501
Number of successful extensions: 459
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 450
Number of HSP's gapped (non-prelim): 11
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)