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= 023289
(284 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 = 431 bits (1108), Expect = e-121, Method: Compositional matrix adjust.
Identities = 203/227 (89%), Positives = 220/227 (96%)
Query: 47 GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
G APKPSSGPHKSRECLPLIL++RNRLKYALTYREVI+ILMQRHVLVDGKVRTDKTYPA
Sbjct: 25 GAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPA 84
Query: 107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
GFMDV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDG
Sbjct: 85 GFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDG 144
Query: 167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
RTIRYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGS
Sbjct: 145 RTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGS 204
Query: 227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 273
FETIH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE
Sbjct: 205 FETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEE 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 = 325 bits (833), Expect = 2e-89, Method: Compositional matrix adjust.
Identities = 154/227 (67%), Positives = 184/227 (81%)
Query: 47 GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
G AP+PS+GPHK RE LPLI+ LRNRLKYAL REV AILMQRHV VDGKVRTD TYPA
Sbjct: 25 GCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPA 84
Query: 107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
GFMDV+++ TNENFRL+YD KGRF +H + DEEA +KL KV+ VQ G+KG+PY+ T+DG
Sbjct: 85 GFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDG 144
Query: 167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
RTIRYPDP IK NDT+K+DL KITDFIKFD G +V VTGGRN GR+G I ++E+H G
Sbjct: 145 RTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGG 204
Query: 227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 273
F+ +HI+D+L + F TRL NVF IG+ KP++SLPKGKGIKLSI EE
Sbjct: 205 FDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEE 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 = 257 bits (656), Expect = 7e-69, Method: Compositional matrix adjust.
Identities = 126/229 (55%), Positives = 164/229 (71%), Gaps = 2/229 (0%)
Query: 47 GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAIL--MQRHVLVDGKVRTDKTY 104
G+ A +PS GPHK RE LPL ++L+ RL YAL R+V IL +++V VDGKVR DK Y
Sbjct: 25 GIWATRPSQGPHKLRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKVRRDKGY 84
Query: 105 PAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTY 164
P G MDVV I KT+++FR+LYDTKGRF L SL EEAK+KL KV + G IPYI T+
Sbjct: 85 PTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVTH 144
Query: 165 DGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK 224
D RTIR+P+P IK DT+K DL NKI +F + GN+ + G N GRVGII++ EKH+
Sbjct: 145 DSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKHQ 204
Query: 225 GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 273
GSF+ H++DA G+ FATRLGN+F +G+G K W+ LP G G++ +I+EE
Sbjct: 205 GSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRETILEE 253
>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 273
Score = 236 bits (601), Expect = 1e-62, Method: Compositional matrix adjust.
Identities = 119/228 (52%), Positives = 155/228 (67%), Gaps = 1/228 (0%)
Query: 47 GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
G+ AP+P +GPHK RECL L++++RNRLKYAL E IL Q V VDGK R D YPA
Sbjct: 22 GVFAPRPRAGPHKLRECLSLLIIIRNRLKYALNALEAQMILRQGLVCVDGKPRKDGKYPA 81
Query: 107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
GFMDVV IPKT + FR+LYD KGRF L + + E+ K+ KV +V G IP T+DG
Sbjct: 82 GFMDVVEIPKTGDRFRILYDVKGRFALVRVSEAESSIKMMKVVNVYTGTGRIPVAVTHDG 141
Query: 167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
IRYPDP DT+ D++E K+ D IK G +VMVTGG NRGR+G I + E+H G+
Sbjct: 142 HRIRYPDPRTSRGDTLVYDVKEKKVLDLIKIGNGKVVMVTGGANRGRIGEIVSIERHPGA 201
Query: 227 FETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEE 273
F+ ++DA GHEFATR N+F IGK S V+LPK +G+++++I+E
Sbjct: 202 FDIARLKDASGHEFATRATNIFVIGKDMSSVPVTLPKQQGLRINVIQE 249
>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 = 115 bits (287), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 75/217 (34%), Positives = 118/217 (54%), Gaps = 7/217 (3%)
Query: 50 APKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 109
A +P GPH R +PL+ ++R+ L YA T RE IL + LVDG+VR D +P G M
Sbjct: 29 AVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIM 88
Query: 110 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR-- 167
DVVSIP+T E++R+L + G+ LH + ++EA K ++R+ + + +N +DG
Sbjct: 89 DVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQLNFHDGTNH 148
Query: 168 --TIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVG-IIKNREKHK 224
+I D + T+ + + E +I + + F+ G V VT G+N R G I++ +
Sbjct: 149 IVSIAEKDNYFTSY-TVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPM 207
Query: 225 GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 261
G + + I+D G F T F +G KP +SLP
Sbjct: 208 GWPDVVTIEDEEGELFDTLKEYAFVVGT-DKPKISLP 243
>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 = 93.2 bits (230), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 65/206 (31%), Positives = 99/206 (48%), Gaps = 7/206 (3%)
Query: 58 HKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 117
H + + L+ ++R+ LK + RE IL V VDGK +K + GF DV+ I
Sbjct: 2 HPKDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEI--N 59
Query: 118 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIK 177
E++R++Y+ +G L E A KL KVRS + T+DGRT D IK
Sbjct: 60 GESYRVVYNDQGALVLXKETKERASXKLLKVRSKVIAPGNRIQLGTHDGRTFITDDKSIK 119
Query: 178 ANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET-IHIQDAL 236
D + + + + KI++ IK GN +T G + + G I E +GS +H Q+
Sbjct: 120 VGDVLAVSVPDXKISEIIKXQPGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQEG- 178
Query: 237 GHEFATRLGNVFTIGKGSKPWVSLPK 262
F+T +VF IG +V P+
Sbjct: 179 ---FSTIKDHVFXIGSSKFSFVLSPE 201
>pdb|4H3V|A Chain A, Crystal Structure Of Oxidoreductase Domain Protein From
Kribbella Flavida
pdb|4H3V|B Chain B, Crystal Structure Of Oxidoreductase Domain Protein From
Kribbella Flavida
Length = 390
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 73 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM-DVVSIPKTNENFRLLYDTKG 129
R TYR V AI + R ++ DGK+ T + A ++ D ++ P+ ++RL D G
Sbjct: 131 RSXVGFTYRRVPAIALARKLVADGKIGTVRHVRAQYLQDWIADPEAPLSWRLDKDKAG 188
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 0.140 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,862,057
Number of Sequences: 62578
Number of extensions: 315858
Number of successful extensions: 551
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 541
Number of HSP's gapped (non-prelim): 7
length of query: 284
length of database: 14,973,337
effective HSP length: 98
effective length of query: 186
effective length of database: 8,840,693
effective search space: 1644368898
effective search space used: 1644368898
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)