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= 025354
(254 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 = 430 bits (1105), Expect = e-121, Method: Compositional matrix adjust.
Identities = 202/224 (90%), Positives = 219/224 (97%)
Query: 20 APKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 79
APKPSSGPHKSRECLPLIL++RNRLKYALTYREVI+ILMQRHVLVDGKVRTDKTYPAGFM
Sbjct: 28 APKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFM 87
Query: 80 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 139
DV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88 DVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147
Query: 140 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 199
RYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207
Query: 200 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 243
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 = 328 bits (840), Expect = 3e-90, Method: Compositional matrix adjust.
Identities = 156/233 (66%), Positives = 187/233 (80%)
Query: 11 LVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRT 70
L+ L C AP+PS+GPHK RE LPLI+ LRNRLKYAL REV AILMQRHV VDGKVRT
Sbjct: 19 LLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRT 78
Query: 71 DKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPY 130
D TYPAGFMDV+++ TNENFRL+YD KGRF +H + DEEA +KL KV+ VQ G+KG+PY
Sbjct: 79 DTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPY 138
Query: 131 INTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNR 190
+ T+DGRTIRYPDP IK NDT+K+DL KITDFIKFD G +V VTGGRN GR+G I ++
Sbjct: 139 VVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHK 198
Query: 191 EKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 243
E+H G F+ +HI+D+L + F TRL NVF IG+ KP++SLPKGKGIKLSI EE
Sbjct: 199 ERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEE 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 = 254 bits (649), Expect = 3e-68, Method: Compositional matrix adjust.
Identities = 125/226 (55%), Positives = 162/226 (71%), Gaps = 2/226 (0%)
Query: 20 APKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAIL--MQRHVLVDGKVRTDKTYPAG 77
A +PS GPHK RE LPL ++L+ RL YAL R+V IL +++V VDGKVR DK YP G
Sbjct: 28 ATRPSQGPHKLRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKVRRDKGYPTG 87
Query: 78 FMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 137
MDVV I KT+++FR+LYDTKGRF L SL EEAK+KL KV + G IPYI T+D R
Sbjct: 88 LMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVTHDSR 147
Query: 138 TIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF 197
TIR+P+P IK DT+K DL NKI +F + GN+ + G N GRVGII++ EKH+GSF
Sbjct: 148 TIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKHQGSF 207
Query: 198 ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 243
+ H++DA G+ FATRLGN+F +G+G K W+ LP G G++ +I+EE
Sbjct: 208 DICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRETILEE 253
>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 273
Score = 234 bits (596), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 118/225 (52%), Positives = 153/225 (68%), Gaps = 1/225 (0%)
Query: 20 APKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 79
AP+P +GPHK RECL L++++RNRLKYAL E IL Q V VDGK R D YPAGFM
Sbjct: 25 APRPRAGPHKLRECLSLLIIIRNRLKYALNALEAQMILRQGLVCVDGKPRKDGKYPAGFM 84
Query: 80 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 139
DVV IPKT + FR+LYD KGRF L + + E+ K+ KV +V G IP T+DG I
Sbjct: 85 DVVEIPKTGDRFRILYDVKGRFALVRVSEAESSIKMMKVVNVYTGTGRIPVAVTHDGHRI 144
Query: 140 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 199
RYPDP DT+ D++E K+ D IK G +VMVTGG NRGR+G I + E+H G+F+
Sbjct: 145 RYPDPRTSRGDTLVYDVKEKKVLDLIKIGNGKVVMVTGGANRGRIGEIVSIERHPGAFDI 204
Query: 200 IHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEE 243
++DA GHEFATR N+F IGK S V+LPK +G+++++I+E
Sbjct: 205 ARLKDASGHEFATRATNIFVIGKDMSSVPVTLPKQQGLRINVIQE 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 = 3e-26, Method: Compositional matrix adjust.
Identities = 75/217 (34%), Positives = 118/217 (54%), Gaps = 7/217 (3%)
Query: 20 APKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 79
A +P GPH R +PL+ ++R+ L YA T RE IL + LVDG+VR D +P G M
Sbjct: 29 AVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIM 88
Query: 80 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR-- 137
DVVSIP+T E++R+L + G+ LH + ++EA K ++R+ + + +N +DG
Sbjct: 89 DVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQLNFHDGTNH 148
Query: 138 --TIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVG-IIKNREKHK 194
+I D + T+ + + E +I + + F+ G V VT G+N R G I++ +
Sbjct: 149 IVSIAEKDNYFTSY-TVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPM 207
Query: 195 GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 231
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: 28 HKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87
H + + L+ ++R+ LK + RE IL V VDGK +K + GF DV+ I
Sbjct: 2 HPKDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEI--N 59
Query: 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIK 147
E++R++Y+ +G L E A KL KVRS + T+DGRT D IK
Sbjct: 60 GESYRVVYNDQGALVLXKETKERASXKLLKVRSKVIAPGNRIQLGTHDGRTFITDDKSIK 119
Query: 148 ANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET-IHIQDAL 206
D + + + + KI++ IK GN +T G + + G I E +GS +H Q+
Sbjct: 120 VGDVLAVSVPDXKISEIIKXQPGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQEG- 178
Query: 207 GHEFATRLGNVFTIGKGSKPWVSLPK 232
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 = 0.17, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 43 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM-DVVSIPKTNENFRLLYDTKG 99
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 0.141 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,507,264
Number of Sequences: 62578
Number of extensions: 312142
Number of successful extensions: 562
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: 552
Number of HSP's gapped (non-prelim): 7
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
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: 50 (23.9 bits)