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= 029041
(200 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 = 363 bits (931), Expect = e-101, Method: Compositional matrix adjust.
Identities = 170/190 (89%), Positives = 183/190 (96%)
Query: 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
MQRHVLVD KVRTDKTYPAGFMDV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCK
Sbjct: 66 MQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCK 125
Query: 61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
VRSVQFGQKGIPY+NTYDGRTIRYPDP+IKANDTIK+DLETNKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTG 185
Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
GRN GRVG+IKNREKHKGSFETIH++DALGH+FATRLGNVFTIGKG KPWVSLPKGKGIK
Sbjct: 186 GRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIK 245
Query: 181 LSIIEEARKR 190
LSIIEE RKR
Sbjct: 246 LSIIEEQRKR 255
>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 = 268 bits (684), Expect = 2e-72, Method: Compositional matrix adjust.
Identities = 125/192 (65%), Positives = 155/192 (80%)
Query: 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
MQRHV VD KVRTD TYPAGFMDV+++ TNENFRL+YD KGRF +H I DEEA +KL K
Sbjct: 66 MQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGK 125
Query: 61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
V+ VQ G+KG+PY+ T+DGRTIRYPDP IK NDT+K+DL + KIT+FIKFD G +V VTG
Sbjct: 126 VKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTG 185
Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
GRN GR+G I ++E+H G F+ +HI+D+L + F TRL NVF IG+ KP++SLPKGKGIK
Sbjct: 186 GRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIK 245
Query: 181 LSIIEEARKRQA 192
LSI EE +R+A
Sbjct: 246 LSIAEERDRRRA 257
>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 = 216 bits (549), Expect = 9e-57, Method: Compositional matrix adjust.
Identities = 105/190 (55%), Positives = 137/190 (72%), Gaps = 1/190 (0%)
Query: 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKV 61
+++V VD KVR DK YP G MDVV I KT+++FR+LYDTKGRF L S+ EEAK+KL KV
Sbjct: 69 EQNVFVDGKVRRDKGYPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKV 128
Query: 62 RSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGG 121
+ G IPYI T+D RTIR+P+P IK DT+K DL NKI F + GNV + G
Sbjct: 129 TAKAIGPNQIPYIVTHDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQG 188
Query: 122 RNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKL 181
N GRVGII++ EKH+GSF+ H++DA G+ FATRLGN+F +G+G K W+ LP G G++
Sbjct: 189 NNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRE 248
Query: 182 SIIEEARKRQ 191
+I+EE RKR+
Sbjct: 249 TILEE-RKRK 257
>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 273
Score = 180 bits (456), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 91/183 (49%), Positives = 120/183 (65%), Gaps = 1/183 (0%)
Query: 5 VLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSV 64
V VD K R D YPAGFMDVV IPKT + FR+LYD KGRF L + + E+ K+ KV +V
Sbjct: 67 VCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVRVSEAESSIKMMKVVNV 126
Query: 65 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNR 124
G IP T+DG IRYPDP DT+ D++ K+ + IK G VVMVTGG NR
Sbjct: 127 YTGTGRIPVAVTHDGHRIRYPDPRTSRGDTLVYDVKEKKVLDLIKIGNGKVVMVTGGANR 186
Query: 125 GRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPW-VSLPKGKGIKLSI 183
GR+G I + E+H G+F+ ++DA GHEFATR N+F IGK V+LPK +G+++++
Sbjct: 187 GRIGEIVSIERHPGAFDIARLKDASGHEFATRATNIFVIGKDMSSVPVTLPKQQGLRINV 246
Query: 184 IEE 186
I+E
Sbjct: 247 IQE 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 = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 58/174 (33%), Positives = 92/174 (52%), Gaps = 7/174 (4%)
Query: 6 LVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQ 65
LVD +VR D +P G MDVVSIP+T E++R+L + G+ LH I ++EA K ++R+ +
Sbjct: 72 LVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKR 131
Query: 66 FGQKGIPYINTYDGR----TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGG 121
+ +N +DG +I D + T+ + + +I E + F+ G V VT G
Sbjct: 132 MIKGARVQLNFHDGTNHIVSIAEKDNYFTSY-TVLMKVPEREILEVLPFEKGAYVFVTQG 190
Query: 122 RNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLP 174
+N R G I++ + G + + I+D G F T F +G KP +SLP
Sbjct: 191 KNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGT-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 = 77.4 bits (189), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 56/172 (32%), Positives = 81/172 (47%), Gaps = 7/172 (4%)
Query: 5 VLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSV 64
V VD K +K + GF DV+ I E++R++Y+ +G L E A KL KVRS
Sbjct: 36 VKVDGKTVREKKFAVGFXDVIEI--NGESYRVVYNDQGALVLXKETKERASXKLLKVRSK 93
Query: 65 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNR 124
+ T+DGRT D IK D + + + KI+E IK GN +T G +
Sbjct: 94 VIAPGNRIQLGTHDGRTFITDDKSIKVGDVLAVSVPDXKISEIIKXQPGNKAYITAGSHV 153
Query: 125 GRVGIIKNREKHKGSFET-IHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 175
+ G I E +GS +H Q+ F+T +VF IG +V P+
Sbjct: 154 NQTGTISKIEAKEGSSANLVHFQEG----FSTIKDHVFXIGSSKFSFVLSPE 201
>pdb|3JYB|A Chain A, Crystal Structure Of The Rets Periplasmic Domain
pdb|3JYB|B Chain B, Crystal Structure Of The Rets Periplasmic Domain
Length = 145
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 21/42 (50%)
Query: 25 VSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQF 66
+ P N+N+RLL D + R+ + + +F+ RS F
Sbjct: 1 ATTPSANQNWRLLRDESAQLRIADVLQRKEQFRPLAKRSFIF 42
>pdb|2XBZ|A Chain A, Multiple Oligomeric Forms Of The Pseudomonas Aeruginosa
Rets Sensor Domain Modulate Accessibility To The
Ligand- Binding Site
pdb|2XBZ|B Chain B, Multiple Oligomeric Forms Of The Pseudomonas Aeruginosa
Rets Sensor Domain Modulate Accessibility To The
Ligand- Binding Site
Length = 171
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 28 PKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQF 66
P N+N+RLL D + R+ + + +F+ RS F
Sbjct: 30 PSANQNWRLLRDESAQLRIADVLQRKEQFRPLAKRSFIF 68
>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 = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 45 RLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLET 101
+ IRD K + C VR + + + G P+ N I+ PD + +++D+ +
Sbjct: 53 EVQKIRDAIKKGEACSVRLLNYRKDGTPFWNLLTVTPIKTPDGRVSKFVGVQVDVTS 109
>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax
Disease Resistance Protein L6
pdb|3OZI|B Chain B, Crystal Structure Of The Tir Domain From The Flax
Disease Resistance Protein L6
Length = 204
Score = 26.9 bits (58), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 13 TDKTYPAGFMDVVSI--------PKTNENF-RLLYDTKGRFRLHSIRDEEAKFK 57
+D T P+G V P T E F LY + R+++H+ RD++ K
Sbjct: 22 SDSTNPSGSFPSVEYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLK 75
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
0.320 0.138 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,927,466
Number of Sequences: 62578
Number of extensions: 248581
Number of successful extensions: 504
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 492
Number of HSP's gapped (non-prelim): 15
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
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: 49 (23.5 bits)