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= 001763
(1017 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZS|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|W Chain W, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 155
Score = 38.9 bits (89), Expect = 0.014, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 275 EARELFAQMQNPNVVAWNVMISGHAKRGYDAEAVNYFKRMRKAGVKSSRSTLGSVLSGIS 334
++ LF Q +NP +AW V+ H K+G E KR RK VK+ R G+ L I
Sbjct: 35 KSASLFKQRKNPRRIAWTVLFRKHHKKGITEEVAK--KRSRKT-VKAQRPITGASLDLIK 91
Query: 335 SLAAL 339
+L
Sbjct: 92 ERRSL 96
>pdb|2V3A|A Chain A, Crystal Structure Of Rubredoxin Reductase From Pseudomonas
Aeruginosa.
pdb|2V3B|A Chain A, Crystal Structure Of The Electron Transfer Complex
Rubredoxin - Rubredoxin Reductase From Pseudomonas
Aeruginosa
Length = 384
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 7/92 (7%)
Query: 788 DEMAERNYVISWNSMIVGFAKNGYAEDALKVFHEM------KETQAMPDDVTFLGV-LTA 840
+E+ R+ V++W + + G A+DAL +++ ++ A V LG L
Sbjct: 98 EEVRYRDLVLAWGAEPIRVPVEGDAQDALYPINDLEDYARFRQAAAGKRRVLLLGAGLIG 157
Query: 841 CSHAGRVSEGRQIFETMVSCHGIQPRVDHCAC 872
C A +S G + + C + P + H A
Sbjct: 158 CEFANDLSSGGYQLDVVAPCEQVMPGLLHPAA 189
>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
Length = 125
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 22/94 (23%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 224 SWTSMIAGYVQAGLPEAAFELFEKMIKVGCVPDQV-AFVTVINVCFNLGRLDEARELFA- 281
+W ++ Y + G + A E ++K +++ P+ A+ + N + G DEA E +
Sbjct: 11 AWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQK 68
Query: 282 --QMQNPNVVAWNVMISGHAKRGYDAEAVNYFKR 313
++ N AW + + + K+G EA+ Y+++
Sbjct: 69 ALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQK 102
>pdb|2WQH|A Chain A, Crystal Structure Of Ctpr3y3
Length = 125
Score = 31.6 bits (70), Expect = 2.6, Method: Composition-based stats.
Identities = 22/94 (23%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 224 SWTSMIAGYVQAGLPEAAFELFEKMIKVGCVPDQV-AFVTVINVCFNLGRLDEARELFA- 281
+W ++ Y + G + A E ++K +++ P+ A+ + N + G DEA E +
Sbjct: 11 AWYNLGNAYYKQGDYDEAIEYYQKALEL--YPNNAEAWYNLGNAYYKQGDYDEAIEYYQK 68
Query: 282 --QMQNPNVVAWNVMISGHAKRGYDAEAVNYFKR 313
++ N AW + + + K+G EA+ Y+++
Sbjct: 69 ALELYPNNAEAWYNLGNAYYKQGDYDEAIEYYQK 102
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 53/243 (21%), Positives = 99/243 (40%), Gaps = 30/243 (12%)
Query: 130 MYSKRGSFENVFKSFGLL-----CNRGGVPNGFTFAIVLSACSKSMDVSYGRQLHCHVIE 184
+Y R N+ K+ G L C + FA+ S ++ + Q +
Sbjct: 134 LYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWS----NLGCVFNAQGEIWLAI 189
Query: 185 LGFESSSFCKGALIDMYAKLNNVSDARRVFDGAVD--LDTVSWT---SMIAG-----YVQ 234
FE + +D Y L NV R+FD AV L +S + +++ G Y +
Sbjct: 190 HHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYE 249
Query: 235 AGLPEAAFELFEKMIKVGC-VPDQVAFVTVINVCFNLGRLDEARELF---AQMQNPNVVA 290
GL + A + + + I++ PD A+ + N G + EA + + ++ + +
Sbjct: 250 QGLIDLAIDTYRRAIELQPHFPD--AYCNLANALKEKGSVAEAEDCYNTALRLCPTHADS 307
Query: 291 WNVMISGHAKRGYDAEAVNYFKRMRK--AGVKSSRSTLGSVLSGISSLAALDFGLIVHAE 348
N + + ++G EAV +++ + ++ S L SVL L L+ + E
Sbjct: 308 LNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQE---ALMHYKE 364
Query: 349 AIK 351
AI+
Sbjct: 365 AIR 367
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 0.135 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,874,865
Number of Sequences: 62578
Number of extensions: 1165749
Number of successful extensions: 2387
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2381
Number of HSP's gapped (non-prelim): 16
length of query: 1017
length of database: 14,973,337
effective HSP length: 108
effective length of query: 909
effective length of database: 8,214,913
effective search space: 7467355917
effective search space used: 7467355917
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: 56 (26.2 bits)