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= 008711
(557 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2V9K|A Chain A, Crystal Structure Of Human Pus10, A Novel Pseudouridine
Synthase
Length = 530
Score = 253 bits (646), Expect = 2e-67, Method: Compositional matrix adjust.
Identities = 159/455 (34%), Positives = 250/455 (54%), Gaps = 43/455 (9%)
Query: 102 NICRSCLGILQFTYCGDKERVVENESACDFAVAIAELVKKEGHQIDSFSLEVSMPPTILE 161
N+C CLGILQ +C DF + + V+ G + S VS PP +
Sbjct: 108 NVCNVCLGILQ-EFCEK-----------DFIKKVCQKVEASGFEFTSLVFSVSFPPQLSV 155
Query: 162 NENKLSLYVKRKYRSEAWFKDRSISECSSTKDALKFALTNPL--ETLLDVKCGISTFHIR 219
E+ L VK++ ++ R + K+A K+ +T+PL E L G S F +
Sbjct: 156 REHAAWLLVKQEMGKQSLSLGRD--DIVQLKEAYKW-ITHPLFSEELGVPIDGKSLFEVS 212
Query: 220 LTYSRVEASIRIQNFVEKIEGCKRRKVDAKNCLDTVKDKSAITGVENSVVSTTEVIPVDE 279
+ ++ E +E C +C K+K SV + V+
Sbjct: 213 VVFAHPET----------VEDCHFLAAICPDCFKPAKNK-------QSVFTRMAVM---- 251
Query: 280 KSSNGLQDNEPSETHEFPLKKVNEPCR-LECLCFRTPIYFGGRYLKYSRNVSQTRWIIDE 338
K+ N +++ + + P C LE C ++ GRY KYSRN+ QT WIID
Sbjct: 252 KALNKIKEEDFLKQFPCPPNSPKAVCAVLEIECAHGAVFVAGRYNKYSRNLPQTPWIIDG 311
Query: 339 ERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVP-SE 397
ER E+S+EE+I ++L + + +S+ F ++GRED+DVR LG+GRPF E+ N V +
Sbjct: 312 ERKLESSVEELISDHLLAVFKAESFNFSSSGREDVDVRTLGNGRPFAIELVNPHRVHFTS 371
Query: 398 LLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDF 457
+KE++ KIN+ NK ++V++L++V + M+EGE EK K Y+AL+W ++ +Q +D
Sbjct: 372 QEIKELQQKINNSSNK-IQVRDLQLVTREAIGHMKEGEEEKTKTYSALIWTNKAIQKKDI 430
Query: 458 QTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIK 517
+ ++ +K+ +I QKTP+RVLHRR R ++I++M+ + + +F LH+ TQAGTYIK
Sbjct: 431 EFLNDIKDLKIDQKTPLRVLHRRPLAVRARVIHFMETQYV--DEHHFRLHLKTQAGTYIK 488
Query: 518 EFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMN 552
EFVHGD GRT P+IGS++ A+IL+LDV V ++
Sbjct: 489 EFVHGDFGRTKPNIGSLMNVTADILELDVESVDVD 523
>pdb|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
pdb|2AUS|A Chain A, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
Length = 334
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 52/105 (49%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + + E +I+Q+ P+R +R R + + +++I +I G
Sbjct: 108 KEYVALMHLHGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEILEIDG 165
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 166 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMAEL 200
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
pdb|2EY4|B Chain B, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
Length = 333
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + E +I+Q+ P+R +R R + + ++++ +I G
Sbjct: 108 KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEVLEIEG 165
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 166 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMSEL 200
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
Length = 340
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + E +I+Q+ P+R +R R + + ++++ +I G
Sbjct: 108 KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEVLEIEG 165
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 166 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMSEL 200
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|A Chain A, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|A Chain A, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 346
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + E +I+Q+ P+R +R R + + ++++ +I G
Sbjct: 108 KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEVLEIEG 165
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 166 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMSEL 200
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + E +I+Q+ P+R +R R + + ++++ +I G
Sbjct: 104 KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEVLEIEG 161
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 162 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMSEL 196
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + E +I+Q+ P+R +R R + + ++++ +I G
Sbjct: 101 KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEVLEIEG 158
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 159 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMSEL 193
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
pdb|3HJY|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 327
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 12/105 (11%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y AL+ + + ++ + E +I+Q+ P+R +R R + + ++++ +I G
Sbjct: 101 KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRR--LRTRKVYYIEVLEIEG 158
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 544
L + +AGTYI+ +H IG LG A + +L
Sbjct: 159 RD--VLFRVGVEAGTYIRSLIH--------HIGLALGVGAHMSEL 193
>pdb|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5
Nop10 Complex
Length = 357
Score = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 50/115 (43%), Gaps = 14/115 (12%)
Query: 440 KQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG 499
K+Y L+ + R +ED + +I Q+ P++ +R R +I ++E +
Sbjct: 128 KEYVCLMHLHRDASEEDILRVFKEFTGRIYQRPPLKAAVKR----RLRIRKIHELELLDK 183
Query: 500 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMNCF 554
+ L + Q+GTYI++ IG LG A + +L T K CF
Sbjct: 184 DGKDVLFRVKCQSGTYIRKLCE--------DIGEALGTSAHMQELRRT--KSGCF 228
>pdb|3CMZ|A Chain A, Tem-1 Class-A Beta-Lactamase L201p Mutant Apo Structure
Length = 263
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 481 SPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKE 518
+P R+++I+WM+ +K+AG LL AG +I +
Sbjct: 175 TPASRQQLIDWMEADKVAGP----LLRSALPAGWFIAD 208
>pdb|1YGR|A Chain A, Crystal Structure Of The Tandem Phosphatase Domain Of Rptp
Cd45
pdb|1YGR|B Chain B, Crystal Structure Of The Tandem Phosphatase Domain Of Rptp
Cd45
pdb|1YGU|A Chain A, Crystal Structure Of The Tandem Phosphatase Domains Of
Rptp Cd45 With A Ptyr Peptide
pdb|1YGU|B Chain B, Crystal Structure Of The Tandem Phosphatase Domains Of
Rptp Cd45 With A Ptyr Peptide
Length = 610
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 376 RMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRV 417
++ GRPFL E Q+ V S+ +KE N +N+ V +
Sbjct: 22 KIADEGRPFLAEFQSIPRVFSKFPIKEARKPFNQNKNRYVDI 63
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
0.318 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,384,484
Number of Sequences: 62578
Number of extensions: 617749
Number of successful extensions: 1542
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1526
Number of HSP's gapped (non-prelim): 16
length of query: 557
length of database: 14,973,337
effective HSP length: 104
effective length of query: 453
effective length of database: 8,465,225
effective search space: 3834746925
effective search space used: 3834746925
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)