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= psy2073
(126 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 51/92 (55%), Positives = 68/92 (73%), Gaps = 1/92 (1%)
Query: 28 LLQVAHLEKDGR-YLTIKDNQVVQLHPSTCLDHKPEWVVYNEFVLTTKNYIRTVTDVKPE 86
+QVA + Y+T+KDNQ V +HPST L H EWV+YNEFVLT+KNYIRTVT V+PE
Sbjct: 657 FMQVAKKRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPE 716
Query: 87 WLIKLAPQYYELQNFPQCEAKRQLEILQAKME 118
WLI++AP YY+L NF + + K LE ++ K++
Sbjct: 717 WLIEIAPAYYDLSNFQKGDVKLSLERIKEKVD 748
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 51/92 (55%), Positives = 68/92 (73%), Gaps = 1/92 (1%)
Query: 28 LLQVAHLEKDGR-YLTIKDNQVVQLHPSTCLDHKPEWVVYNEFVLTTKNYIRTVTDVKPE 86
+QVA + Y+T+KDNQ V +HPST L H EWV+YNEFVLT+KNYIRTVT V+PE
Sbjct: 657 FMQVAKKRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPE 716
Query: 87 WLIKLAPQYYELQNFPQCEAKRQLEILQAKME 118
WLI++AP YY+L NF + + K LE ++ K++
Sbjct: 717 WLIEIAPAYYDLSNFQKGDVKLSLERIKEKVD 748
>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain
Length = 270
Score = 71.6 bits (174), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 31/60 (51%), Positives = 45/60 (75%), Gaps = 1/60 (1%)
Query: 40 YLTIKDNQVVQLHPSTCL-DHKPEWVVYNEFVLTTKNYIRTVTDVKPEWLIKLAPQYYEL 98
Y T+ D QVV +HPS+ L + +PEWVVY+E VLTTK Y+R VT + P WL++ AP ++++
Sbjct: 190 YRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFKV 249
>pdb|1BOO|A Chain A, Pvuii Dna Methyltransferase (Cytosine-N4-Specific)
Length = 323
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 30/59 (50%)
Query: 7 PFGFIYNKNYSILFYSTLSESLLQVAHLEKDGRYLTIKDNQVVQLHPSTCLDHKPEWVV 65
P G K++S ++ +LLQ+++ E +G+YL ++ HP+ PE+ +
Sbjct: 188 PSGHDIGKSFSKDNGGSIPPNLLQISNSESNGQYLANCKLMGIKAHPARFPAKLPEFFI 246
>pdb|3NGB|H Chain H, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|B Chain B, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|E Chain E, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|J Chain J, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
Length = 224
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 68 EFVLTTKNYIRTVTDVKPEWLIKLAPQ 94
EF+ T N+IR +PEW+ L P+
Sbjct: 28 EFIDCTLNWIRLAPGKRPEWMGWLKPR 54
>pdb|3K1Q|D Chain D, Backbone Model Of An Aquareovirus Virion By Cryo-Electron
Microscopy And Bioinformatics
pdb|3K1Q|E Chain E, Backbone Model Of An Aquareovirus Virion By Cryo-Electron
Microscopy And Bioinformatics
pdb|3IYL|U Chain U, Atomic Cryoem Structure Of A Nonenveloped Virus Suggests
How Penetration Protein Is Primed For Cell Entry
pdb|3IYL|V Chain V, Atomic Cryoem Structure Of A Nonenveloped Virus Suggests
How Penetration Protein Is Primed For Cell Entry
Length = 412
Score = 25.8 bits (55), Expect = 6.9, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 21/49 (42%)
Query: 41 LTIKDNQVVQLHPSTCLDHKPEWVVYNEFVLTTKNYIRTVTDVKPEWLI 89
+T +D + L P + P W V +L + NY V ++ W I
Sbjct: 90 ITWRDPVLSSLAPVPAIQPPPVWAVAENVLLDSNNYPTYVLNLSSMWPI 138
>pdb|2P97|A Chain A, Crystal Structure Of A Putative Metal-Dependent Hydrolase
(Ava_3068) From Anabaena Variabilis Atcc 29413 At 1.65 A
Resolution
pdb|2P97|B Chain B, Crystal Structure Of A Putative Metal-Dependent Hydrolase
(Ava_3068) From Anabaena Variabilis Atcc 29413 At 1.65 A
Resolution
Length = 201
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 69 FVLTTKNYIRTVTDVKPEWLIKLAPQYYELQNFP 102
VLT +++R+ ++ + K+A E +NFP
Sbjct: 60 IVLTNSDHVRSAKEIADQTYTKIAGPVAEKENFP 93
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 25.0 bits (53), Expect = 9.7, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 39 RYLTIKDNQVVQLH---PSTCLDHKPEWVVYNEFVLTTKNYIRTVTDVKPEWL 88
+YLT KD +++ S D W+ + ++TT + ++ +PEWL
Sbjct: 91 KYLTFKDWELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWL 143
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
0.321 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,886,770
Number of Sequences: 62578
Number of extensions: 144963
Number of successful extensions: 307
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 294
Number of HSP's gapped (non-prelim): 14
length of query: 126
length of database: 14,973,337
effective HSP length: 87
effective length of query: 39
effective length of database: 9,529,051
effective search space: 371632989
effective search space used: 371632989
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: 45 (21.9 bits)