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= 011961
(474 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3VOX|A Chain A, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
pdb|3VOX|B Chain B, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
pdb|3VOX|C Chain C, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
pdb|3VOX|D Chain D, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
pdb|3VP5|A Chain A, X-Ray Crystal Structure Of Wild Type Hrtr In The Holo Form
pdb|3VOK|A Chain A, X-Ray Crystal Structure Of Wild Type Hrtr In The Apo Form
With The Target Dna
Length = 189
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 332 NPICQVVRAVINNQTYLTRDLTKLNRTYIENTVRQAYLNWRELEVAEGVLN 382
NPI QV+++V++N Y +T+IEN ++ L V EG+LN
Sbjct: 138 NPISQVLKSVVHNLVYRLFSENWTEKTFIENYDKEIKL------VTEGLLN 182
>pdb|4DNS|A Chain A, Crystal Structure Of Bermuda Grass Isoallergen Bg60
Provides Insight Into The Various Cross-Allergenicity Of
The Pollen Group 4 Allergens
pdb|4DNS|B Chain B, Crystal Structure Of Bermuda Grass Isoallergen Bg60
Provides Insight Into The Various Cross-Allergenicity Of
The Pollen Group 4 Allergens
Length = 497
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 346 TYLTRDLTKLNRTYIENTVRQAYLNWRELEVA 377
T TRD+ Y+ RQAY+N+R+L++
Sbjct: 414 TQWTRDIYDFMTPYVSKNPRQAYVNYRDLDLG 445
>pdb|1Z82|A Chain A, Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase
(Tm0378) From Thermotoga Maritima At 2.00 A Resolution
pdb|1Z82|B Chain B, Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase
(Tm0378) From Thermotoga Maritima At 2.00 A Resolution
Length = 335
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 7/53 (13%)
Query: 185 GVAPIGDIEFTDNSSWIRSRKFRIGAKVARGSYQGVRICEA----ITDAFVVK 233
G+A IGD+ T NS + R+R+F G +ARG + +++ E+ + AF VK
Sbjct: 238 GLAGIGDLXVTCNSRYSRNRRF--GELIARG-FNPLKLLESSNQVVEGAFTVK 287
>pdb|1OLA|A Chain A, The Structural Basis Of Multispecificity In The
Oligopeptide-binding Protein Oppa
pdb|2OLB|A Chain A, Oligopeptide Binding Protein (Oppa) Complexed With Tri-
Lysine
pdb|1OLC|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With
Lys-Lys- Lys-Ala
pdb|1JEV|A Chain A, Oligo-peptide Binding Protein (oppa) Complexed With Kwk
pdb|1JET|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kak
pdb|1JEU|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kek
pdb|2RKM|A Chain A, Structure Of Oppa Complexed With Lys-Lys
pdb|1B32|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kmk
pdb|1B3F|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Khk
pdb|1B3G|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kik
pdb|1B3L|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kgk
pdb|1B3L|C Chain C, Oligo-Peptide Binding Protein (Oppa) Complexed With Kgk
pdb|1B7H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Norleucyl-Lysine
pdb|1B0H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Napthylalanyl-Lysine
pdb|1B1H|A Chain A, Oligo-Peptide Binding ProteinTRIPEPTIDE (LYS HPE LYS)
Complex
pdb|1B2H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Ornithyl-Lysine
pdb|1B3H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Cyclohexylalanyl-Lysine
pdb|1B4H|A Chain A, Oligo-Peptide Binding Protein Complexed With Lysyl-
Diaminobutyric Acid-Lysine
pdb|1B5H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Diaminopropanoic Acid-Lysine
pdb|1B6H|A Chain A, Oligo-Peptide Binding Protein Complexed With
Lysyl-Norvalyl- Lysine
pdb|1B52|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Ktk
pdb|1B51|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Ksk
pdb|1B5I|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Knk
pdb|1B5J|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kqk
pdb|1B46|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kpk
pdb|1B9J|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Klk
pdb|1QKA|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Krk
pdb|1QKB|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kvk
pdb|1B4Z|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kdk
pdb|1B58|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kyk
pdb|1B40|A Chain A, Oligo-Peptide Binding Protein (Oppa) Complexed With Kfk
pdb|1B05|A Chain A, Structure Of Oligo-Peptide Binding Protein Complexed With
Lys-Cys-Lys
pdb|1RKM|A Chain A, Structure Of Oppa
Length = 517
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 69 RSLTRSSSLRIQALEPSSLKLIFSQKLSLPIFTGSKITDVENNP 112
++L R++ +Q+L+P ++ + +S +F G I+DVE +P
Sbjct: 13 QTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHP 56
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 59/129 (45%), Gaps = 29/129 (22%)
Query: 179 NVTARDGVAPIGDI-EFTDNSSWIRSRKFRIGAKVARGSYQGV--RICEAITDAFVVKDH 235
+ A+ G+AP GD+ + + W+ + RI +V S G+ RI + + +
Sbjct: 578 EICAKYGIAP-GDLRRIVETAEWLSNAMNRIAEEVGNTSVSGLTERIKHGVKEELL---- 632
Query: 236 RGELYKKHHPPMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILG 295
E+ R+ IG+ A +KL AGI+ +D ++ +++ ++G
Sbjct: 633 ---------------ELVRIRHIGRVRA--RKLYNAGIRNAEDIVR----HREKVASLIG 671
Query: 296 PGMSEKMWE 304
G++E++ E
Sbjct: 672 RGIAERVVE 680
>pdb|3KLN|A Chain A, Vibrio Cholerae Vpst
pdb|3KLN|B Chain B, Vibrio Cholerae Vpst
pdb|3KLN|C Chain C, Vibrio Cholerae Vpst
pdb|3KLN|D Chain D, Vibrio Cholerae Vpst
pdb|3KLO|A Chain A, Vibrio Cholerae Vpst Bound To C-Di-Gmp
pdb|3KLO|B Chain B, Vibrio Cholerae Vpst Bound To C-Di-Gmp
pdb|3KLO|C Chain C, Vibrio Cholerae Vpst Bound To C-Di-Gmp
pdb|3KLO|D Chain D, Vibrio Cholerae Vpst Bound To C-Di-Gmp
Length = 225
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 229 AFVVKDHRGELYKKHHPPMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQ 288
F + D L K +L+DE+W K+ ++ H + + + T Q + KL+ E Q
Sbjct: 109 VFYIDDDMDTLIKGM-SKILQDEMWLTRKLAQEYILHYR-AGNSVVTSQMYAKLTKRE-Q 165
Query: 289 RLRKILGPGMS 299
++ K+LG G S
Sbjct: 166 QIIKLLGSGAS 176
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
0.317 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,280,560
Number of Sequences: 62578
Number of extensions: 586969
Number of successful extensions: 1446
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1442
Number of HSP's gapped (non-prelim): 13
length of query: 474
length of database: 14,973,337
effective HSP length: 102
effective length of query: 372
effective length of database: 8,590,381
effective search space: 3195621732
effective search space used: 3195621732
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: 53 (25.0 bits)