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= 018680
(352 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 1.5, 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|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 = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 230 FVVKDHRGELYKKHHPPMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQR 289
F + D L K +L+DE+W K+ ++ H + + + T Q + KL+ E Q+
Sbjct: 110 FYIDDDMDTLIKGM-SKILQDEMWLTRKLAQEYILHYR-AGNSVVTSQMYAKLTKRE-QQ 166
Query: 290 LRKILGPGMS 299
+ K+LG G S
Sbjct: 167 IIKLLGSGAS 176
>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 = 2.0, 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|4I43|B Chain B, Crystal Structure Of Prp8:aar2 Complex
Length = 1564
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 15/87 (17%)
Query: 35 MVNSFQNFFSALEPLLRRVVNEEVQRGVSKYNPCRSLTRSSSLRI-QALEPSSLKLIFSQ 93
M +++ N+F+ L+PL++ + R + K NP + R RI + L+ I+
Sbjct: 934 MYDAYGNWFNGLKPLIQNSM-----RTIMKANPALYVLRE---RIRKGLQ------IYQS 979
Query: 94 KLSLPIFTGSKITDVENNPLQIVVVDT 120
+ P S ++ NN +++ V DT
Sbjct: 980 SVQEPFLNSSNYAELFNNDIKLFVDDT 1006
>pdb|3ZEF|B Chain B, Crystal Structure Of Prp8:aar2 Complex: Second Crystal
Form At 3.1 Angstrom Resolution
pdb|3ZEF|E Chain E, Crystal Structure Of Prp8:aar2 Complex: Second Crystal
Form At 3.1 Angstrom Resolution
Length = 1531
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 15/87 (17%)
Query: 35 MVNSFQNFFSALEPLLRRVVNEEVQRGVSKYNPCRSLTRSSSLRI-QALEPSSLKLIFSQ 93
M +++ N+F+ L+PL++ + R + K NP + R RI + L+ I+
Sbjct: 901 MYDAYGNWFNGLKPLIQNSM-----RTIMKANPALYVLRE---RIRKGLQ------IYQS 946
Query: 94 KLSLPIFTGSKITDVENNPLQIVVVDT 120
+ P S ++ NN +++ V DT
Sbjct: 947 SVQEPFLNSSNYAELFNNDIKLFVDDT 973
>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 = 28.9 bits (63), Expect = 4.5, 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
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 0.137 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,661,106
Number of Sequences: 62578
Number of extensions: 438321
Number of successful extensions: 1094
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1091
Number of HSP's gapped (non-prelim): 10
length of query: 352
length of database: 14,973,337
effective HSP length: 100
effective length of query: 252
effective length of database: 8,715,537
effective search space: 2196315324
effective search space used: 2196315324
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: 52 (24.6 bits)