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= 037972
(480 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3G33|B Chain B, Crystal Structure Of Cdk4CYCLIN D3
pdb|3G33|D Chain D, Crystal Structure Of Cdk4CYCLIN D3
Length = 306
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 44/188 (23%), Positives = 87/188 (46%), Gaps = 27/188 (14%)
Query: 16 VEEKSMPAAGYAYINEANFLRPRAIKVI----LQNSKSNKRNAYIPYLALNYFDRFISKH 71
+EE+ +P A Y + ++P K++ L+ + + + LA+NY DR++S
Sbjct: 48 LEERYVPRASYFQCVQRE-IKPHMRKMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLS-- 104
Query: 72 TLPEVLGNVEDDLVLAANCCLIIAWKLRDQSFSFSDFMAGNNLPRNYSKHAL------NM 125
+ + L L C+++A KLR+ + + + Y+ HA+ +
Sbjct: 105 ----CVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLC------IYTDHAVSPRQLRDW 154
Query: 126 ELQILNGLEWRSRAVVAVNFVPFFLNISSA----KGIKRRHVNRIIIEAQADLSFASCKP 181
E+ +L L+W AV+A +F+ F L+ S + + ++H + D +FA P
Sbjct: 155 EVLVLGKLKWDLAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPP 214
Query: 182 SVIAAAAL 189
S+IA ++
Sbjct: 215 SMIATGSI 222
>pdb|2W96|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
pdb|2W99|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
pdb|2W9F|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
Length = 271
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 73/178 (41%), Gaps = 15/178 (8%)
Query: 14 FDVEEKSMPAAGYAYINEANFLRPRAIKVI----LQNSKSNKRNAYIPYLALNYFDRFIS 69
EE P+ Y + L P K++ L+ + K + LA+NY DRF+S
Sbjct: 32 LKAEETCAPSVSYFKCVQKEVL-PSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLS 90
Query: 70 KHTLPEVLGNVEDDLVLAANCCLIIAWKLRDQSFSFSDFMAGNNLPRNYSKHALNMELQI 129
+ + L L C+ +A K+++ ++ + + L MEL +
Sbjct: 91 LEPVKK------SRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLL 144
Query: 130 LNGLEWRSRAVVAVNFVPFFLN----ISSAKGIKRRHVNRIIIEAQADLSFASCKPSV 183
+N L+W A+ +F+ FL+ K I R+H + D+ F S PS+
Sbjct: 145 VNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSM 202
>pdb|2W9Z|A Chain A, Crystal Structure Of Cdk4 In Complex With A D-Type Cyclin
Length = 257
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 73/178 (41%), Gaps = 15/178 (8%)
Query: 14 FDVEEKSMPAAGYAYINEANFLRPRAIKVI----LQNSKSNKRNAYIPYLALNYFDRFIS 69
EE P+ Y + L P K++ L+ + K + LA+NY DRF+S
Sbjct: 18 LKAEETCAPSVSYFKCVQKEVL-PSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLS 76
Query: 70 KHTLPEVLGNVEDDLVLAANCCLIIAWKLRDQSFSFSDFMAGNNLPRNYSKHALNMELQI 129
+ + L L C+ +A K+++ ++ + + L MEL +
Sbjct: 77 LEPVKK------SRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLL 130
Query: 130 LNGLEWRSRAVVAVNFVPFFLN----ISSAKGIKRRHVNRIIIEAQADLSFASCKPSV 183
+N L+W A+ +F+ FL+ K I R+H + D+ F S PS+
Sbjct: 131 VNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSM 188
>pdb|1W98|B Chain B, The Structural Basis Of Cdk2 Activation By Cyclin E
Length = 283
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 49/101 (48%), Gaps = 15/101 (14%)
Query: 58 YLALNYFDRFISKH-----TLPEVLGNVEDDLVLAANCCLIIAWKLRDQSFSFSDFMAGN 112
YLA ++FDR+++ TL +++G L +AA I KL ++ +G+
Sbjct: 72 YLAQDFFDRYMATQENVVKTLLQLIGI--SSLFIAAKLEEIYPPKLHQFAYVTDGACSGD 129
Query: 113 NLPRNYSKHALNMELQILNGLEWRSRAVVAVNFVPFFLNIS 153
+ L MEL I+ L+WR + V+++ ++ ++
Sbjct: 130 EI--------LTMELMIMKALKWRLSPLTIVSWLNVYMQVA 162
>pdb|3P0S|A Chain A, Crystal Structure Of Bombyx Mori Densovirus 1 Capsid
Length = 494
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 6/62 (9%)
Query: 44 LQNSKSNKRNAYIPYLALNYF-DRFISKHTLPE-VLGNV----EDDLVLAANCCLIIAWK 97
L S SN NA++ Y+ NYF ++ + ++P+ ++G V ED+ +L A ++I +
Sbjct: 332 LNQSASNNLNAFVDYMGYNYFGEQKCAPQSMPKFMIGFVNIRNEDNSLLNAKWDILIKTR 391
Query: 98 LR 99
+R
Sbjct: 392 IR 393
>pdb|2LP7|A Chain A, Structure Of Gp41-m-mat, A Membrane Associated Mper Trimer
From Hiv-1 Gp41.
pdb|2LP7|B Chain B, Structure Of Gp41-m-mat, A Membrane Associated Mper Trimer
From Hiv-1 Gp41.
pdb|2LP7|C Chain C, Structure Of Gp41-m-mat, A Membrane Associated Mper Trimer
From Hiv-1 Gp41
Length = 59
Score = 28.5 bits (62), Expect = 7.7, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 249 FLSDVGGFHVLLNLDDAQQLWSLYDFKEWWWVI 281
FL G LL LD LW+ ++ W W I
Sbjct: 26 FLGSSGNEQELLELDKWASLWNWFNITNWLWYI 58
>pdb|4EXM|A Chain A, The Crystal Structure Of An Engineered Phage Lysin
Containing The Binding Domain Of Pesticin And The
Killing Domain Of T4-Lysozyme
pdb|4EXM|B Chain B, The Crystal Structure Of An Engineered Phage Lysin
Containing The Binding Domain Of Pesticin And The
Killing Domain Of T4-Lysozyme
pdb|4EXM|C Chain C, The Crystal Structure Of An Engineered Phage Lysin
Containing The Binding Domain Of Pesticin And The
Killing Domain Of T4-Lysozyme
pdb|4EXM|D Chain D, The Crystal Structure Of An Engineered Phage Lysin
Containing The Binding Domain Of Pesticin And The
Killing Domain Of T4-Lysozyme
Length = 347
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 20/34 (58%)
Query: 136 RSRAVVAVNFVPFFLNISSAKGIKRRHVNRIIIE 169
R+R V+A N V F NIS K RR VN +I E
Sbjct: 155 RNRIVLADNTVINFDNISQLKEFLRRSVNIVIFE 188
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 0.134 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,175,492
Number of Sequences: 62578
Number of extensions: 504480
Number of successful extensions: 854
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 845
Number of HSP's gapped (non-prelim): 8
length of query: 480
length of database: 14,973,337
effective HSP length: 103
effective length of query: 377
effective length of database: 8,527,803
effective search space: 3214981731
effective search space used: 3214981731
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: 53 (25.0 bits)