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= 040367
(400 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/123 (21%), Positives = 49/123 (39%), Gaps = 11/123 (8%)
Query: 36 VLSLFKRLNSTGLFPDLYTYNILINCFCKMGR----------VSHGFVVLGRILRSCFTP 85
L L+ G+ Y YN+L+ C + +S GF + +++ P
Sbjct: 45 ALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVP 103
Query: 86 NAVTFTSLIKGLCAESRIMEAAALFTKLRVFGCEPNVFTYNTLINGLYRTGHTIVALNLF 145
N TFT+ + A+ A + +++ FG +P + +Y + G R G A +
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD 163
Query: 146 EEM 148
M
Sbjct: 164 AHM 166
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 59/133 (44%), Gaps = 16/133 (12%)
Query: 103 IMEAAALFTKLRVFGCEPNVFTYNTLINGLYRTGHTIVALNLFEEMASGNGEFGV-EGFV 161
++EA L+ + R G + + + YN L+ +L E + G+ GF
Sbjct: 42 VLEALRLYDEARRNGVQLSQYHYNVLL----------YVCSLAEAATESSPNPGLSRGF- 90
Query: 162 DKAKELFLQMKDENINPDVVTYTSVIRGFCYANDWNEAKCLLIEMMDQGVQPNVVTFNVI 221
++F QM + + P+ T+T+ R +D A ++ +M G+QP + ++
Sbjct: 91 ----DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPA 146
Query: 222 MDELCKNGKMDEA 234
+ C+ G D+A
Sbjct: 147 LFGFCRKGDADKA 159
>pdb|2ILR|A Chain A, Crystal Structure Of Human Fanconi Anemia Protein E C-
Terminal Domain
Length = 264
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 171 MKDENINPDVVTYTSVIRGFCYANDWNEAKCLLIE-MMDQGVQPNVVTFNVIMDELCKNG 229
+K E++ PD ++ G W E L+++ ++++ V+ F+V+M++LCK G
Sbjct: 152 VKMESLEPDAQV---LMLGQILELPWKEETFLVLQSLLERQVEMTPEKFSVLMEKLCKKG 208
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 28/133 (21%), Positives = 56/133 (42%), Gaps = 16/133 (12%)
Query: 103 IMEAAALFTKLRVFGCEPNVFTYNTLINGLYRTGHTIVALNLFEEMASGNGEFGV-EGFV 161
++EA L+ + R G + + + YN L+ +L E + G+ GF
Sbjct: 42 VLEALRLYDEARRNGVQLSQYHYNVLL----------YVCSLAEAATESSPNPGLSRGF- 90
Query: 162 DKAKELFLQMKDENINPDVVTYTSVIRGFCYANDWNEAKCLLIEMMDQGVQPNVVTFNVI 221
++F Q + + P+ T+T+ R +D A + + G+QP + ++
Sbjct: 91 ----DIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPA 146
Query: 222 MDELCKNGKMDEA 234
+ C+ G D+A
Sbjct: 147 LFGFCRKGDADKA 159
>pdb|1PD6|A Chain A, The Nmr Structure Of Domain C2 Of Human Cardiac Myosin
Binding Protein C
Length = 104
Score = 28.5 bits (62), Expect = 6.8, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 368 NSYIVEAVELFRTLRILKCEL-DIRAYNCLIDG 399
+ YI E++ RTL I +C L D AY C++ G
Sbjct: 61 SKYIFESIGAKRTLTISQCSLADDAAYQCVVGG 93
>pdb|3HSB|A Chain A, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
pdb|3HSB|B Chain B, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
pdb|3HSB|C Chain C, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
pdb|3HSB|D Chain D, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
pdb|3HSB|E Chain E, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
pdb|3HSB|F Chain F, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
pdb|3AHU|A Chain A, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer.
pdb|3AHU|B Chain B, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer.
pdb|3AHU|C Chain C, Crystal Structure Of Ymah (Hfq) From Bacillus Subtilis In
Complex With An Rna Aptamer
Length = 78
Score = 28.1 bits (61), Expect = 10.0, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 247 RPNAFVYNTLMDGFCLTGRVNRAKELFVSMESMGCTHTVFSYSILINGYCKNKEIE 302
+ N +V L++GF L G+V V +ES G ++ ++I KN ++E
Sbjct: 21 KENTYVTVFLLNGFQLRGQVKGFDNFTVLLESEGKQQLIYKHAISTFAPQKNVQLE 76
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
0.327 0.142 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,332,294
Number of Sequences: 62578
Number of extensions: 454161
Number of successful extensions: 1317
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1302
Number of HSP's gapped (non-prelim): 19
length of query: 400
length of database: 14,973,337
effective HSP length: 101
effective length of query: 299
effective length of database: 8,652,959
effective search space: 2587234741
effective search space used: 2587234741
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)