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= 047932
(598 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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/169 (21%), Positives = 68/169 (40%), Gaps = 9/169 (5%)
Query: 188 IDGVCKEGFVDKAMELFLQMKDENINPNVVTYNSLIHCFSHADDWNEAK---------RL 238
+D K+G V +A+ L+ + + + + YN L++ S A+ E+ +
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 239 FIKMMDQGVHPNVVTFSVIVDELCKNGKMEEASRLLDLMIQIGVHPNTFVYNTLMDGFCL 298
F +M+ V PN TF+ E A ++ M G+ P Y + GFC
Sbjct: 93 FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 299 TGRVNHAKELFVSMESNGCMHDVVSYTTLINGYCKTKNVEEALNLYRKM 347
G + A E+ M + + + L+ TKN ++ +++
Sbjct: 153 KGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRL 201
Score = 37.4 bits (85), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 55/127 (43%), Gaps = 9/127 (7%)
Query: 398 IDGLCKNGFVLEALELF-----CAIGNSKYELDIISYSC-LIDGLCKIGK---LETAWEL 448
+D K G VLEAL L+ + S+Y +++ Y C L + + L +++
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 449 FQSLSRVGLLPNVVTYNIMIHGLCNDGQMDKAHDLFLDMEAKGVEPDCVIFNTIMLGFIR 508
F+ + ++PN T+ + A D+ M+A G++P + + GF R
Sbjct: 93 FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 509 NNETSKS 515
+ K+
Sbjct: 153 KGDADKA 159
Score = 35.8 bits (81), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 342 NLYRKMLPKGIR--PTVVTYSTLFLGLFEVHQVEHALKLFDEMQHNDVAADTYIYNT--F 397
NL RK K I+ P + L + + V AL+L+DE + N V Y YN +
Sbjct: 11 NLSRKAKKKAIQQSPEALLKQKLDM-CSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY 69
Query: 398 IDGLCK-------NGFVLEALELFCAIGNSKYELDIISYSCLIDGLCKIGKLETAWELFQ 450
+ L + N + ++F + K + +++ E A+++ +
Sbjct: 70 VCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVK 129
Query: 451 SLSRVGLLPNVVTYNIMIHGLCNDGQMDKAHDL 483
+ G+ P + +Y + G C G DKA+++
Sbjct: 130 QMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/151 (17%), Positives = 68/151 (45%), Gaps = 3/151 (1%)
Query: 184 YNTIIDGVCKEGFVDKAMELFLQMKDENINPNVVTYNSLIHCFSHAD-DWNEAKRLFIKM 242
YN ++ G ++G + + + +KD + P++++Y + + C D D +R +M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 243 MDQGVHPNVVTFSVIVDELCKNGKMEEASRLLD-LMIQIGVHPNTFVYNTLMDGFCLTGR 301
+G+ + +V++ E + ++ ++ + + P L D + GR
Sbjct: 228 SQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGR 287
Query: 302 VNHAKELFVSMESNGCMHDVVSYTTLINGYC 332
V++ K L + +++ C+ + + L + C
Sbjct: 288 VSYPK-LHLPLKTLQCLFEKQLHMELASRVC 317
>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 = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 28/127 (22%), Positives = 52/127 (40%), Gaps = 9/127 (7%)
Query: 398 IDGLCKNGFVLEALELF-----CAIGNSKYELDIISYSC-LIDGLCKIGK---LETAWEL 448
+D K G VLEAL L+ + S+Y +++ Y C L + + L +++
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 449 FQSLSRVGLLPNVVTYNIMIHGLCNDGQMDKAHDLFLDMEAKGVEPDCVIFNTIMLGFIR 508
F+ ++PN T+ + A D +A G++P + + GF R
Sbjct: 93 FKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCR 152
Query: 509 NNETSKS 515
+ K+
Sbjct: 153 KGDADKA 159
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 33/169 (19%), Positives = 64/169 (37%), Gaps = 9/169 (5%)
Query: 188 IDGVCKEGFVDKAMELFLQMKDENINPNVVTYNSLIHCFSHADDWNEAK---------RL 238
+D K+G V +A+ L+ + + + + YN L++ S A+ E+ +
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 239 FIKMMDQGVHPNVVTFSVIVDELCKNGKMEEASRLLDLMIQIGVHPNTFVYNTLMDGFCL 298
F + + V PN TF+ E A + G+ P Y + GFC
Sbjct: 93 FKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCR 152
Query: 299 TGRVNHAKELFVSMESNGCMHDVVSYTTLINGYCKTKNVEEALNLYRKM 347
G + A E+ + + + L+ TKN ++ +++
Sbjct: 153 KGDADKAYEVDAHXVESEVVPEEPELAALLKVSXDTKNADKVYKTLQRL 201
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 26/121 (21%), Positives = 49/121 (40%), Gaps = 9/121 (7%)
Query: 372 VEHALKLFDEMQHNDVAADTYIYNT--FIDGLCK-------NGFVLEALELFCAIGNSKY 422
V AL+L+DE + N V Y YN ++ L + N + ++F K
Sbjct: 42 VLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXIVDKV 101
Query: 423 ELDIISYSCLIDGLCKIGKLETAWELFQSLSRVGLLPNVVTYNIMIHGLCNDGQMDKAHD 482
+ +++ E A++ + G+ P + +Y + G C G DKA++
Sbjct: 102 VPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYE 161
Query: 483 L 483
+
Sbjct: 162 V 162
>pdb|2DJ6|A Chain A, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3
pdb|2DJ6|B Chain B, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3
pdb|2DJ6|C Chain C, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3
pdb|2DTT|A Chain A, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3 Complexed With
(1'r,2's)-Biopterin
pdb|2DTT|B Chain B, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3 Complexed With
(1'r,2's)-Biopterin
pdb|2DTT|C Chain C, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3 Complexed With
(1'r,2's)-Biopterin
pdb|2DTT|D Chain D, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3 Complexed With
(1'r,2's)-Biopterin
pdb|2DTT|E Chain E, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3 Complexed With
(1'r,2's)-Biopterin
pdb|2DTT|F Chain F, Crystal Structure Of 6-Pyruvoyl Tetrahydrobiopterin
Synthase From Pyrococcus Horikoshii Ot3 Complexed With
(1'r,2's)-Biopterin
Length = 115
Score = 32.0 bits (71), Expect = 0.91, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 374 HALKLFDEMQHNDVAADTYIYNTFIDGLCKNGFVLEALELFCAIGNSKYELD 425
HA+K+ D + DV T+ I+G KNG+V++ LEL + ELD
Sbjct: 15 HAVKVGDHWE--DVHGHTFFLEVAIEGEIKNGYVMDFLELRKIVEEITKELD 64
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
0.322 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: 17,550,800
Number of Sequences: 62578
Number of extensions: 722590
Number of successful extensions: 1795
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1774
Number of HSP's gapped (non-prelim): 15
length of query: 598
length of database: 14,973,337
effective HSP length: 104
effective length of query: 494
effective length of database: 8,465,225
effective search space: 4181821150
effective search space used: 4181821150
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)