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= 042941
(481 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 = 0.013, Method: Compositional matrix adjust.
Identities = 31/122 (25%), Positives = 56/122 (45%), Gaps = 16/122 (13%)
Query: 219 SKARNLHKVLRLFDQMKRMGIECDRKVYNAVIHALAKGRLVKDA---------ISLMKSM 269
SK ++ + LRL+D+ +R G++ + YN +++ + ++ + K M
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 270 EEKGVAPNVVTYNSLIKPLCKARKLDEARQAFD---EMLQRGISPTIRTY-HAFLDIIRT 325
V PN T+ + + L A+ D+ AFD +M GI P +R+Y A R
Sbjct: 97 IVDKVVPNEATFTNGAR-LAVAK--DDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRK 153
Query: 326 GE 327
G+
Sbjct: 154 GD 155
Score = 36.2 bits (82), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 84/183 (45%), Gaps = 16/183 (8%)
Query: 183 CNIIGSSREAERVWMEMSQRGIC-----YDVVSFSCIISCYSKARNLHKVL-RLFDQMKR 236
C+ G EA R++ E + G+ Y+V+ + C ++ + + + L R FD K+
Sbjct: 36 CSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQ 95
Query: 237 MGIECDRKVYN-AVIHALAKGRLVKD----AISLMKSMEEKGVAPNVVTYNSLIKPLCKA 291
M + D+ V N A A+ + KD A ++K M+ G+ P + +Y + C+
Sbjct: 96 MIV--DKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRK 153
Query: 292 RKLDEARQAFDEMLQRGISPTIRTYHAFLDI---IRTGEEVFGLLESMRKMGCQPTNDTY 348
D+A + M++ + P A L + + ++V+ L+ +R + Q + T+
Sbjct: 154 GDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTF 213
Query: 349 IML 351
M+
Sbjct: 214 DMI 216
>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 = 36.6 bits (83), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 16/122 (13%)
Query: 219 SKARNLHKVLRLFDQMKRMGIECDRKVYNAVIHALAKGRLVKDA---------ISLMKSM 269
SK ++ + LRL+D+ +R G++ + YN +++ + ++ + K
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQX 96
Query: 270 EEKGVAPNVVTYNSLIKPLCKARKLDEARQAFDEMLQR---GISPTIRTY-HAFLDIIRT 325
V PN T+ + + L A+ D+ AFD + Q GI P +R+Y A R
Sbjct: 97 IVDKVVPNEATFTNGAR-LAVAK--DDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRK 153
Query: 326 GE 327
G+
Sbjct: 154 GD 155
>pdb|2FXV|A Chain A, Bacillus Subtilis Xanthine Phosphoribosyltransferase In
Complex With Guanosine 5'-monophosphate (gmp)
pdb|2FXV|B Chain B, Bacillus Subtilis Xanthine Phosphoribosyltransferase In
Complex With Guanosine 5'-monophosphate (gmp)
Length = 194
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 257 RLVKDAISLMKSMEEKGVAPNVVTYNSLIKPLCKARK 293
R KD I+ + ++E G+AP V+T L P+ ARK
Sbjct: 45 RFAKDGITKIVTIESSGIAPAVMTGLKLGVPVVFARK 81
>pdb|2E9L|A Chain A, Crystal Structure Of Human Cytosolic Neutral
Beta-Glycosylceramidase (Klotho-Related Prote:klrp)
Complex With Glucose And Fatty Acids
pdb|2E9M|A Chain A, Crystal Structure Of Human Cytosolic Neutral Beta-
Glycosylceramidase (Klotho-Related Prote:klrp) Complex
With Galactose And Fatty Acids
Length = 469
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 21/87 (24%)
Query: 292 RKLDEARQAFDEMLQRGISPTIRTYHAFLDIIRTGEEVFGLLESMRKMGCQPTNDTYIML 351
+ +D + D++L+ G++P + YH D+ +T E+ G L +
Sbjct: 95 KGIDYYNKIIDDLLKNGVTPIVTLYH--FDLPQTLEDQGGWLSE--------------AI 138
Query: 352 IKKFSRWRQ-----FGNVFKVWNEISE 373
I+ F ++ Q FG+ K W I+E
Sbjct: 139 IESFDKYAQFCFSTFGDRVKQWITINE 165
>pdb|2JFE|X Chain X, The Crystal Structure Of Human Cytosolic Beta-Glucosidase
Length = 469
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 21/87 (24%)
Query: 292 RKLDEARQAFDEMLQRGISPTIRTYHAFLDIIRTGEEVFGLLESMRKMGCQPTNDTYIML 351
+ +D + D++L+ G++P + YH D+ +T E+ G L +
Sbjct: 95 KGIDYYNKIIDDLLKNGVTPIVTLYH--FDLPQTLEDQGGWLSE--------------AI 138
Query: 352 IKKFSRWRQ-----FGNVFKVWNEISE 373
I+ F ++ Q FG+ K W I+E
Sbjct: 139 IESFDKYAQFCFSTFGDRVKQWITINE 165
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 11/73 (15%)
Query: 265 LMKSMEEKGVAPNVVTYNSLIKPLCKARKL-DEARQAFDEMLQRGI-----SPTIR--TY 316
L+K MEEKG+APNV +++ + R + DE A +E++ + +PT+
Sbjct: 657 LLKKMEEKGIAPNVKAARRMLE---RQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI 713
Query: 317 HAFLDIIRTGEEV 329
AF ++ G+ +
Sbjct: 714 QAFQPVLVEGQSI 726
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 11/73 (15%)
Query: 265 LMKSMEEKGVAPNVVTYNSLIKPLCKARKL-DEARQAFDEMLQRGI-----SPTIR--TY 316
L+K MEEKG+APNV +++ + R + DE A +E++ + +PT+
Sbjct: 657 LLKKMEEKGIAPNVKAARRMLE---RQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI 713
Query: 317 HAFLDIIRTGEEV 329
AF ++ G+ +
Sbjct: 714 QAFQPVLVEGQSI 726
>pdb|3TIA|A Chain A, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir
pdb|3TIA|B Chain B, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir
pdb|3TIA|C Chain C, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir
pdb|3TIA|D Chain D, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir
pdb|3TIB|A Chain A, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir Octanoate
pdb|3TIB|B Chain B, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir Octanoate
pdb|3TIB|C Chain C, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir Octanoate
pdb|3TIB|D Chain D, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Laninamivir Octanoate
pdb|3TIC|A Chain A, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Zanamivir
pdb|3TIC|B Chain B, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Zanamivir
pdb|3TIC|C Chain C, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Zanamivir
pdb|3TIC|D Chain D, Crystal Structure Of 1957 Pandemic H2n2 Neuraminidase
Complexed With Zanamivir
Length = 469
Score = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 240 ECDRKVYNAVI--HALAKGRLVKDAISLMKSMEEKGVAPNVVTYNSLIKPLCK 290
ECD N V+ + R + + + L + EK + P VV Y + KP C+
Sbjct: 41 ECDSPASNQVMPCEPIIIERNITEIVYLNNTTIEKEICPKVVEYRNWSKPQCQ 93
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
0.323 0.136 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,763,094
Number of Sequences: 62578
Number of extensions: 551504
Number of successful extensions: 1034
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1029
Number of HSP's gapped (non-prelim): 11
length of query: 481
length of database: 14,973,337
effective HSP length: 103
effective length of query: 378
effective length of database: 8,527,803
effective search space: 3223509534
effective search space used: 3223509534
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)