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= 018706
(351 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XO8|A Chain A, Solution Structure Of At1g01470 From Arabidopsis Thaliana
Length = 151
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 57/125 (45%)
Query: 86 KPTADVTAVHIPKINLERADIVIDVXXXXXXXXXXXXXXXXXXVESDGRKLVSGLIPDSG 145
KP VT V + +N + + + V S GR++ G IPD G
Sbjct: 21 KPEGSVTDVDLKDVNRDSVEYLAKVSVTNPYSHSIPICEISFTFHSAGREIGKGKIPDPG 80
Query: 146 TIHAHGEETVKIPVTLIYDDIKNAYDDIKPGMIIPYKIKVDLIVDVPVFGRLTLPLEKNG 205
++ A + IPV + Y + N D+ I Y++++ L +D+PV G T+P+ G
Sbjct: 81 SLKAKDMTALDIPVVVPYSILFNLARDVGVDWDIDYELQIGLTIDLPVVGEFTIPISSKG 140
Query: 206 EIPIP 210
EI +P
Sbjct: 141 EIKLP 145
>pdb|1YYC|A Chain A, Solution Structure Of A Putative Late Embryogenesis
Abundant (Lea) Protein At2g46140.1
Length = 174
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 44/82 (53%)
Query: 129 VESDGRKLVSGLIPDSGTIHAHGEETVKIPVTLIYDDIKNAYDDIKPGMIIPYKIKVDLI 188
++S R + SG IPD G++ G + +PV + Y + D+ I Y++ + L
Sbjct: 87 LKSATRTIASGTIPDPGSLVGSGTTVLDVPVKVAYSIAVSLMKDMCTDWDIDYQLDIGLT 146
Query: 189 VDVPVFGRLTLPLEKNGEIPIP 210
D+PV G +T+P+ GEI +P
Sbjct: 147 FDIPVVGDITIPVSTQGEIKLP 168
>pdb|3UGX|A Chain A, Crystal Structure Of Visual Arrestin
pdb|3UGX|B Chain B, Crystal Structure Of Visual Arrestin
pdb|3UGX|C Chain C, Crystal Structure Of Visual Arrestin
pdb|3UGX|D Chain D, Crystal Structure Of Visual Arrestin
Length = 414
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 166 IKNAYDDIKPGMIIPYKIKVDLIVDVPVFGRLTLPLEKNGEIPI------PYKPDIDLEK 219
IK D G+++ Y+IKV L V + G LT E E+P P PD E
Sbjct: 322 IKEGIDKTVMGILVSYQIKVKLTVS-GLLGELTSS-EVATEVPFRLMHPQPEDPDTAKES 379
Query: 220 IKFERFSFEE 229
+ E F FEE
Sbjct: 380 FQDENFVFEE 389
>pdb|1CF1|A Chain A, Arrestin From Bovine Rod Outer Segments
pdb|1CF1|B Chain B, Arrestin From Bovine Rod Outer Segments
pdb|1CF1|C Chain C, Arrestin From Bovine Rod Outer Segments
pdb|1CF1|D Chain D, Arrestin From Bovine Rod Outer Segments
Length = 404
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 166 IKNAYDDIKPGMIIPYKIKVDLIVDVPVFGRLTLPLEKNGEIPI------PYKPDIDLEK 219
IK D G+++ Y+IKV L V + G LT E E+P P PD E
Sbjct: 312 IKEGIDKTVMGILVSYQIKVKLTVS-GLLGELTSS-EVATEVPFRLMHPQPEDPDTAKES 369
Query: 220 IKFERFSFEE 229
+ E F FEE
Sbjct: 370 FQDENFVFEE 379
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1119
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 27/116 (23%), Positives = 52/116 (44%), Gaps = 13/116 (11%)
Query: 155 VKIPVTLIYDDIKNAYDDIKPGMIIPYKI-KVDLIVDVPVFGRLTLPLEKNGEIPIPYKP 213
V+ P+ Y + D +P +++ ++ K DL+ D P L L +N + I
Sbjct: 621 VEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAI---- 676
Query: 214 DIDLEKIKFERFSFEETVAILHLKLENKNDFDLALNSLDYEVWLSDASIGAAELTK 269
+ F+ ++FE+ + I L K DF +++ YE+ D +G +T+
Sbjct: 677 ------MPFDGYNFEDAIVISEELL--KRDFYTSIHIERYEIEARDTKLGPERITR 724
>pdb|2D7I|A Chain A, Crsytal Structure Of Pp-Galnac-T10 With Udp, Galnac And
Mn2+
pdb|2D7R|A Chain A, Crystal Structure Of Pp-galnac-t10 Complexed With
Galnac-ser On Lectin Domain
Length = 570
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 268 TKSAKIDKNGISYIDIPITFRPKDFGSALWDMIRGKGTGYTMKGHIDVDTPFGAMKLPIS 327
KS K I++ D+P + P + +A W IR GTG + DT GA+ P+
Sbjct: 399 CKSFKWFMTKIAW-DLPKFYPPVEPPAAAWGEIRNVGTG------LCADTKHGALGSPLR 451
Query: 328 KEG 330
EG
Sbjct: 452 LEG 454
>pdb|3EUP|A Chain A, The Crystal Structure Of The Transcriptional Regulator,
Tetr Family From Cytophaga Hutchinsonii
pdb|3EUP|B Chain B, The Crystal Structure Of The Transcriptional Regulator,
Tetr Family From Cytophaga Hutchinsonii
Length = 204
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 23/50 (46%)
Query: 203 KNGEIPIPYKPDIDLEKIKFERFSFEETVAILHLKLENKNDFDLALNSLD 252
K G ++PD D+ KI F + E ++H +N+ D SL+
Sbjct: 144 KKGIQAKEFRPDTDVTKIAFSMIALVEGAILIHRATKNRAYSDYVFESLE 193
>pdb|3M07|A Chain A, 1.4 Angstrom Resolution Crystal Structure Of Putative
Alpha Amylase From Salmonella Typhimurium
Length = 618
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 252 DYEVWLSDASIGAAELTKSAKIDKNGISYIDIP--ITFRPKDFGSALWDMIRGKGTGYTM 309
+Y LSD + +++ K D NG SY+ P T+R + + W+ + Y M
Sbjct: 87 EYNFVLSDGMVVPDPASRAQKTDVNGPSYVVDPGSYTWRNTGWKGSRWE----QAVVYEM 142
Query: 310 KGHIDVDTPFGAMKLPISK 328
H TP G + I+K
Sbjct: 143 --HTGTFTPEGTFRAAIAK 159
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
0.318 0.139 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,357,056
Number of Sequences: 62578
Number of extensions: 380116
Number of successful extensions: 841
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 835
Number of HSP's gapped (non-prelim): 19
length of query: 351
length of database: 14,973,337
effective HSP length: 100
effective length of query: 251
effective length of database: 8,715,537
effective search space: 2187599787
effective search space used: 2187599787
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)