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= 044048
(269 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A8T|A Chain A, Plant Adenylate Isopentenyltransferase In Complex With Atp
Length = 339
Score = 204 bits (518), Expect = 5e-53, Method: Compositional matrix adjust.
Identities = 117/295 (39%), Positives = 164/295 (55%), Gaps = 30/295 (10%)
Query: 1 MGATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDP 60
MGAT TGK++LSIDLA HF E INSDK+QVYKGLDI TNK++ +R GVPHHLLG VDP
Sbjct: 46 MGATGTGKSRLSIDLAAHFPLEVINSDKMQVYKGLDITTNKISVPDRGGVPHHLLGEVDP 105
Query: 61 -EADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALVED---------------S 104
+ +F A +A+ +I LP++VGGSN++I AL+ D S
Sbjct: 106 ARGELTPADFRSLAGKAVSEITGRRKLPVLVGGSNSFIHALLVDRFDSSGPGVFEEGSHS 165
Query: 105 IINFRANYDCCFIWMDVDPLVLYKYVGIRVDKMVETGLVDEVRDMFDP-------NADYN 157
+++ YDCCF+W+DV VL Y+ RVD M+E G+ DE+ + + P ++
Sbjct: 166 VVSSELRYDCCFLWVDVSVKVLTDYLAKRVDDMLELGMFDELAEFYSPEDEDHDEDSATR 225
Query: 158 RGIRRSIGAPELHEYLKLESNVKNETTNNNKDLLLKKAIQE----IKDNTCKLVDKQVQK 213
G+R++IG PE Y + E + +D + + A +E IK+NTC L +Q+ K
Sbjct: 226 TGLRKAIGVPEFDRYFEKFRPGDVEGEDPGRDRVRRGAFEEAVRAIKENTCHLAKRQIGK 285
Query: 214 IKRLRNELGWKIHRIDATYVLEGRMKXXXXXXXXX--XXVVLKPGVAIVEDFLNK 266
I RL+ GW + R+DAT M VL+P V IV FL++
Sbjct: 286 ILRLKGA-GWDLRRLDATESFRAAMTSDSGEKCTEIWEKQVLEPSVKIVSRFLDE 339
>pdb|3D3Q|A Chain A, Crystal Structure Of Trna
Delta(2)-Isopentenylpyrophosphate Transferase (Se0981)
From Staphylococcus Epidermidis. Northeast Structural
Genomics Consortium Target Ser100
pdb|3D3Q|B Chain B, Crystal Structure Of Trna
Delta(2)-Isopentenylpyrophosphate Transferase (Se0981)
From Staphylococcus Epidermidis. Northeast Structural
Genomics Consortium Target Ser100
Length = 340
Score = 97.1 bits (240), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 45/101 (44%), Positives = 67/101 (66%)
Query: 1 MGATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDP 60
+G TA+GKT+LSI++A F+GE I+ D QVY+G DI T KVT E +G+PH+ + + P
Sbjct: 13 VGPTASGKTELSIEVAKKFNGEIISGDSXQVYQGXDIGTAKVTTEEXEGIPHYXIDILPP 72
Query: 61 EADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALV 101
+A + EF + A + I I G +PII GG+ YI++L+
Sbjct: 73 DASFSAYEFKKRAEKYIKDITRRGKVPIIAGGTGLYIQSLL 113
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 105 IINFRANYDCCFIWMDVDPLVLYKYVGIRVDKMVETGLVDEVRDMFDPNADYNRGIRRSI 164
+ F NYD I ++ LY + RVD + GL +EV+ + + + ++ ++I
Sbjct: 189 VQQFTENYDTLLIGIEXSRETLYLRINKRVDIXLGHGLFNEVQHLVEQGFEASQSX-QAI 247
Query: 165 GAPEL 169
G EL
Sbjct: 248 GYKEL 252
>pdb|2QGN|A Chain A, Crystal Structure Of Trna Isopentenylpyrophosphate
Transferase (Bh2366) From Bacillus Halodurans, Northeast
Structural Genomics Consortium Target Bhr41.
pdb|3EXA|A Chain A, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41.
pdb|3EXA|B Chain B, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41.
pdb|3EXA|C Chain C, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41.
pdb|3EXA|D Chain D, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41
Length = 322
Score = 96.7 bits (239), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 49/114 (42%), Positives = 69/114 (60%), Gaps = 1/114 (0%)
Query: 1 MGATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDP 60
+G TA GKTK S+ LA +GE I+ D QVY+G DI T K+T E GVPHHL+ DP
Sbjct: 9 VGPTAVGKTKTSVXLAKRLNGEVISGDSXQVYRGXDIGTAKITAEEXDGVPHHLIDIKDP 68
Query: 61 EADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALVED-SIINFRANYD 113
+ V +F + A I +I E G LP +VGG+ Y+ A++ ++ + RA+ D
Sbjct: 69 SESFSVADFQDLATPLITEIHERGRLPFLVGGTGLYVNAVIHQFNLGDIRADED 122
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 53/105 (50%), Gaps = 24/105 (22%)
Query: 112 YDCCFIWMDVDPLVLYKYVGIRVDKMVETGLVDEVRDMFDPNADYNRGIR-----RSIGA 166
Y+ I + + VLY + RVD+ VE GL+DE + ++D RGIR ++IG
Sbjct: 190 YNLVXIGLTXERDVLYDRINRRVDQXVEEGLIDEAKKLYD------RGIRDCQSVQAIGY 243
Query: 167 PELHEYLKLESNVKNETTNNNKDLLLKKAIQEIKDNTCKLVDKQV 211
E ++YL + ++ L++AI +K N+ + +Q+
Sbjct: 244 KEXYDYL-------------DGNVTLEEAIDTLKRNSRRYAKRQL 275
>pdb|3EPH|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPH|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPJ|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPJ|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPK|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPK|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPL|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPL|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
Length = 409
Score = 96.3 bits (238), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 45/99 (45%), Positives = 63/99 (63%)
Query: 2 GATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDPE 61
G T GK++LSI LA F+GE INSD +QVYK + I TNK ER+G+PHH++ VD
Sbjct: 9 GTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHPLQEREGIPHHVMNHVDWS 68
Query: 62 ADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEAL 100
+Y F + AI+ I G +PI+VGG++ Y++ L
Sbjct: 69 EEYYSHRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTL 107
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 55/114 (48%), Gaps = 17/114 (14%)
Query: 112 YDCCFIWMDVDPLVLYKYVGIRVDKMVETGLVDEVRDM--------FDPNADYNRGIRRS 163
+D F+W+ P L++ + RVD M+E G + E++ + F P N G+ +
Sbjct: 187 FDTLFLWLYSKPEPLFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCEN-GVWQV 245
Query: 164 IGAPELHEYLKLESNVKNETTNNNKDLLLKKAIQEIKDNTCKLVDKQVQKIKRL 217
IG E +L +T +N + L+ I+ +K T + +QV+ IK++
Sbjct: 246 IGFKEFLPWL------TGKTDDNT--VKLEDCIERMKTRTRQYAKRQVKWIKKM 291
>pdb|3FOZ|A Chain A, Structure Of E. Coli Isopentenyl-Trna Transferase In
Complex With E. Coli Trna(Phe)
pdb|3FOZ|B Chain B, Structure Of E. Coli Isopentenyl-Trna Transferase In
Complex With E. Coli Trna(Phe)
pdb|2ZXU|A Chain A, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe) And Dmaspp
pdb|2ZXU|B Chain B, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe) And Dmaspp
Length = 316
Score = 77.4 bits (189), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 41/102 (40%), Positives = 55/102 (53%)
Query: 1 MGATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDP 60
MG TA+GKT L+I+L E I+ D +YKG+DI T K E PH LL DP
Sbjct: 16 MGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDP 75
Query: 61 EADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALVE 102
Y +F AL + I G +P++VGG+ Y +AL+E
Sbjct: 76 SQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLE 117
>pdb|2ZM5|A Chain A, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe)
pdb|2ZM5|B Chain B, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe)
Length = 316
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 40/101 (39%), Positives = 52/101 (51%)
Query: 2 GATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDPE 61
G TA+GKT L+I+L E I+ D +YKG DI T K E PH LL DP
Sbjct: 17 GPTASGKTALAIELRKILPVELISVDSALIYKGXDIGTAKPNAEELLAAPHRLLDIRDPS 76
Query: 62 ADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALVE 102
Y +F AL I G +P++VGG+ Y +AL+E
Sbjct: 77 QAYSAADFRRDALAEXADITAAGRIPLLVGGTXLYFKALLE 117
>pdb|3CRM|A Chain A, Structure Of Trna Dimethylallyltransferase: Rna
Modification Through A Channel
pdb|3CRQ|A Chain A, Structure Of Trna Dimethylallyltransferase: Rna
Modification Through A Channel
pdb|3CRR|A Chain A, Structure Of Trna Dimethylallyltransferase: Rna
Modification Through A Channel
Length = 323
Score = 68.6 bits (166), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 40/102 (39%), Positives = 55/102 (53%)
Query: 1 MGATATGKTKLSIDLAIHFSGEAINSDKIQVYKGLDIATNKVTESERQGVPHHLLGFVDP 60
MG TA GKT L++ LA E I+ D +Y+G+DI T K + PH L+ DP
Sbjct: 11 MGPTAAGKTDLAMALADALPCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDP 70
Query: 61 EADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALVE 102
Y EF AL A+ K G +P++VGG+ Y +AL+E
Sbjct: 71 AESYSAAEFRADALAAMAKATARGRIPLLVGGTMLYYKALLE 112
>pdb|3FF1|A Chain A, Structure Of Glucose 6-Phosphate Isomerase From
Staphylococcus Aureus
pdb|3FF1|B Chain B, Structure Of Glucose 6-Phosphate Isomerase From
Staphylococcus Aureus
Length = 446
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 46 ERQGVPHHLLGFVDPEADYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYI--EALVED 103
E G LG+VD DY EEF + A +I EN + +++G +Y+ A +E
Sbjct: 39 EGTGAGSDFLGWVDLPVDYDKEEFS-RIVEASKRIKENSDVLVVIGIGGSYLGARAAIEX 97
Query: 104 SIINFR 109
+FR
Sbjct: 98 LTSSFR 103
>pdb|1TCE|A Chain A, Solution Nmr Structure Of The Shc Sh2 Domain Complexed
With A Tyrosine-Phosphorylated Peptide From The T-Cell
Receptor, Minimized Average Structure
Length = 107
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 42 VTESERQGVPHHLLGFVDPEADYPVEEFCEHALRAIDKIIE---NGHLPIIVGGSNTYIE 98
V + G P HLL VDPE V +H ++ +I + HLPII GS ++
Sbjct: 42 VLTGSQSGQPKHLL-LVDPEG---VVRTKDHRFESVSHLISYHMDNHLPIISAGSELCLQ 97
Query: 99 ALVEDSII 106
VE ++
Sbjct: 98 QPVERKLL 105
>pdb|1MIL|A Chain A, Transforming Protein
Length = 104
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 47 RQGVPHHLLGFVDPEADYPVEEFCEHALRAIDKIIE---NGHLPIIVGGSNTYIEALVE 102
+ G P HLL VDPE V +H ++ +I + HLPII GS ++ VE
Sbjct: 47 QSGQPKHLL-LVDPEG---VVRTKDHRFESVSHLISYHMDNHLPIISAGSELCLQQPVE 101
>pdb|2AKO|A Chain A, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
pdb|2AKO|B Chain B, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
pdb|2AKO|C Chain C, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
pdb|2AKO|D Chain D, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
Length = 251
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 63 DYPVEEFCEHALRAIDKIIENGHLPIIVGGSNTYIEALV---EDSIINFRANY---DCCF 116
D+ + +HA AID I G LPII T IE +V DS+ + ++ D
Sbjct: 100 DFDSRKATKHAKNAIDXXINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLV 159
Query: 117 IWMDVD 122
I D+D
Sbjct: 160 ILSDID 165
>pdb|2O9B|A Chain A, Crystal Structure Of Bacteriophytochrome Chromophore
Binding Domain
pdb|2O9C|A Chain A, Crystal Structure Of Bacteriophytochrome Chromophore
Binding Domain At 1.45 Angstrom Resolution
Length = 342
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 22 EAINSDKIQVYKGLDIATNKV-TESERQGVPHHLLGFVDPEADYPVEE---FCEHALR 75
E D++ +YK AT +V E+ R+G+ H LG P +D P + + H LR
Sbjct: 181 ELTGFDRVMLYKFAPDATGEVIAEARREGL-HAFLGHRFPASDIPAQARALYTRHLLR 237
>pdb|1ZTU|A Chain A, Structure Of The Chromophore Binding Domain Of Bacterial
Phytochrome
Length = 341
Score = 28.1 bits (61), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 22 EAINSDKIQVYKGLDIATNKV-TESERQGVPHHLLGFVDPEADYPVEE---FCEHALR 75
E D++ +YK AT +V E+ R+G+ H LG P +D P + + H LR
Sbjct: 180 ELTGFDRVXLYKFAPDATGEVIAEARREGL-HAFLGHRFPASDIPAQARALYTRHLLR 236
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
0.319 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,957,582
Number of Sequences: 62578
Number of extensions: 337520
Number of successful extensions: 945
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 929
Number of HSP's gapped (non-prelim): 20
length of query: 269
length of database: 14,973,337
effective HSP length: 97
effective length of query: 172
effective length of database: 8,903,271
effective search space: 1531362612
effective search space used: 1531362612
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)