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= 042984
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
pdb|3OZI|B Chain B, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
Length = 204
Score = 88.6 bits (218), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 45/114 (39%), Positives = 72/114 (63%), Gaps = 10/114 (8%)
Query: 21 SFRED-------EISPSLSSAIEGSKISIVIFSEGYASSRWCLNELVKILEIKNKYG-QI 72
+FR+D EI P+L AI+ SKI + I S GYA S+WCL EL +I+ + + +I
Sbjct: 66 TFRDDDELLKGKEIGPNLLRAIDQSKIYVPIISSGYADSKWCLMELAEIVRRQEEDPRRI 125
Query: 73 VVPVFYRVDPSDVRNQTGTFGDSFSELEERFKEKIDMLQTWRIAMREAANLSGF 126
++P+FY VDPSDVR+QTG + +F + +F + +Q W+ A+++ +L G+
Sbjct: 126 ILPIFYMVDPSDVRHQTGCYKKAFRKHANKFDGQ--TIQNWKDALKKVGDLKGW 177
>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana
Length = 176
Score = 86.7 bits (213), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 71/144 (49%), Gaps = 34/144 (23%)
Query: 14 TKYDVFLSFREDE--------------------------------ISPSLSSAIEGSKIS 41
TKYDVFLSFR + SP L S IE S+ +
Sbjct: 7 TKYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFA 66
Query: 42 IVIFSEGYASSRWCLNELVKILEIKNKYGQIVVPVFYRVDPSDVRNQTGTFGDSFSELEE 101
+V+ SE YA+S WCL+ELV I++ + K V+P+FY V+P+ VR QTG + F +
Sbjct: 67 VVVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHAS 126
Query: 102 RFKEKIDMLQTWRIAMREAANLSG 125
R E + + WR A+ A LSG
Sbjct: 127 R--EDPEKVLKWRQALTNFAQLSG 148
>pdb|3H16|A Chain A, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|B Chain B, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|C Chain C, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|D Chain D, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
Length = 154
Score = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 38/82 (46%)
Query: 16 YDVFLSFREDEISPSLSSAIEGSKISIVIFSEGYASSRWCLNELVKILEIKNKYGQIVVP 75
YD F D + S+ + S+ IV+ S + W EL + ++++ ++P
Sbjct: 52 YDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILP 111
Query: 76 VFYRVDPSDVRNQTGTFGDSFS 97
++++V +V + + T D +
Sbjct: 112 IWHKVSKDEVASFSPTMADKLA 133
>pdb|3TY5|A Chain A, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain In
Complex With Atp
pdb|3TY5|B Chain B, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain In
Complex With Atp
Length = 413
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 51 SSRWCLNELVKILEIKNKYGQIVVPVFYRVDPSDVRNQTGTFGDSFSELEERFKEKIDML 110
S R L+E VK+L K + V + DV QT +EL +RF E+ +M+
Sbjct: 172 SGRVVLDEAVKLL----KQASLNKTVSF-----DVSRQTSGKNADINELLQRFTERSEMM 222
Query: 111 QTWRIAMRE 119
Q + A R+
Sbjct: 223 QKYVEAYRK 231
>pdb|3TY8|A Chain A, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Apo Form
pdb|3TY8|B Chain B, Crystal Structure Of C. Thermocellum Pnkp Ligase Domain
Apo Form
Length = 413
Score = 27.3 bits (59), Expect = 2.5, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 51 SSRWCLNELVKILEIKNKYGQIVVPVFYRVDPSDVRNQTGTFGDSFSELEERFKEKIDML 110
S R L+E VK+L K + V + DV QT +EL +RF E+ +M+
Sbjct: 172 SGRVVLDEAVKLL----KQASLNKTVSF-----DVSRQTSGKNADINELLQRFTERSEMM 222
Query: 111 QTWRIAMRE 119
Q + A R+
Sbjct: 223 QKYVEAYRK 231
>pdb|3RBJ|A Chain A, Crystal Structure Of The Lid-Mutant Of Streptococcus
Agalactiae Sortase C1
pdb|3RBJ|B Chain B, Crystal Structure Of The Lid-Mutant Of Streptococcus
Agalactiae Sortase C1
Length = 230
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 14 TKYDVFLSFREDEISPSLSSAIEGSKIS----IVIFSEGYASSRWCLNELVKILEIKNKY 69
TK D R E++ + +++I G+K + +I + G + + E ++LE+K +
Sbjct: 25 TKIDRVEINRRLELAYAYNASIAGAKTNGEYPALIPNTGAEQKQAGVVEYARMLEVKEQI 84
Query: 70 GQIVVP 75
G +++P
Sbjct: 85 GHVIIP 90
>pdb|3TN7|A Chain A, Crystal Structure Of Short-Chain Alcohol Dehydrogenase
From Hyperthermophilic Archaeon Thermococcus Sibiricus
Complexed With 5- Hydroxy-Nadp
pdb|3TN7|B Chain B, Crystal Structure Of Short-Chain Alcohol Dehydrogenase
From Hyperthermophilic Archaeon Thermococcus Sibiricus
Complexed With 5- Hydroxy-Nadp
Length = 257
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 42 IVIFSEGYASSRWCLNELVKILEIKN 67
++ + GY S++W LV+ +I+N
Sbjct: 166 LIPYGGGYVSTKWAARALVRTFQIEN 191
>pdb|3L77|A Chain A, X-Ray Structure Alcohol Dehydrogenase From Archaeon
Thermococcus Sibiricus Complexed With 5-Hydroxy-Nadp
Length = 235
Score = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 42 IVIFSEGYASSRWCLNELVKILEIKN 67
++ + GY S++W LV+ +I+N
Sbjct: 144 LIPYGGGYVSTKWAARALVRTFQIEN 169
>pdb|3AYX|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An H2-Reduced Condition
pdb|3AYX|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An H2-Reduced Condition
pdb|3AYY|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In A Ferricyanide-Oxidized
Condition
pdb|3AYY|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In A Ferricyanide-Oxidized
Condition
pdb|3AYZ|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An Air-Oxidized Condition
pdb|3AYZ|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An Air-Oxidized Condition
Length = 596
Score = 26.6 bits (57), Expect = 4.8, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 50 ASSRWCLNELVKILEIKNKYGQIVVPVFYRVDPSDVRNQTGTFGDSFSELE-ERFKEKID 108
A+ R L + I + K K Q VVP + P D + G F S ER E ++
Sbjct: 520 AAPRGALAHWIVIEKGKIKNYQCVVPTTWNGSPRDPKGNIGAFEASLMGTPMERPDEPVE 579
Query: 109 MLQT 112
+L+T
Sbjct: 580 VLRT 583
>pdb|3RGW|L Chain L, Crystal Structure At 1.5 A Resolution Of An H2-Reduced,
O2-Tolerant Hydrogenase From Ralstonia Eutropha Unmasks
A Novel Iron-Sulfur Cluster
Length = 603
Score = 26.2 bits (56), Expect = 5.0, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 50 ASSRWCLNELVKILEIKNKYGQIVVPVFYRVDPSDVRNQTGTFGDSF 96
A+ R L ++I + + + Q VVP + P D + Q G F S
Sbjct: 527 AAPRGALGHWIRIKDGRIENYQCVVPTTWNGSPRDYKGQIGAFEASL 573
>pdb|3IPW|A Chain A, Crystal Structure Of Hydrolase Tatd Family Protein From
Entamoeba Histolytica
Length = 325
Score = 26.2 bits (56), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 22 FREDEISPSLSSAIEGSKISIVIFSEGYASSRWCLNELVKILEIKNKY 69
+ E++I L A E + +S +I + G CLN+ K +EI NKY
Sbjct: 49 YHEEDIDVVLQRA-ERNGLSHIIITSG------CLNDFKKAIEIINKY 89
>pdb|2DPI|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|2DPJ|A Chain A, Structure Of Hpoli With Dna And Dttp
pdb|2FLN|A Chain A, Binary Complex Of Catalytic Core Of Human Dna Polymerase
Iota With Dna (Template A)
pdb|2FLP|A Chain A, Binary Complex Of The Catalytic Core Of Human Dna
Polymerase Iota With Dna (Template G)
pdb|2FLL|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Dna And
Dttp
pdb|3EPG|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine
pdb|3EPI|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine And Incoming Ttp
pdb|3G6V|A Chain A, Dna Synthesis Across An Abasic Lesion By Human Dna
Polymerase-Iota
pdb|3G6X|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dgtp With An
Abasic Site At The Templating Position
pdb|3G6Y|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dttp With An
Abasic Site At The Templating Position
pdb|3GV7|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Dttp
pdb|3GV8|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Dgtp
pdb|3NGD|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3OSN|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3Q8P|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite
8-Oxo-Guanine
pdb|3Q8Q|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite
8-Oxo-Guanine
pdb|3Q8R|B Chain B, Human Dna Polymerase Iota Incorporating Dgtp Opposite
8-Oxo-Guanine
pdb|3Q8S|B Chain B, Human Dna Polymerase Iota Incorporating Dttp Opposite
8-Oxo-Guanine
pdb|4EBC|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBD|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBE|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4FS1|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dttp By
Human Polymerase Iota
pdb|4FS2|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dctp By
Human Polymerase Iota
pdb|4EYH|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
pdb|4EYI|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
Length = 420
Score = 25.4 bits (54), Expect = 8.6, Method: Composition-based stats.
Identities = 31/148 (20%), Positives = 69/148 (46%), Gaps = 21/148 (14%)
Query: 1 MASSSSSINMIPHTKYDVFLSFREDEISPSLSSAIEGSKISIVIFSEGYASSRWCLNELV 60
+ + ++S +I H D F + E +P L G + ++ + Y + + + +L+
Sbjct: 20 LPTPNASSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGVKKLM 79
Query: 61 KILEIKNKYGQIVV----------PVFYRV-----DPSDVRNQTGTFGDSFSELEERFKE 105
+ + K K Q+V+ + Y+V + S V + G F ++F +L E ++
Sbjct: 80 NVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLG-FDENFVDLTEMVEK 138
Query: 106 KIDMLQTWRIAMREAANLSG--FDSHSI 131
++ LQ+ ++ A +SG +++ SI
Sbjct: 139 RLQQLQSDELS---AVTVSGHVYNNQSI 163
>pdb|3TFH|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - Apo
pdb|3TFH|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - Apo
pdb|3TFI|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - With Substrate
Dmsp
pdb|3TFI|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - With Substrate
Dmsp
pdb|3TFJ|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - With Cofactor
Thf
pdb|3TFJ|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - With Cofactor
Thf
Length = 369
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 95 SFSELEERFKEKIDMLQTWRIAMREAANLSGFDS 128
+F +E+ +K + +Q W +A +SG DS
Sbjct: 40 AFGSIEDSYKHLKEHVQIWDVAAERQVEISGKDS 73
>pdb|3PIH|A Chain A, T. Maritima Uvra In Complex With Fluorescein-Modified Dna
Length = 916
Score = 25.4 bits (54), Expect = 9.5, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 93 GDSFSELEERFKEKIDMLQTWRIAMREAANLSGFDSHSIR 132
G+ E+E+R + +D+ + R A LSG +S IR
Sbjct: 435 GELLKEIEKRLEFLVDVGLEYLTLSRSATTLSGGESQRIR 474
>pdb|4DRF|A Chain A, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
pdb|4DRF|C Chain C, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
pdb|4E6N|A Chain A, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
pdb|4E6N|C Chain C, Crystal Structure Of Bacterial Pnkp-CHEN1-N Heterodimer
Length = 427
Score = 25.4 bits (54), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 51 SSRWCLNELVKILEIKNKYGQIVVPVFYRVDPSDVRNQTGTFGDSFSELEERFKEKIDML 110
S R L+E VK+L K + V + DV QT +EL +RF E+ +M+
Sbjct: 186 SGRVVLDEAVKLL----KQASLNKTVSF-----DVSRQTSGKNADINELLQRFTERSEMM 236
Query: 111 QTWRIAMRE 119
Q + A R+
Sbjct: 237 QKYVEAYRK 245
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 0.132 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,665,119
Number of Sequences: 62578
Number of extensions: 134741
Number of successful extensions: 383
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 368
Number of HSP's gapped (non-prelim): 19
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)