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= 043831
(243 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CV8|A Chain A, Crystal Structure Of Trna-Intron Endonuclease From
Sulfolobus Tokodaii
pdb|2CV8|B Chain B, Crystal Structure Of Trna-Intron Endonuclease From
Sulfolobus Tokodaii
Length = 180
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 39/101 (38%), Positives = 53/101 (52%), Gaps = 4/101 (3%)
Query: 67 TAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDE-LWQYMKAKKETFPLLYKAY 125
+AE+ L + EG YL K L+IV N + D E L+Q + F +LY Y
Sbjct: 38 SAEEINSELILSLIEGVYLVKKGK-LEIV--SNGERLDFERLYQIGVTQIPRFRILYSVY 94
Query: 126 SHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAE 166
LR+K +VVRSG +YG DF Y P + H+ Y V+ L E
Sbjct: 95 EDLREKGYVVRSGIKYGADFAVYTIGPGIEHAPYLVIALDE 135
>pdb|2ZYZ|B Chain B, Pyrobaculum Aerophilum Splicing Endonuclease
pdb|2ZYZ|D Chain D, Pyrobaculum Aerophilum Splicing Endonuclease
Length = 183
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 50/173 (28%), Positives = 74/173 (42%), Gaps = 18/173 (10%)
Query: 39 LAGYSALLAVEAEQTELLNR----ACFGRHIV-------TAEKDKQWYQLGMEEGFYLCH 87
+ GY LAV E E R +GR + EK LG+ E YL
Sbjct: 1 MIGYLRGLAVIVEDVEFARRLYKEGFYGRFLGYDKVKRDEVEKINAPLILGLYEALYLAE 60
Query: 88 SLKCLKIVGEDNSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVA 147
+ LK++GED +EL + + F +YK Y + R +VV+SG ++G F
Sbjct: 61 KGR-LKVMGEDGREVAPEELAALGRERMRNFDEIYKIYKYFRDLGYVVKSGLKFGALFSV 119
Query: 148 YRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKTLLILTI 200
Y P + H+ V+V E + G + +DI RL V KT + T+
Sbjct: 120 YEKGPGIDHAP-MVVVFLEPDKGISA-----TDITRGGRLSHSVRKTWTLATV 166
>pdb|1A79|A Chain A, Crystal Structure Of The Trna Splicing Endonuclease From
Methanococcus Jannaschii
pdb|1A79|B Chain B, Crystal Structure Of The Trna Splicing Endonuclease From
Methanococcus Jannaschii
pdb|1A79|C Chain C, Crystal Structure Of The Trna Splicing Endonuclease From
Methanococcus Jannaschii
pdb|1A79|D Chain D, Crystal Structure Of The Trna Splicing Endonuclease From
Methanococcus Jannaschii
Length = 171
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 66/135 (48%), Gaps = 9/135 (6%)
Query: 73 QWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKN 132
+ L + E YL + L L++ +DN + +EL++Y + +E L Y Y LR +
Sbjct: 33 NFLSLSLVEALYLIN-LGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRG 91
Query: 133 WVVRSGSQYGVDFVAYRHHPSL--VHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGG 190
++V++G +YG DF Y ++ HS Y V V E + S++ VR+
Sbjct: 92 YIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSS------FLLSELTGFVRVAHS 145
Query: 191 VAKTLLILTINKNGQ 205
V K LLI ++ +G
Sbjct: 146 VRKKLLIAIVDADGD 160
>pdb|3P1Z|B Chain B, Crystal Structure Of The Aperopyrum Pernix Rna Splicing
Endonuclease
pdb|3P1Z|D Chain D, Crystal Structure Of The Aperopyrum Pernix Rna Splicing
Endonuclease
pdb|3P1Z|F Chain F, Crystal Structure Of The Aperopyrum Pernix Rna Splicing
Endonuclease
pdb|3P1Z|H Chain H, Crystal Structure Of The Aperopyrum Pernix Rna Splicing
Endonuclease
pdb|3P1Z|J Chain J, Crystal Structure Of The Aperopyrum Pernix Rna Splicing
Endonuclease
pdb|3P1Z|L Chain L, Crystal Structure Of The Aperopyrum Pernix Rna Splicing
Endonuclease
Length = 186
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 62/133 (46%), Gaps = 8/133 (6%)
Query: 34 EAHAVLAGYSALLAVEAEQTELLNRACFGRHIVTAEKDKQW-----YQLGMEEGFYLCHS 88
+A VL G ++L + EQ L + + EK + +L + E YL
Sbjct: 9 KASGVLIG-DSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEK 67
Query: 89 LKCLKIVGEDNSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAY 148
L++ D S+ ++L ++ F +LY Y LR++ +VVRSG ++G DF Y
Sbjct: 68 -GVLEVAKPDGSSVGVEDLRTAVRGNPR-FSMLYNIYRDLRERGFVVRSGLKFGSDFAVY 125
Query: 149 RHHPSLVHSEYAV 161
R P + H+ + V
Sbjct: 126 RLGPGIDHAPFIV 138
>pdb|3AJV|B Chain B, Splicing Endonuclease From Aeropyrum Pernix
pdb|3AJV|D Chain D, Splicing Endonuclease From Aeropyrum Pernix
Length = 186
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 61/133 (45%), Gaps = 8/133 (6%)
Query: 34 EAHAVLAGYSALLAVEAEQTELLNRACFGRHIVTAEKDKQW-----YQLGMEEGFYLCHS 88
+A VL G S L+ + EQ L + + EK + +L + E YL
Sbjct: 9 KASGVLIGDSVLVT-DVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEK 67
Query: 89 LKCLKIVGEDNSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAY 148
L++ D S+ ++L ++ F +LY Y LR++ +VVRSG ++G DF Y
Sbjct: 68 -GVLEVAKPDGSSVGVEDLRTAVRGNPR-FSMLYNIYRDLRERGFVVRSGLKFGSDFAVY 125
Query: 149 RHHPSLVHSEYAV 161
R P + + + V
Sbjct: 126 RLGPGIDAAPFIV 138
>pdb|2OHC|A Chain A, Structural And Mutational Analysis Of Trna-Intron Splicing
Endonuclease From Thermoplasma Acidophilum Dsm1728
pdb|2OHC|B Chain B, Structural And Mutational Analysis Of Trna-Intron Splicing
Endonuclease From Thermoplasma Acidophilum Dsm1728
Length = 289
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 9/80 (11%)
Query: 124 AYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHC 183
YS L + +V++G +YG +F Y S H+EY V V+ E E W I
Sbjct: 205 VYSDLVGRGCIVKTGFKYGANFRVYLGRDSQ-HAEYLVSVMPEEER--------WYSISR 255
Query: 184 TVRLCGGVAKTLLILTINKN 203
VR+ V KT++ +I KN
Sbjct: 256 GVRVASSVRKTMIYASIYKN 275
>pdb|2OHE|A Chain A, Structural And Mutational Analysis Of Trna-Intron Splicing
Endonuclease From Thermoplasma Acidophilum Dsm 1728
Length = 290
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 9/80 (11%)
Query: 124 AYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHC 183
YS L + +V++G +YG +F Y S H+EY V V+ E E W I
Sbjct: 206 VYSDLVGRGCIVKTGFKYGANFRVYLGRDSQ-HAEYLVSVMPEEER--------WYSISR 256
Query: 184 TVRLCGGVAKTLLILTINKN 203
VR+ V KT++ +I KN
Sbjct: 257 GVRVASSVRKTMIYASIYKN 276
>pdb|3IEY|A Chain A, Crystal Structure Of The Functional Nanoarchaeum Equitans
Trna Splicing Endonuclease
Length = 154
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 60 CFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAKKETFP 119
FG ++ +K +L + E +YL + V ED+ + +E + E F
Sbjct: 5 LFGNRVLVDDK-----ELPLIEAYYLLDKGELE--VYEDDKKLSKEEFLKKCLTYDERFL 57
Query: 120 LLYKAYSHLRKKNWVVRSGSQYGVDFVAY 148
+ YKAY LR K + + + ++G DF Y
Sbjct: 58 IRYKAYKELRDKGYTLGTALKFGADFRVY 86
>pdb|1F11|A Chain A, F124 Fab Fragment From A Monoclonal Anti-Pres2 Antibody
pdb|1F11|C Chain C, F124 Fab Fragment From A Monoclonal Anti-Pres2 Antibody
Length = 218
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 203 NGQGTATPSCLEQYAVEERTISRWSPEQCREDPATVANGIK 243
+G G+ T L + VEE + + +Q EDP T +G K
Sbjct: 67 SGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPFTFGSGTK 107
>pdb|3DDM|A Chain A, Crystal Structure Of Mandelate RacemaseMUCONATE
Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
pdb|3DDM|B Chain B, Crystal Structure Of Mandelate RacemaseMUCONATE
Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
pdb|3DDM|C Chain C, Crystal Structure Of Mandelate RacemaseMUCONATE
Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
pdb|3DDM|D Chain D, Crystal Structure Of Mandelate RacemaseMUCONATE
Lactonizing Enzyme From Bordetella Bronchiseptica Rb50
Length = 392
Score = 27.3 bits (59), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 155 VHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKTLLILTI 200
+H AVLV E DG G W ++ C CG + L+ T+
Sbjct: 35 MHDRPAVLVEVEDSDGAVG----WGEVWCNFPACGAEHRARLVETV 76
>pdb|3TT1|L Chain L, Crystal Structure Of Leut In The Outward-Open Conformation
In Complex With Fab
pdb|3TT1|M Chain M, Crystal Structure Of Leut In The Outward-Open Conformation
In Complex With Fab
Length = 218
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 203 NGQGTATPSCLEQYAVEERTISRWSPEQCREDPATVANGIK 243
+G G+ T L + VEE + + +Q EDP T G K
Sbjct: 67 SGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPYTFGGGTK 107
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 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,710,547
Number of Sequences: 62578
Number of extensions: 310015
Number of successful extensions: 649
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 633
Number of HSP's gapped (non-prelim): 18
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
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: 50 (23.9 bits)