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= 020786
(321 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DK3|C Chain C, Structure Of Editosome Protein
pdb|4DK3|D Chain D, Structure Of Editosome Protein
pdb|4DK6|C Chain C, Structure Of Editosome Protein
pdb|4DK6|D Chain D, Structure Of Editosome Protein
pdb|4DKA|C Chain C, Structure Of Editosome Protein
pdb|4DKA|D Chain D, Structure Of Editosome Protein
Length = 105
Score = 31.6 bits (70), Expect = 0.59, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 91 ILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHG--VPKSLVVKLMLIQPRT 148
++ R+ D L A+ VLE D E ++ G P SL+ + + R
Sbjct: 8 MIGRIADVQHGFLGAMTVTQYVLEVDGGASGEKEFIVIRCMGDNFPASLLKDQVKLGSRV 67
Query: 149 LLQSTARLNKIIDEVKK 165
L+Q T R+N+ +D+V K
Sbjct: 68 LVQGTLRMNRHVDDVSK 84
>pdb|2BR6|A Chain A, Crystal Structure Of Quorum-Quenching N-Acyl Homoserine
Lactone Lactonase
pdb|2BTN|A Chain A, Crystal Structure And Catalytic Mechanism Of The Quorum-
Quenching N-Acyl Homoserine Lactone Hydrolase
Length = 252
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 127 ILVNHGVPKSLVVKLMLIQPR----TLLQSTARLNKIIDEVKKLGFDPTNLLFVLA 178
ILV+ G+P+S V L +L ++I++ +K++G++P +LL++++
Sbjct: 49 ILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIIS 104
>pdb|3DHA|A Chain A, An Ultral High Resolution Structure Of N-Acyl Homoserine
Lactone Hydrolase With The Product
N-Hexanoyl-L-Homoserine Bound At An Alternative Site
pdb|3DHB|A Chain A, 1.4 Angstrom Structure Of N-Acyl Homoserine Lactone
Hydrolase With The Product N-Hexanoyl-L-Homoserine Bound
At The Catalytic Metal Center
pdb|3DHC|A Chain A, 1.3 Angstrom Structure Of N-Acyl Homoserine Lactone
Hydrolase With The Product N-Hexanoyl-L-Homocysteine
Bound To The Catalytic Metal Center
Length = 254
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 127 ILVNHGVPKSLVVKLMLIQPR----TLLQSTARLNKIIDEVKKLGFDPTNLLFVLA 178
ILV+ G+P+S V L +L ++I++ +K++G++P +LL++++
Sbjct: 51 ILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIIS 106
>pdb|2A7M|A Chain A, 1.6 Angstrom Resolution Structure Of The Quorum-Quenching
N-Acyl Homoserine Lactone Hydrolase Of Bacillus
Thuringiensis
Length = 250
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 127 ILVNHGVPKSLVVKLMLIQPR----TLLQSTARLNKIIDEVKKLGFDPTNLLFVLA 178
ILV+ G+P+S V L +L ++I++ +K++G++P +LL++++
Sbjct: 47 ILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIIS 102
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 47/113 (41%), Gaps = 7/113 (6%)
Query: 126 AILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTNLLFVLAIRSMAVM 185
+ + H P V K++ P L+QST R+ I+ ++ + L VL A +
Sbjct: 169 GLSLGHNDPADFVRKIIFKNPAILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEI 228
Query: 186 SKALWEKKLEAYMN-------FGLTKDEVYSAFRRQPMFMIVSEQKISKLMDC 231
+ +Y N G T++EV P + ++E+K + +DC
Sbjct: 229 LDLSNDAARRSYANIKEKLFSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDC 281
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 41/214 (19%), Positives = 86/214 (40%), Gaps = 39/214 (18%)
Query: 26 SDSQIKSITVKRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENH 84
SD +I +I + P+ F+ N ++ ++F S+G + + L++ P SL
Sbjct: 99 SDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSL--- 155
Query: 85 IIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 144
D ++ +++ ++A L L H P V K++
Sbjct: 156 ------------DLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFK 187
Query: 145 QPRTLLQSTARLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAY 197
P L+QST R+ I+ ++ + LL ++ ++ ++ + E
Sbjct: 188 NPFILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKL 247
Query: 198 MNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDC 231
+ G T++EV P + ++E+K + +DC
Sbjct: 248 FSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDC 281
>pdb|3N6S|A Chain A, Crystal Structure Of Human Mitochondrial Mterf In Complex
With A 15- Mer Dna Encompassing The Trnaleu(Uur) Binding
Sequence
Length = 353
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 42/214 (19%), Positives = 88/214 (41%), Gaps = 39/214 (18%)
Query: 26 SDSQIKSITVKRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENH 84
SD +I +I + P+ F+ N ++ ++F S+G + + L++ P R+ N
Sbjct: 100 SDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAP----RTFSNS 155
Query: 85 IIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 144
LD ++ +++ ++A L L H P V K++
Sbjct: 156 -----------LDLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFK 188
Query: 145 QPRTLLQSTARLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAY 197
P L+QST R+ I+ ++ + LL ++ ++ ++ + E
Sbjct: 189 NPFILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKL 248
Query: 198 MNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDC 231
+ G T++EV P + ++E+K + +DC
Sbjct: 249 FSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDC 282
>pdb|3N7Q|A Chain A, Crystal Structure Of Human Mitochondrial Mterf Fragment
(Aa 99-399) In Complex With A 12-Mer Dna Encompassing
The Trnaleu(Uur) Binding Sequence
Length = 310
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 42/214 (19%), Positives = 88/214 (41%), Gaps = 39/214 (18%)
Query: 26 SDSQIKSITVKRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENH 84
SD +I +I + P+ F+ N ++ ++F S+G + + L++ P R+ N
Sbjct: 57 SDLEIVNILERSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAP----RTFSNS 112
Query: 85 IIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 144
LD ++ +++ ++A L L H P V K++
Sbjct: 113 -----------LDLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFK 145
Query: 145 QPRTLLQSTARLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAY 197
P L+QST R+ I+ ++ + LL ++ ++ ++ + E
Sbjct: 146 NPFILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKL 205
Query: 198 MNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDC 231
+ G T++EV P + ++E+K + +DC
Sbjct: 206 FSLGCTEEEVQKFVLSYPDVIFLAEKKFNDKIDC 239
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 50/228 (21%), Positives = 82/228 (35%), Gaps = 55/228 (24%)
Query: 44 NLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVL 103
+ +K +K L F K +G + Q+ FL+ I LEN
Sbjct: 36 DFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-------------------- 75
Query: 104 KAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEV 163
L+ +A L + K+ V +++ P L S RL+
Sbjct: 76 -----------------LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLD------ 112
Query: 164 KKLGFDPTNL-LFVLAIRSMAVMSKALWEKKLEAY--------MNFGLTKDEVYSAFRRQ 214
+LGF L L V R + V L LE + G +E+ R
Sbjct: 113 NRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRI 172
Query: 215 PMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLL---LFSLEKRIL 259
P + ++ K+++ D N +S+ II K P + LF +++R L
Sbjct: 173 PKMLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRLFKVKERHL 220
>pdb|3SNP|A Chain A, Crystal Structure Analysis Of Iron Regulatory Protein 1 In
Complex With Ferritin H Ire Rna
pdb|3SNP|B Chain B, Crystal Structure Analysis Of Iron Regulatory Protein 1 In
Complex With Ferritin H Ire Rna
pdb|3SN2|A Chain A, Crystal Structure Analysis Of Iron Regulatory Protein 1 In
Complex With Transferrin Receptor Ire B Rna
Length = 908
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 111 LVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDP 170
LV + DIE +L N+ +N VP +++Q T + S + D VKKLG DP
Sbjct: 73 LVKKEDIENILNWNVTQHMNIEVP--FKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDP 130
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 50/228 (21%), Positives = 82/228 (35%), Gaps = 55/228 (24%)
Query: 44 NLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVL 103
+ +K +K L F K +G + Q+ FL+ I LEN
Sbjct: 64 DFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-------------------- 103
Query: 104 KAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEV 163
L+ +A L + K+ V +++ P L S RL+
Sbjct: 104 -----------------LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLD------ 140
Query: 164 KKLGFDPTNL-LFVLAIRSMAVMSKALWEKKLEAY--------MNFGLTKDEVYSAFRRQ 214
+LGF L L V R + V L LE + G +E+ R
Sbjct: 141 NRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRI 200
Query: 215 PMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLL---LFSLEKRIL 259
P + ++ K+++ D N +S+ II K P + LF +++R L
Sbjct: 201 PKMLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRLFKVKERHL 248
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
0.324 0.139 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,141,503
Number of Sequences: 62578
Number of extensions: 298059
Number of successful extensions: 1025
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 1022
Number of HSP's gapped (non-prelim): 30
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)