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= 013135
(449 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 = 0.90, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 219 ILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHG--VPKSLVVKLMLIQPRT 276
++ R+ D L A+ VLE D E ++ G P SL+ + + R
Sbjct: 8 MIGRIADVQHGFLGAMTVTQYVLEVDGGASGEKEFIVIRCMGDNFPASLLKDQVKLGSRV 67
Query: 277 LLQSTARLNKIIDEVKK 293
L+Q T R+N+ +D+V K
Sbjct: 68 LVQGTLRMNRHVDDVSK 84
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 52/264 (19%), Positives = 110/264 (41%), Gaps = 43/264 (16%)
Query: 108 TLEPNLKLFK-SLGITGANLAEMLNKEHRVLE---SDAYATVEFFRTNGFSDSQIKSITV 163
T E +LK+F S G + +A ++++ R + + + +R SD +I +I
Sbjct: 49 TNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPENLSKRWDLWRKIVTSDLEIVNILE 108
Query: 164 KRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRR 222
+ P+ F+ N ++ ++F S+G + + L++ P R+ N
Sbjct: 109 RSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAP----RTFSNS---------- 154
Query: 223 VLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTA 282
LD ++ +++ ++A L L H P V K++ P L+QST
Sbjct: 155 -LDLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFKNPFILIQSTK 197
Query: 283 RLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAYMNFGLTKDEV 335
R+ I+ ++ + LL ++ ++ ++ + E + G T++EV
Sbjct: 198 RVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEV 257
Query: 336 YSAFRRQPMFMIVSEQKISKLMDC 359
P + ++E+K + +DC
Sbjct: 258 QKFVLSYPDVIFLAEKKFNDKIDC 281
>pdb|2CWE|A Chain A, Crystal Structure Of Hypothetical Transcriptional
Regulator Protein, Ph1932 From Pyrococcus Horikoshii Ot3
Length = 192
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 57/129 (44%), Gaps = 20/129 (15%)
Query: 62 VSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLGI 121
++ E ++V D +LKLLR +T SQ++ + K P T+ +++ K G+
Sbjct: 8 ITDPEVIKVMLEDTRRKILKLLRNKEMTISQLSEILGKTPQ-----TIYHHIEKLKEAGL 62
Query: 122 TGANLAEMLNKEHRVLESDAYATVEFFRTNGF-SDSQIKSITVKRPKFYVYNLKKCMKPK 180
EM + ++E T + F N + D +++ I R +K K
Sbjct: 63 VEVKRTEM---KGNLVEKYYGRTADVFYINLYLGDEELRYIARSR-----------LKTK 108
Query: 181 LEFFKSLGF 189
++ FK LG+
Sbjct: 109 IDIFKRLGY 117
>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 = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 52/264 (19%), Positives = 110/264 (41%), Gaps = 43/264 (16%)
Query: 108 TLEPNLKLFK-SLGITGANLAEMLNKEHRVLE---SDAYATVEFFRTNGFSDSQIKSITV 163
T E +LK+F S G + +A ++++ R + + + +R SD +I +I
Sbjct: 50 TNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPENLSKRWDLWRKIVTSDLEIVNILE 109
Query: 164 KRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRR 222
+ P+ F+ N ++ ++F S+G + + L++ P R+ N
Sbjct: 110 RSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAP----RTFSNS---------- 155
Query: 223 VLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTA 282
LD ++ +++ ++A L L H P V K++ P L+QST
Sbjct: 156 -LDLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFKNPFILIQSTK 198
Query: 283 RLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAYMNFGLTKDEV 335
R+ I+ ++ + LL ++ ++ ++ + E + G T++EV
Sbjct: 199 RVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEV 258
Query: 336 YSAFRRQPMFMIVSEQKISKLMDC 359
P + ++E+K + +DC
Sbjct: 259 QKFVLSYPDVIFLAEKKFNDKIDC 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 = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 52/264 (19%), Positives = 110/264 (41%), Gaps = 43/264 (16%)
Query: 108 TLEPNLKLFK-SLGITGANLAEMLNKEHRVLE---SDAYATVEFFRTNGFSDSQIKSITV 163
T E +LK+F S G + +A ++++ R + + + +R SD +I +I
Sbjct: 7 TNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPENLSKRWDLWRKIVTSDLEIVNILE 66
Query: 164 KRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRR 222
+ P+ F+ N ++ ++F S+G + + L++ P R+ N
Sbjct: 67 RSPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAP----RTFSNS---------- 112
Query: 223 VLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTA 282
LD ++ +++ ++A L L H P V K++ P L+QST
Sbjct: 113 -LDLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFKNPFILIQSTK 155
Query: 283 RLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAYMNFGLTKDEV 335
R+ I+ ++ + LL ++ ++ ++ + E + G T++EV
Sbjct: 156 RVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFSLGCTEEEV 215
Query: 336 YSAFRRQPMFMIVSEQKISKLMDC 359
P + ++E+K + +DC
Sbjct: 216 QKFVLSYPDVIFLAEKKFNDKIDC 239
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 52/264 (19%), Positives = 109/264 (41%), Gaps = 43/264 (16%)
Query: 108 TLEPNLKLFK-SLGITGANLAEMLNKEHRVLE---SDAYATVEFFRTNGFSDSQIKSITV 163
T E +LK+F S G + +A ++++ R + + + +R SD +I +I
Sbjct: 49 TNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPENLSKRWDLWRKIVTSDLEIVNILE 108
Query: 164 KRPK-FYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRR 222
P+ F+ N ++ ++F S+G + + L++ P R+ N
Sbjct: 109 ASPESFFRSNNNLNLENNIKFLYSVGLTRKCLCRLLTNAP----RTFSNS---------- 154
Query: 223 VLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTA 282
LD ++ +++ ++A L L H P V K++ P L+QST
Sbjct: 155 -LDLNKQMVEFLQAAGLSL----------------GHNDPADFVRKIIFKNPAILIQSTK 197
Query: 283 RLNKIIDEVKK-LGFDPTNLLFVLAIRSMAVM------SKALWEKKLEAYMNFGLTKDEV 335
R+ I+ ++ + LL ++ ++ ++ + E + G T++EV
Sbjct: 198 RVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDAARRSYANIKEKLFSLGCTEEEV 257
Query: 336 YSAFRRQPMFMIVSEQKISKLMDC 359
P + ++E+K + +DC
Sbjct: 258 QKFVLSYPDVIFLAEKKFNDKIDC 281
>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 = 4.0, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 255 ILVNHGVPKSLVVKLMLIQPR----TLLQSTARLNKIIDEVKKLGFDPTNLLFVLA 306
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 = 4.0, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 255 ILVNHGVPKSLVVKLMLIQPR----TLLQSTARLNKIIDEVKKLGFDPTNLLFVLA 306
ILV+ G+P+S V L +L ++I++ +K++G++P +LL++++
Sbjct: 47 ILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIIS 102
>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 = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 255 ILVNHGVPKSLVVKLMLIQPR----TLLQSTARLNKIIDEVKKLGFDPTNLLFVLA 306
ILV+ G+P+S V L +L ++I++ +K++G++P +LL++++
Sbjct: 49 ILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIIS 104
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 28.5 bits (62), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 50/228 (21%), Positives = 82/228 (35%), Gaps = 55/228 (24%)
Query: 172 NLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVL 231
+ +K +K L F K +G + Q+ FL+ I LEN
Sbjct: 36 DFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-------------------- 75
Query: 232 KAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEV 291
L+ +A L + K+ V +++ P L S RL+
Sbjct: 76 -----------------LKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLD------ 112
Query: 292 KKLGFDPTNL-LFVLAIRSMAVMSKALWEKKLEAY--------MNFGLTKDEVYSAFRRQ 342
+LGF L L V R + V L LE + G +E+ R
Sbjct: 113 NRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRI 172
Query: 343 PMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLL---LFSLEKRIL 387
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 = 28.5 bits (62), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 239 LVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDP 298
LV + DIE +L N+ +N VP +++Q T + S + D VKKLG DP
Sbjct: 73 LVKKEDIENILNWNVTQHMNIEVP--FKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDP 130
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
0.322 0.137 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,563,741
Number of Sequences: 62578
Number of extensions: 434406
Number of successful extensions: 1134
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1126
Number of HSP's gapped (non-prelim): 19
length of query: 449
length of database: 14,973,337
effective HSP length: 102
effective length of query: 347
effective length of database: 8,590,381
effective search space: 2980862207
effective search space used: 2980862207
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)