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= 025227
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SNG|A Chain A, X-ray Structure Of Fully Glycosylated Bifunctional
Nuclease Tbn1 From Solanum Lycopersicum (tomato)
Length = 277
Score = 275 bits (702), Expect = 2e-74, Method: Compositional matrix adjust.
Identities = 136/255 (53%), Positives = 168/255 (65%), Gaps = 5/255 (1%)
Query: 5 QSRLREAAADAVKQLLPESADNDLGSVCTWADHVK--FHYHWSSALHFIDTPDNLCTYQY 62
Q L + AA AVK LLPE + DL ++C W D V+ + Y W+S LHFIDTPD C + Y
Sbjct: 14 QGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDY 73
Query: 63 NRDCKDEDGVKGRCVAGAINNYTTQLLXXXXXXXXXXEYNLTEALLFLSHFIGDIHQPLH 122
RDC D+ GVK CVAGAI N+TTQL YN+TEALLFLSHF+GDIHQP+H
Sbjct: 74 ERDCHDQHGVKDMCVAGAIQNFTTQL-SHYREGTSDRRYNMTEALLFLSHFMGDIHQPMH 132
Query: 123 VGFTSDRGGNTIDVHWYTRKQVLHHVWDNNIIETAEERFYNSNIDGLVDAIQQNITTD-W 181
VGFTSD GGN+ID+ W+ K LHHVWD II TA + +Y +I+ L + I+ N T W
Sbjct: 133 VGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGNFTDGIW 192
Query: 182 ADLVKKWETCSANNTACPDVYASEGIKAACDWAYKGVSEGSVLEDEYFNSRLPIVKLRLA 241
+D + W C N +C + +A+E I AC W YKGV G L D+YFNSRLPIV R+A
Sbjct: 193 SDDLASWREC-GNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVA 251
Query: 242 QGGVRLAATLNRIFG 256
QGG+RLA LN +FG
Sbjct: 252 QGGIRLAMLLNNVFG 266
>pdb|4DJ4|A Chain A, X-ray Structure Of Mutant N211d Of Bifunctional Nuclease
Tbn1 From Solanum Lycopersicum (tomato)
pdb|4DJ4|B Chain B, X-ray Structure Of Mutant N211d Of Bifunctional Nuclease
Tbn1 From Solanum Lycopersicum (tomato)
Length = 277
Score = 273 bits (697), Expect = 8e-74, Method: Compositional matrix adjust.
Identities = 135/255 (52%), Positives = 168/255 (65%), Gaps = 5/255 (1%)
Query: 5 QSRLREAAADAVKQLLPESADNDLGSVCTWADHVK--FHYHWSSALHFIDTPDNLCTYQY 62
Q L + AA AVK LLPE + DL ++C W D V+ + Y W+S LHFIDTPD C + Y
Sbjct: 14 QGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDY 73
Query: 63 NRDCKDEDGVKGRCVAGAINNYTTQLLXXXXXXXXXXEYNLTEALLFLSHFIGDIHQPLH 122
RDC D+ GVK CVAGAI N+TTQL YN+TEALLFLSHF+GDIHQP+H
Sbjct: 74 ERDCHDQHGVKDMCVAGAIQNFTTQL-SHYREGTSDRRYNMTEALLFLSHFMGDIHQPMH 132
Query: 123 VGFTSDRGGNTIDVHWYTRKQVLHHVWDNNIIETAEERFYNSNIDGLVDAIQQNITTD-W 181
VGFTSD GGN+ID+ W+ K LHHVWD II TA + +Y +I+ L + I+ + T W
Sbjct: 133 VGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGDFTDGIW 192
Query: 182 ADLVKKWETCSANNTACPDVYASEGIKAACDWAYKGVSEGSVLEDEYFNSRLPIVKLRLA 241
+D + W C N +C + +A+E I AC W YKGV G L D+YFNSRLPIV R+A
Sbjct: 193 SDDLASWREC-GNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVA 251
Query: 242 QGGVRLAATLNRIFG 256
QGG+RLA LN +FG
Sbjct: 252 QGGIRLAMLLNNVFG 266
>pdb|1AK0|A Chain A, P1 Nuclease In Complex With A Substrate Analog
Length = 270
Score = 76.3 bits (186), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 77/250 (30%), Positives = 104/250 (41%), Gaps = 54/250 (21%)
Query: 34 WADHVKFHY--HWSSALHFIDTPDNL---CTYQYNRDCKDEDGVKGRCVAGAINNYTTQL 88
WAD + WS++LHFID DN C Y RDC G G C AI NYT ++
Sbjct: 43 WADEYRLTSAGKWSASLHFIDAEDNPPTNCNVDYERDC----GSSG-CSISAIANYTQRV 97
Query: 89 LXXXXXXXXXXEYNLTEALLFLSHFIGDIHQPLHVGFTSDRGGNTIDVHWYTRKQVLHHV 148
N EAL FL HFIGD+ QPLH + GGN I+V + LH
Sbjct: 98 -----SDSSLSSENHAEALRFLVHFIGDMTQPLHDEAYA-VGGNKINVTFDGYHDNLHSD 151
Query: 149 WD--------------------NNIIETAEERFYNSNIDGLV--DAIQQNITTDWADLVK 186
WD +++ E Y + G + D I + ITT
Sbjct: 152 WDTYMPQKLIGGHALSDAESWAKTLVQNIESGNYTAQAIGWIKGDNISEPITT-----AT 206
Query: 187 KWETCSANNTACPDVYASEGIKAACDWAYKGVSEGSVLEDEYFNSRLPIVKLRLAQGGVR 246
+W + AN C V G A + L Y++S + ++L++A+GG R
Sbjct: 207 RWAS-DANALVCT-VVMPHGAAAL---------QTGDLYPTYYDSVIDTIELQIAKGGYR 255
Query: 247 LAATLNRIFG 256
LA +N I G
Sbjct: 256 LANWINEIHG 265
>pdb|1AH7|A Chain A, Phospholipase C From Bacillus Cereus
Length = 245
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 20/81 (24%)
Query: 47 ALHFIDTPDNLCTYQYNRDCKDEDGVKGRCVAGAINNYTTQLLXXXXXXXXXXEYNLTEA 106
A HF D PDN TY E G K +AG +Y + ++ +A
Sbjct: 67 ASHFYD-PDNGKTYIPFAKQAKETGAKYFKLAG--ESYKNK--------------DMKQA 109
Query: 107 LLFLS---HFIGDIHQPLHVG 124
+L H++GD++QP+H
Sbjct: 110 FFYLGLSLHYLGDVNQPMHAA 130
>pdb|2HUC|A Chain A, Structural Studies Examining The Substrate Specificity
Profiles Of Pc-Plcbc Protein Variants
Length = 245
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 20/80 (25%)
Query: 47 ALHFIDTPDNLCTYQYNRDCKDEDGVKGRCVAGAINNYTTQLLXXXXXXXXXXEYNLTEA 106
A HF D PDN TY E G K +AG +Y + ++ +A
Sbjct: 67 ASHFYD-PDNGKTYIPFAKQAKETGAKYFKLAG--ESYKNK--------------DMKQA 109
Query: 107 LLFLS---HFIGDIHQPLHV 123
+L H++GD++QP+H
Sbjct: 110 FFYLGLSLHYLGDVNQPMHA 129
>pdb|2FFZ|A Chain A, Structural Studies Examining The Substrate Specificity
Profiles Of Pc-Plcbc Protein Variants
Length = 245
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 20/81 (24%)
Query: 47 ALHFIDTPDNLCTYQYNRDCKDEDGVKGRCVAGAINNYTTQLLXXXXXXXXXXEYNLTEA 106
A HF D PDN TY E G K +AG +Y + ++ +A
Sbjct: 67 ASHFYD-PDNGKTYIPFAKQAKETGAKYFKLAG--ESYKNK--------------DMKQA 109
Query: 107 LLFLS---HFIGDIHQPLHVG 124
+L H++GD++QP+H
Sbjct: 110 FFYLGLSLHYLGDVNQPMHAA 130
>pdb|1ESC|A Chain A, The Molecular Mechanism Of Enantiorecognition By Esterases
pdb|1ESD|A Chain A, The Molecular Mechanism Of Enantiorecognition By Esterases
pdb|1ESE|A Chain A, The Molecular Mechanism Of Enantiorecognition By Esterases
Length = 306
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 200 DVYASEGIKAACDWAYKGVSEGSVLED---EYFNSRLP 234
D+YA G ACD A +G+ G +LED E +++P
Sbjct: 244 DLYAGTGANTACDGADRGI--GGLLEDSQLELLGTKIP 279
>pdb|1GXP|A Chain A, Phob Effector Domain In Complex With Pho Box Dna.
pdb|1GXP|B Chain B, Phob Effector Domain In Complex With Pho Box Dna.
pdb|1GXP|E Chain E, Phob Effector Domain In Complex With Pho Box Dna.
pdb|1GXP|F Chain F, Phob Effector Domain In Complex With Pho Box Dna.
pdb|1GXQ|A Chain A, Crystal Structure Of The Phob Effector Domain
Length = 106
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 111 SHFIGDIHQPLHVGFTSDRGGNTIDVH---WYTRKQVLHHVWDNNIIETAEERFYNSNID 167
SH + +PL +G T + + H Y+R+Q+L+HVW N+ E+R + +I
Sbjct: 20 SHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVY--VEDRTVDVHIR 77
Query: 168 GLVDAIQ 174
L A++
Sbjct: 78 RLRKALE 84
>pdb|1QQI|A Chain A, Solution Structure Of The Dna-Binding And Transactivation
Domain Of Phob From Escherichia Coli
pdb|2Z33|A Chain A, Solution Structure Of The Dna Complex Of Phob Dna-
BindingTRANSACTIVATION DOMAIN
Length = 104
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 111 SHFIGDIHQPLHVGFTSDRGGNTIDVH---WYTRKQVLHHVWDNNIIETAEERFYNSNID 167
SH + +PL +G T + + H Y+R+Q+L+HVW N+ E+R + +I
Sbjct: 18 SHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVY--VEDRTVDVHIR 75
Query: 168 GLVDAIQ 174
L A++
Sbjct: 76 RLRKALE 82
>pdb|3T72|A Chain A, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|B Chain B, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|E Chain E, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|F Chain F, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|I Chain I, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|J Chain J, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|M Chain M, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|N Chain N, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|R Chain R, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|S Chain S, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|V Chain V, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|W Chain W, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|Z Chain Z, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|1 Chain 1, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|4 Chain 4, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|5 Chain 5, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|8 Chain 8, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|9 Chain 9, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|CC Chain c, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|DD Chain d, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|GG Chain g, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|HH Chain h, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|KK Chain k, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|LL Chain l, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
Length = 102
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 111 SHFIGDIHQPLHVGFTSDRGGNTIDVH---WYTRKQVLHHVWDNNIIETAEERFYNSNID 167
SH + +PL +G T + + H Y+R+Q+L+HVW N+ E+R + +I
Sbjct: 16 SHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVY--VEDRTVDVHIR 73
Query: 168 GLVDAIQ 174
L A++
Sbjct: 74 RLRKALE 80
>pdb|3I7F|A Chain A, Aspartyl Trna Synthetase From Entamoeba Histolytica
pdb|3I7F|B Chain B, Aspartyl Trna Synthetase From Entamoeba Histolytica
Length = 548
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 116 DIHQPLHVGFTSDRGGNTIDVHWYTRKQVL 145
+IH P +G +S+ G N +V ++ RK L
Sbjct: 265 EIHTPKLIGCSSEGGSNIFEVKYFDRKAYL 294
>pdb|3SHS|A Chain A, Three N-Terminal Domains Of The Bacteriophage Rb49 Highly
Immunogenic Outer Capsid Protein (Hoc)
Length = 304
Score = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 33 TWADHVKFHYHWSSALHFIDTPDNLCTYQYNRD 65
T AD+ + HY WS IDT ++ ++ D
Sbjct: 123 TPADNYELHYSWSKGEDVIDTTQDITIQEFTAD 155
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
0.320 0.135 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,891,823
Number of Sequences: 62578
Number of extensions: 315813
Number of successful extensions: 874
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 859
Number of HSP's gapped (non-prelim): 14
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)