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= psy5651
(843 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3K44|A Chain A, Crystal Structure Of Drosophila Melanogaster Pur-Alpha
pdb|3K44|B Chain B, Crystal Structure Of Drosophila Melanogaster Pur-Alpha
pdb|3K44|C Chain C, Crystal Structure Of Drosophila Melanogaster Pur-Alpha
pdb|3K44|D Chain D, Crystal Structure Of Drosophila Melanogaster Pur-Alpha
Length = 146
Score = 106 bits (264), Expect = 7e-23, Method: Composition-based stats.
Identities = 55/136 (40%), Positives = 84/136 (61%), Gaps = 3/136 (2%)
Query: 311 TKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNAL--LTA 368
TKM Q +K+FY D+KQ++ +FIK++E+ D R+QI++++S RDHL++ A
Sbjct: 7 TKMLQIQSKRFYLDVKQNRRGRFIKVAEIGADGRRSQIYLALSTAAEFRDHLSSFSDYYA 66
Query: 369 HQNTPR-HRYRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPA 427
P + +KSE++IKD RRY+LDLK+N R RF+ +SQ + GG S IA PA
Sbjct: 67 SLGPPNTDNLPEDGKLKSEMMIKDYRRYYLDLKENARGRFLRVSQTITRGGPRSQIALPA 126
Query: 428 QDLGPIIGLISDLQQE 443
Q + ++DL +E
Sbjct: 127 QGMIEFRDALTDLLEE 142
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/110 (23%), Positives = 57/110 (51%), Gaps = 6/110 (5%)
Query: 383 IKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGK------LSSIAFPAQDLGPIIGL 436
+ +++L ++R++LD+K N R RF+ ++++ G + LS+ A L
Sbjct: 5 LATKMLQIQSKRFYLDVKQNRRGRFIKVAEIGADGRRSQIYLALSTAAEFRDHLSSFSDY 64
Query: 437 ISDLQQEHSCPEDEDGAPEGNYMRCNNKRFFFNVSKNGKGTFMRISEIST 486
+ L ++ EDG + M + +R++ ++ +N +G F+R+S+ T
Sbjct: 65 YASLGPPNTDNLPEDGKLKSEMMIKDYRRYYLDLKENARGRFLRVSQTIT 114
>pdb|2FBT|A Chain A, Wrn Exonuclease
pdb|2FBV|A Chain A, Wrn Exonuclease, Mn Complex
pdb|2FBX|A Chain A, Wrn Exonuclease, Mg Complex
pdb|2FBY|A Chain A, Wrn Exonuclease, Eu Complex
pdb|2FC0|A Chain A, Wrn Exonuclease, Mn Dgmp Complex
Length = 205
Score = 55.1 bits (131), Expect = 2e-07, Method: Composition-based stats.
Identities = 53/168 (31%), Positives = 78/168 (46%), Gaps = 23/168 (13%)
Query: 41 VGLDLEGMDL---GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKV 97
VG D+E L G GKV+L+ L + K ++F V S + +F L +LE+ + K
Sbjct: 48 VGFDMEWPPLYNRGKLGKVALIQLCVSESKCYLFHVSS--MSVFPQGLKMLLENKAVKKA 105
Query: 98 IHGAFGDAGGLLSNFNIRLKNVYD-TQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYK 156
G GD LL +F+I+LKN + T A L+ ++ L+ LV H +G LLK
Sbjct: 106 GVGIEGDQWKLLRDFDIKLKNFVELTDVANKKLKCTETWSLNS-LVKHLLG-KQLLKDKS 163
Query: 157 ISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204
I +N W PLT D LYAA D + ++ +
Sbjct: 164 IRCSN---------------WSKFPLTEDQKLYAATDAYAGFIIYRNL 196
>pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain
pdb|2E6M|A Chain A, Structure Of Mouse Werner Exonuclease Domain
Length = 208
Score = 49.7 bits (117), Expect = 7e-06, Method: Composition-based stats.
Identities = 47/168 (27%), Positives = 79/168 (47%), Gaps = 23/168 (13%)
Query: 41 VGLDLEGMDL---GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKV 97
VG D+E + G +V+++ L + K ++F + S + +F L +LE+ I K
Sbjct: 43 VGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHISS--MSVFPQGLKMLLENKSIKKA 100
Query: 98 IHGAFGDAGGLLSNFNIRLKNVYD-TQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYK 156
G GD LL +F+++L++ + T A L+ ++ L+ LV H +G LLK
Sbjct: 101 GVGIEGDQWKLLRDFDVKLESFVELTDVANEKLKCAETWSLN-GLVKHVLG-KQLLKDKS 158
Query: 157 ISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204
I +N W PLT D LYAA D + L ++ ++
Sbjct: 159 IRCSN---------------WSNFPLTEDQKLYAATDAYAGLIIYQKL 191
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 38/123 (30%), Positives = 56/123 (45%), Gaps = 20/123 (16%)
Query: 85 LHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPH 144
L+E L I+KV HGA D L +F + + N++DT A L L H
Sbjct: 174 LNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGR----------H 223
Query: 145 TIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204
+ L+ LLK Y +N + + + W+ RPL +ML YA D LL ++ +M
Sbjct: 224 S--LDHLLKLYCNVDSNKQYQLAD--------WRIRPLPEEMLSYARDDTHYLLYIYDKM 273
Query: 205 TKE 207
E
Sbjct: 274 RLE 276
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 37/123 (30%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 85 LHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPH 144
L+E L I+KV HGA D L +F + + N++DT A L L H
Sbjct: 174 LNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGR----------H 223
Query: 145 TIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204
+ L+ LLK Y +N + + + W+ RPL +ML A D LL ++ +M
Sbjct: 224 S--LDHLLKLYCNVDSNKQYQLAD--------WRIRPLPEEMLSAARDDTHYLLYIYDKM 273
Query: 205 TKE 207
E
Sbjct: 274 RLE 276
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 67/260 (25%), Positives = 113/260 (43%), Gaps = 52/260 (20%)
Query: 27 EAQSAMATILNESKVGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKL 85
E +S + + N ++ +DLE D G V L+ ++ + + ++ D + L
Sbjct: 95 ELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRE-RDYLVDT-----LKLRENL 148
Query: 86 H---EVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLV 142
H EV + I+KV HGAF D L + + + ++DT A A+ L PR
Sbjct: 149 HILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGL--PR------- 199
Query: 143 PHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFH 202
H++ LL+ + NFK + + + W+ RPL+ M A AD LL ++
Sbjct: 200 -HSLAY--LLENFA----NFKTSKKYQLAD----WRIRPLSKPMTAAARADTHFLLNIYD 248
Query: 203 RMTKEYALKQNRLLLDNLIYETLFNHVVPLNIRKRRQFRQNQLRRWRKDLMSSKRPYPYI 262
++ +N+L+ N + L+ N+ KRR F ++ R L S Y I
Sbjct: 249 QL-------RNKLIESNKLAGVLYES---RNVAKRR-FEYSKYR----PLTPSSEVYSPI 293
Query: 263 EEVNSNEYIWR---NDYNVP 279
E+ E W+ YN+P
Sbjct: 294 EK----ESPWKILMYQYNIP 309
>pdb|3NU1|A Chain A, Structure Of Holo Form Of A Periplasmic Heme Binding
Protein
pdb|3NU1|B Chain B, Structure Of Holo Form Of A Periplasmic Heme Binding
Protein
Length = 254
Score = 33.9 bits (76), Expect = 0.43, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 412 QLLPVGGKLSSIAFPAQDLGPIIGLISDLQQEHSCPEDEDGAPEGNYMRCNNKRFFFNVS 471
+++ +GG ++ IA+ I+ S QQ P+ P+ YMR N +
Sbjct: 3 RIVTIGGDVTEIAYALGAGDEIVARDSTSQQ----PQAAQKLPDVGYMRTLNAEGILAM- 57
Query: 472 KNGKGTFMRISEISTPSKVLTNIG 495
K T + +SE++ PS VLT I
Sbjct: 58 ---KPTMLLVSELAQPSLVLTQIA 78
>pdb|3MD9|A Chain A, Structure Of Apo Form Of A Periplasmic Heme Binding
Protein
pdb|3MD9|B Chain B, Structure Of Apo Form Of A Periplasmic Heme Binding
Protein
Length = 255
Score = 33.9 bits (76), Expect = 0.43, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 412 QLLPVGGKLSSIAFPAQDLGPIIGLISDLQQEHSCPEDEDGAPEGNYMRCNNKRFFFNVS 471
+++ +GG ++ IA+ I+ S QQ P+ P+ YMR N +
Sbjct: 4 RIVTIGGDVTEIAYALGAGDEIVARDSTSQQ----PQAAQKLPDVGYMRTLNAEGILAM- 58
Query: 472 KNGKGTFMRISEISTPSKVLTNIG 495
K T + +SE++ PS VLT I
Sbjct: 59 ---KPTMLLVSELAQPSLVLTQIA 79
>pdb|1AGN|A Chain A, X-Ray Structure Of Human Sigma Alcohol Dehydrogenase
pdb|1AGN|B Chain B, X-Ray Structure Of Human Sigma Alcohol Dehydrogenase
pdb|1AGN|C Chain C, X-Ray Structure Of Human Sigma Alcohol Dehydrogenase
pdb|1AGN|D Chain D, X-Ray Structure Of Human Sigma Alcohol Dehydrogenase
pdb|1D1S|A Chain A, Wild-type Human Sigma (class Iv) Alcohol Dehydrogenase
pdb|1D1S|B Chain B, Wild-type Human Sigma (class Iv) Alcohol Dehydrogenase
pdb|1D1S|C Chain C, Wild-type Human Sigma (class Iv) Alcohol Dehydrogenase
pdb|1D1S|D Chain D, Wild-type Human Sigma (class Iv) Alcohol Dehydrogenase
Length = 373
Score = 33.5 bits (75), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 325 IKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALLTAHQN 371
I STK ISEV + T N + + V+GHL ++AL + H N
Sbjct: 240 ISPKDSTK--PISEVLSEMTGNNVGYTFEVIGHLETMIDALASCHMN 284
>pdb|1D1T|A Chain A, Mutant Of Human Sigma Alcohol Dehydrogenase With Leucine
At Position 141
pdb|1D1T|B Chain B, Mutant Of Human Sigma Alcohol Dehydrogenase With Leucine
At Position 141
pdb|1D1T|C Chain C, Mutant Of Human Sigma Alcohol Dehydrogenase With Leucine
At Position 141
pdb|1D1T|D Chain D, Mutant Of Human Sigma Alcohol Dehydrogenase With Leucine
At Position 141
Length = 373
Score = 33.5 bits (75), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 325 IKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALLTAHQN 371
I STK ISEV + T N + + V+GHL ++AL + H N
Sbjct: 240 ISPKDSTK--PISEVLSEMTGNNVGYTFEVIGHLETMIDALASCHMN 284
>pdb|1J4B|A Chain A, Recombinant Mouse-muscle Adenylosuccinate Synthetase
pdb|1IWE|A Chain A, Imp Complex Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase
pdb|1IWE|B Chain B, Imp Complex Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase
pdb|1LNY|A Chain A, Crystal Structure Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase Complexed With 6-Phosphoryl-
Imp, Gdp And Mg
pdb|1LNY|B Chain B, Crystal Structure Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase Complexed With 6-Phosphoryl-
Imp, Gdp And Mg
pdb|1LON|A Chain A, Crystal Structure Of The Recombinant Mouse-Muscle
Adenylosuccinate Synthetase Complexed With
6-Phosphoryl-Imp, Gdp And Hadacidin
pdb|1LOO|A Chain A, Crystal Structure Of The Mouse-Muscle Adenylosuccinate
Synthetase Ligated With Gtp
pdb|1MEZ|A Chain A, Structure Of The Recombinant Mouse-Muscle Adenylosuccinate
Synthetase Complexed With Samp, Gdp, So4(2-), And Mg(2+)
pdb|1MF0|A Chain A, Structure Of The Recombinant Mouse-Muscle Adenylosuccinate
Synthetase Complexed With Amp, Gdp, Hpo4(2-), And Mg(2+)
pdb|1MF1|A Chain A, Structure Of The Recombinant Mouse-Muscle Adenylosuccinate
Synthetase Complexed With Amp
pdb|2DGN|A Chain A, Mouse Muscle Adenylosuccinate Synthetase Partially Ligated
Complex With Gtp, 2'-Deoxy-Imp
Length = 457
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 377 YRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPAQDLGPIIGL 436
Y H +VL++ LD+ D G FVT S VGG + + P Q++G + G+
Sbjct: 240 YEALHGPPKKVLVEGANAALLDI-DFGTYPFVTSSNCT-VGGVCTGLGIPPQNIGDVYGV 297
Query: 437 I 437
+
Sbjct: 298 V 298
>pdb|2V40|A Chain A, Human Adenylosuccinate Synthetase Isozyme 2 In Complex
With Gdp
Length = 459
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 377 YRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPAQDLGPIIGL 436
Y H ++L++ LD+ D G FVT S VGG + + P Q++G + G+
Sbjct: 242 YEALHGPPKKILVEGANAALLDI-DFGTYPFVTSSNCT-VGGVCTGLGMPPQNVGEVYGV 299
Query: 437 I 437
+
Sbjct: 300 V 300
>pdb|2YXL|A Chain A, Crystal Structure Of Ph0851
Length = 450
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 25 VQEAQSAMATILNESKVGLDLEGMDLGVDGKVSLVSLALQN-GKIFIFDV 73
VQE SA+A+I+ + K G + + GK + ++ ++N GKI+ FDV
Sbjct: 243 VQEEASAVASIVLDPKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDV 292
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 0.134 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,215,346
Number of Sequences: 62578
Number of extensions: 644158
Number of successful extensions: 1366
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1348
Number of HSP's gapped (non-prelim): 17
length of query: 843
length of database: 14,973,337
effective HSP length: 107
effective length of query: 736
effective length of database: 8,277,491
effective search space: 6092233376
effective search space used: 6092233376
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: 56 (26.2 bits)