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= psy4458
(303 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B4T|P Chain P, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 445
Score = 212 bits (540), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 118/298 (39%), Positives = 195/298 (65%), Gaps = 3/298 (1%)
Query: 1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60
+K++EG + EAA+I+ ELQVETYGSME EK+ ILEQM L + K DY + ++S+KI
Sbjct: 146 IKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILK 205
Query: 61 KFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQN 120
K F + K + LKL+YY L++++ H+ YL ++ + I T I+SD + VL +
Sbjct: 206 KTFKNPK--YESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSH 263
Query: 121 VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELF 180
+V +L+L+PY N Q+DL H++ D L ++ + L++ FT EL++W +++ YE L
Sbjct: 264 IVYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLN 323
Query: 181 KTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS 240
+ + E + ++ L+ RV+EHN+RV+++YY+RITL R+ +LL L +TE ++S
Sbjct: 324 EDDLAF-GGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLTESQTETYISD 382
Query: 241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIH 298
+V I AK++RPA I+NF + K+ ++LNEWS +++EL++ + HLI KE+++H
Sbjct: 383 LVNQGIIYAKVNRPAKIVNFEKPKNSSQLLNEWSHNVDELLEHIETIGHLITKEEIMH 440
>pdb|1UFM|A Chain A, Solution Structure Of The Pci Domain
Length = 84
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 198 MLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI 257
+L V+EHN+ +K Y IT + + LL +P + E+ S M+ + ID+ GI
Sbjct: 11 ILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGI 70
Query: 258 INFARNKDPG 267
++F + G
Sbjct: 71 VHFETREASG 80
>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 523
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 67/140 (47%), Gaps = 21/140 (15%)
Query: 154 KGLLQWFTNPELIKWSGLRQL------YEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHN 207
K LL ++ + +K L++ Y++ L K + Q C + L+ V++
Sbjct: 340 KSLLPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTY-------QLCVR-LRSNVIKTG 391
Query: 208 IRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVV-SKTITAKIDRPAGII------NF 260
IR+++ Y +I+L+ +C L L E+T E++ S + I AKI+ G I N
Sbjct: 392 IRIISLTYKKISLRDICLKLNLDSEQTVEYMVSRAIRDGVIEAKINHEDGFIETTELLNI 451
Query: 261 ARNKDPGEILNEWSASLNEL 280
++DP ++ +E N+L
Sbjct: 452 YDSEDPQQVFDERIKFANQL 471
>pdb|3A4Z|A Chain A, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution
pdb|3A4Z|B Chain B, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution
pdb|3A4Z|C Chain C, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution
pdb|3A4Z|D Chain D, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution
pdb|3A4Z|E Chain E, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution
pdb|3A50|A Chain A, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound Vitamin D3
pdb|3A50|B Chain B, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound Vitamin D3
pdb|3A50|C Chain C, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound Vitamin D3
pdb|3A50|D Chain D, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound Vitamin D3
pdb|3A50|E Chain E, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound Vitamin D3
pdb|3A51|A Chain A, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound 25-Hydroxyvitamin D3
pdb|3A51|B Chain B, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound 25-Hydroxyvitamin D3
pdb|3A51|C Chain C, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound 25-Hydroxyvitamin D3
pdb|3A51|D Chain D, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound 25-Hydroxyvitamin D3
pdb|3A51|E Chain E, Structure Of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained
By Directed Evolution With Bound 25-Hydroxyvitamin D3
Length = 411
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 9/69 (13%)
Query: 198 MLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEF--LSSMVVSKTITAKIDRPA 255
+L + + +M +Y +I +Q +C+LLGLP E+ ++F SS++V D PA
Sbjct: 125 LLAGLPTDGPVDLMREYAFQIPVQVICELLGLPAEDRDDFSAWSSVLVD-------DSPA 177
Query: 256 GIINFARNK 264
N A K
Sbjct: 178 DDKNAAMGK 186
>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
Gd(3+) Complex
pdb|3TXN|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
Native Data
Length = 394
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 34/56 (60%)
Query: 203 VVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGII 258
++E N+ + + Y+R+ + + + + LP+ + E+ LS M++ K + +D+ G++
Sbjct: 302 MLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVL 357
>pdb|3A4G|A Chain A, Structure Of Cytochrome P450 Vdh From Pseudonocardia
Autotrophica (Trigonal Crystal Form)
pdb|3A4H|A Chain A, Structure Of Cytochrome P450 Vdh From Pseudonocardia
Autotrophica (Orthorhombic Crystal Form)
Length = 411
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 9/69 (13%)
Query: 198 MLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEF--LSSMVVSKTITAKIDRPA 255
+L + + +M +Y +I +Q +C+LLG+P E+ ++F SS++V D PA
Sbjct: 125 LLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVD-------DSPA 177
Query: 256 GIINFARNK 264
N A K
Sbjct: 178 DDKNAAMGK 186
>pdb|3FRV|A Chain A, Structure Of Human Chmp3 (Residues 1-150)
Length = 152
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 256 GIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQ 295
G+ + K P E++NEWS + + M++V+ I +E+
Sbjct: 4 GLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREE 43
>pdb|3FRT|A Chain A, The Structure Of Human Chmp3 (Residues 8 - 222).
pdb|3FRT|B Chain B, The Structure Of Human Chmp3 (Residues 8 - 222)
Length = 218
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 264 KDPGEILNEWSASLNELMKLVNNTTHLINKEQ 295
K P E++NEWS + + M++V+ I +E+
Sbjct: 6 KPPKELVNEWSLKIRKEMRVVDRQIRDIQREE 37
>pdb|2D8C|A Chain A, Solution Structure Of The Sam-Domain Of Mouse Phosphatidyl
Ceramidecholinephosphotransferase 1
Length = 97
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 146 LLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVE 205
L N +P Y L+ FT +LI L +E+ K ++ S++ GQ+ M++ +E
Sbjct: 30 LENAMPEYCEPLEHFTGQDLI------NLTQEDFKKPPLYRVSSDNGQRLLDMIETLKME 83
Query: 206 HNIRV 210
H++
Sbjct: 84 HHMEA 88
>pdb|4FFB|A Chain A, A Tog:alphaBETA-Tubulin Complex Structure Reveals
Conformation-Based Mechanisms For A Microtubule
Polymerase
Length = 447
Score = 27.7 bits (60), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 81 MIELDQHEGSYLATCKHYRAILTTPCIQ 108
M++ D +G Y+ATC YR + T +Q
Sbjct: 303 MVKCDPRDGKYMATCLLYRGDVVTRDVQ 330
>pdb|1R8W|A Chain A, Native Structure Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R8W|B Chain B, Native Structure Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9D|A Chain A, Glycerol Bound Form Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9D|B Chain B, Glycerol Bound Form Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9E|A Chain A, Structure Of The B12-Independent Glycerol Dehydratase With
1,2-Propanediol Bound
pdb|1R9E|B Chain B, Structure Of The B12-Independent Glycerol Dehydratase With
1,2-Propanediol Bound
Length = 787
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%)
Query: 227 LGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLV 284
LGLP +E + +VS+ +T + R GII + PG+ ++ L ++V
Sbjct: 400 LGLPAYYNDEVIIPALVSRGLTLEDARDYGIIGCVEPQKPGKTEGWHDSAFFNLARIV 457
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
0.319 0.134 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,604,969
Number of Sequences: 62578
Number of extensions: 340543
Number of successful extensions: 929
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 912
Number of HSP's gapped (non-prelim): 38
length of query: 303
length of database: 14,973,337
effective HSP length: 98
effective length of query: 205
effective length of database: 8,840,693
effective search space: 1812342065
effective search space used: 1812342065
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)