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= psy4398
(306 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
Flavin
Length = 318
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 52/204 (25%), Positives = 87/204 (42%), Gaps = 19/204 (9%)
Query: 32 KIILAPMVRMNTLPFRLLALDYGADLVYSEELVDHKLVKTERKVNDLLNTIDFVDPLDGS 91
K+ LAP FR LA ++GAD +SE + + +K +LL
Sbjct: 6 KVGLAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEELLPQ---------- 55
Query: 92 VVFRTCPREKNKIILQIGTADPERALEAAKKVEHDVAAIDINMGCPKQFSLTGGMGAALL 151
P E+N + +QI ++P EAA+ + ID+N GCP + + G G ALL
Sbjct: 56 ------PHERN-VAVQIFGSEPNELSEAARILSEKYKWIDLNAGCPVRKVVKEGAGGALL 108
Query: 152 STPDIACNILTTLISNLSIPVSCKIRVFHNEADTIALCKRLEACGIIAIGVHGRTKAERP 211
I+ L ++S S K R+ + + + + L G+ + +H RT +
Sbjct: 109 KDLRHFRYIVRELRKSVSGKFSVKTRLGWEKNEVEEIYRILVEEGVDEVFIHTRTVVQSF 168
Query: 212 RHRNRIEMIRTLTQHLKIPVIANG 235
R + + L + +IP +G
Sbjct: 169 TGRAEWKALSVLEK--RIPTFVSG 190
>pdb|3B0P|A Chain A, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0P|B Chain B, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0U|X Chain X, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
pdb|3B0U|Y Chain Y, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
Length = 350
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 49/181 (27%), Positives = 82/181 (45%), Gaps = 24/181 (13%)
Query: 32 KIILAPMVRMNTLPFRLLALDYGADL-VYSEELVDHKLVKTERKVNDLLNTIDFVDPLDG 90
++ +APMV FR L + +Y+E VD +++ R +
Sbjct: 5 RLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNR---------------ER 49
Query: 91 SVVFRTCPREKNKIILQIGTADPERALEAAKKVE-HDVAAIDINMGCPKQFSLTGGMGAA 149
+ FR E++ I LQ+ +DP+ EAA+ E I++N+GCP + + GG GA
Sbjct: 50 LLAFRP---EEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGAC 106
Query: 150 LLSTPDIACNILTTLISNLSIPVSCKIRVFHNEADTI-ALCKRLEA---CGIIAIGVHGR 205
LL IL + + +PV+ K+R+ +T L + +EA G+ VH R
Sbjct: 107 LLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHAR 166
Query: 206 T 206
+
Sbjct: 167 S 167
>pdb|3B0V|C Chain C, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
pdb|3B0V|D Chain D, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
Length = 363
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 48/181 (26%), Positives = 79/181 (43%), Gaps = 24/181 (13%)
Query: 32 KIILAPMVRMNTLPFRLLALDYGADL-VYSEELVDHKLVKTERKVNDLLNTIDFVDPLDG 90
++ +AP V FR L + +Y+E VD +++ R +
Sbjct: 26 RLSVAPXVDRTDRHFRFLVRQVSLGVRLYTEXTVDQAVLRGNR---------------ER 70
Query: 91 SVVFRTCPREKNKIILQIGTADPERALEAAKKVE-HDVAAIDINMGCPKQFSLTGGMGAA 149
+ FR E++ I LQ+ +DP+ EAA+ E I++N+GCP + + GG GA
Sbjct: 71 LLAFRP---EEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGAC 127
Query: 150 LLSTPDIACNILTTLISNLSIPVSCKIRVFHNEADTI-ALCKRLEA---CGIIAIGVHGR 205
LL IL + +PV+ K R+ +T L + +EA G+ VH R
Sbjct: 128 LLLDLARVREILKAXGEAVRVPVTVKXRLGLEGKETYRGLAQSVEAXAEAGVKVFVVHAR 187
Query: 206 T 206
+
Sbjct: 188 S 188
>pdb|1WHN|A Chain A, Solution Structure Of The Dsrbd From Hypothetical Protein
Bab26260
Length = 128
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 253 FLRNHYPVEKLPKTILYAHCKYKRFEVPKYETVQY--EKLFRSLVTVNGKQYTS 304
F R YP + PK L C+ ++ P YETVQ +++F S+VTV ++Y S
Sbjct: 17 FDRRAYPPQITPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQS 70
>pdb|2Z6J|A Chain A, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk) In Complex With An Inhibitor
pdb|2Z6J|B Chain B, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk) In Complex With An Inhibitor
Length = 332
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 185 TIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIPVIANGG 236
++AL KR+E G A+ G + ++R + + IPVIA GG
Sbjct: 119 SVALAKRMEKIGADAVIAEGMEAGGHIGKLTTMTLVRQVATAISIPVIAAGG 170
>pdb|2Z6I|A Chain A, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk)
pdb|2Z6I|B Chain B, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk)
Length = 332
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 23/52 (44%)
Query: 185 TIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIPVIANGG 236
++AL KR E G A+ G ++R + + IPVIA GG
Sbjct: 119 SVALAKRXEKIGADAVIAEGXEAGGHIGKLTTXTLVRQVATAISIPVIAAGG 170
>pdb|3BH6|B Chain B, Crystal Structure Of The Rp2-Arl3 Complex Bound To Gppnhp
pdb|3BH7|B Chain B, Crystal Structure Of The Rp2-Arl3 Complex Bound To
Gdp-Alf4
Length = 352
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 63 LVDHKLVKTERKVNDLLNTIDFVDPLDGSVVFRTC 97
+ DH T ++D N I F+ P+ GSV FR C
Sbjct: 76 IFDHSATVT---IDDCTNCIIFLGPVKGSVFFRNC 107
>pdb|2BX6|A Chain A, Crystal Structure Of The Human Retinitis Pigmentosa
Protein 2 (Rp2)
Length = 350
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 63 LVDHKLVKTERKVNDLLNTIDFVDPLDGSVVFRTC 97
+ DH T ++D N I F+ P+ GSV FR C
Sbjct: 74 IFDHSATVT---IDDCTNCIIFLGPVKGSVFFRNC 105
>pdb|1AGX|A Chain A, Refined Crystal Structure Of Acinetobacter
Glutaminasificans Glutaminase-Asparaginase
Length = 331
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 58 VYSEELVDHKLVKTERKVNDLLN--TIDFV------DPLDGSVVFRTCPREKNKIILQIG 109
V SE + D +L+ R+VNDL+ +++ V D ++ + F +K I+ +G
Sbjct: 57 VASESITDKELLSLARQVNDLVKKPSVNGVVITHGTDTMEETAFFLNLVVHTDKPIVLVG 116
Query: 110 TADPERALEA 119
+ P AL A
Sbjct: 117 SMRPSTALSA 126
>pdb|1JCF|A Chain A, Mreb From Thermotoga Maritima, Trigonal
pdb|1JCG|A Chain A, Mreb From Thermotoga Maritima, Amppnp
pdb|2WUS|A Chain A, Bacterial Actin Mreb Assembles In Complex With Cell Shape
Protein Rodz
pdb|2WUS|B Chain B, Bacterial Actin Mreb Assembles In Complex With Cell Shape
Protein Rodz
Length = 344
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 99 REKNKIILQIGTADPERALEAAKKVEHDVAAIDINMGCPKQFSLTGG 145
R ++ ++IG P + + ++E V+ ID++ G P++ +L GG
Sbjct: 201 RTAERVKIEIGNVFPSKEND---ELETTVSGIDLSTGLPRKLTLKGG 244
>pdb|1JCE|A Chain A, Mreb From Thermotoga Maritima
Length = 344
Score = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 99 REKNKIILQIGTADPERALEAAKKVEHDVAAIDINMGCPKQFSLTGG 145
R ++ ++IG P + + ++E V+ ID++ G P++ +L GG
Sbjct: 201 RTAERVKIEIGNVFPSKEND---ELETTVSGIDLSTGLPRKLTLKGG 244
>pdb|1ZVD|A Chain A, Regulation Of Smurf2 Ubiquitin Ligase Activity By
Anchoring The E2 To The Hect Domain
Length = 380
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 6/35 (17%)
Query: 263 LPKTILYAHCKYKRFEVPKYETVQYEKLFRSLVTV 297
LPK AH + R ++P YE+ YEKL+ L+T
Sbjct: 342 LPK----AHTCFNRIDIPPYES--YEKLYEKLLTA 370
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
0.323 0.139 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,600,365
Number of Sequences: 62578
Number of extensions: 339962
Number of successful extensions: 811
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: 800
Number of HSP's gapped (non-prelim): 15
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)