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= 021001
(318 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
Length = 398
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 37/160 (23%), Positives = 70/160 (43%), Gaps = 38/160 (23%)
Query: 29 NVDGCAMFWKADKFRLLEQTSIEFKEFGL---------------RENVAQLSAFEMRN-- 71
+VDGCA+F+K +KF L+++ ++EF + + ++N+ E+
Sbjct: 122 HVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKEL 181
Query: 72 ----------TKSRRVLVGNIHVLYNPNRGEVKLGQICFLSSRAQIVAEKW--------- 112
+ ++V N H+ ++P +VKL Q S + + EK
Sbjct: 182 FGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTA 241
Query: 113 --GNIPVVLAGDFNITPQSAIYKFLSSSELNIKSYDRRDL 150
+IP+VL D N P S + ++LS+ + D ++L
Sbjct: 242 DPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKEL 281
>pdb|3NGN|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Amp
pdb|3NGO|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Poly(A) Dna
Length = 398
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 37/160 (23%), Positives = 70/160 (43%), Gaps = 38/160 (23%)
Query: 29 NVDGCAMFWKADKFRLLEQTSIEFKEFGL---------------RENVAQLSAFEMRN-- 71
+VDGCA+F+K +KF L+++ ++EF + + ++N+ E+
Sbjct: 122 HVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKEL 181
Query: 72 ----------TKSRRVLVGNIHVLYNPNRGEVKLGQICFLSSRAQIVAEKW--------- 112
+ ++V N H+ ++P +VKL Q S + + EK
Sbjct: 182 FGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTA 241
Query: 113 --GNIPVVLAGDFNITPQSAIYKFLSSSELNIKSYDRRDL 150
+IP+VL D N P S + ++LS+ + D ++L
Sbjct: 242 DPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKEL 281
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 65/139 (46%), Gaps = 27/139 (19%)
Query: 30 VDGCAMFWKADKFRLLEQTSIEF-------KEFGLRENVAQLSAFEMRNT----KSRRVL 78
VDGC +F+K D+F+L+ + +++F K+F E+ A N K + +
Sbjct: 486 VDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLN-RAMNKDNVALFLKLQHIP 544
Query: 79 VGN------IHVLYNPNRGEVKLGQICFLSSRAQIVAEKWGN---------IPVVLAGDF 123
G+ H+ ++P +VK Q+ L + + ++ + PV++ GDF
Sbjct: 545 SGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDF 604
Query: 124 NITPQSAIYKFLSSSELNI 142
N SA+Y+ +++ + I
Sbjct: 605 NSYINSAVYELINTGRVQI 623
>pdb|3MPR|A Chain A, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|B Chain B, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|C Chain C, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
pdb|3MPR|D Chain D, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE
FAMILY Protein From Bacteroides Thetaiotaomicron,
Northeast Structural Genomics Consortium Target Btr318a
Length = 298
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 32/145 (22%), Positives = 54/145 (37%), Gaps = 16/145 (11%)
Query: 17 PGYYLYATAHWDNVDG---CAMFWKADKFRLLEQTSIEFKEF---------GLRENVAQL 64
PGY D D A+F++ DKF ++E+ E + +
Sbjct: 65 PGYDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSW 124
Query: 65 SAFEMRNTKSRRVLVGNIHVLYNPNRGEVKLGQICFLSSRAQIVAEKWGNIPVVLAGDFN 124
F+ ++T L N+H + + V + FL + N+P +L GDFN
Sbjct: 125 GHFKCKDT-GFEFLFFNLHXDHIGKKARV---ESAFLVQEKXKELGRGKNLPAILTGDFN 180
Query: 125 ITPQSAIYKFLSSSELNIKSYDRRD 149
+ Y S + SY++ D
Sbjct: 181 VDQTHQSYDAFVSKGVLCDSYEKCD 205
>pdb|3G6S|A Chain A, Crystal Structure Of The
EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM
Bacteroides Vulgatus. Northeast Structural Genomics
Consortium Target Bvr56d
Length = 267
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 32/125 (25%), Positives = 52/125 (41%), Gaps = 26/125 (20%)
Query: 35 MFWKADKFRLLEQTSIEFKEFGLREN---------------VAQLSAFEMRNTKSRRVLV 79
+F++ DK+ +L+ + F L EN +A + F+ + T V
Sbjct: 81 LFYRKDKYEVLDSNT-----FWLAENPDSVGXXGWDAVCVRIATWAKFKDKATGKIFXAV 135
Query: 80 GNIHVLYNPNRGEVKLGQICFLSSRAQIVAEKWGNIPVVLAGDFNITPQSAIYKFLSSSE 139
N H + GE Q L R + E G P V+ GDFN+T S Y+ ++++E
Sbjct: 136 -NTHF---DHVGEEARRQSALLIIRK--IKEIVGERPAVVTGDFNVTDASDAYETITTNE 189
Query: 140 LNIKS 144
K
Sbjct: 190 FVXKD 194
>pdb|3BYI|A Chain A, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
pdb|3BYI|B Chain B, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
pdb|3BYI|C Chain C, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
pdb|3BYI|D Chain D, Crystal Structure Of Human Rho Gtpase Activating Protein
15 (arhgap15)
Length = 214
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 243 WYTKGLVPTRVLDTLPVDILRRTGGLPCKVRTVERVGFAISCCMTQKLHESVSAWDDIVH 302
W+ K + L VD + R G + T++++ F ++ +KL+ S W+DI
Sbjct: 37 WFVKQCIEAVEKRGLDVDGIYRVSG---NLATIQKLRFIVN--QEEKLNLDDSQWEDIHV 91
Query: 303 FQGFLKVF 310
G LK+F
Sbjct: 92 VTGALKMF 99
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 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,386,121
Number of Sequences: 62578
Number of extensions: 382433
Number of successful extensions: 692
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 678
Number of HSP's gapped (non-prelim): 9
length of query: 318
length of database: 14,973,337
effective HSP length: 99
effective length of query: 219
effective length of database: 8,778,115
effective search space: 1922407185
effective search space used: 1922407185
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: 51 (24.3 bits)