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= 047201
(772 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 = 104 bits (259), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 77/267 (28%), Positives = 127/267 (47%), Gaps = 47/267 (17%)
Query: 163 PRPRPPKPLDYRNWEHSKASLPPYSERFVVLSYNILADYLALSHRSKLYFHIPRHLLDWE 222
P PP+P + + LP S F V+ YN+L D A +LY + P L+WE
Sbjct: 9 PEQLPPRP--WITLKERDQILP--SASFTVMCYNVLCDKYA---TRQLYGYCPSWALNWE 61
Query: 223 WRKRSILFELGLWSADIMCFQEVDRFQDLEV---ELKFRGYTGIWKMRTGNAI------- 272
+RK+ I+ E+ ADI+ QEV+ Q + LK RGY G + ++ I
Sbjct: 62 YRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERK 121
Query: 273 --DGCAIFWRASRFKLLYEEGIEFNKLGL---------------RDNVAQICVLELLSQN 315
DGCAIF++ +F L+ + +EFN++ + +DN+ VLE+ +
Sbjct: 122 HVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKEL 181
Query: 316 FTENSAALPTSSAHSKKVAICNIHVLFNPKRGEIKLGQ-------VRTLLEKAHAV---- 364
F + P +A + + + N H+ ++P+ ++KL Q V+ +LEKA +
Sbjct: 182 F--GAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSP 239
Query: 365 SKTWNDAPVVLCGDFNCTPKSPLYNFI 391
+ N P+VLC D N P S + ++
Sbjct: 240 TADPNSIPLVLCADLNSLPDSGVVEYL 266
>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 = 103 bits (258), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 77/267 (28%), Positives = 127/267 (47%), Gaps = 47/267 (17%)
Query: 163 PRPRPPKPLDYRNWEHSKASLPPYSERFVVLSYNILADYLALSHRSKLYFHIPRHLLDWE 222
P PP+P + + LP S F V+ YN+L D A +LY + P L+WE
Sbjct: 9 PEQLPPRP--WITLKERDQILP--SASFTVMCYNVLCDKYA---TRQLYGYCPSWALNWE 61
Query: 223 WRKRSILFELGLWSADIMCFQEVDRFQDLEV---ELKFRGYTGIWKMRTGNAI------- 272
+RK+ I+ E+ ADI+ QEV+ Q + LK RGY G + ++ I
Sbjct: 62 YRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERK 121
Query: 273 --DGCAIFWRASRFKLLYEEGIEFNKLGL---------------RDNVAQICVLELLSQN 315
DGCAIF++ +F L+ + +EFN++ + +DN+ VLE+ +
Sbjct: 122 HVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKEL 181
Query: 316 FTENSAALPTSSAHSKKVAICNIHVLFNPKRGEIKLGQ-------VRTLLEKAHAV---- 364
F + P +A + + + N H+ ++P+ ++KL Q V+ +LEKA +
Sbjct: 182 F--GAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSP 239
Query: 365 SKTWNDAPVVLCGDFNCTPKSPLYNFI 391
+ N P+VLC D N P S + ++
Sbjct: 240 TADPNSIPLVLCADLNSLPDSGVVEYL 266
>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 = 88.2 bits (217), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 61/226 (26%), Positives = 109/226 (48%), Gaps = 28/226 (12%)
Query: 190 FVVLSYNILADYLALSHRSKLYFHIPRHLLDWEWRKRSILFELGLWSADIMCFQEVD--R 247
F VLSYN L + A K+Y + P L W++R+ + ++ + +D++C QEV+
Sbjct: 395 FTVLSYNTLCQHYA---TPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKT 451
Query: 248 FQDLEVELKFR-GYTGIWKMRT---------GNAIDGCAIFWRASRFKLLYEEGIEFNKL 297
F++ V L + GYTGI+ + +DGC IF++ +FKL+ ++ ++F+
Sbjct: 452 FEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGA 511
Query: 298 GLRDNVAQICVLELLSQNFTENSAALPTSSAH---SKKVAICNIHVLFNPKRGEIKLGQV 354
++ Q + L++ +++ AL H + H+ ++PK ++K QV
Sbjct: 512 WMKHKKFQRTE-DYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQV 570
Query: 355 RTLL---------EKAHAVSKTWNDAPVVLCGDFNCTPKSPLYNFI 391
LL E +H + PV++CGDFN S +Y I
Sbjct: 571 GVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELI 616
Score = 36.2 bits (82), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 11/91 (12%)
Query: 681 LEHPLQLRSTYAEVEDCTGTRDSHGEPLVTSYNRRFKGTVDYI-LRSEGLQTVRVLAPIP 739
H L L+S+Y +C G E T++ F +DYI + L+ +L +
Sbjct: 640 FSHNLALKSSY----NCIG------ELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVD 689
Query: 740 KHAMQWTPGYPTKKWGSDHIALASEVAFVET 770
+ G+P K+ SDHI L + F++T
Sbjct: 690 PEYVSKFIGFPNDKFPSDHIPLLARFEFMKT 720
>pdb|3G6S|A Chain A, Crystal Structure Of The
EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM
Bacteroides Vulgatus. Northeast Structural Genomics
Consortium Target Bvr56d
Length = 267
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 70/176 (39%), Gaps = 12/176 (6%)
Query: 218 LLDWEWRKRSILFELGLWSADIMCFQEV--DRFQDLEVELKFRGYTGIWKMRTGNAIDGC 275
L +W++RK + + DI+ QEV ++FQDL L G+ + A +
Sbjct: 20 LNNWQYRKDRVCQFIKDHELDIVGXQEVLHNQFQDLRAGLPEYDGIGVGRDDGKTAGEYA 79
Query: 276 AIFWRASRFKLLYEEGIEFNKLGLRDNVAQICVLELLSQNFTENSAALPTSSAHSKKVAI 335
+F+R ++++L + N L +N + + + A A K
Sbjct: 80 PLFYRKDKYEVL-----DSNTFWLAENPDSVGXXGWDAVCVRIATWAKFKDKATGKIFXA 134
Query: 336 CNIHVLFNPKRGEIKLGQVRTLLEKAHAVSKTWNDAPVVLCGDFNCTPKSPLYNFI 391
N H F+ E + ++ K + + + P V+ GDFN T S Y I
Sbjct: 135 VNTH--FDHVGEEARRQSALLIIRK---IKEIVGERPAVVTGDFNVTDASDAYETI 185
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
0.315 0.131 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,708,323
Number of Sequences: 62578
Number of extensions: 909987
Number of successful extensions: 1525
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1510
Number of HSP's gapped (non-prelim): 11
length of query: 772
length of database: 14,973,337
effective HSP length: 106
effective length of query: 666
effective length of database: 8,340,069
effective search space: 5554485954
effective search space used: 5554485954
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)