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= 047989
(223 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 59/235 (25%), Positives = 98/235 (41%), Gaps = 53/235 (22%)
Query: 2 YVRSALYPHSPSACLKWKNRSDAVLTVLKSFGADFLCLQELDN---EDFYKGNMETEGYS 58
Y +Y ++PS L W R + + + S+ +D LCLQE+++ E+++ ++ GY+
Sbjct: 407 YATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYT 466
Query: 59 SLYIQRS---------GQKRDGCGIFYKISCAELLVEDRIYYNELVNSIKDGSSCGDDQN 109
++ ++ +K DGC IF+K +L+ +D + +
Sbjct: 467 GIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDF------------------ 508
Query: 110 NTLAGGNNDSDLKSGSW--SKKDSRDHGDLNDPYVRLKRDCVGIMAAFRLKGPFDHVVIV 167
SG+W KK R LN + +D V + + P +
Sbjct: 509 -------------SGAWMKHKKFQRTEDYLNR---AMNKDNVALFLKLQ-HIPSGDTIWA 551
Query: 168 ATTHLYWDPELADVKLAQAKYLSSRLAEF---RTQVSDRYDCVP-SVIVAGDFNS 218
TTHL+WDP+ DVK Q L L T + R D V++ GDFNS
Sbjct: 552 VTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNS 606
>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
Length = 398
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 58/239 (24%), Positives = 103/239 (43%), Gaps = 44/239 (18%)
Query: 2 YVRSALYPHSPSACLKWKNRSDAVLTVLKSFGADFLCLQELDNEDFYK---GNMETEGYS 58
Y LY + PS L W+ R ++ + + AD + LQE++ E ++ ++ GY
Sbjct: 44 YATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYD 103
Query: 59 SLYIQR------SGQKR---DGCGIFYKISCAELLVEDRIYYNELVNSIKDGSSCGDDQN 109
+ + S Q+R DGC IF+K L+ + + +N++ + DGS ++
Sbjct: 104 GFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRV 163
Query: 110 NTLAGGNNDSDLKSGSWSKKDSRDHGDLNDPYVRLKRDCVGIMAAFR-LKGPFDHVVIVA 168
T KD+ + + + ++ G A + + ++IVA
Sbjct: 164 MT-----------------KDNIGVAVV----LEVHKELFG--AGMKPIHAADKQLLIVA 200
Query: 169 TTHLYWDPELADVKLAQAKYLSSRLAEFRTQVSDR-------YDCVPSVIVAGDFNSVP 220
H++WDPE +DVKL Q S + + S R + +P V+ A D NS+P
Sbjct: 201 NAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCA-DLNSLP 258
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 58/239 (24%), Positives = 103/239 (43%), Gaps = 44/239 (18%)
Query: 2 YVRSALYPHSPSACLKWKNRSDAVLTVLKSFGADFLCLQELDNEDFYK---GNMETEGYS 58
Y LY + PS L W+ R ++ + + AD + LQE++ E ++ ++ GY
Sbjct: 44 YATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYD 103
Query: 59 SLYIQR------SGQKR---DGCGIFYKISCAELLVEDRIYYNELVNSIKDGSSCGDDQN 109
+ + S Q+R DGC IF+K L+ + + +N++ + DGS ++
Sbjct: 104 GFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRV 163
Query: 110 NTLAGGNNDSDLKSGSWSKKDSRDHGDLNDPYVRLKRDCVGIMAAFR-LKGPFDHVVIVA 168
T KD+ + + + ++ G A + + ++IVA
Sbjct: 164 MT-----------------KDNIGVAVV----LEVHKELFG--AGMKPIHAADKQLLIVA 200
Query: 169 TTHLYWDPELADVKLAQAKYLSSRLAEFRTQVSDR-------YDCVPSVIVAGDFNSVP 220
H++WDPE +DVKL Q S + + S R + +P V+ A D NS+P
Sbjct: 201 NAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCA-DLNSLP 258
>pdb|4FSX|A Chain A, Crystal Structure Of Se-Substituted Zea Mays Zmet2 In
Complex With Sah
pdb|4FSX|B Chain B, Crystal Structure Of Se-Substituted Zea Mays Zmet2 In
Complex With Sah
Length = 784
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 133 DHGDL---NDPYVRLKRDCVGIMAAFR-LKGPFDHVVIVATTHLYWDPELADVKLAQAKY 188
DH L ND Y R+++ V A FR LKG V + A + WDPE+ VKL+ K
Sbjct: 588 DHQPLRLNNDDYERVQQIPVKKGANFRDLKG----VRVGANNIVEWDPEIERVKLSSGKP 643
Query: 189 L 189
L
Sbjct: 644 L 644
>pdb|4FT2|A Chain A, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-15)k9me2 Peptide And Sah
pdb|4FT2|B Chain B, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-15)k9me2 Peptide And Sah
pdb|4FT4|B Chain B, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-32)k9me2 Peptide And Sah
pdb|4FT4|A Chain A, Crystal Structure Of Zea Mays Zmet2 In Complex
H3(1-32)k9me2 Peptide And Sah
Length = 784
Score = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 133 DHGDL---NDPYVRLKRDCVGIMAAFR-LKGPFDHVVIVATTHLYWDPELADVKLAQAKY 188
DH L ND Y R+++ V A FR LKG V + A + WDPE+ VKL+ K
Sbjct: 588 DHQPLRLNNDDYERVQQIPVKKGANFRDLKG----VRVGANNIVEWDPEIERVKLSSGKP 643
Query: 189 L 189
L
Sbjct: 644 L 644
>pdb|3S62|H Chain H, Structure Of Fab Fragment Of Malaria Transmission
Blocking Antibody 2a8 Against P. Vivax P25 Protein
Length = 216
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 7 LYPHSPSACLKWKNRSDAVLTVLKSFGADFLCLQELDNED 46
++PHS S K +S A LTV KS ++ L L +ED
Sbjct: 51 IHPHSGSTNYNEKFKSKATLTVDKSSSTAYMQLSSLTSED 90
>pdb|1Z3G|H Chain H, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
pdb|1Z3G|I Chain I, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
Length = 216
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 7 LYPHSPSACLKWKNRSDAVLTVLKSFGADFLCLQELDNED 46
++PHS S K +S A LTV KS ++ L L +ED
Sbjct: 51 IHPHSGSTNYNEKFKSKATLTVDKSSSTAYMQLSSLTSED 90
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
0.318 0.136 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,273,667
Number of Sequences: 62578
Number of extensions: 302334
Number of successful extensions: 625
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 613
Number of HSP's gapped (non-prelim): 13
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)