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= 014403
(425 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W4S|A Chain A, Crystal Structure Of The Proximal Bah Domain Of Polybromo
Length = 174
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 51/110 (46%), Gaps = 15/110 (13%)
Query: 77 VHDFVYV-LAEEN-KRLIAYLEDMYEDSRGNKMVVVRWFHKIDEVGIFLPHNFNDREIFF 134
V D+VYV AE N + I +E ++EDS G K + WF++ +E F ++E+F
Sbjct: 29 VGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNETFHLATRKFLEKEVFK 88
Query: 135 SLCLQDLSIECIDGLATVLSPQHFEKFMNEATYPQLQPFICDKQFENDDV 184
S + + I G V+ + + K +C + F ++DV
Sbjct: 89 SDYYNKVPVSKILGKCVVMFVKEYFK-------------LCPENFRDEDV 125
>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 = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 60 KKRKHYQSFCRNGVKVSVHDFVYVLAEENKR-LIAYLEDMYEDSRGNKMVVVRWFHKIDE 118
K R HY+S + V + D VYV A EN+ I + + +E + RWF + ++
Sbjct: 43 KARCHYRSAKVDNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAED 102
Query: 119 VGI-------FLPHNFNDREIFFSLCLQDLSIECI 146
I H + R +F S D ++CI
Sbjct: 103 TVINSLVSISVDGHKHDPRRVFLSEEKNDNVLDCI 137
>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 = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 60 KKRKHYQSFCRNGVKVSVHDFVYVLAEENKR-LIAYLEDMYEDSRGNKMVVVRWFHKIDE 118
K R HY+S + V + D VYV A EN+ I + + +E + RWF + ++
Sbjct: 43 KARCHYRSAKVDNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAED 102
Query: 119 VGI-------FLPHNFNDREIFFSLCLQDLSIECI 146
I H + R +F S D ++CI
Sbjct: 103 TVINSLVSISVDGHKHDPRRVFLSEEKNDNVLDCI 137
>pdb|1REQ|B Chain B, Methylmalonyl-Coa Mutase
pdb|1REQ|D Chain D, Methylmalonyl-Coa Mutase
pdb|2REQ|B Chain B, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|D Chain D, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|B Chain B, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|B Chain B, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|D Chain D, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|B Chain B, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|D Chain D, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|B Chain B, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|D Chain D, Methylmalonyl-Coa Mutase Substrate Complex
pdb|5REQ|B Chain B, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|D Chain D, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|1E1C|B Chain B, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|D Chain D, Methylmalonyl-Coa Mutase H244a Mutant
Length = 637
Score = 31.6 bits (70), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 129 DREIFFSLCLQDLSIECIDGLATV--LSPQHFEKFMNEATYPQLQPFICDKQFENDDVKP 186
++++ F+ CL+ L++ +DG+ V P+ K + YP + PF N D+
Sbjct: 49 EKQLTFAECLKRLTVHTVDGIDIVPMYRPKDAPKKLG---YPGVAPFTRGTTVRNGDMDA 105
Query: 187 FDI 189
+D+
Sbjct: 106 WDV 108
>pdb|3AV4|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1
pdb|3AV5|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adohcy
pdb|3AV6|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adomet
Length = 1330
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 51 WLGSSWMSRKKRKHYQSFCRNGVKVSVHDFVYVLAEENKR--LIAYLEDMYEDSRGNKMV 108
WLG + R +YQ + + V D V V+ +++ + +A + ++ED G M
Sbjct: 446 WLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMF 505
Query: 109 VVRWF 113
WF
Sbjct: 506 HAHWF 510
>pdb|3PT9|A Chain A, Crystal Structure Of Mouse Dnmt1(731-1602) In The Free
State
pdb|4DA4|A Chain A, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
pdb|4DA4|B Chain B, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
Length = 873
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 51 WLGSSWMSRKKRKHYQSFCRNGVKVSVHDFVYVLAEENKR--LIAYLEDMYEDSRGNKMV 108
WLG + R +YQ + + V D V V+ +++ + +A + ++ED G M
Sbjct: 7 WLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMF 66
Query: 109 VVRWF 113
WF
Sbjct: 67 HAHWF 71
>pdb|3PT6|A Chain A, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
pdb|3PT6|B Chain B, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
Length = 954
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 51 WLGSSWMSRKKRKHYQSFCRNGVKVSVHDFVYVLAEENKR--LIAYLEDMYEDSRGNKMV 108
WLG + R +YQ + + V D V V+ +++ + +A + ++ED G M
Sbjct: 88 WLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMF 147
Query: 109 VVRWF 113
WF
Sbjct: 148 HAHWF 152
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 0.135 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,797,396
Number of Sequences: 62578
Number of extensions: 525066
Number of successful extensions: 1009
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1008
Number of HSP's gapped (non-prelim): 16
length of query: 425
length of database: 14,973,337
effective HSP length: 102
effective length of query: 323
effective length of database: 8,590,381
effective search space: 2774693063
effective search space used: 2774693063
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)