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= 041152
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RFR|C Chain C, Crystal Structure Of Particulate Methane Monooxygenase
(Pmmo) From Methylocystis Sp. Strain M
pdb|3RFR|G Chain G, Crystal Structure Of Particulate Methane Monooxygenase
(Pmmo) From Methylocystis Sp. Strain M
pdb|3RFR|K Chain K, Crystal Structure Of Particulate Methane Monooxygenase
(Pmmo) From Methylocystis Sp. Strain M
Length = 256
Score = 32.3 bits (72), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 60 IKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHHQLQGLKYNYSQPFFSIWDRLLGTHMPYH 119
+++V D G+W+ + N+F+ Y V GL +++ F + W +L T +P
Sbjct: 15 VESVVDLRGMWIGLAVLNVFYLIVRIYEQVFGWRAGLD-SFAPEFQTYWMSILWTEIPLE 73
Query: 120 LVK 122
LV
Sbjct: 74 LVS 76
>pdb|3IZS|S Chain S, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
Length = 167
Score = 29.6 bits (65), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 34 TLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGN 74
TL GA+ + + M +R V F C +IKT H L N
Sbjct: 100 TLNGAVEQMYTEMASRHRVRFPCIQIIKTATVHFKLCKRDN 140
>pdb|3IZR|S Chain S, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 178
Score = 29.6 bits (65), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 34 TLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGN 74
TL GA+ + + M +R V F C +IKT H L N
Sbjct: 100 TLNGAVEQMYTEMASRHRVRFPCIQIIKTATVHFKLCKRDN 140
>pdb|2GRV|A Chain A, Crystal Structure Of Lpqw
pdb|2GRV|B Chain B, Crystal Structure Of Lpqw
pdb|2GRV|C Chain C, Crystal Structure Of Lpqw
Length = 621
Score = 28.1 bits (61), Expect = 1.5, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 100 YSQPFFSIWDRLLGTHMPYHLVKLPGGGFEARLKK 134
+SQP+ W L +P H+VK GGF A L +
Sbjct: 178 FSQPY-PAWRELFNDILPAHIVKDIPGGFGAGLAR 211
>pdb|1YJL|A Chain A, Reduced Peptidylglycine Alpha-Hydroxylating
Monooxygenase In A New Crystal Form
Length = 306
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 8 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 59
Query: 92 QL 93
L
Sbjct: 60 ML 61
>pdb|1YJK|A Chain A, Reduced Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) In A New Crystal Form
Length = 306
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 8 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 59
Query: 92 QL 93
L
Sbjct: 60 ML 61
>pdb|1YIP|A Chain A, Oxidized Peptidylglycine Alpha-hydroxylating
Monooxygenase (phm) In A New Crystal Form
Length = 311
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 13 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 64
Query: 92 QL 93
L
Sbjct: 65 ML 66
>pdb|4E4Z|A Chain A, Oxidized (cu2+) Peptidylglycine Alpha-hydroxylating
Monooxygenase (phm) In Complex With Hydrogen Peroxide
(1.98 A)
Length = 312
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 13 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 64
Query: 92 QL 93
L
Sbjct: 65 ML 66
>pdb|1YI9|A Chain A, Crystal Structure Analysis Of The Oxidized Form Of The
M314i Mutant Of Peptidylglycine Alpha-Hydroxylating
Monooxygenase
Length = 309
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 11 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 62
Query: 92 QL 93
L
Sbjct: 63 ML 64
>pdb|1SDW|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase With Bound Peptide And Dioxygen
pdb|3MIB|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Nitrite
pdb|3MIC|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide Obtained By
Co-Crystallization
pdb|3MID|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide Obtained By
Soaking (100mm Nan3)
pdb|3MIE|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide Obtained By
Soaking (50mm Nan3)
pdb|3MIF|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Carbon Monooxide (Co)
pdb|3MIG|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Nitrite, Obtained In The
Presence Of Substrate
pdb|3MIH|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide, Obtained In The
Presence Of Substrate
pdb|3MLJ|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Carbon Monooxide (Co)
pdb|3MLK|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Nitrite
pdb|3MLL|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide
Length = 314
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 15 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 66
Query: 92 QL 93
L
Sbjct: 67 ML 68
>pdb|1OPM|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Substrate
pdb|3PHM|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm)
pdb|1PHM|A Chain A, Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm)
From Rat
Length = 310
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 32 LDTLGGALSFLVSGMTARTAVIFFCFAVIKTVDDHSGLWLPGNIFNLFFQNNTAYHDVHH 91
LD AL + G+T + + +FC ++ VD+ + F + F+ + VHH
Sbjct: 13 LDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEA--------FVIDFKPRASMDTVHH 64
Query: 92 QL 93
L
Sbjct: 65 ML 66
>pdb|4GDN|A Chain A, Structure Of Fmta-Like Protein
pdb|4GDN|B Chain B, Structure Of Fmta-Like Protein
pdb|4GDN|C Chain C, Structure Of Fmta-Like Protein
pdb|4GDN|D Chain D, Structure Of Fmta-Like Protein
Length = 342
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 82 NNTAYHD-VHHQLQGLKYNYSQPFFSIWD 109
NN + HD + ++LQG S+P F++WD
Sbjct: 205 NNKSKHDAIGYELQGSTPVVSKPEFNLWD 233
>pdb|3IK2|A Chain A, Crystal Structure Of A Glycoside Hydrolase Family 44
Endoglucanase Produced By Clostridium Acetobutylium Atcc
824
Length = 517
Score = 26.2 bits (56), Expect = 6.3, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 97 KYNYSQP---FFSIWDRLLGTHMPYHLVKLPGGGFEA 130
K Y++P + + D+ L +PY LV L GG+ A
Sbjct: 74 KEKYNEPASVYTAFHDKSLAMGVPYSLVTLQAGGYVA 110
>pdb|1CLK|A Chain A, Crystal Structure Of Streptomyces Diastaticus No.7 Strain
M1033 Xylose Isomerase At 1.9 A Resolution With
Pseudo-I222 Space Group
Length = 387
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 15 VPYAIGALYNHPLEGLLLDTLGGALSFL 42
P+AI N P +LL T+G AL+F+
Sbjct: 175 TPFAIEPKPNEPRGDILLPTIGHALAFI 202
>pdb|1QT1|A Chain A, Crystal Structure Of Xylose Isomerase From Streptomyces
Diastaticus No.7 M1033 At 1.85 A Resolution
pdb|1QT1|B Chain B, Crystal Structure Of Xylose Isomerase From Streptomyces
Diastaticus No.7 M1033 At 1.85 A Resolution
Length = 387
Score = 25.4 bits (54), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 15 VPYAIGALYNHPLEGLLLDTLGGALSFL 42
P+AI N P +LL T+G AL+F+
Sbjct: 175 TPFAIEPKPNEPRGDILLPTIGHALAFI 202
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
0.329 0.145 0.476
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,644,587
Number of Sequences: 62578
Number of extensions: 179828
Number of successful extensions: 468
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 462
Number of HSP's gapped (non-prelim): 20
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)