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= psy4120
(95 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2K8D|A Chain A, Solution Structure Of A Zinc-Binding Methionine Sulfoxide
Reductase
Length = 151
Score = 68.9 bits (167), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 27/41 (65%), Positives = 36/41 (87%)
Query: 51 MVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVP 91
MVR EV C++CDAHLGHVF+DGP PT +R+C+NSA++ F+P
Sbjct: 106 MVRCEVLCARCDAHLGHVFDDGPRPTGKRYCMNSAALKFIP 146
>pdb|2KZN|A Chain A, Solution Nmr Structure Of Peptide Methionine Sulfoxide
Reductase Msrb From Bacillus Subtilis, Northeast
Structural Genomics Consortium Target Sr10
Length = 151
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 29/49 (59%), Positives = 35/49 (71%)
Query: 45 LITNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVPDH 93
L T+ M+RTEV D+HLGHVFNDGP P R+CINSA++ FVP H
Sbjct: 79 LDTSHGMIRTEVRSRTADSHLGHVFNDGPGPNGLRYCINSAALRFVPKH 127
>pdb|3E0O|A Chain A, Crystal Structure Of Msrb
pdb|3E0O|B Chain B, Crystal Structure Of Msrb
pdb|3E0O|C Chain C, Crystal Structure Of Msrb
pdb|3E0O|D Chain D, Crystal Structure Of Msrb
pdb|3E0O|E Chain E, Crystal Structure Of Msrb
pdb|3E0O|F Chain F, Crystal Structure Of Msrb
Length = 144
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 29/49 (59%), Positives = 35/49 (71%)
Query: 45 LITNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVPDH 93
L T+ M+RTEV D+HLGHVFNDGP P R+CINSA++ FVP H
Sbjct: 80 LDTSHGMIRTEVRSRTADSHLGHVFNDGPGPNGLRYCINSAALRFVPKH 128
>pdb|2L1U|A Chain A, Structure-Functional Analysis Of Mammalian Msrb2 Protein
Length = 143
Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 44/130 (33%), Positives = 58/130 (44%), Gaps = 51/130 (39%)
Query: 16 ELKKRLTPMQYHVTQEKGTER-----YI-------------------------------- 38
+ +K+LTP Q++VT+EKGTE Y+
Sbjct: 3 DWQKKLTPEQFYVTREKGTEAPFSGMYLNNKETGMYHCVCCDSPLFSSEKKYCSGTGWPS 62
Query: 39 --------GSN------LLLLITNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINS 84
GS+ L L T+ R EV C +C+AHLGHVF DGP PT +RFCINS
Sbjct: 63 FSEAYGSKGSDESHTGILRRLDTSLGCPRMEVVCKQCEAHLGHVFPDGPKPTGQRFCINS 122
Query: 85 ASVDFVPDHP 94
++ F P P
Sbjct: 123 VALKFKPSKP 132
>pdb|3HCJ|A Chain A, Structure Of Msrb From Xanthomonas Campestris (Oxidized
Form)
pdb|3HCJ|B Chain B, Structure Of Msrb From Xanthomonas Campestris (Oxidized
Form)
Length = 154
Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 34/46 (73%)
Query: 47 TNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVPD 92
T+ M+RTE+ C++CD+HLGHVF DGP PT R C+NS S+ F D
Sbjct: 91 TSYGMIRTEIVCARCDSHLGHVFPDGPPPTGERHCLNSVSLAFTED 136
>pdb|3HCI|A Chain A, Structure Of Msrb From Xanthomonas Campestris
(Complex-Like Form)
pdb|3HCI|B Chain B, Structure Of Msrb From Xanthomonas Campestris
(Complex-Like Form)
Length = 154
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 33/46 (71%)
Query: 47 TNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVPD 92
T+ MVRTE+ C++CD+HLGHVF DGP PT R +NS S+ F D
Sbjct: 91 TSYGMVRTEIVCARCDSHLGHVFPDGPPPTGERHSLNSVSLAFTED 136
>pdb|3CEZ|A Chain A, Crystal Structure Of Methionine-R-Sulfoxide Reductase From
Burkholderia Pseudomallei
pdb|3CEZ|B Chain B, Crystal Structure Of Methionine-R-Sulfoxide Reductase From
Burkholderia Pseudomallei
pdb|3CXK|A Chain A, 1.7 A Crystal Structure Of Methionine-R-Sulfoxide
Reductase From Burkholderia Pseudomallei:
Crystallization In A Microfluidic Crystal Card.
pdb|3CXK|B Chain B, 1.7 A Crystal Structure Of Methionine-R-Sulfoxide
Reductase From Burkholderia Pseudomallei:
Crystallization In A Microfluidic Crystal Card
Length = 164
Score = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 41/122 (33%), Positives = 51/122 (41%), Gaps = 45/122 (36%)
Query: 13 DKEELKKRLTPMQYHVTQ-------------------------------EKGTERYIGSN 41
D EL++RLTPMQY VTQ E G + + G
Sbjct: 36 DDAELRRRLTPMQYEVTQHAATEPPFTGEYTDTEDAGIYHCVVCGTALFESGAKYHSGCG 95
Query: 42 LLLLITNPD-------------MVRTEVTCSKCDAHLGHVFNDGPA-PTRRRFCINSASV 87
D M R EV C++C AHLGHVF DGP T R+CINSA++
Sbjct: 96 WPSYFKPIDGEVIDEKMDYTHGMTRVEVRCNQCGAHLGHVFEDGPRDKTGLRYCINSAAL 155
Query: 88 DF 89
+F
Sbjct: 156 NF 157
>pdb|1L1D|A Chain A, Crystal Structure Of The C-Terminal Methionine Sulfoxide
Reductase Domain (Msrb) Of N. Gonorrhoeae Pilb
pdb|1L1D|B Chain B, Crystal Structure Of The C-Terminal Methionine Sulfoxide
Reductase Domain (Msrb) Of N. Gonorrhoeae Pilb
Length = 152
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 53 RTEVTCSKCDAHLGHVFNDGPAPTRR-RFCINSASVDFVP 91
RTEV D+HLGHVF DGP R+CIN AS+ F+P
Sbjct: 96 RTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIP 135
>pdb|3HCG|A Chain A, Structure Of The C-Terminal Domain (Msrb) Of Neisseria
Meningitidis Pilb (Reduced Form)
pdb|3HCG|B Chain B, Structure Of The C-Terminal Domain (Msrb) Of Neisseria
Meningitidis Pilb (Reduced Form)
pdb|3HCG|C Chain C, Structure Of The C-Terminal Domain (Msrb) Of Neisseria
Meningitidis Pilb (Reduced Form)
pdb|3HCG|D Chain D, Structure Of The C-Terminal Domain (Msrb) Of Neisseria
Meningitidis Pilb (Reduced Form)
Length = 146
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 53 RTEVTCSKCDAHLGHVFNDGPAPTRR-RFCINSASVDFVP 91
RTEV D+HLGHVF DGP R+CIN AS+ F+P
Sbjct: 90 RTEVRSHAADSHLGHVFPDGPRDKGGLRYCINGASLKFIP 129
>pdb|3HCH|A Chain A, Structure Of The C-Terminal Domain (Msrb) Of Neisseria
Meningitidis Pilb (Complex With Substrate)
pdb|3HCH|B Chain B, Structure Of The C-Terminal Domain (Msrb) Of Neisseria
Meningitidis Pilb (Complex With Substrate)
Length = 146
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 45/121 (37%), Gaps = 45/121 (37%)
Query: 16 ELKKRLTPMQYHVTQEKGTE------------------------------RYIGSNLLLL 45
ELK+ LT QY VTQ TE +Y +
Sbjct: 9 ELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGSGWPS 68
Query: 46 ITNP--------------DMVRTEVTCSKCDAHLGHVFNDGPAPTRR-RFCINSASVDFV 90
T P +M RTEV D+HLGHVF DGP R+ IN AS+ F+
Sbjct: 69 FTRPIDAKSVTEHDDFSYNMRRTEVRSHAADSHLGHVFPDGPRDKGGLRYSINGASLKFI 128
Query: 91 P 91
P
Sbjct: 129 P 129
>pdb|3MAO|A Chain A, Crystal Structure Of Human Methionine-R-Sulfoxide
Reductase B1 (Msrb1)
Length = 105
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/47 (51%), Positives = 30/47 (63%), Gaps = 4/47 (8%)
Query: 49 PDMVRTE---VTCSKCDAHLGHVF-NDGPAPTRRRFCINSASVDFVP 91
P+ R+E V+C KC LGH F NDGP P + RF I S+S+ FVP
Sbjct: 52 PEHNRSEALKVSCGKCGNGLGHEFLNDGPKPGQSRFSIFSSSLKFVP 98
>pdb|3E0M|A Chain A, Crystal Structure Of Fusion Protein Of Msra And Msrb
pdb|3E0M|B Chain B, Crystal Structure Of Fusion Protein Of Msra And Msrb
pdb|3E0M|C Chain C, Crystal Structure Of Fusion Protein Of Msra And Msrb
pdb|3E0M|D Chain D, Crystal Structure Of Fusion Protein Of Msra And Msrb
Length = 313
Score = 44.7 bits (104), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/41 (56%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 51 MVRTEVTCSKCDAHLGHVFNDGPAPT-RRRFCINSASVDFV 90
M R EV AHLGHVF DGP R+CINSAS+ FV
Sbjct: 254 MERIEVRSRSGSAHLGHVFTDGPRELGGLRYCINSASLRFV 294
>pdb|2KV1|A Chain A, Insights Into Function, Catalytic Mechanism And Fold
Evolution Of Mouse Selenoprotein Methionine Sulfoxide
Reductase B1 Through Structural Analysis
Length = 124
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/38 (55%), Positives = 26/38 (68%), Gaps = 1/38 (2%)
Query: 55 EVTCSKCDAHLGHVF-NDGPAPTRRRFCINSASVDFVP 91
+V+C KC LGH F NDGP + RFCI S+S+ FVP
Sbjct: 68 KVSCGKCGNGLGHEFLNDGPKRGQSRFCIFSSSLKFVP 105
>pdb|1BP1|A Chain A, Crystal Structure Of Bpi, The Human Bactericidal
Permeability-Increasing Protein
Length = 456
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 43 LLLITNPDMVRTEVTCSKCDAHLGHV 68
L L +NP + +TCS C +H+ V
Sbjct: 117 LKLGSNPTSGKPTITCSSCSSHINSV 142
>pdb|1EWF|A Chain A, The 1.7 Angstrom Crystal Structure Of Bpi
Length = 456
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 43 LLLITNPDMVRTEVTCSKCDAHLGHV 68
L L +NP + +TCS C +H+ V
Sbjct: 117 LKLGSNPTSGKPTITCSSCSSHINSV 142
>pdb|2VPJ|A Chain A, Crystal Structure Of The Kelch Domain Of Human Klhl12
Length = 301
Score = 25.4 bits (54), Expect = 8.0, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 29 TQEKGTERYIGSNLLLLITNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVD 88
T +G + S ++ + D + + K D H GH N P T+R + A V
Sbjct: 148 TAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNVTPMATKR----SGAGVA 203
Query: 89 FVPDH 93
+ DH
Sbjct: 204 LLNDH 208
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
0.320 0.136 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,026,328
Number of Sequences: 62578
Number of extensions: 100099
Number of successful extensions: 152
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 123
Number of HSP's gapped (non-prelim): 24
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
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: 45 (21.9 bits)