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= psy12844
(121 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using
Combined Nmr And Cs-Rosetta Method
Length = 70
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 27/36 (75%), Gaps = 2/36 (5%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQ 49
++G++++FN ++GFGFI DDG KD F HFS IQ
Sbjct: 5 MTGIVKWFNADKGFGFITP--DDGSKDVFVHFSAIQ 38
>pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein
Of Escherichia Coli
Length = 69
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 27/36 (75%), Gaps = 2/36 (5%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQ 49
++G++++FN ++GFGFI DDG KD F HFS IQ
Sbjct: 4 MTGIVKWFNADKGFGFITP--DDGSKDVFVHFSAIQ 37
>pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution
Nmr Structure
Length = 69
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 27/36 (75%), Gaps = 2/36 (5%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQ 49
++G++++FN ++GFGFI DDG KD F HFS IQ
Sbjct: 4 MTGIVKWFNADKGFGFITP--DDGSKDVFVHFSAIQ 37
>pdb|3CAM|A Chain A, Crystal Structure Of The Cold Shock Domain Protein From
Neisseria Meningitidis
pdb|3CAM|B Chain B, Crystal Structure Of The Cold Shock Domain Protein From
Neisseria Meningitidis
Length = 67
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73
+G++++FN +GFGFI D+G +D F HFS I + +K V FD+ P
Sbjct: 2 ATGIVKWFNDAKGFGFITP--DEGGEDLFAHFSAIN---XEGFKTLKEGQRVSFDVTTGP 56
Query: 74 GGRREA 79
G++ A
Sbjct: 57 KGKQAA 62
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 4 HLGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGT 52
H G ++ ++G++++FN ++GFGFI DDG KD F HFS G
Sbjct: 7 HHGSRLQSGKMTGIVKWFNADKGFGFITP--DDGSKDVFVHFSAGSSGA 53
>pdb|3I2Z|B Chain B, Structure Of Cold Shock Protein E From Salmonella
Typhimurium
pdb|3I2Z|A Chain A, Structure Of Cold Shock Protein E From Salmonella
Typhimurium
Length = 71
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 8/47 (17%)
Query: 3 AHLGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQ 49
+H+ KI G +++FN+ +GFGFI +DG KD F HFS IQ
Sbjct: 1 SHMSKI------KGNVKWFNESKGFGFITP--EDGSKDVFVHFSAIQ 39
>pdb|2ES2|A Chain A, Crystal Structure Analysis Of The Bacillus Subtilis Cold
Shock Protein Bs-Cspb In Complex With Hexathymidine
pdb|2F52|A Chain A, Solution Structure Of Cold Shock Protein Cspb From
Bacillus Subtilis In Complex With Heptathymidine
pdb|1CSP|A Chain A, Crystal Structure Of The Bacillus Subtilis Major Cold
Shock Protein, Cspb: A Universal Nucleic-Acid Binding
Domain
pdb|1CSQ|A Chain A, Crystal Structure Of The Bacillus Subtilis Major Cold
Shock Protein, Cspb: A Universal Nucleic-Acid Binding
Domain
pdb|1NMF|A Chain A, Major Cold-Shock Protein, Nmr, 20 Structures
pdb|1NMG|A Chain A, Major Cold-Shock Protein, Nmr, Minimized Average
Structure
pdb|3PF4|A Chain A, Crystal Structure Of Bs-Cspb In Complex With R(Gucuuua)
pdb|3PF4|B Chain B, Crystal Structure Of Bs-Cspb In Complex With R(Gucuuua)
pdb|3PF5|A Chain A, Crystal Structure Of Bs-Cspb In Complex With Ru6
pdb|3PF5|B Chain B, Crystal Structure Of Bs-Cspb In Complex With Ru6
Length = 67
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
+ G +++FN E+GFGFI G D D F HFS IQG
Sbjct: 2 LEGKVKWFNSEKGFGFIEVEGQD---DVFVHFSAIQG 35
>pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Cspb Variant A46k S48r
Length = 67
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
+ G +++FN E+GFGFI G D D F HFS IQG
Sbjct: 2 LEGKVKWFNSEKGFGFIEVEGQD---DVFVHFSAIQG 35
>pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Variant Bs-Cspb M1rE3KK65I
Length = 67
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
+ G +++FN E+GFGFI G D D F HFS IQG
Sbjct: 2 LKGKVKWFNSEKGFGFIEVEGQD---DVFVHFSAIQG 35
>pdb|3A0J|A Chain A, Crystal Structure Of Cold Shock Protein 1 From Thermus
Thermophilus Hb8
pdb|3A0J|B Chain B, Crystal Structure Of Cold Shock Protein 1 From Thermus
Thermophilus Hb8
Length = 73
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
G +++FN E+G+GFI R GD D F H++ I R + +V FD+ G
Sbjct: 4 GRVKWFNAEKGYGFIEREGD---TDVFVHYTAINA---KGFRTLNEGDIVTFDVEPGRNG 57
Query: 76 R-REAVHIKIFD 86
+ +AV++ + +
Sbjct: 58 KGPQAVNVTVVE 69
>pdb|1H95|A Chain A, Solution Structure Of The Single-Stranded Dna-Binding
Cold Shock Domain (Csd) Of Human Y-Box Protein 1 (Yb1)
Determined By Nmr (10 Lowest Energy Structures)
Length = 79
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD-NILRAIKYSLLVIFDI 69
V G +++FN G+GFINR +D ++D F H + I+ LR++ V FD+
Sbjct: 9 VLGTVKWFNVRNGYGFINR--NDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63
>pdb|1HZ9|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZ9|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 4 GKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 35
>pdb|1I5F|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1I5F|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 3/36 (8%)
Query: 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 3 EGKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 35
>pdb|1HZC|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZC|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 3/36 (8%)
Query: 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 3 EGKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 35
>pdb|1HZA|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZA|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 67
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 4 GKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 35
>pdb|1C9O|A Chain A, Crystal Structure Analysis Of The Bacillus Caldolyticus
Cold Shock Protein Bc-Csp
pdb|1C9O|B Chain B, Crystal Structure Analysis Of The Bacillus Caldolyticus
Cold Shock Protein Bc-Csp
pdb|2HAX|A Chain A, Crystal Structure Of Bacillus Caldolyticus Cold Shock
Protein In Complex With Hexathymidine
pdb|2HAX|B Chain B, Crystal Structure Of Bacillus Caldolyticus Cold Shock
Protein In Complex With Hexathymidine
Length = 66
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 4 GKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 35
>pdb|1HZB|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZB|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 34.3 bits (77), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 4 GKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 35
>pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From
The Hyperthermophilic Bacterium Thermotoga Maritima
Length = 66
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 7/71 (9%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
G +++F+ ++G+GFI + D+G D F H+S I+ + +K +V F+I G
Sbjct: 3 GKVKWFDSKKGYGFITK--DEGG-DVFVHWSAIE---MEGFKTLKEGQVVEFEIQEGKKG 56
Query: 76 RREAVHIKIFD 86
+ A H+K+ +
Sbjct: 57 PQ-AAHVKVVE 66
>pdb|3AQQ|A Chain A, Crystal Structure Of Human Crhsp-24
pdb|3AQQ|C Chain C, Crystal Structure Of Human Crhsp-24
pdb|3AQQ|B Chain B, Crystal Structure Of Human Crhsp-24
pdb|3AQQ|D Chain D, Crystal Structure Of Human Crhsp-24
Length = 147
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
GV + F + +G GFI DG D F H S+++G
Sbjct: 65 GVCKCFCRSKGHGFITPA--DGGPDIFLHISDVEG 97
>pdb|2KCM|A Chain A, Solution Nmr Structure Of The N-Terminal Ob-Domain Of
So_1732 From Shewanella Oneidensis. Northeast
Structural Genomics Consortium Target Sor210a
Length = 74
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73
+ G + + + +GFI GDDG YF HFSE+ D + +K S +V FD TP
Sbjct: 1 MKGKVVSYLAAKKYGFIQ--GDDGE-SYFLHFSELLDKKDEG-KLVKGS-MVHFDPTPTP 55
Query: 74 GG 75
G
Sbjct: 56 KG 57
>pdb|1E3M|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With
A G:t Mismatch
pdb|1E3M|B Chain B, The Crystal Structure Of E. Coli Muts Binding To Dna With
A G:t Mismatch
Length = 800
Score = 27.7 bits (60), Expect = 1.9, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 52 TDNILRAIKYSLLVIFDIGVTPGGRREA---VHIKIFDTRLYLEDLRT 96
T N+ + +L + D VTP G R +H + DTR+ LE +T
Sbjct: 280 TQNLAGGAENTLASVLDCTVTPXGSRXLKRWLHXPVRDTRVLLERQQT 327
>pdb|2YTY|A Chain A, Solution Structure Of The Fourth Cold-Shock Domain Of
The Human Kiaa0885 Protein (Unr Protein)
Length = 88
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 27 FGFINRIGDDGRKDYFFHFSEIQGGTDNILRA--IKYSL 63
FGFI D K+ FFH+SE G D++ ++YSL
Sbjct: 30 FGFIETANHD--KEIFFHYSEFSGDVDSLELGDMVEYSL 66
>pdb|2YTV|A Chain A, Solution Structure Of The Fifth Cold-Shock Domain Of The
Human Kiaa0885 Protein (Unr Protein)
Length = 79
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 27 FGFIN-RIGDDGRKDYFFHFSEIQGGTD 53
FGFIN +GD K FFH E+Q G +
Sbjct: 20 FGFINYEVGDS--KKLFFHVKEVQDGIE 45
>pdb|2HFZ|A Chain A, Crystal Structure Of Rna Dependent Rna Polymerase Domain
From West Nile Virus
Length = 639
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 21 FNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNI-LRAIKYSLLVIFDIGVTPGGRREA 79
F + GF+N GRK+ GG + + L+ + Y ++ ++G PGGR A
Sbjct: 219 FLEFEALGFLNEDHWLGRKNS-------GGGVEGLGLQKLGY---ILREVGTRPGGRIYA 268
Query: 80 VHIKIFDTRLYLEDL 94
+DTR+ DL
Sbjct: 269 DDTAGWDTRITRADL 283
>pdb|2HCN|A Chain A, Crystal Structure Of Rna Dependent Rna Polymerase Domain
From West Nile Virus
pdb|2HCS|A Chain A, Crystal Structure Of Rna Dependant Rna Polymerase Domain
Of West Nile Virus
Length = 595
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 21 FNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNI-LRAIKYSLLVIFDIGVTPGGRREA 79
F + GF+N GRK+ GG + + L+ + Y ++ ++G PGGR A
Sbjct: 175 FLEFEALGFLNEDHWLGRKNS-------GGGVEGLGLQKLGY---ILREVGTRPGGRIYA 224
Query: 80 VHIKIFDTRLYLEDL 94
+DTR+ DL
Sbjct: 225 DDTAGWDTRITRADL 239
>pdb|2YTX|A Chain A, Solution Structure Of The Second Cold-Shock Domain Of
The Human Kiaa0885 Protein (Unr Protein)
Length = 97
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 24 ERGFGFINRIGDDGRKDYFFHFSEIQGGTDNI 55
+ FGFI R D K+ FFH+SE +G + +
Sbjct: 27 KEAFGFIER--GDVVKEIFFHYSEFKGDLETL 56
>pdb|1X65|A Chain A, Solution Structure Of The Third Cold-Shock Domain Of The
Human Kiaa0885 Protein (Unr Protein)
Length = 89
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 26 GFGFINRIGDDGRKDYFFHFSEIQGGT 52
GFGFI + D R FFHFSEI G
Sbjct: 19 GFGFIKCVDRDVR--MFFHFSEILDGN 43
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
0.328 0.146 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,796,542
Number of Sequences: 62578
Number of extensions: 156511
Number of successful extensions: 330
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 304
Number of HSP's gapped (non-prelim): 29
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)