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= 005229
(707 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 79.0 bits (193), Expect = 9e-15, Method: Composition-based stats.
Identities = 36/62 (58%), Positives = 42/62 (67%), Gaps = 1/62 (1%)
Query: 638 HFRGVRQRPWGKWAAEIRDP-KKAARIWLGTFDTXXXXXXXXXXXXXRFKGRKAKLNFPE 696
H+RGVRQRPWGK+AAEIRDP K AR+WLGTF+T R +G +A LNFP
Sbjct: 2 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 61
Query: 697 RV 698
RV
Sbjct: 62 RV 63
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
Structures
Length = 70
Score = 78.6 bits (192), Expect = 1e-14, Method: Composition-based stats.
Identities = 36/64 (56%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 638 HFRGVRQRPWGKWAAEIRDP-KKAARIWLGTFDTXXXXXXXXXXXXXRFKGRKAKLNFPE 696
H+RGVRQRPWGK+AAEIRDP K AR+WLGTF+T R +G +A LNFP
Sbjct: 5 HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 64
Query: 697 RVQA 700
RV +
Sbjct: 65 RVNS 68
>pdb|2QZW|A Chain A, Secreted Aspartic Proteinase (Sap) 1 From Candida Albicans
pdb|2QZW|B Chain B, Secreted Aspartic Proteinase (Sap) 1 From Candida Albicans
Length = 341
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 25/52 (48%)
Query: 213 KYIEELNQDPASKDKELRFVQQSIEECSKEIPGKKEELISKGKTIAECSKEV 264
KY L P + D+ELR S++ K I G + L+ G TI ++V
Sbjct: 178 KYSGSLIAVPVTSDRELRITLNSLKAVGKNINGNIDVLLDSGTTITYLQQDV 229
>pdb|3M1T|A Chain A, Crystal Structure Of Putative Phosphohydrolase
(Yp_929327.1) From Shewanella Amazonensis Sb2b At 1.62 A
Resolution
Length = 275
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 36/73 (49%)
Query: 182 SLEQKLDSMRKQQKKYFDDVELKKRELNEIRKYIEELNQDPASKDKELRFVQQSIEECSK 241
+L QK+D + + K + +++ E + ++ E+L+ DP + LR + CS+
Sbjct: 6 ALLQKVDELPRLPKAIAELLDVVNNEDSTVKAVSEKLSHDPVLSARVLRLANSARFGCSR 65
Query: 242 EIPGKKEELISKG 254
E+ + ++ G
Sbjct: 66 EVGTIDDAVVRLG 78
>pdb|1RJV|A Chain A, Solution Structure Of Human Alpha-Parvalbumin Refined With
A Paramagnetism-Based Strategy
pdb|1RK9|A Chain A, Solution Structure Of Human Alpha-Parvalbumin (Minimized
Average Structure)
Length = 110
Score = 29.6 bits (65), Expect = 6.1, Method: Composition-based stats.
Identities = 14/60 (23%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 194 QKKYFDDVELKKRELNEIRKYIEELNQDPAS--KDKELRFVQQSIEECSKEIPGKKEELI 251
KK+F V LKK+ ++++K L++D + ++ EL F+ + ++++ K+ +++
Sbjct: 27 HKKFFQMVGLKKKSADDVKKVFHMLDKDKSGFIEEDELGFILKGFSPDARDLSAKETKML 86
>pdb|1G8A|A Chain A, Pyrococcus Horikoshii Fibrillarin Pre-Rrna Processing
Protein
Length = 227
Score = 29.3 bits (64), Expect = 7.7, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 192 KQQKKYFDDVELKKRELNEIRKYIEELNQDPASKDKELRFVQQS 235
K+ ++ F +VE REL+E + IE LN +P KD L V+++
Sbjct: 187 KEPEQVFREVE---RELSEYFEVIERLNLEPYEKDHALFVVRKT 227
>pdb|2NNW|B Chain B, Alternative Conformations Of Nop56/58-fibrillarin Complex
And Implication For Induced-fit Assenly Of Box C/d Rnps
pdb|2NNW|D Chain D, Alternative Conformations Of Nop56/58-fibrillarin Complex
And Implication For Induced-fit Assenly Of Box C/d Rnps
pdb|3NMU|F Chain F, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NMU|J Chain J, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NVK|I Chain I, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVK|J Chain J, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVM|B Chain B, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 234
Score = 29.3 bits (64), Expect = 8.8, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 192 KQQKKYFDDVELKKRELNEIRKYIEELNQDPASKDKELRFVQQ 234
K+ ++ F +VE REL+E + IE LN +P KD L V++
Sbjct: 194 KEPEQVFKEVE---RELSEYFEVIERLNLEPYEKDHALFVVRK 233
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
0.314 0.130 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,437,014
Number of Sequences: 62578
Number of extensions: 640037
Number of successful extensions: 1795
Number of sequences better than 100.0: 87
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 71
Number of HSP's that attempted gapping in prelim test: 1658
Number of HSP's gapped (non-prelim): 170
length of query: 707
length of database: 14,973,337
effective HSP length: 106
effective length of query: 601
effective length of database: 8,340,069
effective search space: 5012381469
effective search space used: 5012381469
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)