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= 024271
(270 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 37/102 (36%)
Query: 156 VETQRSYKGRHCKKFYTEEGCPYGENCTFLHDEQSKNRESVAISLXXXXXXXXXXXXXXX 215
+ T YK C+ + C YG C F H
Sbjct: 4 MTTSSRYKTELCRTYSESGRCRYGAKCQFAH----------------------------- 34
Query: 216 XNNIGVSNVKPSN----WKTRICNKWELTGYCPFGNKCHFAH 253
G+ ++ +N +KT +C+K++L G CP+G++CHF H
Sbjct: 35 ----GLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIH 72
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 220 GVSNVKPSNWKTRICNKWELTGYCPFGNKCHFAHGIQEF 258
G S +KT +C + +G C +G KC FAHG+ E
Sbjct: 1 GSHMTTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGEL 39
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 38/102 (37%), Gaps = 39/102 (38%)
Query: 87 FKTKLCCKF-RNGTCPYITNCNFAHSIEELRRPPPNWQEIVAAHEEERASTNEIPREEFQ 145
+KT+LC + +G C Y C FAH + ELR+ N P+
Sbjct: 10 YKTELCRTYSESGRCRYGAKCQFAHGLGELRQ------------------ANRHPK---- 47
Query: 146 IPSIVSTNFAVETQRSYKGRHCKKFYTEEGCPYGENCTFLHD 187
YK C KF + CPYG C F+H+
Sbjct: 48 ----------------YKTELCHKFKLQGRCPYGSRCHFIHN 73
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 87 FKTKLCCKFR-NGTCPYITNCNFAHSIEE 114
+KT+LC KF+ G CPY + C+F H+ E
Sbjct: 48 YKTELCHKFKLQGRCPYGSRCHFIHNPTE 76
>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
Rich Element By The Tandem Zinc Finger Domain Of Tis11d
Length = 70
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 32/96 (33%), Gaps = 29/96 (30%)
Query: 162 YKGRHCKKFYTEEGCPYGENCTFLHDEQSKNRESVAISLXXXXXXXXXXXXXXXXNNIGV 221
YK C+ F C YGE C F H
Sbjct: 4 YKTELCRPFEESGTCKYGEKCQFAHGFHELR----------------------------- 34
Query: 222 SNVKPSNWKTRICNKWELTGYCPFGNKCHFAHGIQE 257
S + +KT +C + G+CP+G +CHF H E
Sbjct: 35 SLTRHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE 70
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 227 SNWKTRICNKWELTGYCPFGNKCHFAHGIQEF 258
+ +KT +C +E +G C +G KC FAHG E
Sbjct: 2 TRYKTELCRPFEESGTCKYGEKCQFAHGFHEL 33
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 38/102 (37%), Gaps = 39/102 (38%)
Query: 87 FKTKLCCKFR-NGTCPYITNCNFAHSIEELRRPPPNWQEIVAAHEEERASTNEIPREEFQ 145
+KT+LC F +GTC Y C FAH ELR S P+
Sbjct: 4 YKTELCRPFEESGTCKYGEKCQFAHGFHELR------------------SLTRHPK---- 41
Query: 146 IPSIVSTNFAVETQRSYKGRHCKKFYTEEGCPYGENCTFLHD 187
YK C+ F+T CPYG C F+H+
Sbjct: 42 ----------------YKTELCRTFHTIGFCPYGPRCHFIHN 67
>pdb|2D9M|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 3 In
Zinc Finger Ccch-Type Domain Containing 7a
Length = 69
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 91 LCCKFRNGTCPYITNCNFAHSIEELRRPPPNWQE 124
+C ++ NGTCP +C FAH EL W+E
Sbjct: 22 ICDRYMNGTCPEGNSCKFAHGNAELHE----WEE 51
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 233 ICNKWELTGYCPFGNKCHFAHGIQEF 258
IC+++ + G CP GN C FAHG E
Sbjct: 22 ICDRY-MNGTCPEGNSCKFAHGNAEL 46
>pdb|3QR6|A Chain A, Crystal Structure Analysis Of H185f Mutant Of Human Clic1
Length = 241
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 11/85 (12%)
Query: 55 QTRSNSEQPPNKKSRNGSQDVNSKSKAIGKMFFKTKLCCKFRNGTCP--------YITNC 106
+T + E +K +G++ + + K+F +C K+R T P Y++N
Sbjct: 154 ETSAEDEGVSQRKFLDGNELTLADCNLLPKLFIVQVVCKKYRGFTIPEAFRGVHRYLSN- 212
Query: 107 NFAHSIEELRRPPPNWQEIVAAHEE 131
A++ EE P+ +EI A+E+
Sbjct: 213 --AYAREEFASTCPDDEEIELAYEQ 235
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
0.315 0.131 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,659,335
Number of Sequences: 62578
Number of extensions: 337385
Number of successful extensions: 855
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 835
Number of HSP's gapped (non-prelim): 25
length of query: 270
length of database: 14,973,337
effective HSP length: 97
effective length of query: 173
effective length of database: 8,903,271
effective search space: 1540265883
effective search space used: 1540265883
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)