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= 021137
(317 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 104 IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 161
I ++ + E+F + + E KK I R+ +++++ K LC L N+FK +
Sbjct: 257 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 316
Query: 162 NIIELHGQ 169
I+E HG+
Sbjct: 317 PILEFHGK 324
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 104 IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 161
I ++ + E+F + + E KK I R+ +++++ K LC L N+FK +
Sbjct: 308 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 367
Query: 162 NIIELHGQ 169
I+E HG+
Sbjct: 368 PILEFHGK 375
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 104 IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 161
I ++ + E+F + + E KK I R+ +++++ K LC L N+FK +
Sbjct: 257 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 316
Query: 162 NIIELHGQ 169
I+E HG+
Sbjct: 317 PILEFHGK 324
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 104 IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 161
I ++ + E+F + + E KK I R+ +++++ K LC L N+FK +
Sbjct: 2 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 61
Query: 162 NIIELHGQ 169
I+E HG+
Sbjct: 62 PILEFHGK 69
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 104 IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 161
I ++ + E+F + + E KK I R+ +++++ K LC L N+FK +
Sbjct: 2 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 61
Query: 162 NIIELHGQ 169
I+E HG+
Sbjct: 62 PILEFHGK 69
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 104 IVETKCVPERFCALVKSLSEEKKKAI--REIGFESLLELRCGKLKRKLCHWLVNQFKPER 161
I ++ + E+F + + E KK I R+ +++++ K LC L N+FK +
Sbjct: 2 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 61
Query: 162 NIIELHGQ 169
I+E HG+
Sbjct: 62 PILEFHGK 69
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARY 82
P + G+V + NE +++R+ + DL + K +G + +L P +K RY
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHPDLPFPE-ITKMLGAEWSKLQPAEKQRY 57
>pdb|1P2Z|A Chain A, Refinement Of Adenovirus Type 2 Hexon With Cns
Length = 967
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 131 EIGFESLLELRCGKLKRKLCHW--LVNQFKPERNIIELHGQKLELCPKMFS-KIMGVKDG 187
E+ ++ LL+ G R W V+ + P+ IIE HG + EL F +GV D
Sbjct: 378 ELSYQLLLD-SIGDRTRYFSMWNQAVDSYDPDVRIIENHGTEDELPNYCFPLGGIGVTDT 436
Query: 188 GMAIKING 195
AIK NG
Sbjct: 437 YQAIKANG 444
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 28.9 bits (63), Expect = 3.8, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 89
F+ + +E KRL +N DL L K +GK++K L +K + + ER+
Sbjct: 14 AFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERL 64
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 89
F+ + +E KRL +N DL L K +GK++K L +K + + ER+
Sbjct: 9 AFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERL 59
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 27.7 bits (60), Expect = 8.4, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 89
F+ + +E KRL +N DL L K +GK++K L +K + + ER+
Sbjct: 13 AFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERL 63
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
0.323 0.138 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,398,469
Number of Sequences: 62578
Number of extensions: 312849
Number of successful extensions: 803
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 802
Number of HSP's gapped (non-prelim): 14
length of query: 317
length of database: 14,973,337
effective HSP length: 99
effective length of query: 218
effective length of database: 8,778,115
effective search space: 1913629070
effective search space used: 1913629070
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)