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= 030283
(180 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SAFF+F E+R K E+P S +K PYE KA KLK +Y K
Sbjct: 14 SAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQ-SAKDKQPYEQKAAKLKEKYEKD 72
Query: 120 MNAYNKK 126
+ AY K
Sbjct: 73 IAAYRAK 79
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SAFF+F E R K E+P S +K PYE KA KLK +Y K
Sbjct: 13 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQ-SAKDKQPYEQKAAKLKEKYEKD 71
Query: 120 MNAYNKK 126
+ AY K
Sbjct: 72 IAAYRAK 78
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
S FF+F EFR K NP +++ +EK PY +KA KLK +Y K
Sbjct: 15 SGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWN-NLNDSEKQPYITKAAKLKEKYEKD 73
Query: 120 MNAYNKK 126
+ Y K
Sbjct: 74 VADYKSK 80
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SA+ F E R + ENP+ +++P EK PYE+KA+ K Y +
Sbjct: 26 SAYMFFANENRDIVRSENPDITFGQVGKKLGEKWK-ALTPEEKQPYEAKAQADKKRYESE 84
Query: 120 MNAYN 124
YN
Sbjct: 85 KELYN 89
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
Protein Nhp6a In Complex With Sry Dna
pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
Protein Nhp6a
Length = 93
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SA+ F E R + ENP+ +++P EK PYE+KA+ K Y +
Sbjct: 26 SAYMFFANENRDIVRSENPDITFGQVGKKLGEKWK-ALTPEEKQPYEAKAQADKKRYESE 84
Query: 120 MNAYN 124
YN
Sbjct: 85 KELYN 89
>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
pdb|1NHN|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
Length = 81
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SAFF+F E+R K E+P + + +K PYE KA KLK +Y K
Sbjct: 10 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAA-DDKQPYEKKAAKLKEKYEKD 68
Query: 120 MNAYNKKQDGDEA 132
+ AY K D A
Sbjct: 69 IAAYRAKGKPDAA 81
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
pdb|1HSN|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
Length = 79
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SAFF+F E+R K E+P + + +K PYE KA KLK +Y K
Sbjct: 8 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAA-DDKQPYEKKAAKLKEKYEKD 66
Query: 120 MNAYNKKQDGDEA 132
+ AY K D A
Sbjct: 67 IAAYRAKGKPDAA 79
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 26.6 bits (57), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
+ + FL E R+ + +P+ + PAEK Y +AEK K +Y K+
Sbjct: 13 TGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSK-LQPAEKQRYLDEAEKEKQQYLKE 71
Query: 120 MNAYNK 125
+ AY +
Sbjct: 72 LWAYQQ 77
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
0.300 0.119 0.311
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,946,540
Number of Sequences: 62578
Number of extensions: 74622
Number of successful extensions: 139
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 118
Number of HSP's gapped (non-prelim): 20
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.7 bits)
S2: 48 (23.1 bits)