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= 032101
(147 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 = 37.7 bits (86), Expect = 0.002, 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 SAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWS-EQSAKDKQPYEQKAAKLKEKYEKD 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 = 36.6 bits (83), Expect = 0.005, 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 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWS-EQSAKDKQPYEQKAAKLKEKYEKD 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 = 35.4 bits (80), Expect = 0.012, 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|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 = 30.8 bits (68), Expect = 0.29, 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|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 30.8 bits (68), Expect = 0.31, 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|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
+ + FL E R+ + +P+ + PAEK Y +AEK K +Y K+
Sbjct: 13 TGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSK-LQPAEKQRYLDEAEKEKQQYLKE 71
Query: 120 MNAYNKKQ 127
+ AY + +
Sbjct: 72 LWAYQQSE 79
>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 = 26.6 bits (57), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 1/67 (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 MNAYNKK 126
+ AY K
Sbjct: 69 IAAYRAK 75
>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 = 26.6 bits (57), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 1/67 (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 MNAYNKK 126
+ AY K
Sbjct: 67 IAAYRAK 73
>pdb|4H8S|A Chain A, Crystal Structure Of Human Appl2barph Domain
pdb|4H8S|B Chain B, Crystal Structure Of Human Appl2barph Domain
pdb|4H8S|C Chain C, Crystal Structure Of Human Appl2barph Domain
pdb|4H8S|D Chain D, Crystal Structure Of Human Appl2barph Domain
Length = 407
Score = 26.2 bits (56), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 29/46 (63%)
Query: 96 SMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNLVPFFNSVDAF 141
SM+ + P + + EK+K+E GK++ A +KQ + + ++ +++A
Sbjct: 166 SMAKYSRLPKKKENEKVKTEVGKEVAAARRKQHLSSLQYYCALNAL 211
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEY 116
+AF V+ ++ RK ++NP+ +++ AEK P+ +AE+L+ ++
Sbjct: 13 NAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWK-ALTLAEKRPFVEEAERLRVQH 68
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEY 116
+AF V+ ++ RK ++NP+ +++ AEK P+ +AE+L+ ++
Sbjct: 8 NAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWK-ALTLAEKRPFVEEAERLRVQH 63
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
Length = 77
Score = 25.8 bits (55), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
SAFF+F E+R K E+P + + +K PYE KA KLK +Y K
Sbjct: 12 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAA-DDKQPYEKKAAKLKEKYEKD 70
Query: 120 MNAYNKK 126
+ AY K
Sbjct: 71 IAAYRAK 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
0.311 0.126 0.344
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,820,376
Number of Sequences: 62578
Number of extensions: 67294
Number of successful extensions: 160
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 139
Number of HSP's gapped (non-prelim): 24
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 47 (22.7 bits)