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= 009802
(525 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GCJ|A Chain A, Crystal Structure Of The Pob3 Middle Domain
pdb|2GCJ|B Chain B, Crystal Structure Of The Pob3 Middle Domain
pdb|2GCJ|C Chain C, Crystal Structure Of The Pob3 Middle Domain
pdb|2GCJ|D Chain D, Crystal Structure Of The Pob3 Middle Domain
Length = 261
Score = 181 bits (458), Expect = 1e-45, Method: Compositional matrix adjust.
Identities = 88/254 (34%), Positives = 150/254 (59%), Gaps = 1/254 (0%)
Query: 71 AQVFRDKIMSMADVGAGGEEAVVTFEGIAILTPRGRYSVELHLSFLRLQGQANDFKIQYS 130
A+ F +++ AD+G +A+V+F+ + TPRGRY ++++ + +RL+G+ ++K+Q+
Sbjct: 4 AEAFYEELKEKADIGEVAGDAIVSFQDVFFTTPRGRYDIDIYKNSIRLRGKTYEYKLQHR 63
Query: 131 SVVRLFLLPKSNQPHTFVVVTLDPPIRKGQTLYPHIVLQFETDYVVQSELLMSEELLNTK 190
+ R+ LPK++ H +V+ ++PP+RKGQT YP +VLQF+ D + +L + +E
Sbjct: 64 QIQRIVSLPKADDIHHLLVLAIEPPLRKGQTTYPFLVLQFQKDEETEVQLNLEDEDYEEN 123
Query: 191 YKDKLEPSYKGLIHEVFTTILRGLSGAKITKPGKFRSAQDGYAVKSSLKAEDGVLYPLEK 250
YKDKL+ Y H V + +L+GL+ ++ PG+++S D AV S KA +G LYPL+
Sbjct: 124 YKDKLKKQYDAKTHIVLSHVLKGLTDRRVIVPGEYKSKYDQCAVSCSFKANEGYLYPLDN 183
Query: 251 SFFFLPKPPTLILHEEIDYVEFERHAAGGSNMHYFDLLIRLKTEQ-EHLFRNIQRNEYHN 309
+FFFL KP I ++ V R ++ FDL + L++ + F NI + E
Sbjct: 184 AFFFLTKPTLYIPFSDVSMVNISRAGQTSTSSRTFDLEVVLRSNRGSTTFANISKEEQQL 243
Query: 310 LFDFISGKGLKIMN 323
L F+ K L++ N
Sbjct: 244 LEQFLKSKNLRVKN 257
>pdb|2GCL|A Chain A, Structure Of The Pob3 Middle Domain
pdb|2GCL|B Chain B, Structure Of The Pob3 Middle Domain
Length = 261
Score = 177 bits (449), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 87/254 (34%), Positives = 148/254 (58%), Gaps = 1/254 (0%)
Query: 71 AQVFRDKIMSMADVGAGGEEAVVTFEGIAILTPRGRYSVELHLSFLRLQGQANDFKIQYS 130
A+ F +++ AD+G +A+V+F+ + TPRGRY ++++ + +RL+G+ ++K+Q+
Sbjct: 4 AEAFYEELKEKADIGEVAGDAIVSFQDVFFTTPRGRYDIDIYKNSIRLRGKTYEYKLQHR 63
Query: 131 SVVRLFLLPKSNQPHTFVVVTLDPPIRKGQTLYPHIVLQFETDYVVQSELLMSEELLNTK 190
+ R+ LPK++ H V ++PP+R+GQT YP +VLQF+ D + +L + +E
Sbjct: 64 QIQRIVSLPKADDIHHXXVXAIEPPLRQGQTTYPFLVLQFQKDEETEVQLNLEDEDYEEN 123
Query: 191 YKDKLEPSYKGLIHEVFTTILRGLSGAKITKPGKFRSAQDGYAVKSSLKAEDGVLYPLEK 250
YKDKL+ Y H V + +L+GL+ ++ PG+++S D AV S KA +G LYPL+
Sbjct: 124 YKDKLKKQYDAKTHIVLSHVLKGLTDRRVIVPGEYKSKYDQCAVSCSFKANEGYLYPLDN 183
Query: 251 SFFFLPKPPTLILHEEIDYVEFERHAAGGSNMHYFDLLIRLKTEQ-EHLFRNIQRNEYHN 309
+FFFL KP I ++ V R ++ FDL + L++ + F NI + E
Sbjct: 184 AFFFLTKPTLYIPFSDVSXVNISRAGQTSTSSRTFDLEVVLRSNRGSTTFANISKEEQQL 243
Query: 310 LFDFISGKGLKIMN 323
L F+ K L++ N
Sbjct: 244 LEQFLKSKNLRVKN 257
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 37/71 (52%), Positives = 53/71 (74%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKRA+S ++FF+ R+ ++ NP I F VG+ LGE+WK ++ EE++PYE+KA+AD
Sbjct: 18 PNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77
Query: 498 KKRYKDEISGY 508
KKRY+ E Y
Sbjct: 78 KKRYESEKELY 88
>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 = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 37/71 (52%), Positives = 53/71 (74%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKRA+S ++FF+ R+ ++ NP I F VG+ LGE+WK ++ EE++PYE+KA+AD
Sbjct: 18 PNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77
Query: 498 KKRYKDEISGY 508
KKRY+ E Y
Sbjct: 78 KKRYESEKELY 88
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 31/72 (43%), Positives = 46/72 (63%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
NAPKR SGF F R IK +NPGI+ DV + LGE W ++ E++PY +KA K
Sbjct: 8 NAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLK 67
Query: 499 KRYKDEISGYKN 510
++Y+ +++ YK+
Sbjct: 68 EKYEKDVADYKS 79
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKR S F F R IK +PG++ D + LGE W + S ++++PYE KA
Sbjct: 5 PNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKL 64
Query: 498 KKRYKDEISGYK 509
K++Y+ +I+ Y+
Sbjct: 65 KEKYEKDIAAYR 76
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 65.5 bits (158), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKR S F F R IK +PG++ D + LGE W + S ++++PYE KA
Sbjct: 6 PNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKL 65
Query: 498 KKRYKDEISGYK 509
K++Y+ +I+ Y+
Sbjct: 66 KEKYEKDIAAYR 77
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
Transactivation Domain Interaction And Is Regulated By
The Acidic Tail
Length = 83
Score = 60.5 bits (145), Expect = 2e-09, Method: Composition-based stats.
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNP--GIAFTDVGRVLGERWKKMSVEEREPYESKAR 495
P P+ MS + FF Q RE KK +P + F++ + ERWK MS +E+ +E A+
Sbjct: 5 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
Query: 496 ADKKRYKDEISGYKNPK 512
ADK RY+ E+ Y PK
Sbjct: 65 ADKARYEREMKTYIPPK 81
>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like
Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A)
Length = 97
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 47/73 (64%), Gaps = 2/73 (2%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIA--FTDVGRVLGERWKKMSVEEREPYESKAR 495
PNAPKRA+S ++FF++ +R I NP IA +G+++G W +S EE++PYE +
Sbjct: 20 PNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSD 79
Query: 496 ADKKRYKDEISGY 508
D+ RY+ E + Y
Sbjct: 80 EDRVRYEREKAEY 92
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNP--GIAFTDVGRVLGERWKKMSVEEREPYESKAR 495
P P+ MS + FF Q RE KK +P + F++ + ERWK MS +E+ +E A+
Sbjct: 5 PKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
Query: 496 ADKKRYKDEISGYKNPK 512
ADK RY+ E+ Y PK
Sbjct: 65 ADKARYEREMKTYIPPK 81
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 44/69 (63%), Gaps = 2/69 (2%)
Query: 441 PKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKR 500
PKRA + F+ + RE+IK+ NPGI T++ + GE WK++ +++ +E A DK+R
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQR 61
Query: 501 YKDEISGYK 509
Y DE+ YK
Sbjct: 62 YHDEMRNYK 70
>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 = 59.3 bits (142), Expect = 6e-09, Method: Composition-based stats.
Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKR S F F R IK +PG++ DV + LGE W + ++++PYE KA
Sbjct: 4 PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 63
Query: 498 KKRYKDEISGYK 509
K++Y+ +I+ Y+
Sbjct: 64 KEKYEKDIAAYR 75
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNP--GIAFTDVGRVLGERWKKMSVEEREPYESKAR 495
P P+ MS + FF Q RE KK +P + F++ + ERWK MS +E+ +E A+
Sbjct: 13 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 72
Query: 496 ADKKRYKDEISGYKNPK 512
ADK RY+ E+ Y PK
Sbjct: 73 ADKARYEREMKTYIPPK 89
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKR S F F R IK +PG++ DV + LGE W + ++++PYE KA
Sbjct: 99 PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 158
Query: 498 KKRYKDEISGYK 509
K++Y+ +I+ Y+
Sbjct: 159 KEKYEKDIAAYR 170
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNP--GIAFTDVGRVLGERWKKMSVEEREPYESKAR 495
PN P+ MS + FF Q RE KK +P + F + + ERWK MS +E+ +E A+
Sbjct: 6 PNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAK 65
Query: 496 ADKKRYKDEI 505
+DK RY E+
Sbjct: 66 SDKARYDREM 75
>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 = 57.0 bits (136), Expect = 3e-08, Method: Composition-based stats.
Identities = 28/71 (39%), Positives = 43/71 (60%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
NAPKR S F F R IK +PG++ DV + LGE W + ++++PYE KA K
Sbjct: 3 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK 62
Query: 499 KRYKDEISGYK 509
++Y+ +I+ Y+
Sbjct: 63 EKYEKDIAAYR 73
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PNAPKR S F F R IK +PG++ DV + LGE W + ++++PYE KA
Sbjct: 86 PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 145
Query: 498 KKRYKDEISGYK 509
K++Y+ +I+ Y+
Sbjct: 146 KEKYEKDIAAYR 157
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
KR M+ FI +S+ +R + NP + +++ + LG +WK ++ E+ P+ +A+ + +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 502 KDEISGYK 509
+++ YK
Sbjct: 66 REKYPNYK 73
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 55.8 bits (133), Expect = 6e-08, Method: Composition-based stats.
Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 441 PKRAMSGFIFFSQMERENIKKSNP--GIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
P+ MS + FF Q RE KK +P + F++ + ERWK MS +E+ +E A+ADK
Sbjct: 2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61
Query: 499 KRYKDEISGY 508
RY+ E+ Y
Sbjct: 62 ARYEREMKTY 71
>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 = 54.7 bits (130), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 42/70 (60%)
Query: 440 APKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKK 499
APKR S F F R IK +PG++ DV + LGE W + ++++PYE KA K+
Sbjct: 2 APKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61
Query: 500 RYKDEISGYK 509
+Y+ +I+ Y+
Sbjct: 62 KYEKDIAAYR 71
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 52.4 bits (124), Expect = 6e-07, Method: Composition-based stats.
Identities = 27/66 (40%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 445 MSGFIFFSQMERENIKKSNPGIA--FTDVGRVLGERWKKMSVEEREPYESKARADKKRYK 502
MS + FF Q RE KK NP + F + + ERWK MS +E+ ++ A+ADK RY
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD 79
Query: 503 DEISGY 508
E+ Y
Sbjct: 80 REMKDY 85
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 49.7 bits (117), Expect = 4e-06, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 41/71 (57%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PK ++G++ F RE I+ +P + F ++ ++LG W K+ E++ Y +A +K
Sbjct: 6 SGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEK 65
Query: 499 KRYKDEISGYK 509
++Y E+ Y+
Sbjct: 66 QQYLKELWAYQ 76
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 48.9 bits (115), Expect = 7e-06, Method: Composition-based stats.
Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPY--ESKAR 495
PN KR M+ F+ F++ R + PG + +LG+RWKKM EER Y E+KA
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKAL 74
Query: 496 ADKKR 500
A++++
Sbjct: 75 AEEQK 79
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PKR +S ++ + RE+IK+ NPGI T+V + GE W+ M +++ +E+KA K
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 60
Query: 499 KRYKDEISGYK 509
Y + ++
Sbjct: 61 DDYDRAVKEFE 71
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PKR +S ++ + RE+IK+ NPGI T+V + GE W+ M +++ +E+KA K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 499 KRYKDEISGYK 509
Y + ++
Sbjct: 60 DDYDRAVKEFE 70
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna
pdb|1QRV|B Chain B, Crystal Structure Of The Complex Of Hmg-D And Dna
Length = 73
Score = 48.5 bits (114), Expect = 8e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PKR +S ++ + RE+IK+ NPGI T+V + GE W+ M +++ +E+KA K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 499 KRYKDEISGYK 509
Y + ++
Sbjct: 60 DDYDRAVKEFE 70
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex
pdb|3NM9|D Chain D, Hmgd(M13a)-Dna Complex
pdb|3NM9|G Chain G, Hmgd(M13a)-Dna Complex
pdb|3NM9|J Chain J, Hmgd(M13a)-Dna Complex
pdb|3NM9|M Chain M, Hmgd(M13a)-Dna Complex
pdb|3NM9|P Chain P, Hmgd(M13a)-Dna Complex
Length = 73
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PKR +S + + RE+IK+ NPGI T+V + GE W+ M +++ +E+KA K
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 499 KRYKDEISGYK 509
Y + ++
Sbjct: 60 DDYDRAVKEFE 70
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREP-YESKARADKK 499
KR M+ F+ +++ ER I ++ P + +++ ++LG RWK M+ E++P YE +AR K+
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQ 64
>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
pdb|3TQ6|B Chain B, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
Length = 214
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 43/71 (60%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PK+ +S ++ FS+ + K NP T++ R + +RW+++ +++ Y+ RA+
Sbjct: 8 SCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEW 67
Query: 499 KRYKDEISGYK 509
+ YK+EIS +K
Sbjct: 68 QVYKEEISRFK 78
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 43/71 (60%)
Query: 439 NAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ PK+ +S ++ FS+ + K NP T++ R + +RW+++ +++ Y+ RA+
Sbjct: 40 SCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEW 99
Query: 499 KRYKDEISGYK 509
+ YK+EIS +K
Sbjct: 100 QVYKEEISRFK 110
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 41/68 (60%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
+R M+ F+ +++ ER+ + + NP + ++ ++LG+ WK +++ E+ P+ +A + ++
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH 63
Query: 502 KDEISGYK 509
+ YK
Sbjct: 64 MQDHPNYK 71
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 42/69 (60%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
+R M+ F+ +++ ER+ + + NP + ++ ++LG+ WK +++ E+ P+ +A + ++
Sbjct: 9 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH 68
Query: 502 KDEISGYKN 510
+ YK+
Sbjct: 69 MQDHPNYKS 77
>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High
Mobility Group Box Protein Tox From Mouse
Length = 102
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
PN P++ +S + F + + IK NP F +V +++ W + E+++ Y+ K A
Sbjct: 15 PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAA 74
Query: 498 KKRYKDEISGYK 509
KK Y +++ Y+
Sbjct: 75 KKEYLKQLAAYR 86
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 35/53 (66%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKA 494
+R M+ F+ +++ ER+ + + NP + ++ ++LG+ WK +++ E+ P+ +A
Sbjct: 8 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEA 60
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 33/53 (62%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKA 494
KR M+ F+ +SQ+ER I + +P + ++ + LG+RWK + ++ P+ +A
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEA 56
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 88
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 438 PNAPKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARAD 497
P+ KR M+ F+ +S+ +R + + NP + +++ + LG WK +S E+ P+ +A+
Sbjct: 5 PDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRL 64
Query: 498 KKRYKDEISGYK 509
+ + E YK
Sbjct: 65 RALHMKEHPDYK 76
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr
pdb|1HRY|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multid-Dimensional Heteronuclear-Edited And-Filtered Nmr
Length = 76
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
KR M+ FI +S+ +R + NP + +++ + LG +WK ++ E+ P+ +A+ + +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 502 KDEISGYK 509
+++ YK
Sbjct: 66 REKYPNYK 73
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPY 490
KR M+ F+ +S+ +R + + NP + +++ + LG WK +S E+ P+
Sbjct: 5 KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPF 53
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPY 490
KR M+ F+ +S+ +R + + NP + +++ + LG WK +S E+ P+
Sbjct: 4 KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPF 52
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box Domain
Of The Human Male Sex Determining Factor Sry Complexed
To Dna
Length = 85
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
KR M+ FI +S+ +R + NP + +++ + LG +WK ++ E+ P+ +A+ + +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 502 KDEISGYK 509
+++ YK
Sbjct: 66 REKYPNYK 73
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The Hmg-Box
Domain Of The Human Male Sex Determining Factor Sry
Complexed To Dna
Length = 85
Score = 36.2 bits (82), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 40/68 (58%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
KR ++ FI +S+ +R + NP + +++ + LG +WK ++ E+ P+ +A+ + +
Sbjct: 6 KRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 502 KDEISGYK 509
+++ YK
Sbjct: 66 REKYPNYK 73
>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor
Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77
A RESOLUTION
Length = 106
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
KR M+ F+ ++Q R + P + ++ + LG+ W+ ++ E+ P+ +A + ++
Sbjct: 31 KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQH 90
Query: 502 KDEISGYK 509
K + YK
Sbjct: 91 KKDHPDYK 98
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 33.5 bits (75), Expect = 0.30, Method: Composition-based stats.
Identities = 15/67 (22%), Positives = 33/67 (49%)
Query: 442 KRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKRY 501
K+ ++ F+ + + R N+ + + ++LG RW +S EE+ Y AR +++ +
Sbjct: 4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLH 63
Query: 502 KDEISGY 508
G+
Sbjct: 64 MQLYPGW 70
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 33/56 (58%)
Query: 441 PKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARA 496
PKR +S FS+ +R +++ P ++ +++ R+L W +S +++ Y+++ A
Sbjct: 21 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAA 76
>pdb|3F5R|A Chain A, The Crystal Structure Of A Subunit Of The Heterodimeric
Fact Complex (Spt16p-Pob3p)
Length = 191
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 4 FMVGQKQAFEVSLADVSQTQLQGKNDVILEFHVDD 38
F + K FE+ A ++ T L KN+V +EF++ D
Sbjct: 146 FALNGKPTFEIPYARINNTNLTSKNEVGIEFNIQD 180
>pdb|2YUK|A Chain A, Solution Structure Of The Hmg Box Of Human MyeloidLYMPHOID
Or Mixed-Lineage Leukemia Protein 3 Homolog
Length = 90
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 449 IFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADK 498
+ ++ + N+K+ P +T + + + W+K S +ER PY KAR ++
Sbjct: 31 VLYTNINFPNLKEEFPD--WTTRVKQIAKLWRKASSQERAPYVQKARDNR 78
>pdb|3T61|A Chain A, Crystal Structure Of A Gluconokinase From Sinorhizobium
Meliloti 1021
pdb|3T61|B Chain B, Crystal Structure Of A Gluconokinase From Sinorhizobium
Meliloti 1021
Length = 202
Score = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 10/54 (18%)
Query: 457 ENIKKSNPGIAFTDVGRVLGERWKKMS-----VEEREPYESKARADKKRYKDEI 505
ENI+K + GI TD +RW ++ + REP A K+ Y+D++
Sbjct: 56 ENIRKXSEGIPLTD-----DDRWPWLAAIGERLASREPVVVSCSALKRSYRDKL 104
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 28.5 bits (62), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 441 PKRAMSGFIFFSQMERENIKKSNPGIAFTDVGRVLGERWKKMSVEEREPYESKARADKKR 500
PKR S + + + K +P + + E WK +S E+E Y A+ D+ R
Sbjct: 3 PKRPRSAYNVYVAERFQEAKGDSPQEKL----KTVKENWKNLSDSEKELYIQHAKEDETR 58
Query: 501 YKDEISGY 508
Y +E+ +
Sbjct: 59 YHNEMKSW 66
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
0.317 0.136 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,699,935
Number of Sequences: 62578
Number of extensions: 547052
Number of successful extensions: 1200
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1146
Number of HSP's gapped (non-prelim): 53
length of query: 525
length of database: 14,973,337
effective HSP length: 103
effective length of query: 422
effective length of database: 8,527,803
effective search space: 3598732866
effective search space used: 3598732866
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: 54 (25.4 bits)