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= 044275
(168 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 56.2 bits (134), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
NAPKRP S +F+F +FR K + P S+ + K G+ W +++++EK PY+ KA
Sbjct: 8 NAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKL 66
Query: 100 KAEYELALEAYK 111
K +YE + YK
Sbjct: 67 KEKYEKDVADYK 78
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKRP SA+F+F ++R K P S+ K G+ W S +K PY QKA
Sbjct: 5 DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 63
Query: 98 NKKAEYELALEAYK 111
K +YE + AY+
Sbjct: 64 KLKEKYEKDIAAYR 77
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKRP SA+F+F + R K P S+ K G+ W S +K PY QKA
Sbjct: 4 DPNAPKRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 62
Query: 98 NKKAEYELALEAYK 111
K +YE + AY+
Sbjct: 63 KLKEKYEKDIAAYR 76
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKR LSAY F + R + PD + +GK G+KWK+++ EK PY KA
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 98 NKKAEYELALEAYKKQL 114
K YE E Y L
Sbjct: 76 ADKKRYESEKELYNATL 92
>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 = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKR LSAY F + R + PD + +GK G+KWK+++ EK PY KA
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 98 NKKAEYELALEAYKKQL 114
K YE E Y L
Sbjct: 76 ADKKRYESEKELYNATL 92
>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 = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKRP SA+F+F ++R K P S+ + K G+ W + + +K PY +KA
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 61
Query: 98 NKKAEYELALEAYK 111
K +YE + AY+
Sbjct: 62 KLKEKYEKDIAAYR 75
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKRP SA+F+F ++R K P S+ + K G+ W + + +K PY +KA
Sbjct: 98 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 156
Query: 98 NKKAEYELALEAYK 111
K +YE + AY+
Sbjct: 157 KLKEKYEKDIAAYR 170
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
D P+ +S+Y F++ R+ K+ PD + + + K ++WK+MS EK + A
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 97 LNKKAEYELALEAY 110
KA YE ++ Y
Sbjct: 72 KADKARYEREMKTY 85
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
SNAPKRP SA+F+F ++R K P S+ + K G+ W + + +K PY +KA
Sbjct: 2 SNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 60
Query: 99 KKAEYELALEAYK 111
K +YE + AY+
Sbjct: 61 LKEKYEKDIAAYR 73
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
D NAPKR LS+Y F ++ R P+ K VAA+GK G W ++S+ EK PY + +
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 97 LNKKAEYE 104
+ YE
Sbjct: 79 DEDRVRYE 86
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D NAPKRP SA+F+F ++R K P S+ + K G+ W + + +K PY +KA
Sbjct: 85 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 143
Query: 98 NKKAEYELALEAYK 111
K +YE + AY+
Sbjct: 144 KLKEKYEKDIAAYR 157
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
KRP++A+ ++ D R+ P ++ + + K G +WK ++EAEK P+ Q+A +A
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 103 YELALEAYK 111
+ YK
Sbjct: 65 HREKYPNYK 73
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S+ PKRPLSAY +++ R+S K P K V + K GG+ W++M +K+ + KA
Sbjct: 1 SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 57
Query: 99 KKAEYELALEAY 110
K +Y+ A++ +
Sbjct: 58 AKDDYDRAVKEF 69
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S+ PKRPLSAY +++ R+S K P K V + K GG+ W++M +K+ + KA
Sbjct: 2 SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 58
Query: 99 KKAEYELALEAY 110
K +Y+ A++ +
Sbjct: 59 AKDDYDRAVKEF 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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S+ PKRPLSAY +++ R+S K P K V + K GG+ W++M +K+ + KA
Sbjct: 1 SDKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 57
Query: 99 KKAEYELALEAY 110
K +Y+ A++ +
Sbjct: 58 AKDDYDRAVKEF 69
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
PKRPLSAY +++ R+S K P K V + K GG+ W++M +K+ + KA K
Sbjct: 4 PKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKD 60
Query: 102 EYELALEAY 110
+Y+ A++ +
Sbjct: 61 DYDRAVKEF 69
>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 = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
APKRP SA+F+F ++R K P S+ + K G+ W + + +K PY +KA K
Sbjct: 2 APKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK 60
Query: 101 AEYELALEAYK 111
+YE + AY+
Sbjct: 61 EKYEKDIAAYR 71
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
+RP++A+ ++ +D RK + PD + A + K G+ WK+++ AEK P+V++A + +
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 103 Y 103
+
Sbjct: 63 H 63
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S+ +RP++A+ ++ +D RK + PD + A + K G+ WK+++ AEK P+V++A
Sbjct: 5 SSGIRRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAER 63
Query: 99 KKAEY 103
+ ++
Sbjct: 64 LRVQH 68
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQ 94
KRP++A+ ++ +D R+ ++FPD + + + K G +WK+M+ EK PY +
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYE 56
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
+RP++A+ ++ +D RK + PD + A + K G+ WK+++ AEK P+V++A + +
Sbjct: 8 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
Query: 103 Y 103
+
Sbjct: 67 H 67
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S PKRP+SA FIF E+ R+ +E P+ S + + + + W +SE +KA Y +
Sbjct: 18 SEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAA 76
Query: 99 KKAEYE 104
KA+ E
Sbjct: 77 LKAQSE 82
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
KRP++A+ ++ + R+ E PD + A + K G++WK + +++K P++Q+A
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHN-AEISKRLGKRWKLLKDSDKIPFIQEA 56
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
D N P+ +S+Y F++ R+ K+ PD+ + A K ++WK+MS EK+ + A
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 97 LNKKAEYELAL 107
+ KA Y+ +
Sbjct: 65 KSDKARYDREM 75
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
KRP++A+ ++ + R+ + +P + A + K G+ W+ ++E+EK P+V++A + +
Sbjct: 31 KRPMNAFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNESEKRPFVEEAERLRVQ 89
Query: 103 YELALEAYKKQ 113
++ YK Q
Sbjct: 90 HKKDHPDYKYQ 100
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S+ PKR +A+ +++ D R+S K P K V + K GG+ WK + +K+ + A
Sbjct: 1 SHMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELK--DKSKWEDAAAK 57
Query: 99 KKAEYELALEAYK 111
K Y + YK
Sbjct: 58 DKQRYHDEMRNYK 70
>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 = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
D P+ +S+Y F++ R+ K+ PD + + + K ++WK+MS EK + A
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 97 LNKKAEYELALEAY 110
KA YE ++ Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
S+ PK P++ Y F+ + R+ + PD + K G +W + AEK Y+ +A
Sbjct: 5 SSGPKAPVTGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDEAEK 63
Query: 99 KKAEYELALEAYKK 112
+K +Y L AY++
Sbjct: 64 EKQQYLKELWAYQQ 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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D N P++P+SAY +F D + + K P N + + K W + E +K Y +K
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNP-NATFGEVSKIVASMWDGLGEEQKQVYKKKTE 72
Query: 98 NKKAEYELALEAYKKQL 114
K EY L AY+ L
Sbjct: 73 AAKKEYLKQLAAYRASL 89
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
D P+ +S+Y F++ R+ K+ PD + + + K ++WK+MS EK + A
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 97 LNKKAEYELALEAY 110
KA YE ++ Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 42 PKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
P+ +S+Y F++ R+ K+ PD + + + K ++WK+MS EK + A K
Sbjct: 2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61
Query: 101 AEYELALEAY 110
A YE ++ Y
Sbjct: 62 ARYEREMKTY 71
>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 = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
KRP++A+ ++ D R+ P ++ + + K G +WK ++EAEK P+ Q+A +A
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 103 YELALEAYK 111
+ YK
Sbjct: 65 HREKYPNYK 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 = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
KRP++A+ ++ D R+ P ++ + + K G +WK ++EAEK P+ Q+A
Sbjct: 6 KRPINAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEA 58
>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 = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
KRP++A+ ++ D R+ P ++ + + K G +WK ++EAEK P+ Q+A
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEA 58
>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 = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 44/77 (57%), Gaps = 5/77 (6%)
Query: 42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
PKRP SAY +++ + F+E+ D S K + WK++S++EK Y+Q A +
Sbjct: 115 PKRPRSAYNVYVAE---RFQEAKGD--SPQEKLKTVKENWKNLSDSEKELYIQHAKEDET 169
Query: 102 EYELALEAYKKQLNDNG 118
Y ++++++Q+ + G
Sbjct: 170 RYHNEMKSWEEQMIEVG 186
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPY 92
++ PK+P+S+Y F ++ FK PD K+ + + Q+W+ + +++K Y
Sbjct: 7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPDSKKKIY 59
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
PK+PL+ YF F + R + + P+ S + K +K+K + E +K Y+Q +K
Sbjct: 11 PKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ 69
Query: 102 EYELALEAYK 111
E+E L ++
Sbjct: 70 EFERNLARFR 79
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 33.9 bits (76), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
S+ KRP++A+ ++ R+ + P + + + K G +WK +SE EK P++ +A
Sbjct: 1 SDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEA 57
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 33.1 bits (74), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
PKRP SAY +++ + F+E+ D S K + WK++S++EK Y+Q A +
Sbjct: 147 PKRPRSAYNVYVAE---RFQEAKGD--SPQEKLKTVKENWKNLSDSEKELYIQHAKEDET 201
Query: 102 EYELALEAYKKQLNDNG 118
Y +++++Q + G
Sbjct: 202 RYHNEXKSWEEQXIEVG 218
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPY 92
++ PK+P+S+Y F ++ FK PD K+ + + Q+W+ + +++K Y
Sbjct: 39 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPDSKKKIY 91
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 33.1 bits (74), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
PKRP SAY +++ + + K P K K + WK++S++EK Y+Q A +
Sbjct: 3 PKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDET 57
Query: 102 EYELALEAY 110
Y ++++
Sbjct: 58 RYHNEMKSW 66
>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 = 33.1 bits (74), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
KRP++A+ ++ R+ + P + + + K G +WK +SE EK P++ +A
Sbjct: 9 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEA 61
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 33.1 bits (74), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
KRP++A+ ++ R+ + P + + + K G +WK +SE EK P++ +A
Sbjct: 4 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEA 56
>pdb|2YUK|A Chain A, Solution Structure Of The Hmg Box Of Human MyeloidLYMPHOID
Or Mixed-Lineage Leukemia Protein 3 Homolog
Length = 90
Score = 31.6 bits (70), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 59 SFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND 116
+ KE FPD V + K W+ S E+APYVQKA + +A AL K Q+++
Sbjct: 40 NLKEEFPDWTTRVKQIAKL----WRKASSQERAPYVQKARDNRA----ALRINKVQMSN 90
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 30.4 bits (67), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 46 LSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYE 104
+SAY F++ R+ K+ P+ + A K ++WK+MS EK+ + + A K Y+
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD 79
Query: 105 LALEAY 110
++ Y
Sbjct: 80 REMKDY 85
>pdb|1V64|A Chain A, Solution Structure Of The 3rd Hmg Box Of Mouse Ubf1
Length = 108
Score = 30.0 bits (66), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
D K P ++Y ++ + + K+ + V Q+WK +S+ EK Y +K
Sbjct: 14 DGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLC-----SQQWKLLSQKEKDAYHKKCD 68
Query: 98 NKKAEYELAL 107
KK +YE+ L
Sbjct: 69 QKKKDYEVEL 78
>pdb|2DSJ|A Chain A, Crystal Structure Of Project Id Tt0128 From Thermus
Thermophilus Hb8
pdb|2DSJ|B Chain B, Crystal Structure Of Project Id Tt0128 From Thermus
Thermophilus Hb8
Length = 423
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 56 FRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ 113
F K+ +E+ K++ A+G+ G++ +++ + +AP + +A+ E A+EA K +
Sbjct: 206 FMKTLEEARLLAKTMVAIGQGAGRRVRALLTSMEAP-LGRAVGNAIEVREAIEALKGE 262
>pdb|3E8K|A Chain A, Crystal Structure Of Hk97 Prohead Ii
pdb|3E8K|B Chain B, Crystal Structure Of Hk97 Prohead Ii
pdb|3E8K|C Chain C, Crystal Structure Of Hk97 Prohead Ii
pdb|3E8K|D Chain D, Crystal Structure Of Hk97 Prohead Ii
pdb|3E8K|E Chain E, Crystal Structure Of Hk97 Prohead Ii
pdb|3E8K|F Chain F, Crystal Structure Of Hk97 Prohead Ii
pdb|3E8K|G Chain G, Crystal Structure Of Hk97 Prohead Ii
Length = 273
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 86 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 118
>pdb|2FS3|A Chain A, Bacteriophage Hk97 K169y Head I
pdb|2FS3|B Chain B, Bacteriophage Hk97 K169y Head I
pdb|2FS3|C Chain C, Bacteriophage Hk97 K169y Head I
pdb|2FS3|D Chain D, Bacteriophage Hk97 K169y Head I
pdb|2FS3|E Chain E, Bacteriophage Hk97 K169y Head I
pdb|2FS3|F Chain F, Bacteriophage Hk97 K169y Head I
pdb|2FS3|G Chain G, Bacteriophage Hk97 K169y Head I
Length = 282
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 95 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 127
>pdb|1OHG|A Chain A, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|1OHG|B Chain B, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|1OHG|C Chain C, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|1OHG|D Chain D, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|1OHG|E Chain E, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|1OHG|F Chain F, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|1OHG|G Chain G, Structure Of The Dsdna Bacteriophage Hk97 Mature Empty
Capsid
pdb|2FRP|A Chain A, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FRP|B Chain B, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FRP|C Chain C, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FRP|D Chain D, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FRP|E Chain E, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FRP|F Chain F, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FRP|G Chain G, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FSY|A Chain A, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FSY|B Chain B, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FSY|C Chain C, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FSY|D Chain D, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FSY|E Chain E, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FSY|F Chain F, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FSY|G Chain G, Bacteriophage Hk97 Pepsin-Treated Expansion Intermediate
Iv
pdb|2FT1|A Chain A, Bacteriophage Hk97 Head Ii
pdb|2FT1|B Chain B, Bacteriophage Hk97 Head Ii
pdb|2FT1|C Chain C, Bacteriophage Hk97 Head Ii
pdb|2FT1|D Chain D, Bacteriophage Hk97 Head Ii
pdb|2FT1|E Chain E, Bacteriophage Hk97 Head Ii
pdb|2FT1|F Chain F, Bacteriophage Hk97 Head Ii
pdb|2FT1|G Chain G, Bacteriophage Hk97 Head Ii
pdb|2FTE|A Chain A, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FTE|B Chain B, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FTE|C Chain C, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FTE|D Chain D, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FTE|E Chain E, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FTE|F Chain F, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|2FTE|G Chain G, Bacteriophage Hk97 Expansion Intermediate Iv
pdb|3DDX|A Chain A, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
pdb|3DDX|B Chain B, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
pdb|3DDX|C Chain C, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
pdb|3DDX|D Chain D, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
pdb|3DDX|E Chain E, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
pdb|3DDX|F Chain F, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
pdb|3DDX|G Chain G, Hk97 Bacteriophage Capsid Expansion Intermediate-Ii Model
Length = 282
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 95 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 127
>pdb|2GP1|A Chain A, Bacteriophage Hk97 Prohead Ii Crystal Structure
pdb|2GP1|B Chain B, Bacteriophage Hk97 Prohead Ii Crystal Structure
pdb|2GP1|C Chain C, Bacteriophage Hk97 Prohead Ii Crystal Structure
pdb|2GP1|D Chain D, Bacteriophage Hk97 Prohead Ii Crystal Structure
pdb|2GP1|E Chain E, Bacteriophage Hk97 Prohead Ii Crystal Structure
pdb|2GP1|F Chain F, Bacteriophage Hk97 Prohead Ii Crystal Structure
pdb|2GP1|G Chain G, Bacteriophage Hk97 Prohead Ii Crystal Structure
Length = 282
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 95 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 127
>pdb|2W5X|A Chain A, Structure Of Tab5 Alkaline Phosphatase Mutant His 135 Glu
With Mg Bound In The M3 Site.
pdb|2W5X|B Chain B, Structure Of Tab5 Alkaline Phosphatase Mutant His 135 Glu
With Mg Bound In The M3 Site
Length = 375
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 5/99 (5%)
Query: 70 VAAMG--KAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLN-DNGAGVSEDSW 126
+AA+ K G S++EA A + ALN+ E E+A++ + L+ G G++ +
Sbjct: 117 IAALNNIKTGVVATSSITEATPASFYAHALNRGLEEEIAMDMTESDLDFFAGGGLNYFTK 176
Query: 127 KXXXXXXXXXXXXXE--INDEAEQEFSSQVSSYFMGFYC 163
+ + IN A +FSS S+ MGF
Sbjct: 177 RKDKKDVLAILKGNQFTINTTALTDFSSIASNRKMGFLL 215
>pdb|3J1A|A Chain A, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
pdb|3J1A|B Chain B, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
pdb|3J1A|C Chain C, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
pdb|3J1A|D Chain D, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
pdb|3J1A|E Chain E, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
pdb|3J1A|F Chain F, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
pdb|3J1A|G Chain G, Hk97-Like Fold Fitted Into 3d Reconstruction Of
Bacteriophage Cw02
Length = 199
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 17 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 49
>pdb|1IF0|A Chain A, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
pdb|1IF0|B Chain B, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
pdb|1IF0|C Chain C, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
pdb|1IF0|D Chain D, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
pdb|1IF0|E Chain E, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
pdb|1IF0|F Chain F, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
pdb|1IF0|G Chain G, Pseudo-Atomic Model Of Bacteriophage Hk97 Procapsid
(Prohead Ii)
Length = 256
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 71 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 103
>pdb|3QPR|A Chain A, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
pdb|3QPR|B Chain B, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
pdb|3QPR|C Chain C, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
pdb|3QPR|D Chain D, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
pdb|3QPR|E Chain E, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
pdb|3QPR|F Chain F, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
pdb|3QPR|G Chain G, Hk97 Prohead I Encapsidating Inactive Virally Encoded
Protease
Length = 385
Score = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 88 EKAPYVQKALNKKAEYELALEAYKKQLNDNGAG 120
+ AP +Q +N + Y LAL+ + LN +G G
Sbjct: 198 DDAPMLQSYINNRLMYGLALKEEGQLLNGDGTG 230
>pdb|2W5V|A Chain A, Structure Of Tab5 Alkaline Phosphatase Mutant His 135 Asp
With Mg Bound In The M3 Site.
pdb|2W5V|B Chain B, Structure Of Tab5 Alkaline Phosphatase Mutant His 135 Asp
With Mg Bound In The M3 Site.
pdb|2W5W|A Chain A, Structure Of Tab5 Alkaline Phosphatase Mutant His 135 Asp
With Zn Bound In The M3 Site.
pdb|2W5W|B Chain B, Structure Of Tab5 Alkaline Phosphatase Mutant His 135 Asp
With Zn Bound In The M3 Site
Length = 375
Score = 26.2 bits (56), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 5/99 (5%)
Query: 70 VAAMG--KAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLN-DNGAGVSEDSW 126
+AA+ K G S+++A A + ALN+ E E+A++ + L+ G G++ +
Sbjct: 117 IAALNNIKTGVVATSSITDATPASFYAHALNRGLEEEIAMDMTESDLDFFAGGGLNYFTK 176
Query: 127 KXXXXXXXXXXXXXE--INDEAEQEFSSQVSSYFMGFYC 163
+ + IN A +FSS S+ MGF
Sbjct: 177 RKDKKDVLAILKGNQFTINTTALTDFSSIASNRKMGFLL 215
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
0.312 0.126 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,947,626
Number of Sequences: 62578
Number of extensions: 123575
Number of successful extensions: 257
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 176
Number of HSP's gapped (non-prelim): 61
length of query: 168
length of database: 14,973,337
effective HSP length: 92
effective length of query: 76
effective length of database: 9,216,161
effective search space: 700428236
effective search space used: 700428236
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)