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= psy15633
(129 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 150 bits (379), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 71/83 (85%), Positives = 78/83 (93%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
D +KRPMNAFMVWSR QRRK+AQ+NPKMHNSEISKRLGAEWKLL+E EKRP+IDEAKRLR
Sbjct: 6 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 65
Query: 82 AMHMKDHPDYKYRPRRKPKTLRK 104
A+HMK+HPDYKYRPRRK KTL K
Sbjct: 66 ALHMKEHPDYKYRPRRKTKTLMK 88
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 149 bits (375), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 69/80 (86%), Positives = 76/80 (95%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
D +KRPMNAFMVWSR QRRK+AQ+NPKMHNSEISKRLGAEWKLL+E EKRP+IDEAKRLR
Sbjct: 2 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 61
Query: 82 AMHMKDHPDYKYRPRRKPKT 101
A+HMK+HPDYKYRPRRK KT
Sbjct: 62 ALHMKEHPDYKYRPRRKTKT 81
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 148 bits (374), Expect = 7e-37, Method: Compositional matrix adjust.
Identities = 69/80 (86%), Positives = 76/80 (95%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
D +KRPMNAFMVWSR QRRK+AQ+NPKMHNSEISKRLGAEWKLL+E EKRP+IDEAKRLR
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60
Query: 82 AMHMKDHPDYKYRPRRKPKT 101
A+HMK+HPDYKYRPRRK KT
Sbjct: 61 ALHMKEHPDYKYRPRRKTKT 80
>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 = 115 bits (289), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 53/83 (63%), Positives = 69/83 (83%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKR 79
+ D +KRPMNAF+VWSR QRRK+A +NP+M NSEISK+LG +WK+LTE EK P+ EA++
Sbjct: 1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60
Query: 80 LRAMHMKDHPDYKYRPRRKPKTL 102
L+AMH + +P+YKYRPRRK K L
Sbjct: 61 LQAMHREKYPNYKYRPRRKAKML 83
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 115 bits (288), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 53/78 (67%), Positives = 66/78 (84%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
HIKRPMNAFMVWS+++RRKI + +P MHN+EISKRLG WKLL +++K P+I EA+RLR
Sbjct: 2 HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRL 61
Query: 83 MHMKDHPDYKYRPRRKPK 100
HM D+PDYKYRPR+K K
Sbjct: 62 KHMADYPDYKYRPRKKVK 79
>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 = 114 bits (284), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 52/83 (62%), Positives = 69/83 (83%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKR 79
+ D +KRP+NAF+VWSR QRRK+A +NP+M NSEISK+LG +WK+LTE EK P+ EA++
Sbjct: 1 MQDRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60
Query: 80 LRAMHMKDHPDYKYRPRRKPKTL 102
L+AMH + +P+YKYRPRRK K L
Sbjct: 61 LQAMHREKYPNYKYRPRRKAKML 83
>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 = 111 bits (278), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 48/76 (63%), Positives = 63/76 (82%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
H+KRPMNAFMVW++ RRK+A P +HN+E+SK LG W+LL E+EKRP+++EA+RLR
Sbjct: 29 HVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRV 88
Query: 83 MHMKDHPDYKYRPRRK 98
H KDHPDYKY+PRR+
Sbjct: 89 QHKKDHPDYKYQPRRR 104
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 47/75 (62%), Positives = 64/75 (85%)
Query: 24 IKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAM 83
I+RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK LT EKRP+++EA+RLR
Sbjct: 7 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
Query: 84 HMKDHPDYKYRPRRK 98
HM+DHP+YKYRPRR+
Sbjct: 67 HMQDHPNYKYRPRRR 81
>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 = 108 bits (271), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 48/76 (63%), Positives = 64/76 (84%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKR 79
+ D +KRPMNAF+VWSR QRRK+A +NP+M NSEISK+LG +WK+LTE EK P+ EA++
Sbjct: 1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60
Query: 80 LRAMHMKDHPDYKYRP 95
L+AMH + +P+YKYRP
Sbjct: 61 LQAMHREKYPNYKYRP 76
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 106 bits (264), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 47/75 (62%), Positives = 63/75 (84%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKR 79
+ D +KRPMNAF+VWSR QRRK+A +NP+M NSEISK+LG +WK+LTE EK P+ EA++
Sbjct: 1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60
Query: 80 LRAMHMKDHPDYKYR 94
L+AMH + +P+YKYR
Sbjct: 61 LQAMHREKYPNYKYR 75
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+ +
Sbjct: 90 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 149
Query: 85 MKDHPDYK 92
KD Y+
Sbjct: 150 EKDIAAYR 157
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 43/72 (59%), Positives = 59/72 (81%)
Query: 24 IKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAM 83
I+RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK LT EKRP+++EA+RLR
Sbjct: 8 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 67
Query: 84 HMKDHPDYKYRP 95
HM+DHP+YK P
Sbjct: 68 HMQDHPNYKSGP 79
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 100 bits (250), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 42/69 (60%), Positives = 58/69 (84%)
Query: 24 IKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAM 83
I+RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK LT EKRP+++EA+RLR
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 84 HMKDHPDYK 92
HM+DHP+YK
Sbjct: 63 HMQDHPNYK 71
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 97.4 bits (241), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 46/76 (60%), Positives = 57/76 (75%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
HIKRPMNAFMVW++ +RRKI Q P MHNS ISK LG+ WK +T EK+PY +E RL
Sbjct: 4 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSK 63
Query: 83 MHMKDHPDYKYRPRRK 98
H++ +PDYKY+PR K
Sbjct: 64 QHLEKYPDYKYKPRPK 79
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 42/70 (60%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP + F ++ R KI NP + +++K+LG W L ++EK+PYI +A +L+ +
Sbjct: 11 KRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKY 70
Query: 85 MKDHPDYKYR 94
KD DYK +
Sbjct: 71 EKDVADYKSK 80
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
+RPMNAF+++ + R + Q++P++ N +K L W +L EK+ Y D AK +
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAF 68
Query: 85 MKDHPDYKYRP 95
MK +P Y+ P
Sbjct: 69 MKANPGYRSGP 79
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 43/72 (59%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
HIK+P+NAFM++ + R + ++ ++ I++ LG W L+ E+ Y + A++ R
Sbjct: 2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQ 61
Query: 83 MHMKDHPDYKYR 94
+HM+ +P + R
Sbjct: 62 LHMQLYPGWSAR 73
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 37/69 (53%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
+ KRPMNAFM++++ R + Q P N IS LG WK + E+R Y EAK L
Sbjct: 16 NKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALA 75
Query: 82 AMHMKDHPD 90
+ +PD
Sbjct: 76 EEQKRLNPD 84
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPY 73
KR ++A+M ++ R + +NP + ++ K+LG +WK LT EK+PY
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 70
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPY 73
KR ++A+M ++ R + +NP + ++ K+LG +WK LT EK+PY
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 70
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 38/63 (60%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
K P+ ++ + +R +I +P + EI+K LGAEW L EK+ Y+DEA++ + +
Sbjct: 9 KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQY 68
Query: 85 MKD 87
+K+
Sbjct: 69 LKE 71
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + + +K+LG W + +K+PY +A +L+ +
Sbjct: 9 KRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKY 68
Query: 85 MKDHPDYKYR 94
KD Y+ +
Sbjct: 69 EKDIAAYRAK 78
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 38/68 (55%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + + +K+LG W + +K+PY +A +L+ +
Sbjct: 10 KRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKY 69
Query: 85 MKDHPDYK 92
KD Y+
Sbjct: 70 EKDIAAYR 77
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHN--SEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
KR ++++M +++ +R +I +NP++ + I K +GA W L++ EK+PY + R
Sbjct: 24 KRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRV 83
Query: 83 MHMKDHPDYKYR 94
+ ++ +Y R
Sbjct: 84 RYEREKAEYAQR 95
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+ +
Sbjct: 6 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 65
Query: 85 MKDHPDYKYRPRRKP 99
KD YR + KP
Sbjct: 66 EKDIA--AYRAKGKP 78
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 30/48 (62%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTE 67
+ D KRP++A+M+W R I ++NP + +E++KR G W+ + +
Sbjct: 1 MSDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 48
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+ +
Sbjct: 4 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 63
Query: 85 MKDHPDYKYRPRRKP 99
KD YR + KP
Sbjct: 64 EKDIA--AYRAKGKP 76
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTE 67
D KRP++A+M+W R I ++NP + +E++KR G W+ + +
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 47
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTE 67
D KRP++A+M+W R I ++NP + +E++KR G W+ + +
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 47
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+ +
Sbjct: 8 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 67
Query: 85 MKDHPDYK 92
KD Y+
Sbjct: 68 EKDIAAYR 75
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP++A ++S +RR++ ++ P++ SE+++ L W L+E +K Y + R
Sbjct: 22 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY-----KAREAA 76
Query: 85 MKDHPDYKYRP 95
+K + K P
Sbjct: 77 LKAQSERKSGP 87
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+ +
Sbjct: 103 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 162
Query: 85 MKDHPDYK 92
KD Y+
Sbjct: 163 EKDIAAYR 170
Score = 29.6 bits (65), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 30 AFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHMKDHP 89
AF V + + K + ++ SE SK+ WK ++ EK + D AK +A + ++
Sbjct: 24 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 83
Query: 90 DY 91
Y
Sbjct: 84 TY 85
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEK 70
KR AFM+W R I ++NP + +EI+K+ G WK L + K
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK 50
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTE 67
D KRP++A+ +W R I ++NP + +E++KR G W+ + +
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 47
>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 = 0.013, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 7/80 (8%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEA 77
KK D K+P+ + + +R K A+ +P+M N +++K L ++K L E +K YI +
Sbjct: 5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDF 64
Query: 78 KRLR-------AMHMKDHPD 90
+R + A +DHPD
Sbjct: 65 QREKQEFERNLARFREDHPD 84
>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 = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
++P++A+ ++ R + I NP E+SK + + W L E +K+ Y + + + +
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEY 78
Query: 85 MKDHPDYK 92
+K Y+
Sbjct: 79 LKQLAAYR 86
>pdb|3QPB|A Chain A, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|B Chain B, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|C Chain C, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|D Chain D, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|E Chain E, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|F Chain F, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|G Chain G, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|H Chain H, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|I Chain I, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|J Chain J, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|K Chain K, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|L Chain L, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|M Chain M, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|N Chain N, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|O Chain O, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|P Chain P, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|Q Chain Q, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
pdb|3QPB|R Chain R, Crystal Structure Of Streptococcus Pyogenes Uridine
Phosphorylase Reveals A Subclass Of The Np-I Superfamily
Length = 282
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 26 RPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAE-WKLLTENEK 70
R + F+V +R + DNP H++E + ++ E + L EN+K
Sbjct: 235 RCGSDFLVVGNQERNALGMDNPMAHDTEAAIQVAVEALRTLIENDK 280
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 30 AFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHMKDHP 89
AF V + + K + ++ SE SK+ WK ++ EK + D AK +A + ++
Sbjct: 16 AFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 75
Query: 90 DY 91
Y
Sbjct: 76 TY 77
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 30/51 (58%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYID 75
K+P+++++ +S+ Q NP +E+ +R+ W+ L +++K+ Y D
Sbjct: 43 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 93
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAK 78
KRP +A+ V+ + ++ D+P+ E K + WK L+++EK YI AK
Sbjct: 148 KRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAK 197
>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 = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 30 AFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHMKDHP 89
AF V + + K + ++ SE SK+ WK ++ EK + D AK +A + ++
Sbjct: 16 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 75
Query: 90 DY 91
Y
Sbjct: 76 TY 77
>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 = 29.3 bits (64), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 30/51 (58%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYID 75
K+P+++++ +S+ Q NP +E+ +R+ W+ L +++K+ Y D
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 61
Score = 26.6 bits (57), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 22/87 (25%)
Query: 10 PNTLLSPEKKI-DDHIKR-----------------PMNAFMVWSRLQRRKIAQDNPKMHN 51
P+ ++S EK+I D H+KR P +A+ V+ + ++ D+P+
Sbjct: 83 PSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ--- 139
Query: 52 SEISKRLGAEWKLLTENEKRPYIDEAK 78
E K + WK L+++EK YI AK
Sbjct: 140 -EKLKTVKENWKNLSDSEKELYIQHAK 165
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 28.5 bits (62), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 30 AFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHMKDHP 89
AF V + + K + ++ SE SK+ WK ++ EK + D AK +A + ++
Sbjct: 10 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 69
Query: 90 DY 91
Y
Sbjct: 70 TY 71
>pdb|2D7L|A Chain A, Solution Structure Of The Hmg Box Domain From Human Wd
Repeat And Hmg-Box Dna Binding Protein 1
Length = 81
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 26 RPMNAFMVWSRLQRRKIAQDNPKMHN-SEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
RP F +W R I DNP + ++I K +++L+ E++ + ++AK A
Sbjct: 8 RPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 67
Query: 85 MKDHPDYKYRP 95
+ K P
Sbjct: 68 GTEAKKRKSGP 78
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 30 AFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
AF V + + K + ++ +E SK+ WK ++ EK + D AK +A
Sbjct: 17 AFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKA 69
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 28 MNAFMVWSRLQRRKIAQDNPKM--HNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHM 85
M+A+ + + R + + NP++ + +E SK+ WK ++ EK + + AK + +
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD 79
Query: 86 KDHPDY 91
++ DY
Sbjct: 80 REMKDY 85
>pdb|2W3P|A Chain A, Boxc Crystal Structure
pdb|2W3P|B Chain B, Boxc Crystal Structure
Length = 556
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 39 RRKIAQDNPKMHNSEISKRLGAE---WKLLTENEKRPYIDEAKRLRAMHMKDHPDYKYRP 95
+RK+ D + + + G W+L+ E K D+A + RA+ + D
Sbjct: 187 KRKVRHDRADIFCTVVEGVRGERAKAWRLVDEVVKPNQFDQAIQARALELAAQSDRPAHA 246
Query: 96 RRKP-----KTLRKDGYTYPAVSV 114
+ P +T R+DG TY + V
Sbjct: 247 QGVPLTRIERTDREDGLTYKTLDV 270
>pdb|2B9L|A Chain A, Crystal Structure Of Prophenoloxidase Activating Factor-Ii
From The Beetle Holotrichia Diomphalia
Length = 394
Score = 27.3 bits (59), Expect = 2.3, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 19/44 (43%)
Query: 46 NPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHMKDHP 89
N N + K EW LTE E+ PY + R +H +P
Sbjct: 182 NSYQSNLDAIKIRAGEWDTLTEKERLPYQERKIRQVIIHSNFNP 225
>pdb|3TW5|A Chain A, Crystal Structure Of The Gp42 Transglutaminase From
Phytophthora Sojae
pdb|3TW5|B Chain B, Crystal Structure Of The Gp42 Transglutaminase From
Phytophthora Sojae
Length = 367
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 87 DHPDYKYRPRRKP--KTLRKDGYTYPAVSV 114
DHPD+ + P+ KP T+ G +Y VS+
Sbjct: 328 DHPDFLWLPKAKPAANTVTSVGLSYADVSM 357
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAK 78
KRP +A+ V+ + ++ D+P+ E K + WK L+++EK YI AK
Sbjct: 4 KRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAK 53
>pdb|3ZTV|A Chain A, Structure Of Haemophilus Influenzae Nad Nucleotidase
(Nadn)
pdb|3ZU0|A Chain A, Structure Of Haemophilus Influenzae Nad Nucleotidase
(Nadn)
pdb|3ZU0|B Chain B, Structure Of Haemophilus Influenzae Nad Nucleotidase
(Nadn)
Length = 579
Score = 25.8 bits (55), Expect = 6.3, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 40 RKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMHMKDH 88
RKI H ++ G +W LT +E++ +D K ++++ + DH
Sbjct: 288 RKIPHVLMSSHKLQVKNSEG-KWAELTGDERKKALDTLKSMKSISLDDH 335
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 0.133 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,351,280
Number of Sequences: 62578
Number of extensions: 160824
Number of successful extensions: 401
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 44
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 353
Number of HSP's gapped (non-prelim): 55
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
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: 45 (21.9 bits)