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= psy12430
(146 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 136 bits (343), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 62/73 (84%), Positives = 70/73 (95%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDERRKIL+A PDMHNSNISKILG+RWKAM+N EKQPYYEEQ+RLSK H+EK
Sbjct: 9 MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 68
Query: 61 HPDYRYRPRPKRT 73
+PDY+Y+PRPKRT
Sbjct: 69 YPDYKYKPRPKRT 81
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 95.1 bits (235), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 40/69 (57%), Positives = 55/69 (79%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDER+++ + PD+HN+ +SK+LG WKA++ AEK+P+ EE RL HM+
Sbjct: 11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 70
Query: 61 HPDYRYRPR 69
HP+Y+YRPR
Sbjct: 71 HPNYKYRPR 79
>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 = 94.4 bits (233), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 42/76 (55%), Positives = 56/76 (73%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVW++ +RRK+ + P MHNS ISK LGA WK +S EK+P+ +E RL LHM++
Sbjct: 12 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 71
Query: 61 HPDYRYRPRPKRTCIV 76
HPDY+YRPR K ++
Sbjct: 72 HPDYKYRPRRKTKTLM 87
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 42/71 (59%), Positives = 54/71 (76%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVW++ +RRK+ + P MHNS ISK LGA WK +S EK+P+ +E RL LHM++
Sbjct: 8 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 67
Query: 61 HPDYRYRPRPK 71
HPDY+YRPR K
Sbjct: 68 HPDYKYRPRRK 78
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 93.6 bits (231), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 42/71 (59%), Positives = 54/71 (76%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVW++ +RRK+ + P MHNS ISK LGA WK +S EK+P+ +E RL LHM++
Sbjct: 7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66
Query: 61 HPDYRYRPRPK 71
HPDY+YRPR K
Sbjct: 67 HPDYKYRPRRK 77
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 89.0 bits (219), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 40/71 (56%), Positives = 53/71 (74%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVW++ ERRKI++ PDMHN+ ISK LG RWK + +++K P+ +E RL HM
Sbjct: 7 MNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMAD 66
Query: 61 HPDYRYRPRPK 71
+PDY+YRPR K
Sbjct: 67 YPDYKYRPRKK 77
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 88.2 bits (217), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 37/68 (54%), Positives = 52/68 (76%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDER+++ + PD+HN+ +SK+LG WKA++ AEK+P+ EE RL HM+
Sbjct: 12 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 71
Query: 61 HPDYRYRP 68
HP+Y+ P
Sbjct: 72 HPNYKSGP 79
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 85.9 bits (211), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 36/65 (55%), Positives = 51/65 (78%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDER+++ + PD+HN+ +SK+LG WKA++ AEK+P+ EE RL HM+
Sbjct: 7 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 66
Query: 61 HPDYR 65
HP+Y+
Sbjct: 67 HPNYK 71
>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 = 84.0 bits (206), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 37/71 (52%), Positives = 53/71 (74%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYRPRPK 71
+P+Y+YRPR K
Sbjct: 69 YPNYKYRPRRK 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 = 82.8 bits (203), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 36/71 (50%), Positives = 53/71 (74%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+NAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 INAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYRPRPK 71
+P+Y+YRPR K
Sbjct: 69 YPNYKYRPRRK 79
>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 = 82.4 bits (202), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 35/68 (51%), Positives = 51/68 (75%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYRP 68
+P+Y+YRP
Sbjct: 69 YPNYKYRP 76
>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 = 79.7 bits (195), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWA+ RRK+ P +HN+ +SK LG W+ ++ +EK+P+ EE RL H +
Sbjct: 34 MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKD 93
Query: 61 HPDYRYRPRPKRT 73
HPDY+Y+PR +++
Sbjct: 94 HPDYKYQPRRRKS 106
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 79.0 bits (193), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 34/67 (50%), Positives = 50/67 (74%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYR 67
+P+Y+YR
Sbjct: 69 YPNYKYR 75
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYE 48
+AF ++ + R KI P + +++K LG W + +KQPY +
Sbjct: 94 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEK 140
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 40/67 (59%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+NAFM++ K+ R ++ ++ I++ILG RW A+S E+ YYE + +LHM+
Sbjct: 7 LNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQL 66
Query: 61 HPDYRYR 67
+P + R
Sbjct: 67 YPGWSAR 73
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 35/63 (55%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFM++AK R + + P N IS ILG RWK M N E++ Y E L++
Sbjct: 22 MNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRL 81
Query: 61 HPD 63
+PD
Sbjct: 82 NPD 84
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPY 46
++A+M +A + R + PD+ + K LG +WKA++ EKQPY
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPY 46
++A+M +A + R + PD+ + K LG +WKA++ EKQPY
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 70
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+++ K R + + P + N +KIL W + EKQ Y + M+
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKA 71
Query: 61 HPDYRYRP 68
+P YR P
Sbjct: 72 NPGYRSGP 79
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 34/48 (70%), Gaps = 2/48 (4%)
Query: 1 MNAFMVWAKDERRKILKACPDMHN--SNISKILGARWKAMSNAEKQPY 46
++++M +AK++R +I+ P++ + I K++GA W A+S+ EK+PY
Sbjct: 27 LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPY 74
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 37/66 (56%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKH 61
+ F ++ + R KI P + +++K LG W ++++EKQPY + ++L + + +
Sbjct: 15 SGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDV 74
Query: 62 PDYRYR 67
DY+ +
Sbjct: 75 ADYKSK 80
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHM 58
+ ++ + + R +I PD+ I+K+LGA W + AEKQ Y +E + + ++
Sbjct: 12 VTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYL 69
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKH 61
+AF ++ + R KI P + + +K LG W S +KQPY ++ ++L + + +
Sbjct: 13 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDI 72
Query: 62 PDYRYR 67
YR +
Sbjct: 73 AAYRAK 78
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 33.5 bits (75), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKH 61
+AF ++ + R KI P + + +K LG W S +KQPY ++ ++L + + +
Sbjct: 14 SAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDI 73
Query: 62 PDYR 65
YR
Sbjct: 74 AAYR 77
>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 = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKH 61
+AF ++ + R KI P + +++K LG W + +KQPY ++ ++L + + +
Sbjct: 10 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI 69
Query: 62 PDYRYRPRP 70
YR + +P
Sbjct: 70 AAYRAKGKP 78
>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 = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKH 61
+AF ++ + R KI P + +++K LG W + +KQPY ++ ++L + + +
Sbjct: 8 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI 67
Query: 62 PDYRYRPRP 70
YR + +P
Sbjct: 68 AAYRAKGKP 76
>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 = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 33/65 (50%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++A+ ++ +D + I P+ +SKI+ + W + +KQ Y ++ K ++++
Sbjct: 22 VSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQ 81
Query: 61 HPDYR 65
YR
Sbjct: 82 LAAYR 86
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/53 (20%), Positives = 32/53 (60%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRL 53
++A ++++++RR++ + P++ S ++++L W +S +K Y ++ L
Sbjct: 25 VSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAAL 77
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 21/42 (50%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEK 43
AFM+W D R I + P + + I+K G WK + + K
Sbjct: 9 TAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK 50
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 29.6 bits (65), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYE 48
+AF ++ + R KI P + +++K LG W + +KQPY +
Sbjct: 107 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEK 153
>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 = 29.6 bits (65), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYE 48
+AF ++ + R KI P + +++K LG W + +KQPY +
Sbjct: 12 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEK 58
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
Upstream Binding Factor
Length = 99
Score = 28.9 bits (63), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 28/52 (53%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSR 52
+ + + ++R K K P+M N +++KIL ++K + +K Y ++ R
Sbjct: 15 LTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQR 66
>pdb|3LEH|A Chain A, The Crystal Structure Of Smu.943c From Streptococcus
Mutans Ua159
Length = 425
Score = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 27 ISKILGARWKAMSNAEKQPYYEEQSRL--SKLHMEKHPDYR 65
+ +LG + A S K+ Y + L +KLH+EKHPD R
Sbjct: 126 VHSLLGIQPFARSFEMKEACYSATAALNYAKLHVEKHPDTR 166
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSN 40
++A+M+W R I + P + + ++K G W+AM +
Sbjct: 8 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 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 = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSN 40
++A+M+W R I + P + + ++K G W+AM +
Sbjct: 8 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 47
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSN 40
++A+M+W R I + P + + ++K G W+AM +
Sbjct: 9 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 48
>pdb|2B9L|A Chain A, Crystal Structure Of Prophenoloxidase Activating Factor-Ii
From The Beetle Holotrichia Diomphalia
Length = 394
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 19 CPDMHNSNIS--KILGARWKAMSNAEKQPYYEEQSRLSKLHMEKHP 62
C + + SN+ KI W ++ E+ PY E + R +H +P
Sbjct: 180 CVNSYQSNLDAIKIRAGEWDTLTEKERLPYQERKIRQVIIHSNFNP 225
>pdb|1V63|A Chain A, Solution Structure Of The 6th Hmg Box Of Mouse Ubf1
Length = 101
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 22/32 (68%), Gaps = 3/32 (9%)
Query: 31 LGARWKAMSNAEKQPY---YEEQSRLSKLHME 59
+G+RW+ +S ++K+ Y EEQ R K+H++
Sbjct: 41 IGSRWQRISQSQKEHYKKLAEEQQRQYKVHLD 72
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
0.318 0.131 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,184,688
Number of Sequences: 62578
Number of extensions: 132736
Number of successful extensions: 330
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 286
Number of HSP's gapped (non-prelim): 48
length of query: 146
length of database: 14,973,337
effective HSP length: 90
effective length of query: 56
effective length of database: 9,341,317
effective search space: 523113752
effective search space used: 523113752
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)