RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3437
(132 letters)
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein, DNA
sequence specific, testis determining.; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 81
Score = 106 bits (267), Expect = 1e-31
Identities = 32/92 (34%), Positives = 51/92 (55%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ RR + +P +HN+ +SK LG WK +++
Sbjct: 9 MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWK--------------------AMTN 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
+K+P+ EE RL + H ++P+YKY+PR ++
Sbjct: 49 LEKQPYYEEQARLSKQHLEKYPDYKYKPRPKR 80
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional
regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus
musculus}
Length = 79
Score = 105 bits (265), Expect = 3e-31
Identities = 43/92 (46%), Positives = 55/92 (59%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVW+Q RR + Q P +HNAE+SK LG WK L D
Sbjct: 7 MNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWK--------------------LLKD 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
SDK PFI+EAERLR H +++P+YKY+PR++
Sbjct: 47 SDKIPFIQEAERLRLKHMADYPDYKYRPRKKV 78
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX
domain, structural genomics, NPPSFA, riken structural
genomics/proteomics initiative; NMR {Mus musculus}
Length = 82
Score = 104 bits (263), Expect = 5e-31
Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 20/90 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+++ + R + ++P L N +K L W L
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWA--------------------VLDP 51
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRR 90
+K+ + + A+ + +P Y+ P
Sbjct: 52 KEKQKYTDMAKEYKDAFMKANPGYRSGPSS 81
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain,
endodermal, activator, DNA- nucleus, transcription
regulation, transcrip complex; HET: DNA; 2.75A {Mus
musculus} PDB: 2yul_A
Length = 83
Score = 104 bits (263), Expect = 6e-31
Identities = 48/92 (52%), Positives = 57/92 (61%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ R+ LA Q P LHNAELSK LG WK L+
Sbjct: 11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWK--------------------ALTL 50
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
++K+PF+EEAERLR H +HPNYKY+PRRRK
Sbjct: 51 AEKRPFVEEAERLRVQHMQDHPNYKYRPRRRK 82
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus
musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B
Length = 80
Score = 103 bits (260), Expect = 1e-30
Identities = 41/92 (44%), Positives = 58/92 (63%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVW++ RR +A + P +HN+E+SK LG WK L S+
Sbjct: 7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLL--------------------SE 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
++K+PFI+EA+RLR +H EHP+YKY+PRR+
Sbjct: 47 TEKRPFIDEAKRLRALHMKEHPDYKYRPRRKT 78
>1j46_A SRY, sex-determining region Y protein; MALE sex determining
factor, SRY, sex-reversal mutation; NMR {Homo sapiens}
SCOP: a.21.1.1 PDB: 1j47_A
Length = 85
Score = 103 bits (259), Expect = 3e-30
Identities = 34/96 (35%), Positives = 56/96 (58%), Gaps = 20/96 (20%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+VW++ RR +A + P + N+E+SK LG WK L ++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKML--------------------TE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKN 96
++K PF +EA++L+ +H+ ++PNYKY+PRR+
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLP 84
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain,
activator, DNA-binding, NUC transcription; HET: DNA;
2.77A {Homo sapiens}
Length = 106
Score = 103 bits (258), Expect = 5e-30
Identities = 56/92 (60%), Positives = 65/92 (70%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWAQAARR LA+QYP LHNAELSKTLG LW+ L++
Sbjct: 34 MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWR--------------------LLNE 73
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
S+K+PF+EEAERLR HK +HP+YKYQPRRRK
Sbjct: 74 SEKRPFVEEAERLRVQHKKDHPDYKYQPRRRK 105
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA
complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1
PDB: 1hrz_A*
Length = 76
Score = 101 bits (253), Expect = 2e-29
Identities = 32/88 (36%), Positives = 53/88 (60%), Gaps = 20/88 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+VW++ RR +A + P + N+E+SK LG WK L++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWK--------------------MLTE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQP 88
++K PF +EA++L+ +H+ ++PNYKY+P
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYRP 76
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG,
TCR-A, transcription factor; HET: DNA; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 86
Score = 99 bits (250), Expect = 5e-29
Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 20/95 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+NAFM++ + R + + +A +++ LG W LS
Sbjct: 7 LNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHA--------------------LSR 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSK 95
++ + E A + RQ+H +P + + K K
Sbjct: 47 EEQAKYYELARKERQLHMQLYPGWSARDNYGKKKK 81
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 95.3 bits (238), Expect = 2e-27
Identities = 42/85 (49%), Positives = 50/85 (58%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ R+ LA Q P LHNAELSK LG WK L+
Sbjct: 7 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWK--------------------ALTL 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
++K+PF+EEAERLR H +HPNYK
Sbjct: 47 AEKRPFVEEAERLRVQHMQDHPNYK 71
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box
transcription factor 1, high mobility group box
transcription factor 1, structural genomics; NMR {Homo
sapiens}
Length = 87
Score = 89.8 bits (223), Expect = 6e-25
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 20/83 (24%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFM++A+ R YP N +S LG WK K+ +
Sbjct: 22 MNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWK--------------------KMKN 61
Query: 61 SDKKPFIEEAERLRQIHKSEHPN 83
+++ + EA+ L + K +P+
Sbjct: 62 EERRMYTLEAKALAEEQKRLNPD 84
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 90
Score = 80.5 bits (199), Expect = 3e-21
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A ++++ RR L + P L +EL++ L +W LS+
Sbjct: 25 VSAMFIFSEEKRRQLQEERPELSESELTRLLARMWN--------------------DLSE 64
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
K + L+ + +
Sbjct: 65 KKKAKYKAREAALKAQSERKSGPSS 89
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX,
amphoterin, DNA/structural protein complex; NMR {Homo
sapiens} SCOP: a.21.1.1 a.21.1.1
Length = 159
Score = 81.8 bits (202), Expect = 6e-21
Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 20/87 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+AF ++ R + ++P L +++K LG +W +
Sbjct: 93 PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN--------------------NTAA 132
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQ 87
DK+P+ ++A +L++ ++ + Y+ +
Sbjct: 133 DDKQPYEKKAAKLKEKYEKDIAAYRAK 159
Score = 79.1 bits (195), Expect = 6e-20
Identities = 32/96 (33%), Positives = 53/96 (55%), Gaps = 20/96 (20%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+VW++ RR +A + P + N+E+SK LG WK L++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKM--------------------LTE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKN 96
++K PF +EA++L+ +H+ ++PNYKY+ K
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFK 84
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of
chromatin subfamily...; structural DNA-binding protein
BRAF35, DNA-bending; NMR {Mus musculus}
Length = 92
Score = 72.0 bits (177), Expect = 7e-18
Identities = 19/101 (18%), Positives = 43/101 (42%), Gaps = 20/101 (19%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+ ++ + R + ++P L E++K LG W KL
Sbjct: 12 VTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWS--------------------KLQP 51
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSA 101
++K+ +++EAE+ +Q + E Y+ + C+++ +S
Sbjct: 52 AEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCTESGPSSG 92
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A
1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A
Length = 77
Score = 68.0 bits (167), Expect = 2e-16
Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 20/87 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+AF ++ R + ++P L +++K LG +W +
Sbjct: 11 PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN--------------------NTAA 50
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQ 87
DK+P+ ++A +L++ ++ + Y+ +
Sbjct: 51 DDKQPYEKKAAKLKEKYEKDIAAYRAK 77
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 65.9 bits (161), Expect = 1e-15
Identities = 15/96 (15%), Positives = 32/96 (33%), Gaps = 20/96 (20%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
M+A ++ Q R + P + + + LWK LS+
Sbjct: 12 MSASALFVQDHRPQFLIENPKTSLEDATLQIEELWK--------------------TLSE 51
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKN 96
+K + E+A + + + S+ Q + +
Sbjct: 52 EEKLKYEEKATKDLERYNSQMKRAIEQESQMSLKDS 87
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 60.4 bits (147), Expect = 2e-13
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 22/85 (25%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
AFM+W R ++ + P + E++K G +WK L
Sbjct: 8 TTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL---------------------- 45
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
DK + + A + +Q + E NYK
Sbjct: 46 KDKSKWEDAAAKDKQRYHDEMRNYK 70
>3nm9_A HMG-D, high mobility group protein D; DNA bending,
non-sequence-specific, HMG chromosomal protein; HET:
DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A*
1hma_A 1qrv_A*
Length = 73
Score = 58.5 bits (142), Expect = 6e-13
Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 22/85 (25%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A+ +W +AR ++ + P + E++K G LW+ +
Sbjct: 8 LSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM---------------------- 45
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
DK + +A + + + ++
Sbjct: 46 KDKSEWEAKAAKAKDDYDRAVKEFE 70
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 59.0 bits (143), Expect = 1e-12
Identities = 12/101 (11%), Positives = 38/101 (37%), Gaps = 20/101 (19%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A+ ++ + + + Q P+ E+SK + +W L +
Sbjct: 22 VSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWD--------------------GLGE 61
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSA 101
K+ + ++ E ++ + + Y+ + + + +S
Sbjct: 62 EQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYTDSGPSSG 102
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 57.4 bits (139), Expect = 4e-12
Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 22/89 (24%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHN--AELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKL 58
++++M +A+ R + + P + A + K +G W L
Sbjct: 27 LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWN--------------------AL 66
Query: 59 SDSDKKPFIEEAERLRQIHKSEHPNYKYQ 87
SD +KKP+ ++ R ++ E Y +
Sbjct: 67 SDEEKKPYERMSDEDRVRYEREKAEYAQR 95
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein; NMR
{Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A
1lwm_A
Length = 93
Score = 54.2 bits (131), Expect = 5e-11
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
++A+M +A R + ++ P + ++ K LG WK L+
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWK--------------------ALTP 64
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
+K+P+ +A+ ++ ++SE Y
Sbjct: 65 EEKQPYEAKAQADKKRYESEKELYN 89
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 52.0 bits (125), Expect = 5e-10
Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+ + + R A +P + N +L+K L +K +L +
Sbjct: 15 LTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYK--------------------ELPE 54
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
K +I++ +R +Q + ++
Sbjct: 55 KKKMKYIQDFQREKQEFERNLARFR 79
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding,
helix-turn-helix motif, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 173
Score = 50.0 bits (119), Expect = 9e-09
Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 20/87 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+AF ++ R + ++P L +++K LG +W +
Sbjct: 106 PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN--------------------NTAA 145
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQ 87
DK+P+ ++A +L++ ++ + Y+ +
Sbjct: 146 DDKQPYEKKAAKLKEKYEKDIAAYRAK 172
Score = 31.9 bits (72), Expect = 0.032
Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 1 MNAFMVWAQAARRTLANQYP--SLHNAELSKTLGVLWKTL--KVETHYHHVMSPFEDTYT 56
M+++ + Q R ++P S++ +E SK WKT+ K + + + + Y
Sbjct: 20 MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE 79
Query: 57 KLSDSDKKPFIEEAERLRQIHKSEHP 82
+ + P E ++ + + + P
Sbjct: 80 REMKTYIPPKGETKKKFKDPNAPKRP 105
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 45.8 bits (109), Expect = 7e-08
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 22/87 (25%)
Query: 1 MNAFMVWAQAARRTLANQYP--SLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKL 58
M+++ + Q +R ++P S++ +E SK WK +
Sbjct: 12 MSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWK--------------------TM 51
Query: 59 SDSDKKPFIEEAERLRQIHKSEHPNYK 85
S +K F + A+ + ++ E Y
Sbjct: 52 SAKEKGKFEDMAKADKARYEREMKTYI 78
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT
DNA, protein-drug-DNA compl regulation-DNA complex;
HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1
PDB: 1j3x_A
Length = 71
Score = 45.5 bits (108), Expect = 9e-08
Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 22/86 (25%)
Query: 1 MNAFMVWAQAARRTLANQYP--SLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKL 58
M+++ + Q R ++P S++ +E SK WKT+
Sbjct: 6 MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTM-------------------- 45
Query: 59 SDSDKKPFIEEAERLRQIHKSEHPNY 84
S +K F + A+ + ++ E Y
Sbjct: 46 SAKEKGKFEDMAKADKARYEREMKTY 71
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 42.7 bits (101), Expect = 1e-06
Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 22/86 (25%)
Query: 1 MNAFMVWAQAARRTLANQYP--SLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKL 58
M+A+ + Q R + P ++ AE SK WKT+
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTM-------------------- 59
Query: 59 SDSDKKPFIEEAERLRQIHKSEHPNY 84
S +K F E A+ + + E +Y
Sbjct: 60 SGKEKSKFDEMAKADKVRYDREMKDY 85
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group
box domain, helix-turn-helix, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 40.9 bits (95), Expect = 5e-06
Identities = 15/99 (15%), Positives = 34/99 (34%), Gaps = 28/99 (28%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHN-AELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLS 59
F +W + R + + P + A++ K + ++ LS
Sbjct: 10 KTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFR--------------------VLS 49
Query: 60 DSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLG 98
++K + +A K E + + ++RK + G
Sbjct: 50 TEERKVWANKA-------KGETASEGTEAKKRKSGPSSG 81
>3tq6_A Transcription factor A, mitochondrial; transcription,
transcription regulation, mitochondrion; HET: DNA BRU
1PE; 2.45A {Homo sapiens}
Length = 214
Score = 39.7 bits (92), Expect = 8e-05
Identities = 15/96 (15%), Positives = 32/96 (33%), Gaps = 20/96 (20%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+++++ +++ Q P EL + + W+ L D
Sbjct: 14 VSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRE--------------------LPD 53
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKN 96
S KK + + Q++K E +K Q +
Sbjct: 54 SKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSL 89
Score = 29.7 bits (66), Expect = 0.18
Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 24/85 (28%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+A+ V+ + + E KT+ WK LSD
Sbjct: 119 RSAYNVYVAERFQ----EAKGDSPQEKLKTVKENWK--------------------NLSD 154
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
S+K+ +I+ A+ + +E +++
Sbjct: 155 SEKELYIQHAKEDETRYHNEMKSWE 179
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group,
transcription, LSP1, mitochon transcription-DNA complex;
HET: DNA; 2.50A {Homo sapiens}
Length = 238
Score = 39.8 bits (92), Expect = 8e-05
Identities = 15/96 (15%), Positives = 32/96 (33%), Gaps = 20/96 (20%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+++++ +++ Q P EL + + W+ L D
Sbjct: 46 VSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRE--------------------LPD 85
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKN 96
S KK + + Q++K E +K Q +
Sbjct: 86 SKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSL 121
Score = 32.5 bits (73), Expect = 0.029
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 24/85 (28%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+A+ V+ + P E KT+ WK LSD
Sbjct: 151 RSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWK--------------------NLSD 186
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
S+K+ +I+ A+ + +E +++
Sbjct: 187 SEKELYIQHAKEDETRYHNEMKSWE 211
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 36.9 bits (86), Expect = 1e-04
Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 24/84 (28%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+A+ V+ + P E KT+ WK LSD
Sbjct: 7 RSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWK--------------------NLSD 42
Query: 61 SDKKPFIEEAERLRQIHKSEHPNY 84
S+K+ +I+ A+ + +E ++
Sbjct: 43 SEKELYIQHAKEDETRYHNEMKSW 66
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 36.8 bits (84), Expect = 0.001
Identities = 13/85 (15%), Positives = 25/85 (29%), Gaps = 22/85 (25%)
Query: 28 SKTLGVLWKTLKVETHYHHVMSPFEDTYTK-LSDSDKKPFI-----------EEAERLRQ 75
+ L ++W + VM + L + K + E
Sbjct: 389 TILLSLIWFDVIKSD----VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444
Query: 76 IHKS--EHPNYKYQPRRRKCSKNLG 98
+H+S +H Y + S +L
Sbjct: 445 LHRSIVDH----YNIPKTFDSDDLI 465
Score = 32.1 bits (72), Expect = 0.043
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 4/67 (5%)
Query: 41 ETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTS 100
+Y +MSP + + S + +IE+ +RL + KY R + L +
Sbjct: 88 RINYKFLMSPIKTEQRQPSM-MTRMYIEQRDRL---YNDNQVFAKYNVSRLQPYLKLRQA 143
Query: 101 ANNLSKS 107
L +
Sbjct: 144 LLELRPA 150
Score = 26.7 bits (58), Expect = 2.7
Identities = 22/120 (18%), Positives = 32/120 (26%), Gaps = 32/120 (26%)
Query: 7 WAQAARRTL--ANQYP-SL------HNAELSKTLGVLWKTLKVETHYHHVMSPF-EDTYT 56
QA R L + Y L NA+ + K L + T + V T T
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL-LTTRFKQVTDFLSAATTT 287
Query: 57 KLS-DSDKKPFIE-EAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSL 114
+S D E + L K L +L + + N
Sbjct: 288 HISLDHHSMTLTPDEVKSL-------------------LLKYLDCRPQDLPREVLTTNPR 328
Score = 26.0 bits (56), Expect = 4.7
Identities = 10/66 (15%), Positives = 18/66 (27%), Gaps = 18/66 (27%)
Query: 43 HYHHVMSPFEDTYTKLSDSD-----KKPFIEE------AERLRQIHKSEH-------PNY 84
H+HH FE + D + F++ + + I E +
Sbjct: 1 HHHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA 60
Query: 85 KYQPRR 90
R
Sbjct: 61 VSGTLR 66
>1v63_A Nucleolar transcription factor 1; DNA binding, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, DNA binding protein; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 101
Score = 32.6 bits (74), Expect = 0.009
Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 22/85 (25%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MN + ++Q + L E +G W+ ++S
Sbjct: 13 MNGYQKFSQELLSNGELNHLPL--KERMVEIGSRWQ--------------------RISQ 50
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
S K+ + + AE ++ +K +
Sbjct: 51 SQKEHYKKLAEEQQRQYKVHLDLWV 75
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics,
riken structural genomics/proteomics initiative, RSGI;
NMR {Mus musculus} SCOP: a.21.1.1
Length = 108
Score = 28.4 bits (63), Expect = 0.31
Identities = 12/110 (10%), Positives = 32/110 (29%), Gaps = 24/110 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
N++ ++ + + + E WK LS
Sbjct: 22 PNSYSLYCAELMANM----KDVPSTERMVLCSQQWK--------------------LLSQ 57
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSS 110
+K + ++ ++ ++ ++ E + + + LG SS
Sbjct: 58 KEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNISGPSS 107
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 29.2 bits (65), Expect = 0.43
Identities = 13/86 (15%), Positives = 23/86 (26%), Gaps = 9/86 (10%)
Query: 3 AFMVWAQAARRTLANQYPSL-----HNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTK 57
A VW +A S+ +N L + + K + + + +T
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINNP---VNLTIHFGGEKGKRIRENYSAMIFETIVD 1698
Query: 58 LSDSDKKPFIEEAERLRQIHKSEHPN 83
+K F E E
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTF-RSEK 1723
>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer
aging, hydrolase; HET: FLC; 2.00A {Sulfolobus
acidocaldarius} PDB: 3crw_1*
Length = 551
Score = 28.1 bits (62), Expect = 1.0
Identities = 7/74 (9%), Positives = 14/74 (18%), Gaps = 3/74 (4%)
Query: 35 WKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCS 94
TL + V + + + + + KY R
Sbjct: 322 SGTLPPREYMEKVWGIKRNMLYLDVER---EIQKRVSGSYECYIGVDVTSKYDMRSDNMW 378
Query: 95 KNLGTSANNLSKST 108
K +
Sbjct: 379 KRYADYLLKIYFQA 392
>3ugc_A Tyrosine-protein kinase JAK2; small molecule inhibitor, ATP
binding, transferase-transfera inhibitor complex; HET:
046; 1.34A {} PDB: 3krr_A* 3lpb_A* 4aqc_A* 3q32_A*
3rvg_A* 3tjc_A* 3tjd_A* 2b7a_A* 3fup_A* 3e64_A* 3e62_A*
3e63_A* 2xa4_A* 3iok_A* 3io7_A* 3kck_A* 3jy9_A*
Length = 295
Score = 25.7 bits (57), Expect = 4.6
Identities = 10/48 (20%), Positives = 13/48 (27%), Gaps = 20/48 (41%)
Query: 36 KTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPN 83
K L+ T D F E E L+ + H N
Sbjct: 45 KKLQHST-----EEHLRD------------FEREIEILKSLQ---HDN 72
>2x6h_A GH13170P, VPS34, phosphotidylinositol 3 kinase 59F; transferase;
2.90A {Drosophila melanogaster} PDB: 2x6f_A 2x6i_A*
2x6j_A* 2x6k_A*
Length = 696
Score = 26.0 bits (56), Expect = 5.1
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 2/49 (4%)
Query: 45 HHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKC 93
HH ++ + +SD D KP ++L I P Y +
Sbjct: 18 HHRLA--RSERSGISDRDAKPTASIRDQLHTIVYRYPPTYVLSSEEQDL 64
>2w1i_A JAK2; chromosomal rearrangement, nucleotide-binding,
tyrosine-protein kinase, proto-oncogene, phosphoprotein,
disease mutation, SH2 domain; HET: PTR L0I; 2.60A {Homo
sapiens}
Length = 326
Score = 25.4 bits (56), Expect = 6.0
Identities = 10/48 (20%), Positives = 13/48 (27%), Gaps = 20/48 (41%)
Query: 36 KTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPN 83
K L+ T D F E E L+ + H N
Sbjct: 76 KKLQHST-----EEHLRD------------FEREIEILKSLQ---HDN 103
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 25.5 bits (55), Expect = 6.9
Identities = 11/56 (19%), Positives = 14/56 (25%), Gaps = 14/56 (25%)
Query: 18 QYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKK-------PF 66
Y K V ++S E + TK KK PF
Sbjct: 123 NYS-----SEVKENSVDSDDKAKVPPLIRIVSGLELSDTK--QKGKKFLVIAYEPF 171
>1mqb_A Ephrin type-A receptor 2; tyrosine protein kinase, transferase;
HET: ANP; 2.30A {Homo sapiens} SCOP: d.144.1.7
Length = 333
Score = 25.0 bits (55), Expect = 8.3
Identities = 10/48 (20%), Positives = 15/48 (31%), Gaps = 19/48 (39%)
Query: 36 KTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPN 83
KTLK ++ + F+ EA + Q H N
Sbjct: 79 KTLKAGY----------------TEKQRVDFLGEAGIMGQFS---HHN 107
>3r8r_A Transaldolase; pentose phosphate pathway, schiff bases; 1.90A
{Bacillus subtilis}
Length = 212
Score = 24.8 bits (55), Expect = 8.4
Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 12/42 (28%)
Query: 49 SPFEDTYTKLSDSDKKPF------------IEEAERLRQIHK 78
F D +++D K IEE + L +I
Sbjct: 38 VSFHDRLREITDVVKGSVSAEVISLKAEEMIEEGKELAKIAP 79
>3pls_A Macrophage-stimulating protein receptor; protein kinase, CIS
autophosphorylation conformation, recept tyrosine
kinase, AMP-PNP, unphosphorylated; HET: ANP; 2.24A
{Homo sapiens}
Length = 298
Score = 24.9 bits (55), Expect = 8.9
Identities = 9/48 (18%), Positives = 15/48 (31%), Gaps = 19/48 (39%)
Query: 36 KTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPN 83
K+L T + F+ E +R ++ HPN
Sbjct: 55 KSLSRIT----------------EMQQVEAFLREGLLMRGLN---HPN 83
>3kul_A Ephrin type-A receptor 8; ATP-binding, kinase, nucleotide-binding,
transfera phosphorylation, transmembrane,
tyrosine-protein kinase; HET: PTR; 2.15A {Homo sapiens}
Length = 325
Score = 25.0 bits (55), Expect = 9.1
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 19/48 (39%)
Query: 36 KTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPN 83
K LK ++ ++ F+ EA + Q HPN
Sbjct: 83 KALKAGY----------------TERQRRDFLSEASIMGQFD---HPN 111
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.313 0.126 0.361
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,895,167
Number of extensions: 93931
Number of successful extensions: 236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 59
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (23.9 bits)