RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15633
(129 letters)
>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 = 143 bits (363), Expect = 3e-46
Identities = 54/85 (63%), Positives = 70/85 (82%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKR 79
+ D +KRPMNAF+VWSR QRRK+A +NP+M NSEISK+LG +WK+LTE EK P+ EA++
Sbjct: 1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60
Query: 80 LRAMHMKDHPDYKYRPRRKPKTLRK 104
L+AMH + +P+YKYRPRRK K L K
Sbjct: 61 LQAMHREKYPNYKYRPRRKAKMLPK 85
>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 = 143 bits (362), Expect = 3e-46
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
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation,
transcription-DNA CO; HET: DNA; 2.40A {Mus musculus}
Length = 79
Score = 141 bits (359), Expect = 1e-45
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
>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 = 140 bits (356), Expect = 4e-45
Identities = 46/77 (59%), Positives = 57/77 (74%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
HIKRPMNAFMVW++ +RRKI Q P MHNS ISK LG+ WK +T EK+PY +E RL
Sbjct: 3 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLS 62
Query: 82 AMHMKDHPDYKYRPRRK 98
H++ +PDYKY+PR K
Sbjct: 63 KQHLEKYPDYKYKPRPK 79
>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 = 140 bits (355), Expect = 5e-45
Identities = 25/77 (32%), Positives = 41/77 (53%)
Query: 21 DDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRL 80
+RPMNAF+++ + R + Q++P++ N +K L W +L EK+ Y D AK
Sbjct: 5 SSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEY 64
Query: 81 RAMHMKDHPDYKYRPRR 97
+ MK +P Y+ P
Sbjct: 65 KDAFMKANPGYRSGPSS 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 = 139 bits (353), Expect = 8e-45
Identities = 47/79 (59%), Positives = 65/79 (82%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
I+RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK LT EKRP+++EA+RLR
Sbjct: 5 SRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 64
Query: 82 AMHMKDHPDYKYRPRRKPK 100
HM+DHP+YKYRPRR+ +
Sbjct: 65 VQHMQDHPNYKYRPRRRKQ 83
>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 = 139 bits (353), Expect = 2e-44
Identities = 49/84 (58%), Positives = 64/84 (76%)
Query: 15 SPEKKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYI 74
K H+KRPMNAFMVW++ RRK+A P +HN+E+SK LG W+LL E+EKRP++
Sbjct: 21 FQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFV 80
Query: 75 DEAKRLRAMHMKDHPDYKYRPRRK 98
+EA+RLR H KDHPDYKY+PRR+
Sbjct: 81 EEAERLRVQHKKDHPDYKYQPRRR 104
>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 = 138 bits (349), Expect = 3e-44
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
>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 = 136 bits (346), Expect = 1e-43
Identities = 25/82 (30%), Positives = 46/82 (56%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
HIK+P+NAFM++ + R + ++ ++ I++ LG W L+ E+ Y + A++ R
Sbjct: 2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQ 61
Query: 83 MHMKDHPDYKYRPRRKPKTLRK 104
+HM+ +P + R K RK
Sbjct: 62 LHMQLYPGWSARDNYGKKKKRK 83
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 132 bits (334), Expect = 6e-42
Identities = 42/70 (60%), Positives = 58/70 (82%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
I+RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK LT EKRP+++EA+RLR
Sbjct: 2 SIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 61
Query: 83 MHMKDHPDYK 92
HM+DHP+YK
Sbjct: 62 QHMQDHPNYK 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 = 129 bits (326), Expect = 1e-40
Identities = 28/84 (33%), Positives = 42/84 (50%)
Query: 7 GTYPNTLLSPEKKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLT 66
G+ ++ + + KRPMNAFM++++ R + Q P N IS LG WK +
Sbjct: 1 GSSGSSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMK 60
Query: 67 ENEKRPYIDEAKRLRAMHMKDHPD 90
E+R Y EAK L + +PD
Sbjct: 61 NEERRMYTLEAKALAEEQKRLNPD 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 = 113 bits (284), Expect = 4e-34
Identities = 19/75 (25%), Positives = 38/75 (50%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEA 77
K + KRP++A ++S +RR++ ++ P++ SE+++ L W L+E +K Y
Sbjct: 15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKARE 74
Query: 78 KRLRAMHMKDHPDYK 92
L+A +
Sbjct: 75 AALKAQSERKSGPSS 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 = 109 bits (275), Expect = 4e-32
Identities = 23/94 (24%), Positives = 45/94 (47%)
Query: 1 MCENSGGTYPNTLLSPEKKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGA 60
+ Y + K + KRP +AF ++ R KI ++P + +++K+LG
Sbjct: 66 REKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGE 125
Query: 61 EWKLLTENEKRPYIDEAKRLRAMHMKDHPDYKYR 94
W ++K+PY +A +L+ + KD Y+ +
Sbjct: 126 MWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 159
Score = 109 bits (274), Expect = 6e-32
Identities = 49/94 (52%), Positives = 66/94 (70%)
Query: 20 IDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKR 79
+ D +KRPMNAF+VWSR QRRK+A +NP+M NSEISK+LG +WK+LTE EK P+ EA++
Sbjct: 1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60
Query: 80 LRAMHMKDHPDYKYRPRRKPKTLRKDGYTYPAVS 113
L+AMH + +P+YKYR K + S
Sbjct: 61 LQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPS 94
>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 = 100 bits (252), Expect = 3e-29
Identities = 24/84 (28%), Positives = 42/84 (50%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEA 77
K P+ ++ + +R +I +P + EI+K LGAEW L EK+ Y+DEA
Sbjct: 2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEA 61
Query: 78 KRLRAMHMKDHPDYKYRPRRKPKT 101
++ + ++K+ Y+ K T
Sbjct: 62 EKEKQQYLKELWAYQQSEAYKVCT 85
>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 = 92.7 bits (231), Expect = 3e-26
Identities = 21/73 (28%), Positives = 41/73 (56%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
+ KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+
Sbjct: 5 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK 64
Query: 82 AMHMKDHPDYKYR 94
+ KD Y+ +
Sbjct: 65 EKYEKDIAAYRAK 77
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 90.6 bits (225), Expect = 3e-25
Identities = 17/78 (21%), Positives = 35/78 (44%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
IK+PM+A ++ + R + +NPK + + ++ WK L+E EK Y ++A +
Sbjct: 7 GIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLE 66
Query: 83 MHMKDHPDYKYRPRRKPK 100
+ + +
Sbjct: 67 RYNSQMKRAIEQESQMSL 84
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 83.1 bits (206), Expect = 1e-22
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KR AFM+W R I ++NP + +EI+K+ G WK L +K + D A + + +
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRY 62
Query: 85 MKDHPDYK 92
+ +YK
Sbjct: 63 HDEMRNYK 70
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 82.8 bits (205), Expect = 4e-22
Identities = 22/79 (27%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHN--SEISKRLGAEWKLLTENEKRPYID 75
KK + KR ++++M +++ +R +I +NP++ + I K +GA W L++ EK+PY
Sbjct: 17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYER 76
Query: 76 EAKRLRAMHMKDHPDYKYR 94
+ R + ++ +Y R
Sbjct: 77 MSDEDRVRYEREKAEYAQR 95
>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 = 80.4 bits (199), Expect = 2e-21
Identities = 17/71 (23%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
D KRP++A+ +W R I ++NP + +E++KR G W+ + +K + +A + +
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAK 59
Query: 82 AMHMKDHPDYK 92
+ + +++
Sbjct: 60 DDYDRAVKEFE 70
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 80.9 bits (200), Expect = 3e-21
Identities = 18/80 (22%), Positives = 38/80 (47%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
+ ++P++A+ ++ R + I NP E+SK + + W L E +K+ Y + + +
Sbjct: 16 NEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAK 75
Query: 82 AMHMKDHPDYKYRPRRKPKT 101
++K Y+ K T
Sbjct: 76 KEYLKQLAAYRASLVSKSYT 95
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 78.6 bits (194), Expect = 2e-20
Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 7/90 (7%)
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 KRLRAMHMKD-------HPDYKYRPRRKPK 100
+R + ++ HPD ++
Sbjct: 65 QREKQEFERNLARFREDHPDLIQNAKKLEH 94
>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 = 75.8 bits (187), Expect = 2e-19
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEA 77
KK + KR ++A+M ++ R + +NP + ++ K+LG +WK LT EK+PY +A
Sbjct: 15 KKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKA 74
Query: 78 KRLRAMHMKDHPDYK 92
+ + + + Y
Sbjct: 75 QADKKRYESEKELYN 89
>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 = 71.6 bits (175), Expect = 6e-17
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
KRP +AF ++ R KI ++P + +++K+LG W ++K+PY +A +L+
Sbjct: 101 APKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 160
Query: 83 MHMKDHPDYKYR 94
+ KD Y+ +
Sbjct: 161 KYEKDIAAYRAK 172
Score = 53.5 bits (128), Expect = 5e-10
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNP--KMHNSEISKRLGAEWKLLTENEKRPYID 75
K + M+++ + + R + + +P ++ SE SK+ WK ++ EK + D
Sbjct: 10 KGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFED 69
Query: 76 EAKRLRAMHMKDHPDYKYRPRRKP 99
AK +A + ++ Y
Sbjct: 70 MAKADKARYEREMKTYIPPKGETK 93
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 68.1 bits (167), Expect = 2e-16
Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNP--KMHNSEISKRLGAEWKLLTENEKRPYID 75
K + M+++ + + R + + +P ++ SE SK+ WK ++ EK + D
Sbjct: 2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFED 61
Query: 76 EAKRLRAMHMKDHPDYK 92
AK +A + ++ Y
Sbjct: 62 MAKADKARYEREMKTYI 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 = 67.0 bits (164), Expect = 3e-16
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNP--KMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
+ M+++ + + R + + +P ++ SE SK+ WK ++ EK + D AK +A
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62
Query: 83 MHMKDHPDY 91
+ ++ Y
Sbjct: 63 RYEREMKTY 71
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 64.3 bits (157), Expect = 5e-15
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNS--EISKRLGAEWKLLTENEKRPYID 75
K K M+A+ + + R + + NP++ + E SK+ WK ++ EK + +
Sbjct: 10 KGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDE 69
Query: 76 EAKRLRAMHMKDHPDY 91
AK + + ++ DY
Sbjct: 70 MAKADKVRYDREMKDY 85
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription
regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo
sapiens}
Length = 214
Score = 60.9 bits (147), Expect = 1e-12
Identities = 14/76 (18%), Positives = 38/76 (50%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
K+P+++++ +S+ Q NP +E+ +R+ W+ L +++K+ Y D + ++
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVY 70
Query: 85 MKDHPDYKYRPRRKPK 100
++ +K +
Sbjct: 71 KEEISRFKEQLTPSQI 86
Score = 49.4 bits (117), Expect = 2e-08
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
KRP +A+ V+ + ++ D+P+ E K + WK L+++EK YI AK
Sbjct: 113 GKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDE 168
Query: 82 AMHMKDHPDYK 92
+ + ++
Sbjct: 169 TRYHNEMKSWE 179
>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 = 57.5 bits (138), Expect = 3e-12
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHN-SEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
RP F +W R I DNP + ++I K +++L+ E++ + ++AK
Sbjct: 5 SSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGET 64
Query: 82 AMHMKDHPDYK 92
A + K
Sbjct: 65 ASEGTEAKKRK 75
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 56.9 bits (138), Expect = 3e-12
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
KRP +A+ V+ + ++ D+P+ E K + WK L+++EK YI AK +
Sbjct: 4 KRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59
Query: 85 MKDHPDY 91
+ +
Sbjct: 60 HNEMKSW 66
>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 = 60.2 bits (145), Expect = 4e-12
Identities = 14/82 (17%), Positives = 39/82 (47%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEA 77
+ K+P+++++ +S+ Q NP +E+ +R+ W+ L +++K+ Y D
Sbjct: 36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAY 95
Query: 78 KRLRAMHMKDHPDYKYRPRRKP 99
+ ++ ++ +K +
Sbjct: 96 RAEWQVYKEEISRFKEQLTPSQ 117
Score = 53.3 bits (127), Expect = 1e-09
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 22 DHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
KRP +A+ V+ + ++ D+P+ E K + WK L+++EK YI AK
Sbjct: 145 GKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDE 200
Query: 82 AMHMKDHPDYK 92
+ + ++
Sbjct: 201 TRYHNEMKSWE 211
>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 = 48.4 bits (115), Expect = 1e-08
Identities = 11/68 (16%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAMH 84
K PMN + +S+ ++ + E +G+ W+ +++++K Y A+ + +
Sbjct: 10 KPPMNGYQKFSQELLSNGELNHLPL--KERMVEIGSRWQRISQSQKEHYKKLAEEQQRQY 67
Query: 85 MKDHPDYK 92
+
Sbjct: 68 KVHLDLWV 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 = 45.0 bits (106), Expect = 3e-07
Identities = 14/101 (13%), Positives = 36/101 (35%), Gaps = 6/101 (5%)
Query: 7 GTYPNTLLSPEKKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLT 66
G+ ++ +K K P N++ ++ + E +WKLL+
Sbjct: 1 GSSGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPST----ERMVLCSQQWKLLS 56
Query: 67 ENEKRPYIDEAKRLRAMHMKDHPDYK--YRPRRKPKTLRKD 105
+ EK Y + + + + + + + + L ++
Sbjct: 57 QKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEE 97
>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 = 35.0 bits (80), Expect = 0.005
Identities = 30/146 (20%), Positives = 47/146 (32%), Gaps = 58/146 (39%)
Query: 18 KKIDDHIKRPMNAFMVWSRLQRRKIAQDNPK---MHNSEISKRLGAEWKLLTENEKRPYI 74
+ D+H K +S L I +NP +H G + K + EN Y
Sbjct: 1647 NRADNHFKDTYG----FSIL---DIVINNPVNLTIHFG------GEKGKRIREN----YS 1689
Query: 75 DEAKRLRAMHMKDHPDYKYRPRRKPKTLRKD--GYTY--------------PA---VSV- 114
AM + D K + + K + + YT+ PA +
Sbjct: 1690 -------AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA 1742
Query: 115 PYQ------SVPVDALRAG-----YA 129
++ +P DA AG YA
Sbjct: 1743 AFEDLKSKGLIPADATFAGHSLGEYA 1768
Score = 33.1 bits (75), Expect = 0.021
Identities = 26/135 (19%), Positives = 41/135 (30%), Gaps = 42/135 (31%)
Query: 8 TYPNTLLSPEKKIDDHIKR------PMNAFMVWSRLQR----RKIAQDNPKMHNSE---I 54
YPNT L P ++D ++ PM + S L + + + N + + I
Sbjct: 313 AYPNTSLPPS-ILEDSLENNEGVPSPM--LSI-SNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 55 SKRLGAEWKLLTENEKRPYI---------DEAKRLRAMHMKDHPDYKYRP--RRKPKTLR 103
S L N + + LR D P RK K
Sbjct: 369 S---------LV-NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKF-- 416
Query: 104 KDGYTYPAVSVPYQS 118
+ V+ P+ S
Sbjct: 417 --SNRFLPVASPFHS 429
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 93
Score = 32.9 bits (74), Expect = 0.008
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 25 KRPMNAFMVWSRLQRRKI-AQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAM 83
K NA+ + + + ++ + P ++ ++W LL E EK Y + A+ RA
Sbjct: 12 KASRNAYYFFVQEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAA 71
Query: 84 HMKD-HPDYKYRPRRKP 99
KD P K +P
Sbjct: 72 QGKDPGPSEKQKPVFTS 88
>3chj_A Alpha-14 giardin; calcium-binding, annexin, metal binding protein;
1.60A {Giardia lamblia} PDB: 3chk_A 3chl_A
Length = 337
Score = 27.7 bits (61), Expect = 1.1
Identities = 8/64 (12%), Positives = 17/64 (26%), Gaps = 5/64 (7%)
Query: 34 WSRLQRRKIAQDNPKMHNSEISKRL-----GAEWKLLTENEKRPYIDEAKRLRAMHMKDH 88
+ Q R + + + + + L L+ K + +R
Sbjct: 39 YPPNQLRNMQRTFQAITGTFLDAFLKKHLSKDFESLVLMLYKPRAQLLCELIRGATKGAG 98
Query: 89 PDYK 92
D K
Sbjct: 99 TDEK 102
>3s6b_A Methionine aminopeptidase; malaria, proteolysis, "PITA bread" fold,
structur genomics, structural genomics consortium, SGC,
hydrolase; 1.95A {Plasmodium falciparum}
Length = 368
Score = 26.9 bits (60), Expect = 2.1
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 6/54 (11%)
Query: 14 LSPEKKIDDHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSE-ISK-----RLGAE 61
LS + HI+RP A + + + ++N E I + LG +
Sbjct: 68 LSKINHVPSHIERPDYAISSIPESELIYKRKSDIYVNNEEEIQRIREACILGRK 121
>3nuq_A Protein SSM1, putative nucleotide phosphatase; suppresses the
6-AU sensitivity of transcription elongation II; 1.70A
{Saccharomyces cerevisiae} PDB: 3onn_A 3opx_A*
Length = 282
Score = 25.9 bits (56), Expect = 4.2
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 11 NTLLSPEKKIDDHIKRPMNAFMV 33
N L +I D +++ + F
Sbjct: 66 NCLYKSSTRIHDLMQQSILRFFQ 88
>1tx2_A DHPS, dihydropteroate synthase; folate biosynthesis, pterine, MA
transferase; HET: 680; 1.83A {Bacillus anthracis} SCOP:
c.1.21.1 PDB: 1tww_A* 1twz_A* 1tx0_A* 1tws_A* 3h21_A*
3h22_A* 3h23_A* 3h24_A* 3h26_A* 3h2a_A* 3h2c_A* 3h2e_A*
3h2f_A* 3h2m_A* 3h2n_A* 3h2o_A* 3tya_A* 3tyb_A* 3tyc_A*
3tyd_A* ...
Length = 297
Score = 25.9 bits (58), Expect = 4.4
Identities = 4/9 (44%), Positives = 7/9 (77%)
Query: 83 MHMKDHPDY 91
MH +D+ +Y
Sbjct: 165 MHNRDNMNY 173
>3ckc_A SUSD; TPR repeat, carbohydrate binding, starch binding, sugar BIND
protein; HET: MES; 1.50A {Bacteroides thetaiotaomicron}
SCOP: a.118.8.6 PDB: 3ck8_A* 3ck9_A* 3ckb_A* 3ck7_A*
Length = 527
Score = 25.6 bits (56), Expect = 5.8
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 65 LTENEKRPYIDEAKRLRAMHM 85
+T+ E E + LRA+H
Sbjct: 119 MTDAETLRQRAEIRFLRALHY 139
>2ii2_A Alpha-11 giardin; helix-turn-helix, metal binding protein; 1.10A
{Giardia intestinalis} PDB: 2iic_A
Length = 310
Score = 25.6 bits (56), Expect = 6.1
Identities = 6/30 (20%), Positives = 10/30 (33%)
Query: 34 WSRLQRRKIAQDNPKMHNSEISKRLGAEWK 63
WS +R+++ E L K
Sbjct: 32 WSAEERKELRTQFQDTTGLEFIAFLKKCIK 61
>2b3h_A Methionine aminopeptidase 1; hydrolase, metalloprotease, pitab;
HET: GOL; 1.10A {Homo sapiens} PDB: 2b3k_A 2b3l_A
2gz5_A* 2nq6_A* 2nq7_A* 2g6p_A*
Length = 329
Score = 25.3 bits (56), Expect = 7.0
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 10 PNTLLSPEKKIDDHIKRP--MNAFMVWSRLQRRKIAQDNPKMHNSE-ISK-----RLGAE 61
P+ L P + + +I+RP + + S ++ K+ +SE I RL E
Sbjct: 34 PHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLARE 93
>2dbq_A Glyoxylate reductase; D-3-phosphoglycerate dehydrogenase, ST
genomics, NPPSFA; HET: NAP; 1.70A {Pyrococcus
horikoshii} PDB: 2dbr_A* 2dbz_A*
Length = 334
Score = 25.2 bits (56), Expect = 7.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 77 AKRLRAMHMKDHPDYKYRPRRKPKTLRKDGYTY 109
AKR + +M+ Y Y RK + R+ +
Sbjct: 166 AKRAKGFNMRIL--Y-YSRTRKEEVERELNAEF 195
>4evf_A Alpha-1 giardin, giardin subunit alpha-1; annexin,
calcium-binding protein, membrane-binding protein,
binding protein; 1.90A {Giardia intestinalis} PDB:
4evh_A
Length = 295
Score = 25.2 bits (55), Expect = 8.1
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 34 WSRLQRRKIAQDNPKMHNSEISKRLGAEWK 63
+S R KIA+ + E+ + K
Sbjct: 30 YSAESREKIAKAYVASYGKELPDDIKKALK 59
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
0.317 0.133 0.406
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,087,754
Number of extensions: 112958
Number of successful extensions: 390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 375
Number of HSP's successfully gapped: 63
Length of query: 129
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,384,350
Effective search space: 201680100
Effective search space used: 201680100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.0 bits)