Psyllid ID: psy15634

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDKGLDITNNICREKMTKM
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccHHHHHHcHHHHHHHHHHccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccHHHHHcHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHccc
Coil and Loop (DISEMBL)
mslsshhqhsyfsmppgldtshlnlgeqhikrpmnaFMVWSRIQRRKIaldnpkmhnsiifnchimhflcpqkielkskrDIHVEACRksnlfdrdkglditNNICREKMTKM
Flexible Loop (DISEMBL)
MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACrksnlfdrdkglditnnicrekmtkm
Low Complexity Region (SEG)
MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDKGLDITNNICREKMTKM
Disordered region (IsUnstruct)
***************************QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDKGLDITNNIC*******
Disordered Region (DISOPRED)
**********************************NAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACR***********DITNNICREKMT**
Disordered Region (DISEMBL)
***********FSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDKGLDITNNICREKMTKM
Disordered Region (DISPRO)
*****************************IKRPMNAFMVWSRI********N**MHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDKGLDITNNICREK****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDKGLDITNNICREKMTKM
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	113	2.2.26 [Sep-21-2011]
Q7SZS1	239	Transcription factor Sox-	yes	N/A	0.283	0.133	0.875	1e-10
Q24533	382	SOX domain-containing pro	no	N/A	0.300	0.089	0.852	2e-10
P53784	375	Transcription factor SOX-	yes	N/A	0.300	0.090	0.764	5e-10
P43267	231	Protein SOX-15 OS=Mus mus	no	N/A	0.530	0.259	0.441	7e-10
Q6TC28	219	Sex-determining region Y	N/A	N/A	0.309	0.159	0.742	8e-10
Q6TC27	219	Sex-determining region Y	N/A	N/A	0.309	0.159	0.742	8e-10
P41225	446	Transcription factor SOX-	yes	N/A	0.300	0.076	0.764	1e-09
P55863	309	Transcription factor Sox-	N/A	N/A	0.398	0.145	0.622	1e-09
Q6RVD7	245	Transcription factor Sox-	no	N/A	0.283	0.130	0.812	2e-09
Q9W7R6	240	Transcription factor SOX-	yes	N/A	0.283	0.133	0.843	2e-09

>sp|Q7SZS1|SX21A_DANRE Transcription factor Sox-21-A OS=Danio rerio GN=sox21a PE=2 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/32 (87%), Positives = 30/32 (93%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          H+KRPMNAFMVWSR QRRK+ALDNPKMHNS I
Sbjct: 7  HVKRPMNAFMVWSRAQRRKMALDNPKMHNSEI 38

May function as a switch in neuronal development (By similarity). Acts as a negative regulator of transcription. Plays a role in dorsoventral patterning of the embryo.
Danio rerio (taxid: 7955)

>sp|Q24533|DICH_DROME SOX domain-containing protein dichaete OS=Drosophila melanogaster GN=D PE=2 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/34 (85%), Positives = 31/34 (91%)

Query: 27  EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           E HIKRPMNAFMVWSR+QRR+IA DNPKMHNS I
Sbjct: 139 EGHIKRPMNAFMVWSRLQRRQIAKDNPKMHNSEI 172

Essential for segmentation and CNS development. May modulate the actions of other transcription factors, including gap and pair-rule proteins.

Drosophila melanogaster (taxid: 7227)

>sp|P53784|SOX3_MOUSE Transcription factor SOX-3 OS=Mus musculus GN=Sox3 PE=1 SV=2

 Score = 63.2 bits (152), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 26/34 (76%), Positives = 30/34 (88%)

Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +  +KRPMNAFMVWSR QRRK+AL+NPKMHNS I
Sbjct: 66 QDRVKRPMNAFMVWSRGQRRKMALENPKMHNSEI 99

Transcription factor required during the formation of the hypothalamo-pituitary axis. May function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation. Required also within the pharyngeal epithelia for craniofacial morphogenesis. Controls a genetic switch in male development. Is necessary for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells.

Mus musculus (taxid: 10090)

>sp|P43267|SOX15_MOUSE Protein SOX-15 OS=Mus musculus GN=Sox15 PE=2 SV=3

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 43/77 (55%), Gaps = 17/77 (22%)

Query: 1  MSLSSHHQHSYFSMPPGLDTSHLNLGEQH-----------------IKRPMNAFMVWSRI 43
          M+L+S  Q   +S+ P   T+ L LG Q                  +KRPMNAFMVWS +
Sbjct: 1  MALTSSSQAETWSLHPRASTASLPLGPQEQEAGGSPGASGGLPLEKVKRPMNAFMVWSSV 60

Query: 44 QRRKIALDNPKMHNSII 60
          QRR++A  NPKMHNS I
Sbjct: 61 QRRQMAQQNPKMHNSEI 77

Mus musculus (taxid: 10090)

>sp|Q6TC28|SRY_LUTLU Sex-determining region Y protein OS=Lutra lutra GN=SRY PE=3 SV=1

 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 26/35 (74%), Positives = 31/35 (88%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G+ HI+RPMNAFMVWSR QRRK+AL+NP+M NS I
Sbjct: 50 GQSHIRRPMNAFMVWSRDQRRKVALENPQMQNSEI 84

Transcriptional regulator that controls a genetic switch in male development. It is necessary and sufficient for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells. In male adult brain involved in the maintenance of motor functions of dopaminergic neurons. Involved in different aspects of gene regulation including promoter activation or repression. Promotes DNA bending. SRY HMG box recognizes DNA by partial intercalation in the minor groove. Also involved in pre-mRNA splicing. Binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'.

Lutra lutra (taxid: 9657)

>sp|Q6TC27|SRY_ENHLU Sex-determining region Y protein OS=Enhydra lutris GN=SRY PE=3 SV=1

 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 26/35 (74%), Positives = 31/35 (88%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G+ HI+RPMNAFMVWSR QRRK+AL+NP+M NS I
Sbjct: 50 GQSHIRRPMNAFMVWSRDQRRKVALENPQMQNSEI 84

Transcriptional regulator that controls a genetic switch in male development. It is necessary and sufficient for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells. In male adult brain involved in the maintenance of motor functions of dopaminergic neurons. Involved in different aspects of gene regulation including promoter activation or repression. Promotes DNA bending. SRY HMG box recognizes DNA by partial intercalation in the minor groove. Also involved in pre-mRNA splicing. Binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'.

Enhydra lutris (taxid: 34882)

>sp|P41225|SOX3_HUMAN Transcription factor SOX-3 OS=Homo sapiens GN=SOX3 PE=1 SV=2

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/34 (76%), Positives = 30/34 (88%)

Query: 27  EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           +  +KRPMNAFMVWSR QRRK+AL+NPKMHNS I
Sbjct: 136 QDRVKRPMNAFMVWSRGQRRKMALENPKMHNSEI 169

Transcription factor required during the formation of the hypothalamo-pituitary axis. May function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation. Required also within the pharyngeal epithelia for craniofacial morphogenesis. Controls a genetic switch in male development. Is necessary for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells.

Homo sapiens (taxid: 9606)

>sp|P55863|SOX3A_XENLA Transcription factor Sox-3-A OS=Xenopus laevis GN=sox3-a PE=1 SV=1

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/45 (62%), Positives = 33/45 (73%)

Query: 16 PGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          PG   +   L +  +KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 26 PGGKGNASTLDQDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 70

Transcription factor with sequence-specific DNA binding activity. Binds to the consensus sequence 5'-[AT][AT]CAA[AT]G-3', showing a preference for 5'-AACAAT-3' and 5'-AACAAAG-3'. Inhibits beta-catenin-mediated dorsal axis specification by binding to sites within the promoter of the beta-catenin-regulated gene nodal5. Acts maternally as a transcriptional repressor of nodal5 and nodal6 to restrict their expression to the vegetal hemisphere of early embryos and thus establish germ layer formation. Acts at multiple points to inhibit nodal signaling, repressing the expression of the other mesoderm-inducing nodal genes nodal, nodal2 and nodal4, and also acting downstream to induce expression of genes including trim33/ectodermin, ema and coco, whose products repress nodal signaling.

Xenopus laevis (taxid: 8355)

>sp|Q6RVD7|SX21B_DANRE Transcription factor Sox-21-B OS=Danio rerio GN=sox21b PE=2 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/32 (81%), Positives = 29/32 (90%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          H+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 7  HVKRPMNAFMVWSRAQRRKMAQENPKMHNSEI 38

Acts as a negative regulator of transcription.

Danio rerio (taxid: 7955)

>sp|Q9W7R6|SOX14_CHICK Transcription factor SOX-14 OS=Gallus gallus GN=SOX14 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/32 (84%), Positives = 29/32 (90%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIKRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 7  HIKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 38

Acts as a negative regulator of transcription.

Gallus gallus (taxid: 9031)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	113
350416776	311	PREDICTED: SOX domain-containing protein	0.513	0.186	0.585	2e-13
340721649	311	PREDICTED: SOX domain-containing protein	0.513	0.186	0.571	4e-12
383864574	206	PREDICTED: SOX domain-containing protein	0.513	0.281	0.547	7e-12
380016546	279	PREDICTED: SOX domain-containing protein	0.513	0.207	0.547	2e-11
345494190	339	PREDICTED: transcription factor Sox-14-l	0.300	0.100	0.941	3e-11
242007463	261	transcription factor Sox-3, putative [Pe	0.380	0.164	0.739	2e-10
391326901	321	PREDICTED: uncharacterized protein LOC10	0.309	0.109	0.857	2e-10
442632266	587	Sox21b, isoform C [Drosophila melanogast	0.300	0.057	0.882	2e-10
195128971	614	GI11537 [Drosophila mojavensis] gi|19392	0.300	0.055	0.882	3e-10
91083767	217	PREDICTED: similar to AGAP010919-PA [Tri	0.309	0.161	0.885	4e-10

>gi|350416776|ref|XP_003491097.1| PREDICTED: SOX domain-containing protein dichaete-like [Bombus impatiens]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/70 (58%), Positives = 46/70 (65%), Gaps = 12/70 (17%)

Query: 3  LSSHHQHSYFSMPPGLDTSHL------------NLGEQHIKRPMNAFMVWSRIQRRKIAL 50
          +SSH QH  +   PG+D   +             L EQHIKRPMNAFMVWSRIQR+KIAL
Sbjct: 2  ISSHQQHPSYGFLPGMDLHSIHRVNQDMNQQTPTLQEQHIKRPMNAFMVWSRIQRKKIAL 61

Query: 51 DNPKMHNSII 60
          DNPKMHNS I
Sbjct: 62 DNPKMHNSEI 71

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721649|ref|XP_003399229.1| PREDICTED: SOX domain-containing protein dichaete-like [Bombus terrestris]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 40/70 (57%), Positives = 44/70 (62%), Gaps = 12/70 (17%)

Query: 3  LSSHHQHSYFSMPPGLD------------TSHLNLGEQHIKRPMNAFMVWSRIQRRKIAL 50
          +SSH QH  +    G+D               L   EQHIKRPMNAFMVWSRIQR+KIAL
Sbjct: 2  ISSHQQHPSYGFLSGMDLHSIHHMGQDINQQSLTPQEQHIKRPMNAFMVWSRIQRKKIAL 61

Query: 51 DNPKMHNSII 60
          DNPKMHNS I
Sbjct: 62 DNPKMHNSEI 71

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383864574|ref|XP_003707753.1| PREDICTED: SOX domain-containing protein dichaete-like [Megachile rotundata]

 Score = 74.3 bits (181), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 47/73 (64%), Gaps = 15/73 (20%)

Query: 3  LSSHHQHSYFSMPPGLD-------TSHLNLG--------EQHIKRPMNAFMVWSRIQRRK 47
          +SSH QH  +    G+D       +  +N+         EQHIKRPMNAFMVWSRIQR+K
Sbjct: 2  MSSHQQHPGYGFLSGMDLHSVHHVSQDMNVAGQQTASSQEQHIKRPMNAFMVWSRIQRKK 61

Query: 48 IALDNPKMHNSII 60
          IALDNPKMHNS I
Sbjct: 62 IALDNPKMHNSEI 74

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380016546|ref|XP_003692243.1| PREDICTED: SOX domain-containing protein dichaete-like [Apis florea]

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 47/73 (64%), Gaps = 15/73 (20%)

Query: 3  LSSHHQHSYFSMPPGLD-------TSHLNLG--------EQHIKRPMNAFMVWSRIQRRK 47
          L+SH QH  +    G+D          +N+G        EQHIKRPMNAFMVWSRIQR+K
Sbjct: 2  LNSHQQHPGYGFLSGMDLHSVHHVGQDMNVGNQPIAASQEQHIKRPMNAFMVWSRIQRKK 61

Query: 48 IALDNPKMHNSII 60
          IAL+NPKMHNS I
Sbjct: 62 IALENPKMHNSEI 74

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345494190|ref|XP_003427240.1| PREDICTED: transcription factor Sox-14-like [Nasonia vitripennis]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/34 (94%), Positives = 33/34 (97%)

Query: 27  EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           EQHIKRPMNAFMVWSRIQR+KIALDNPKMHNS I
Sbjct: 72  EQHIKRPMNAFMVWSRIQRKKIALDNPKMHNSEI 105

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007463|ref|XP_002424559.1| transcription factor Sox-3, putative [Pediculus humanus corporis] gi|212508002|gb|EEB11821.1| transcription factor Sox-3, putative [Pediculus humanus corporis]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/46 (73%), Positives = 37/46 (80%), Gaps = 3/46 (6%)

Query: 18 LDTSHLNLGEQ---HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          ++ SH  L +    HIKRPMNAFMVWSRIQRRKIALDNPKMHNS I
Sbjct: 11 IEPSHDTLSQSEVAHIKRPMNAFMVWSRIQRRKIALDNPKMHNSEI 56

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391326901|ref|XP_003737948.1| PREDICTED: uncharacterized protein LOC100900235 [Metaseiulus occidentalis]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/35 (85%), Positives = 31/35 (88%)

Query: 26  GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           G  HI+RPMNAFMVWSR QRRKIALDNPKMHNS I
Sbjct: 138 GPDHIRRPMNAFMVWSRAQRRKIALDNPKMHNSEI 172

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442632266|ref|NP_001261829.1| Sox21b, isoform C [Drosophila melanogaster] gi|440215768|gb|AGB94522.1| Sox21b, isoform C [Drosophila melanogaster]

 Score = 69.3 bits (168), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/34 (88%), Positives = 32/34 (94%)

Query: 27  EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           E+HIKRPMNAFMVWSR+QRRKIA DNPKMHNS I
Sbjct: 245 EEHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEI 278

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195128971|ref|XP_002008932.1| GI11537 [Drosophila mojavensis] gi|193920541|gb|EDW19408.1| GI11537 [Drosophila mojavensis]

 Score = 68.9 bits (167), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/34 (88%), Positives = 32/34 (94%)

Query: 27  EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           E+HIKRPMNAFMVWSR+QRRKIA DNPKMHNS I
Sbjct: 271 EEHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEI 304

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91083767|ref|XP_972019.1| PREDICTED: similar to AGAP010919-PA [Tribolium castaneum] gi|270008129|gb|EFA04577.1| dichaete [Tribolium castaneum]

 Score = 68.9 bits (167), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 31/35 (88%), Positives = 32/35 (91%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           E HIKRPMNAFMVWSRIQRRKIAL+NPKMHNS I
Sbjct: 16 SEGHIKRPMNAFMVWSRIQRRKIALENPKMHNSEI 50

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	113
FB|FBgn0042630	571	Sox21b "Sox21b" [Drosophila me	0.513	0.101	0.6	2e-11
ZFIN|ZDB-GENE-990715-6	239	sox21a "SRY-box containing gen	0.283	0.133	0.875	3.5e-11
FB|FBgn0036411	388	Sox21a "Sox21a" [Drosophila me	0.477	0.139	0.593	4.2e-11
WB|WBGene00004950	212	sox-3 [Caenorhabditis elegans	0.398	0.212	0.673	7.4e-11
FB|FBgn0000411	382	D "Dichaete" [Drosophila melan	0.300	0.089	0.852	1.8e-10
UNIPROTKB|E1BHN5	204	LOC614121 "Uncharacterized pro	0.283	0.156	0.812	4.1e-10
ZFIN|ZDB-GENE-040429-1	245	sox21b "SRY-box containing gen	0.283	0.130	0.812	6e-10
UNIPROTKB|B0ZTE1	262	sox21 "Transcription factor So	0.283	0.122	0.812	8e-10
ZFIN|ZDB-GENE-051113-268	238	sox14 "SRY-box containing gene	0.283	0.134	0.843	8.9e-10
UNIPROTKB|A4QNG3	239	sox14 "Transcription factor So	0.283	0.133	0.843	9.1e-10

FB|FBgn0042630 Sox21b "Sox21b" [Drosophila melanogaster (taxid:7227)]

 Score = 166 (63.5 bits), Expect = 2.0e-11, P = 2.0e-11
 Identities = 36/60 (60%), Positives = 41/60 (68%)

Query:     1 MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             M+  S     +FS+     T   N  E+HIKRPMNAFMVWSR+QRRKIA DNPKMHNS I
Sbjct:   221 MNSGSSASDVFFSLMIQNTTKRQN--EEHIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEI 278

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008301 "DNA binding, bending" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

ZFIN|ZDB-GENE-990715-6 sox21a "SRY-box containing gene 21a" [Danio rerio (taxid:7955)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 28/32 (87%), Positives = 30/32 (93%)

Query:    29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             H+KRPMNAFMVWSR QRRK+ALDNPKMHNS I
Sbjct:     7 HVKRPMNAFMVWSRAQRRKMALDNPKMHNSEI 38

GO:0009953 "dorsal/ventral pattern formation" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA;ISS;IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA;IMP

GO:0001071 "nucleic acid binding transcription factor activity" evidence=IMP

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

FB|FBgn0036411 Sox21a "Sox21a" [Drosophila melanogaster (taxid:7227)]

 Score = 160 (61.4 bits), Expect = 4.2e-11, P = 4.2e-11
 Identities = 35/59 (59%), Positives = 39/59 (66%)

Query:     6 HHQHSYFSMPPGLDTS----HLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             HH +S+ + P     S    H N    HIKRPMNAFMVWSR QRRK+A DNPKMHNS I
Sbjct:    94 HHGNSHHNAPTSHSNSNTGSHHN-SHDHIKRPMNAFMVWSRGQRRKMAQDNPKMHNSEI 151

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0006911 "phagocytosis, engulfment" evidence=IMP

WB|WBGene00004950 sox-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 151 (58.2 bits), Expect = 7.4e-11, P = 7.4e-11
 Identities = 31/46 (67%), Positives = 33/46 (71%)

Query:    15 PPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             PPG      N    H+KRPMNAFMVWSR QRRK+A DNPKMHNS I
Sbjct:    34 PPGSPVDLQN-SLDHVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEI 78

GO:0003690 "double-stranded DNA binding" evidence=ISS

FB|FBgn0000411 D "Dichaete" [Drosophila melanogaster (taxid:7227)]

 Score = 154 (59.3 bits), Expect = 1.8e-10, P = 1.8e-10
 Identities = 29/34 (85%), Positives = 31/34 (91%)

Query:    27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             E HIKRPMNAFMVWSR+QRR+IA DNPKMHNS I
Sbjct:   139 EGHIKRPMNAFMVWSRLQRRQIAKDNPKMHNSEI 172

GO:0007350 "blastoderm segmentation" evidence=IMP

GO:0007417 "central nervous system development" evidence=IMP

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0008301 "DNA binding, bending" evidence=NAS;IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0035120 "post-embryonic appendage morphogenesis" evidence=IMP

GO:0002168 "instar larval development" evidence=IMP

GO:0007442 "hindgut morphogenesis" evidence=IMP

GO:0007420 "brain development" evidence=IMP

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0003730 "mRNA 3'-UTR binding" evidence=IDA

GO:0009950 "dorsal/ventral axis specification" evidence=IMP

GO:0060810 "intracellular mRNA localization involved in pattern specification process" evidence=IMP

GO:0008134 "transcription factor binding" evidence=IPI

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

UNIPROTKB|E1BHN5 LOC614121 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 26/32 (81%), Positives = 29/32 (90%)

Query:    29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             H+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct:     7 HVKRPMNAFMVWSRAQRRKMAQENPKMHNSEI 38

GO:0048863 "stem cell differentiation" evidence=IEA

GO:0043588 "skin development" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0001942 "hair follicle development" evidence=IEA

ZFIN|ZDB-GENE-040429-1 sox21b "SRY-box containing gene 21 b" [Danio rerio (taxid:7955)]

 Score = 144 (55.7 bits), Expect = 6.0e-10, P = 6.0e-10
 Identities = 26/32 (81%), Positives = 29/32 (90%)

Query:    29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             H+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct:     7 HVKRPMNAFMVWSRAQRRKMAQENPKMHNSEI 38

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

UNIPROTKB|B0ZTE1 sox21 "Transcription factor Sox-21" [Xenopus laevis (taxid:8355)]

 Score = 144 (55.7 bits), Expect = 8.0e-10, P = 8.0e-10
 Identities = 26/32 (81%), Positives = 29/32 (90%)

Query:    29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             H+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct:     7 HVKRPMNAFMVWSRAQRRKMAQENPKMHNSEI 38

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0007399 "nervous system development" evidence=IEP

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

ZFIN|ZDB-GENE-051113-268 sox14 "SRY-box containing gene 14" [Danio rerio (taxid:7955)]

 Score = 142 (55.0 bits), Expect = 8.9e-10, P = 8.9e-10
 Identities = 27/32 (84%), Positives = 29/32 (90%)

Query:    29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             HIKRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct:     7 HIKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 38

GO:0021854 "hypothalamus development" evidence=IMP

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

UNIPROTKB|A4QNG3 sox14 "Transcription factor Sox-14" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 142 (55.0 bits), Expect = 9.1e-10, P = 9.1e-10
 Identities = 27/32 (84%), Positives = 29/32 (90%)

Query:    29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
             HIKRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct:     7 HIKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 38

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0007399 "nervous system development" evidence=ISS

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	113
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	1e-11
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-08
smart00398	70	smart00398, HMG, high mobility group	8e-07
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-05

>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 55.0 bits (133), Expect = 1e-11
 Identities = 17/32 (53%), Positives = 22/32 (68%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIKRPMNAFM++S+  RRK+  + P   N  I
Sbjct: 1  HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAI 32

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif. Length = 72

>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box

 Score = 46.8 bits (112), Expect = 2e-08
 Identities = 13/31 (41%), Positives = 22/31 (70%)

Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           KRP++AF ++S+ QR K+  +NP + N+ I
Sbjct: 1  PKRPLSAFFLFSQEQRAKLKAENPGLKNAEI 31

Length = 69

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 42.7 bits (101), Expect = 8e-07
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
            KRPM+AFM++S+  R KI  +NP + N+
Sbjct: 1  KPKRPMSAFMLFSQENRAKIKAENPDLSNA 30

Length = 70

>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 8/29 (27%), Positives = 18/29 (62%)

Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
           KRP++A+ ++S+  R ++  +NP +   
Sbjct: 1  PKRPLSAYFLFSQEHRAEVKAENPGLSVG 29

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	113
KOG0527|consensus	331		99.97
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.92
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.88
KOG0528|consensus	511		99.87
PTZ00199	94	high mobility group protein; Provisional	99.72
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.68
smart00398	70	HMG high mobility group.	99.66
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.6
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.6
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.54
KOG3248|consensus	421		99.49
KOG0381|consensus	96		99.32
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.29
KOG2746|consensus	683		99.24
KOG0526|consensus	615		99.21
KOG4715|consensus	410		97.91
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	97.25
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	96.8
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	96.03
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	83.11
COG5648	211	NHP6B Chromatin-associated proteins containing the	81.54

>KOG0527|consensus

Probab=99.97  E-value=1.5e-30  Score=207.23  Aligned_cols=83  Identities=37%  Similarity=0.414  Sum_probs=77.2

Q ss_pred             CCCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         20 TSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        20 ~~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      +...++...||||||||||+|++++|++|.++||+|+|+||||.||.+||.       ||.++|+++|..|+++||||||
T Consensus        53 ~~~~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKY  132 (331)
T KOG0527|consen   53 GMKDKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKY  132 (331)
T ss_pred             cccCCCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCccc
Confidence            444678899999999999999999999999999999999999999999985       8999999999999999999999


Q ss_pred             CCCCCCCCCC
Q psy15634         93 FDRDKGLDIT  102 (113)
Q Consensus        93 ~pr~k~~~~~  102 (113)
                      +||||.+...
T Consensus       133 RPRRKkk~~~  142 (331)
T KOG0527|consen  133 RPRRKKKKRP  142 (331)
T ss_pred             cccccccccc
Confidence            9999987643

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=99.92  E-value=1.1e-24  Score=140.21  Aligned_cols=70  Identities=19%  Similarity=0.250  Sum_probs=67.1

Q ss_pred             CCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCC
Q psy15634         29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKG   98 (113)
Q Consensus        29 ~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~   98 (113)
                      |||||+||||||+++.|..|+.+||+++++|||++||++|+.       +|...|++.+..|..++|+|+|.|++++
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p~~~~   77 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTPRKSS   77 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccCCCCC
Confidence            699999999999999999999999999999999999999986       7999999999999999999999999874

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=99.88  E-value=2.2e-22  Score=128.10  Aligned_cols=65  Identities=32%  Similarity=0.445  Sum_probs=62.6

Q ss_pred             CCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        29 ~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      |||||+||||+|++++|..|+.+||++++.|||++||++|+.       +|.+.+++.+..|.+++|||+|+
T Consensus         1 ~iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y~   72 (72)
T cd01388           1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKWR   72 (72)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCCCC
Confidence            699999999999999999999999999999999999999986       79999999999999999999996

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.

>KOG0528|consensus

Probab=99.87  E-value=9.3e-23  Score=167.61  Aligned_cols=80  Identities=36%  Similarity=0.462  Sum_probs=75.4

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCC
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRD   96 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~   96 (113)
                      ...+.||||||||||+|+++.|++|...+|+|+|..||||||.+||.       ||+++-+++-..|.+.||||+|.||-
T Consensus       320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRP  399 (511)
T KOG0528|consen  320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRP  399 (511)
T ss_pred             CCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCC
Confidence            46778999999999999999999999999999999999999999984       89999999999999999999999999


Q ss_pred             CCCCCCC
Q psy15634         97 KGLDITN  103 (113)
Q Consensus        97 k~~~~~~  103 (113)
                      |+.|+.+
T Consensus       400 KRTCvvd  406 (511)
T KOG0528|consen  400 KRTCVVD  406 (511)
T ss_pred             Cceeeec
Confidence            9998765

>PTZ00199 high mobility group protein; Provisional

Probab=99.72  E-value=2.2e-17  Score=110.49  Aligned_cols=69  Identities=13%  Similarity=0.160  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCC--hHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcC
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMH--NSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRK   89 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~--~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~   89 (113)
                      .+..+|++.||||+||||||++++|..|..+||+++  +++||++||++|+.       +|...|++.+..|..+...
T Consensus        14 ~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~   91 (94)
T PTZ00199         14 KRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAE   91 (94)
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345689999999999999999999999999999986  79999999999987       4444444444444444333

>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin

Probab=99.68  E-value=5e-17  Score=101.24  Aligned_cols=62  Identities=26%  Similarity=0.354  Sum_probs=55.3

Q ss_pred             CCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        30 ~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ||||+||||||+++.+..|..+||++++.+|+++||++|++       +|...+++.+..|.+++++|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            79999999999999999999999999999999999999986       688888888888888888774

HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....

>smart00398 HMG high mobility group

Probab=99.66  E-value=3.4e-16  Score=96.95  Aligned_cols=63  Identities=29%  Similarity=0.366  Sum_probs=58.4

Q ss_pred             CCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        29 ~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      .||||+||||+|+++.|..+..++|++++++|+++||.+|+.       +|...+++.+..|..++++|+
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            489999999999999999999999999999999999999986       688888888888999888875

>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

Probab=99.60  E-value=3.4e-15  Score=91.43  Aligned_cols=59  Identities=15%  Similarity=0.229  Sum_probs=51.8

Q ss_pred             CCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhc
Q psy15634         30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACR   88 (113)
Q Consensus        30 ~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p   88 (113)
                      ||||+||||+|+++.|..+..++|+++..+|+++||.+|+.       +|...+++.+..|..++|
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~~   66 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP   66 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            68999999999999999999999999999999999999986       566777777777766653

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

Probab=99.60  E-value=2.7e-15  Score=92.45  Aligned_cols=54  Identities=22%  Similarity=0.329  Sum_probs=47.0

Q ss_pred             CCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHHH
Q psy15634         30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEA   86 (113)
Q Consensus        30 ~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a   86 (113)
                      ||||+||||+|+++.|..+..++|++++.+|+++||++|+.   +.++++..|...+
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~---ls~~eK~~y~~~a   54 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKE---LSEEEKKKYEEKA   54 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHh---CCHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999986   5555555555444

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=99.54  E-value=3.2e-15  Score=112.53  Aligned_cols=72  Identities=19%  Similarity=0.235  Sum_probs=65.5

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHHHhcCCccCCC
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDR   95 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a~p~yky~pr   95 (113)
                      .+..+|++.||||++|||+|+.+.|.+|..++|++.+++|+++||++|++   ++++++++|..+++-++..+-+
T Consensus        62 ~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~---Ltd~eke~y~k~~~~~~erYq~  133 (211)
T COG5648          62 VRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKE---LTDEEKEPYYKEANSDRERYQR  133 (211)
T ss_pred             HHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHh---ccHhhhhhHHHHHhhHHHHHHH
Confidence            34568999999999999999999999999999999999999999999988   8899999999999888875554

>KOG3248|consensus

Probab=99.49  E-value=3e-14  Score=113.90  Aligned_cols=67  Identities=19%  Similarity=0.271  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ....|||.||||||||++++|.+|.+++.....++|.+|||++|.+       .|++.|...+..|++.||+|.
T Consensus       187 ~KkphiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WS  260 (421)
T KOG3248|consen  187 AKKPHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS  260 (421)
T ss_pred             ccCccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcc
Confidence            3677899999999999999999999999988899999999999975       688999999999999999885

>KOG0381|consensus

Probab=99.32  E-value=5.8e-12  Score=83.25  Aligned_cols=61  Identities=23%  Similarity=0.290  Sum_probs=49.8

Q ss_pred             CC--CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHH
Q psy15634         26 GE--QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEA   86 (113)
Q Consensus        26 ~~--~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a   86 (113)
                      ++  +.++||++||++|+.+.|..++.+||+++..||++.||++|++       +|...+...+..+...
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~   86 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKE   86 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            55  5899999999999999999999999999999999999999986       3444444444444433

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins

Probab=99.29  E-value=5.3e-12  Score=80.29  Aligned_cols=57  Identities=14%  Similarity=0.192  Sum_probs=42.8

Q ss_pred             CCCCCCCCchHHHHHHHHHHHHHhh-CCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHHH
Q psy15634         27 EQHIKRPMNAFMVWSRIQRRKIALD-NPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEA   86 (113)
Q Consensus        27 ~~~~KRPlNAFmlf~~~~R~~v~~~-~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a   86 (113)
                      |++||||+|||+||+.+++..+..+ .+.....|+++.||..|++   ++.+++..|..+|
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~---Ls~~EK~~Y~~~A   58 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKS---LSEEEKEPYEERA   58 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHH---S-HHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHh---cCHHHHHHHHHHH
Confidence            5789999999999999999999998 7888899999999999986   4444444444433

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

>KOG2746|consensus

Probab=99.24  E-value=4.2e-12  Score=108.23  Aligned_cols=62  Identities=26%  Similarity=0.371  Sum_probs=51.8

Q ss_pred             CCCCCCCCCCCCCchHHHHHHHHH--HHHHhhCCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHHH
Q psy15634         22 HLNLGEQHIKRPMNAFMVWSRIQR--RKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEA   86 (113)
Q Consensus        22 ~~~k~~~~~KRPlNAFmlf~~~~R--~~v~~~~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a   86 (113)
                      ..+.+..||.|||||||+|++.+|  ..+.+.+|+.+|..||+|||++|   |.+.+.|+..||+.+
T Consensus       174 pnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewW---ytL~~~Ekq~yhdLa  237 (683)
T KOG2746|consen  174 PNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWW---YTLGPNEKQKYHDLA  237 (683)
T ss_pred             CCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhH---hhhCchhhhhHHHHH
Confidence            345789999999999999999999  99999999999999999999999   445555555555433

>KOG0526|consensus

Probab=99.21  E-value=3e-11  Score=101.24  Aligned_cols=73  Identities=11%  Similarity=0.077  Sum_probs=65.4

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-----hhHhhHHHHHHHHHHHhcCCccCCC
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-----PQKIELKSKRDIHVEACRKSNLFDR   95 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-----~y~~~a~~~k~~h~~a~p~yky~pr   95 (113)
                      ++++|||++|||+++|||||.+..|..|+.+  +.+.+||+|.+|++|++     +|...|+.-+..+..+..+|+ .++
T Consensus       527 ~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~k~~we~ka~~dk~ry~~em~~yk-~g~  603 (615)
T KOG0526|consen  527 GKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSAKEEWEDKAAVDKQRYEDEMKEYK-NGQ  603 (615)
T ss_pred             cccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcccchhhHHHHHHHHHHHHHHHhhc-CCC
Confidence            4567899999999999999999999999998  99999999999999985     799999998888888888998 444


Q ss_pred             C
Q psy15634         96 D   96 (113)
Q Consensus        96 ~   96 (113)
                      .
T Consensus       604 ~  604 (615)
T KOG0526|consen  604 M  604 (615)
T ss_pred             c
Confidence            3

>KOG4715|consensus

Probab=97.91  E-value=1.6e-05  Score=63.85  Aligned_cols=48  Identities=17%  Similarity=0.125  Sum_probs=44.0

Q ss_pred             CCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC
Q psy15634         23 LNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC   70 (113)
Q Consensus        23 ~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~   70 (113)
                      ..+.+..|-+||-.||-|++..-..|++.||++.--||+|++|.+|+.
T Consensus        58 ~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~d  105 (410)
T KOG4715|consen   58 RPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLD  105 (410)
T ss_pred             CCCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhh
Confidence            345677788999999999999999999999999999999999999975

>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT)

Probab=97.25  E-value=0.00077  Score=50.98  Aligned_cols=43  Identities=16%  Similarity=0.186  Sum_probs=36.0

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC   70 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~   70 (113)
                      +....+.+||+|+||+|+.-.-    ...|+....++|.+|+..|..
T Consensus        38 ~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~   80 (201)
T PF04769_consen   38 KRSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEK   80 (201)
T ss_pred             cccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhC
Confidence            4566678999999999976554    667888899999999999974

MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus

>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases []

Probab=96.80  E-value=0.0015  Score=39.96  Aligned_cols=36  Identities=19%  Similarity=0.169  Sum_probs=33.5

Q ss_pred             chHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC
Q psy15634         35 NAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC   70 (113)
Q Consensus        35 NAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~   70 (113)
                      ..|=+|.+..|+.|.+.||+...+.|-.+++.+||+
T Consensus        14 t~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrE   49 (55)
T PF08073_consen   14 TNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWRE   49 (55)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999986

; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=96.03  E-value=0.014  Score=43.21  Aligned_cols=46  Identities=13%  Similarity=0.236  Sum_probs=41.1

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC   70 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~   70 (113)
                      +.+.+-.|-++||=.|.++.=.+|++.||+++..|+-+...+.|..
T Consensus       117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h  162 (170)
T PF04690_consen  117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAH  162 (170)
T ss_pred             CCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhh
Confidence            4455556779999999999999999999999999999999999965

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=83.11  E-value=2.6  Score=31.54  Aligned_cols=45  Identities=13%  Similarity=0.097  Sum_probs=35.7

Q ss_pred             CchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHH
Q psy15634         34 MNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVE   85 (113)
Q Consensus        34 lNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~   85 (113)
                      -||||-|.++.|.    .|.+|+..|+-...+..|..   +...++..|-.+
T Consensus        83 nnaYLNFLReFRr----kh~~L~p~dlI~~AAraW~r---LSe~eK~rYrr~  127 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCGLSPQDLIQRAARAWCR---LSEAEKNRYRRM  127 (183)
T ss_pred             chHHHHHHHHHHH----HccCCCHHHHHHHHHHHHHh---CCHHHHHHHHhh
Confidence            5899999987776    57899999999999999964   666666555443

The function of this family is unknown.

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=81.54  E-value=1.5  Score=33.59  Aligned_cols=43  Identities=14%  Similarity=-0.002  Sum_probs=38.8

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC   70 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~   70 (113)
                      -..++|.-.|+-+....|..+...+|+-.-.++.+++|..|.+
T Consensus       142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~e  184 (211)
T COG5648         142 LPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSE  184 (211)
T ss_pred             cCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhh
Confidence            3457888999999999999999999999999999999999976

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	113
2le4_A	81	Solution Structure Of The Hmg Box Dna-Binding Domai		2e-09
1gt0_D	80	Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le		2e-09
1o4x_B	88	Ternary Complex Of The Dna Binding Domains Of The O		2e-09
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		1e-08
1j46_A	85	3d Solution Nmr Structure Of The Wild Type Hmg-Box		2e-08
1hrz_A	76	The 3d Structure Of The Human Sry-Dna Complex Solve		2e-08
1j47_A	85	3d Solution Nmr Structure Of The M9i Mutant Of The		6e-08
3u2b_C	79	Structure Of The Sox4 Hmg Domain Bound To Dna Lengt		9e-08
1i11_A	81	Solution Structure Of The Dna Binding Domain, Sox-5		3e-07
2yul_A	82	Solution Structure Of The Hmg Box Of Human Transcri		3e-06
4euw_A	106	Crystal Structure Of A Hmg Domain Of Transcription		6e-06
4a3n_A	71	Crystal Structure Of Hmg-Box Of Human Sox17 Length		1e-05
3f27_D	83	Structure Of Sox17 Bound To Dna Length = 83		1e-05

>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of Human Stem Cell Transcription Factor Sox2 Length = 81

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/31 (80%), Positives = 28/31 (90%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 4  VKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 34

>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/31 (80%), Positives = 28/31 (90%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 3  VKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 33

>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

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/31 (80%), Positives = 28/31 (90%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 8  VKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 38

>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 23/34 (67%), Positives = 29/34 (85%)
Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +  +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35

>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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/32 (71%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 4  RVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35

>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr Length = 76

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/32 (71%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 4  RVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35

>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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           +KRP+NAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 4  RVKRPINAFIVWSRDQRRKMALENPRMRNSEI 35

>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna Length = 79

Iteration: 1
 Score = 51.6 bits (122), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 23/32 (71%), Positives = 27/32 (84%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIKRPMNAFMVWS+I+RRKI   +P MHN+ I
Sbjct: 2  HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEI 33

>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 26/35 (74%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G  HIKRPMNAFMVW++ +RRKI    P MHNS I
Sbjct: 1  GSPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNI 35

>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17 Length = 82

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 17/35 (48%), Positives = 27/35 (77%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G   I+RPMNAFMVW++ +R+++A  NP +HN+ +
Sbjct: 4  GSSGIRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 38

>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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 18/32 (56%), Positives = 25/32 (78%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          H+KRPMNAFMVW++  RRK+A   P +HN+ +
Sbjct: 29 HVKRPMNAFMVWAQAARRKLADQYPHLHNAEL 60

>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 16/29 (55%), Positives = 25/29 (86%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          I+RPMNAFMVW++ +R+++A  NP +HN+
Sbjct: 3  IRRPMNAFMVWAKDERKRLAQQNPDLHNA 31

>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 16/31 (51%), Positives = 26/31 (83%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          I+RPMNAFMVW++ +R+++A  NP +HN+ +
Sbjct: 7  IRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 37

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	113
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	2e-15
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	3e-15
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	3e-15
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	5e-15
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	1e-14
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	2e-14
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-14
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	3e-14
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	4e-14
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	4e-14
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	8e-14
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-13
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	7e-12
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	4e-06
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-09
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	7e-09
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	1e-07
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	2e-07
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	4e-07
2lhj_A	97	High mobility group protein homolog NHP1; structur	6e-07
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	6e-06
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-05
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-05
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	7e-05
1ckt_A	71	High mobility group 1 protein; high-mobility group	3e-04
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	9e-04

>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 = 64.5 bits (158), Expect = 2e-15
 Identities = 23/35 (65%), Positives = 26/35 (74%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G  HIKRPMNAFMVW++ +RRKI    P MHNS I
Sbjct: 1  GSPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNI 35

>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 = 64.3 bits (157), Expect = 3e-15
 Identities = 12/46 (26%), Positives = 18/46 (39%)

Query: 15 PPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
                +         KRPMNAFM++++  R +     P   N  I
Sbjct: 3  SGSSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAI 48

>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 = 64.2 bits (157), Expect = 3e-15
 Identities = 10/35 (28%), Positives = 20/35 (57%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G    +RPMNAF+++ +  R  +  ++P++ N   
Sbjct: 4  GSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGA 38

>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 = 63.3 bits (155), Expect = 5e-15
 Identities = 23/34 (67%), Positives = 29/34 (85%)

Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +  +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71

 Score = 62.2 bits (152), Expect = 1e-14
 Identities = 16/32 (50%), Positives = 26/32 (81%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           I+RPMNAFMVW++ +R+++A  NP +HN+ +
Sbjct: 2  SIRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 33

>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 = 62.2 bits (152), Expect = 2e-14
 Identities = 16/35 (45%), Positives = 26/35 (74%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
              I+RPMNAFMVW++ +R+++A  NP +HN+ +
Sbjct: 3  FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 37

>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 = 61.8 bits (151), Expect = 2e-14
 Identities = 23/34 (67%), Positives = 29/34 (85%)

Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +  +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35

>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 = 62.4 bits (152), Expect = 3e-14
 Identities = 21/60 (35%), Positives = 31/60 (51%)

Query: 1  MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          M+   HH                +  + H+KRPMNAFMVW++  RRK+A   P +HN+ +
Sbjct: 1  MAHHHHHHVDDDDKMSENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAEL 60

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79

 Score = 61.4 bits (150), Expect = 4e-14
 Identities = 23/32 (71%), Positives = 27/32 (84%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIKRPMNAFMVWS+I+RRKI   +P MHN+ I
Sbjct: 2  HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEI 33

>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 = 61.5 bits (150), Expect = 4e-14
 Identities = 10/32 (31%), Positives = 20/32 (62%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIK+P+NAFM++ +  R  +  ++    ++ I
Sbjct: 2  HIKKPLNAFMLYMKEMRANVVAESTLKESAAI 33

>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 = 60.3 bits (147), Expect = 8e-14
 Identities = 25/32 (78%), Positives = 28/32 (87%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           +KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 2  RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 33

>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 = 60.1 bits (146), Expect = 2e-13
 Identities = 10/35 (28%), Positives = 22/35 (62%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G +  KRP++A  ++S  +RR++  + P++  S +
Sbjct: 17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESEL 51

>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 = 57.5 bits (139), Expect = 7e-12
 Identities = 22/32 (68%), Positives = 28/32 (87%)

Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          +  +KRPMNAF+VWSR QRRK+AL+NP+M NS
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNS 33

>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 = 42.1 bits (99), Expect = 4e-06
 Identities = 11/53 (20%), Positives = 19/53 (35%)

Query: 6   HHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
           H +          +T          KRP +AF ++    R KI  ++P +   
Sbjct: 65  HREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIG 117

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 49.4 bits (118), Expect = 2e-09
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          G   IK+PM+A  ++ +  R +  ++NPK    
Sbjct: 4  GSSGIKKPMSASALFVQDHRPQFLIENPKTSLE 36

>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 = 48.1 bits (115), Expect = 7e-09
 Identities = 5/30 (16%), Positives = 13/30 (43%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
            K P+  ++ +   +R +I   +P +   
Sbjct: 7  GPKAPVTGYVRFLNERREQIRTRHPDLPFP 36

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73

 Score = 44.6 bits (106), Expect = 1e-07
 Identities = 10/28 (35%), Positives = 14/28 (50%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          KR   AFM+W    R  I  +NP +  +
Sbjct: 5  KRATTAFMLWLNDTRESIKRENPGIKVT 32

>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 = 43.8 bits (104), Expect = 2e-07
 Identities = 9/30 (30%), Positives = 15/30 (50%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
            KRP +AF ++    R KI  ++P +   
Sbjct: 6  APKRPPSAFFLFCSEYRPKIKGEHPGLSIG 35

>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 = 43.0 bits (102), Expect = 4e-07
 Identities = 9/28 (32%), Positives = 16/28 (57%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          KRP++A+ +W    R  I  +NP +  +
Sbjct: 5  KRPLSAYALWLNSARESIKRENPGIKVT 32

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97

 Score = 43.1 bits (102), Expect = 6e-07
 Identities = 7/31 (22%), Positives = 20/31 (64%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSI 59
            KR ++++M +++ +R +I  +NP++   +
Sbjct: 22 APKRALSSYMFFAKEKRVEIIAENPEIAKDV 52

>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 = 40.6 bits (94), Expect = 6e-06
 Identities = 9/29 (31%), Positives = 11/29 (37%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHN 57
             RP   F +W    R  I  DNP   +
Sbjct: 5  SSGRPKTGFQMWLEENRSNILSDNPDFSD 33

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102

 Score = 38.9 bits (91), Expect = 3e-05
 Identities = 6/28 (21%), Positives = 14/28 (50%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          ++P++A+ ++ R  +  I   NP     
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFG 46

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99

 Score = 38.5 bits (90), Expect = 3e-05
 Identities = 8/28 (28%), Positives = 15/28 (53%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          K+P+  +  +   +R K A  +P+M N 
Sbjct: 12 KKPLTPYFRFFMEKRAKYAKLHPEMSNL 39

>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 = 37.7 bits (88), Expect = 7e-05
 Identities = 7/28 (25%), Positives = 15/28 (53%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
          KR ++A+M ++   R  +  +NP +   
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFG 49

>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 = 35.4 bits (82), Expect = 3e-04
 Identities = 3/29 (10%), Positives = 12/29 (41%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSI 59
          +  M+++  + +  R +    +P    + 
Sbjct: 3  RGKMSSYAFFVQTCREEHKKKHPDASVNF 31

>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 = 35.7 bits (82), Expect = 9e-04
 Identities = 12/53 (22%), Positives = 22/53 (41%)

Query: 6   HHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
           + +     +PP  +T          KRP +AF ++    R KI  ++P +   
Sbjct: 78  YEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIG 130

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.93
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.92
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.92
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.92
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.91
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.91
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.91
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.91
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.9
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.89
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.88
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.85
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.85
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.85
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.85
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.84
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.82
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.82
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.81
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.81
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.81
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.81
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.81
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.8
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.77
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.77
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.75
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.72
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.71
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.67
2cto_A	93	Novel protein; high mobility group box domain, hel	99.66
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.63
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.62
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.61
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.6
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.59
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.57
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.43
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.4

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=99.93  E-value=6.8e-26  Score=144.84  Aligned_cols=72  Identities=40%  Similarity=0.495  Sum_probs=66.6

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKGL   99 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~~   99 (113)
                      ++||||+||||||++++|..|..++|+++++|||++||++|++       +|...|++.+..|.+++|+|+|+|+++++
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~Prk~~k   79 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRPRKKVK   79 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCCCCCCC
Confidence            5899999999999999999999999999999999999999985       79999999999999999999999998864

>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

Probab=99.92  E-value=8.8e-26  Score=145.38  Aligned_cols=72  Identities=39%  Similarity=0.484  Sum_probs=61.0

Q ss_pred             CCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCC
Q psy15634         27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKG   98 (113)
Q Consensus        27 ~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~   98 (113)
                      .++||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|.++||+|+|.|++++
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~pr~~~   80 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKPRPKR   80 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC--------
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeccCCCC
Confidence            57899999999999999999999999999999999999999986       7999999999999999999999999876

>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

Probab=99.92  E-value=4.5e-25  Score=143.48  Aligned_cols=76  Identities=38%  Similarity=0.509  Sum_probs=72.0

Q ss_pred             CCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCC
Q psy15634         26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKG   98 (113)
Q Consensus        26 ~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~   98 (113)
                      .+++||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|..++|+|+|.|++++
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~prr~~   80 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKA   80 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCCCCcc
Confidence            378999999999999999999999999999999999999999986       7999999999999999999999999988


Q ss_pred             CCC
Q psy15634         99 LDI  101 (113)
Q Consensus        99 ~~~  101 (113)
                      +..
T Consensus        81 ~~~   83 (85)
T 1j46_A           81 KML   83 (85)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            764

>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} SCOP: a.21.1.1 PDB: 2yul_A

Probab=99.92  E-value=2.3e-25  Score=143.70  Aligned_cols=74  Identities=28%  Similarity=0.433  Sum_probs=65.3

Q ss_pred             CCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCC
Q psy15634         26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKG   98 (113)
Q Consensus        26 ~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~   98 (113)
                      .+++||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|.+++|+|+|+|++++
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~P~~kk   82 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRPRRRK   82 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCC--
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCCccCC
Confidence            577899999999999999999999999999999999999999985       7999999999999999999999999886


Q ss_pred             C
Q psy15634         99 L   99 (113)
Q Consensus        99 ~   99 (113)
                      +
T Consensus        83 ~   83 (83)
T 3f27_D           83 Q   83 (83)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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*

Probab=99.91  E-value=9.5e-25  Score=138.73  Aligned_cols=69  Identities=39%  Similarity=0.533  Sum_probs=64.3

Q ss_pred             CCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCC
Q psy15634         26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFD   94 (113)
Q Consensus        26 ~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~p   94 (113)
                      |+++||||+||||||++++|..|+.+||+++++|||++||++|++       +|...|++.+..|.+++|+|+|+|
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~P   76 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCCC-
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCc
Confidence            688999999999999999999999999999999999999999986       799999999999999999999987

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B

Probab=99.91  E-value=2.2e-24  Score=138.39  Aligned_cols=72  Identities=44%  Similarity=0.559  Sum_probs=69.0

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKGL   99 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~~   99 (113)
                      ++||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|.+++|+|+|.|+++++
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~r~~k   79 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK   79 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCCCCCCC
Confidence            4799999999999999999999999999999999999999986       79999999999999999999999999876

>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}

Probab=99.91  E-value=1.7e-24  Score=141.39  Aligned_cols=72  Identities=19%  Similarity=0.123  Sum_probs=68.2

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      .+..+|+++||||+||||||++++|..|+.+||++++.|||++||++|++       +|...|++.+..|.++||+|+|
T Consensus         9 ~~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yky   87 (87)
T 2e6o_A            9 TVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCWK   87 (87)
T ss_dssp             SCCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            34568999999999999999999999999999999999999999999985       8999999999999999999998

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens}

Probab=99.91  E-value=1.7e-24  Score=146.43  Aligned_cols=76  Identities=30%  Similarity=0.412  Sum_probs=63.6

Q ss_pred             CCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCC
Q psy15634         23 LNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDR   95 (113)
Q Consensus        23 ~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr   95 (113)
                      ..+++++||||+||||||++++|..|+.++|+++++|||++||++|+.       +|...|++.+..|.+++|+|+|+|+
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~Pr  102 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPR  102 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC---
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcCCC
Confidence            358999999999999999999999999999999999999999999986       7999999999999999999999999


Q ss_pred             CCC
Q psy15634         96 DKG   98 (113)
Q Consensus        96 ~k~   98 (113)
                      +++
T Consensus       103 rkK  105 (106)
T 4euw_A          103 RRK  105 (106)
T ss_dssp             ---
T ss_pred             CCC
Confidence            875

>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

Probab=99.90  E-value=1.9e-23  Score=135.95  Aligned_cols=71  Identities=18%  Similarity=0.238  Sum_probs=67.0

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKG   98 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~   98 (113)
                      .+||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|.+++|+|+|.|+..+
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~~~   78 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGK   78 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCCCC
Confidence            3799999999999999999999999999999999999999986       7999999999999999999999998554

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus}

Probab=99.89  E-value=1.3e-23  Score=135.41  Aligned_cols=72  Identities=18%  Similarity=0.224  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCC
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRD   96 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~   96 (113)
                      .++++||||+||||||++++|..|+.+||+++++|||++||++|++       +|...|++.+..|.+++|+|+|.|++
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~p~~   81 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGPSS   81 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCCTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCC
Confidence            5789999999999999999999999999999999999999999986       79999999999999999999999986

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1

Probab=99.88  E-value=4.6e-23  Score=137.91  Aligned_cols=76  Identities=13%  Similarity=0.101  Sum_probs=69.0

Q ss_pred             CCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHH-------HHHHh
Q psy15634         22 HLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDI-------HVEAC   87 (113)
Q Consensus        22 ~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~-------h~~a~   87 (113)
                      ++.+|+++||||+||||||+++.|..|+.+||+++++|||++||++|++       +|...|++.+..       |...+
T Consensus         3 kk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~~   82 (99)
T 1k99_A            3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (99)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            4568999999999999999999999999999999999999999999985       788889888887       67779


Q ss_pred             cCCccCCCCC
Q psy15634         88 RKSNLFDRDK   97 (113)
Q Consensus        88 p~yky~pr~k   97 (113)
                      |||+|.|+..
T Consensus        83 P~~~~~~~~~   92 (99)
T 1k99_A           83 PDLIQNAKKL   92 (99)
T ss_dssp             CCCSCCCCC-
T ss_pred             CCccCCCccc
Confidence            9999999864

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0

Probab=99.85  E-value=5.1e-22  Score=124.11  Aligned_cols=64  Identities=31%  Similarity=0.514  Sum_probs=55.1

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ++||||+||||||+++.|..|..++|+++++|||++||++|+.       +|...|++.+..|.+++|+|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            4799999999999999999999999999999999999999985       799999999999999999996

>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

Probab=99.85  E-value=1.6e-21  Score=123.97  Aligned_cols=69  Identities=14%  Similarity=0.081  Sum_probs=65.5

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      ++|+++||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|.+++++|+.
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            47999999999999999999999999999999999999999999975       7999999999999999999974

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus}

Probab=99.85  E-value=8.8e-22  Score=129.66  Aligned_cols=72  Identities=11%  Similarity=0.093  Sum_probs=67.9

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCC
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDR   95 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr   95 (113)
                      .+|+++||||+||||||++++|..|+.+||++++.|||++||++|++       +|...|++.+..|.+++++|++.+.
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~   80 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEA   80 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHH
Confidence            37999999999999999999999999999999999999999999986       7999999999999999999988764

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.85  E-value=1.4e-21  Score=131.05  Aligned_cols=78  Identities=10%  Similarity=0.041  Sum_probs=71.7

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      .+..+|+++||||+||||||++++|..|+.+||++++.|||++||++|++       +|...|++.+..|.+++++|++.
T Consensus         9 kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~   88 (102)
T 2co9_A            9 KKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRAS   88 (102)
T ss_dssp             CSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34468999999999999999999999999999999999999999999986       79999999999999999999987


Q ss_pred             CCCCC
Q psy15634         94 DRDKG   98 (113)
Q Consensus        94 pr~k~   98 (113)
                      +..+.
T Consensus        89 ~~~~~   93 (102)
T 2co9_A           89 LVSKS   93 (102)
T ss_dssp             HTSSC
T ss_pred             ccccc
Confidence            76544

>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

Probab=99.84  E-value=7.3e-21  Score=124.89  Aligned_cols=76  Identities=17%  Similarity=0.222  Sum_probs=65.9

Q ss_pred             CCCCCCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHHHhcCCccCCC
Q psy15634         17 GLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDR   95 (113)
Q Consensus        17 ~~~~~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a~p~yky~pr   95 (113)
                      .....+..+|+++||||+||||||++++|..|+.+||++++.|||++||++|++   +.+++++.|..+|..+..-+.+
T Consensus         8 k~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~---ls~eeK~~Y~~~A~~~k~~y~~   83 (90)
T 1wgf_A            8 KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWND---LSEKKKAKYKAREAALKAQSER   83 (90)
T ss_dssp             SSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHH---SCHHHHHHHHHHHHHHTTTTCC
T ss_pred             CCCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHH
Confidence            334455678999999999999999999999999999999999999999999976   8888899998888776655443

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster}

Probab=99.82  E-value=1.5e-20  Score=118.70  Aligned_cols=65  Identities=18%  Similarity=0.178  Sum_probs=61.0

Q ss_pred             CCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-----hhHhhHHHHHHHHHHHhcCCc
Q psy15634         27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-----PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        27 ~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-----~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      |++||||+||||||++++|..|+.+||+++++|||++||++|++     +|...|++.+..|.+++++|+
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l~eK~~y~~~A~~~k~~y~~e~~~Y~   70 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWEDAAAKDKQRYHDEMRNYK   70 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTCTTHHHHHHHHHHHHHHHHTTTGGGT
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999986     788889999999999999886

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=2.3e-20  Score=121.36  Aligned_cols=72  Identities=10%  Similarity=0.015  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCC--hHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCC
Q psy15634         20 TSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMH--NSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKS   90 (113)
Q Consensus        20 ~~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~--~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~y   90 (113)
                      ..+..+|+++||||+||||||++++|..|+.+||+++  +.|||++||++|++       +|...|++.+..|..+.++|
T Consensus         6 ~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   85 (86)
T 2eqz_A            6 SGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY   85 (86)
T ss_dssp             SSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3445689999999999999999999999999999997  49999999999986       67777777777777777766


Q ss_pred             c
Q psy15634         91 N   91 (113)
Q Consensus        91 k   91 (113)
                      +
T Consensus        86 ~   86 (86)
T 2eqz_A           86 G   86 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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

Probab=99.81  E-value=2e-21  Score=128.29  Aligned_cols=77  Identities=14%  Similarity=0.163  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHh
Q psy15634         15 PPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEAC   87 (113)
Q Consensus        15 p~~~~~~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~   87 (113)
                      |+.....+..+|+++|+||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|..++
T Consensus         6 ~~k~~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~   85 (93)
T 1cg7_A            6 EPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK   85 (93)
T ss_dssp             CCCCCCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHH
T ss_pred             CCCcccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444455678999999999999999999999999999999999999999999986       56666666666677777


Q ss_pred             cCCc
Q psy15634         88 RKSN   91 (113)
Q Consensus        88 p~yk   91 (113)
                      ++|+
T Consensus        86 ~~Y~   89 (93)
T 1cg7_A           86 ELYN   89 (93)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7665

>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}

Probab=99.81  E-value=7.1e-20  Score=118.81  Aligned_cols=62  Identities=19%  Similarity=0.344  Sum_probs=58.4

Q ss_pred             CCCCCCCCCchHHHHHHHHHHHHHhhCCCCC-hHHHHHHhhhhcCChhHhhHHHHHHHHHHHhcCC
Q psy15634         26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMH-NSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKS   90 (113)
Q Consensus        26 ~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~-~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a~p~y   90 (113)
                      ++++|||||||||||++++|..|+.+||+++ ++|||++||++|+.   +.+++++.|..+|..+.
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~---ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRV---LSTEERKVWANKAKGET   64 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSS---SCHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHh
Confidence            6789999999999999999999999999998 99999999999998   99999999999987763

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=99.81  E-value=1.9e-20  Score=118.31  Aligned_cols=64  Identities=17%  Similarity=0.250  Sum_probs=60.8

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-----hhHhhHHHHHHHHHHHhcCCc
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-----PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-----~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      +.||||+||||||++++|..|+.+||+++++|||++||++|++     +|...|++.+..|.+++++|+
T Consensus         2 ~~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~K~~y~~~A~~~k~~y~~~~~~Y~   70 (73)
T 3nm9_A            2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFE   70 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHHHHHH
Confidence            6799999999999999999999999999999999999999975     899999999999999999885

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.7e-20  Score=121.85  Aligned_cols=72  Identities=14%  Similarity=0.101  Sum_probs=66.2

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCC
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRD   96 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~   96 (113)
                      .++++||||+||||||++++|..|+.+||++++.|||++||++|++       +|...|++.+..|.+++++|+....+
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~~   81 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQ   81 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            5789999999999999999999999999999999999999999986       78888998889999999999886443

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1

Probab=99.81  E-value=4.2e-20  Score=119.15  Aligned_cols=69  Identities=7%  Similarity=-0.004  Sum_probs=64.2

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCCh--HHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHN--SIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~--~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      ++|+++||||+||||||++++|..|+.+||++++  +|||++||++|+.       +|...|++.+..|..++++|+-
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   79 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   79 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4799999999999999999999999999999974  9999999999986       7999999999999999999863

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis}

Probab=99.80  E-value=1.4e-20  Score=124.90  Aligned_cols=72  Identities=14%  Similarity=0.130  Sum_probs=67.0

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCC--hHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMH--NSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~--~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      .+..+|+++||||+||||||++++|..|..+||+++  ++|||++||++|++       +|...|++.+..|.+++++|+
T Consensus        14 ~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~   93 (97)
T 2lhj_A           14 RKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYA   93 (97)
T ss_dssp             TCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445689999999999999999999999999999999  99999999999985       799999999999999999986


Q ss_pred             c
Q psy15634         92 L   92 (113)
Q Consensus        92 y   92 (113)
                      .
T Consensus        94 ~   94 (97)
T 2lhj_A           94 Q   94 (97)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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

Probab=99.77  E-value=8.4e-19  Score=109.63  Aligned_cols=62  Identities=8%  Similarity=0.022  Sum_probs=57.1

Q ss_pred             CCCCCCchHHHHHHHHHHHHHhhCCCCCh--HHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCC
Q psy15634         29 HIKRPMNAFMVWSRIQRRKIALDNPKMHN--SIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKS   90 (113)
Q Consensus        29 ~~KRPlNAFmlf~~~~R~~v~~~~P~~~~--~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~y   90 (113)
                      +||||+||||||++++|..|+.+||++++  +|||++||++|++       +|...|++.+..|..+..+|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            58999999999999999999999999987  9999999999985       78888999888888888776

>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

Probab=99.77  E-value=9.5e-19  Score=124.40  Aligned_cols=73  Identities=37%  Similarity=0.518  Sum_probs=67.7

Q ss_pred             CCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCCC
Q psy15634         27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKGL   99 (113)
Q Consensus        27 ~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~~   99 (113)
                      +++||||+||||||+++.|..|..+||+++++|||++||++|+.       +|...|+..+..|..++|+|++.++++++
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~k~~~kk   81 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKK   81 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCCCCCCGG
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccccccccc
Confidence            67899999999999999999999999999999999999999985       79999999999999999999999875543

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.8e-18  Score=124.66  Aligned_cols=72  Identities=14%  Similarity=0.071  Sum_probs=67.1

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      .+..+|+++||||+||||||++++|..|..+||+++++||+++||++|++       +|...|++.+..|..++++|++
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  171 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  171 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34457999999999999999999999999999999999999999999985       7999999999999999999976

>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

Probab=99.72  E-value=7.5e-18  Score=119.74  Aligned_cols=71  Identities=14%  Similarity=0.078  Sum_probs=64.2

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         21 SHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        21 ~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      .+..+|++.||||+||||||++++|..|..+||+++++||+++||++|++       +|...|++.+..|..+.++|+
T Consensus        80 kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~  157 (159)
T 2gzk_A           80 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR  157 (159)
T ss_dssp             GGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34468999999999999999999999999999999999999999999985       788888888888888888775

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=3.4e-17  Score=118.02  Aligned_cols=72  Identities=7%  Similarity=-0.047  Sum_probs=65.1

Q ss_pred             CCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCC--CChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         22 HLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPK--MHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        22 ~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~--~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      ...+|+++||||+||||||++++|..|..+||+  ++++|||++||++|+.       +|...|++.+..|..++++|.-
T Consensus         8 ~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   87 (173)
T 2yrq_A            8 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   87 (173)
T ss_dssp             SSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            346799999999999999999999999999999  6899999999999985       7888888888889999999875


Q ss_pred             C
Q psy15634         93 F   93 (113)
Q Consensus        93 ~   93 (113)
                      .
T Consensus        88 ~   88 (173)
T 2yrq_A           88 P   88 (173)
T ss_dssp             C
T ss_pred             h
Confidence            3

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.67  E-value=5.1e-17  Score=110.14  Aligned_cols=68  Identities=6%  Similarity=-0.064  Sum_probs=61.0

Q ss_pred             CCCCCCCCCC-CCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         21 SHLNLGEQHI-KRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        21 ~~~~k~~~~~-KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      .++.+|+++| |||+||||||++++|..|+    +++++||+++||++|+.       +|...|++.+..|..++++|+-
T Consensus         8 ~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~   83 (108)
T 1v64_A            8 QLKDKFDGRPTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4456899999 9999999999999999987    78999999999999985       7888899988899999988864

>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=5.1e-17  Score=108.03  Aligned_cols=61  Identities=10%  Similarity=0.052  Sum_probs=51.6

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHh---hhhcCChhHhhHHHHHHHHHHHhcC
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCH---IMHFLCPQKIELKSKRDIHVEACRK   89 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~L---G~~Wk~~y~~~a~~~k~~h~~a~p~   89 (113)
                      ..++++|||||||||||++++|..|+.+  +++++|||++|   |++|+.   +.++++++|.++|..+
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~---ls~eEK~pYe~~A~~~   68 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWAL---LREEEKEKYAEMAREW   68 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHH---SCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHH
Confidence            4789999999999999999999999998  89999999999   999976   5566666665555443

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}

Probab=99.63  E-value=1.9e-16  Score=98.13  Aligned_cols=59  Identities=14%  Similarity=0.057  Sum_probs=47.3

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKS   90 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~y   90 (113)
                      ++||||+||||||++++|..|+.++|    +|||++||++|++       +|...|++.+..|..+...|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            47999999999999999999988776    7999999999986       56666666655555554443

>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

Probab=99.62  E-value=6.3e-16  Score=103.57  Aligned_cols=65  Identities=9%  Similarity=-0.145  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ....+||||+||||||+++++.  ..+++++++.||+++||++|+.       +|...|++.+..|..++++|.
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~   75 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWV   75 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4667899999999999999964  3455668889999999999986       788899998899999988886

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-17  Score=109.68  Aligned_cols=59  Identities=10%  Similarity=-0.015  Sum_probs=49.0

Q ss_pred             CCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCC--hHHHHHHhhhhcCChhHhhHHHHHHHHHHHhc
Q psy15634         23 LNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMH--NSIIFNCHIMHFLCPQKIELKSKRDIHVEACR   88 (113)
Q Consensus        23 ~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~--~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a~p   88 (113)
                      ..+|++.||||+|||||||+++|..|+.+||+++  ++|||    ++|+.   +.++++++|..+|..
T Consensus        16 ~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~---ls~eeK~pY~~kA~~   76 (90)
T 2yuk_A           16 WEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRK---ASSQERAPYVQKARD   76 (90)
T ss_dssp             HHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHH---SCHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHc---CCHHHHHHHHHHHHH
Confidence            3579999999999999999999999999999999  99999    99976   445555555544443

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=99.60  E-value=3.1e-16  Score=118.79  Aligned_cols=68  Identities=10%  Similarity=0.145  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ..++++||||+||||||+++.|..|+.+||+++++|||++||++|+.       +|...|...+..|.++..+|.
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~  110 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFK  110 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999999999999985       788888888888888888774

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A

Probab=99.59  E-value=2.5e-15  Score=99.58  Aligned_cols=64  Identities=6%  Similarity=-0.047  Sum_probs=59.1

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      +.|+||++|||||+++.|..+..++|+ +++||||.||++|+.       +|...|++.+..++.+..+|+-
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~   73 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRA   73 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            579999999999999999999999999 999999999999985       7888888888888888888864

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.57  E-value=1.1e-15  Score=114.15  Aligned_cols=67  Identities=10%  Similarity=0.142  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ..+++||||+||||||+++.|..|+.+||+++++|||++||++|+.       +|...|.+.+..|.++.++|.
T Consensus         5 ~~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~   78 (214)
T 3tq6_A            5 VLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFK   78 (214)
T ss_dssp             HHHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhc
Confidence            3577899999999999999999999999999999999999999985       788888888888888888874

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.43  E-value=1.1e-14  Score=108.65  Aligned_cols=65  Identities=12%  Similarity=-0.008  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      +|++.||||+||||||++++|..|..++|+    ||+++||++|++       +|...|++.+..|..+.++|+-.
T Consensus       110 kdp~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~  181 (214)
T 3tq6_A          110 TLLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ  181 (214)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            589999999999999999999998777664    999999999986       79999999999999988888753

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=99.40  E-value=2e-14  Score=108.82  Aligned_cols=65  Identities=12%  Similarity=-0.008  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         25 LGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        25 k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      +|++.||||+||||||++++|..|..++|+    ||+++||++|++       +|...|++.+..|..+.++|+..
T Consensus       142 kdp~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k  213 (238)
T 3tmm_A          142 TLLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ  213 (238)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSCCSSHH----HHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCcHHHHHHHHHHHHHhccCHH----HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            689999999999999999999998877664    999999999985       89999999999999999999764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	113
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	1e-08
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	2e-08
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	2e-08
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	5e-08
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	7e-07
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	1e-06
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-06
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	4e-06
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-05
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-05
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-04

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.9 bits (109), Expect = 1e-08
 Identities = 25/32 (78%), Positives = 28/32 (87%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
           +KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 2  RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 33

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.0 bits (109), Expect = 2e-08
 Identities = 10/32 (31%), Positives = 20/32 (62%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIK+P+NAFM++ +  R  +  ++    ++ I
Sbjct: 2  HIKKPLNAFMLYMKEMRANVVAESTLKESAAI 33

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (107), Expect = 2e-08
 Identities = 22/32 (68%), Positives = 25/32 (78%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          HIKRPMNAFMVW++ +RRKI    P MHNS I
Sbjct: 2  HIKRPMNAFMVWAKDERRKILQAFPDMHNSNI 33

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 5e-08
 Identities = 23/34 (67%), Positives = 29/34 (85%)

Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          +  +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 41.4 bits (97), Expect = 7e-07
 Identities = 9/30 (30%), Positives = 16/30 (53%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          KRP +AF ++    R KI  ++P +    +
Sbjct: 4  KRPPSAFFLFCSEYRPKIKGEHPGLSIGDV 33

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.5 bits (95), Expect = 1e-06
 Identities = 10/30 (33%), Positives = 18/30 (60%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          KRP++A+M+W    R  I  +NP +  + +
Sbjct: 5  KRPLSAYMLWLNSARESIKRENPGIKVTEV 34

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 1e-06
 Identities = 10/35 (28%), Positives = 22/35 (62%)

Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
          G +  KRP++A  ++S  +RR++  + P++  S +
Sbjct: 17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESEL 51

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.9 bits (93), Expect = 4e-06
 Identities = 7/32 (21%), Positives = 16/32 (50%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
            KR ++A+M ++   R  +  +NP +    +
Sbjct: 20 APKRALSAYMFFANENRDIVRSENPDITFGQV 51

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (88), Expect = 3e-05
 Identities = 6/28 (21%), Positives = 12/28 (42%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMH 56
            K PMN +  +S+       L++  + 
Sbjct: 8  PKKPPMNGYQKFSQELLSNGELNHLPLK 35

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (86), Expect = 4e-05
 Identities = 8/32 (25%), Positives = 16/32 (50%)

Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
            K+P+  +  +   +R K A  +P+M N  +
Sbjct: 10 FPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDL 41

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 35.6 bits (82), Expect = 1e-04
 Identities = 3/26 (11%), Positives = 11/26 (42%)

Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMH 56
          +  M+++  + +  R +    +P   
Sbjct: 3  RGKMSSYAFFVQTCREEHKKKHPDAS 28

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	113
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.92
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.91
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.9
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.79
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.76
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.75
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.74
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.73
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.72
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.51
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.48

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.92  E-value=2.3e-25  Score=142.85  Aligned_cols=72  Identities=44%  Similarity=0.559  Sum_probs=68.6

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKGL   99 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~~   99 (113)
                      ++||||+||||||++++|..|.++||+++++|||++||++|++       +|...|++.+..|.+++|+|+|.|+++.+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p~rk~k   79 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK   79 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCCCCCCC
Confidence            5799999999999999999999999999999999999999986       79999999999999999999999998765

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=2e-24  Score=139.74  Aligned_cols=72  Identities=18%  Similarity=0.232  Sum_probs=68.4

Q ss_pred             CCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCCCC
Q psy15634         29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKGLD  100 (113)
Q Consensus        29 ~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~~~  100 (113)
                      |||||+||||||+++.|..|..+||++++++||++||++|++       +|.+.|++.+..|.+++|+|+|.|+++.+.
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~~~~~   80 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKK   80 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCCCCCc
Confidence            899999999999999999999999999999999999999996       799999999999999999999999877654

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=7.7e-24  Score=136.63  Aligned_cols=74  Identities=39%  Similarity=0.526  Sum_probs=69.6

Q ss_pred             CCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCCCCCC
Q psy15634         27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDRDKGL   99 (113)
Q Consensus        27 ~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr~k~~   99 (113)
                      .++||||+||||||++++|..|..+||+++++|||++||++|++       +|...|++.+..|.+++|+|+|.|+++.+
T Consensus         2 ~~~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p~~~~k   81 (85)
T d1j46a_           2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK   81 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCCCCccc
Confidence            47899999999999999999999999999999999999999986       79999999999999999999999987665


Q ss_pred             C
Q psy15634        100 D  100 (113)
Q Consensus       100 ~  100 (113)
                      .
T Consensus        82 ~   82 (85)
T d1j46a_          82 M   82 (85)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=2.5e-23  Score=129.81  Aligned_cols=63  Identities=41%  Similarity=0.536  Sum_probs=60.6

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKS   90 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~y   90 (113)
                      .|||||+||||||++++|..|+.+||+++++|||++||++|++       +|.+.|++.+..|.++||||
T Consensus         1 p~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           1 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            4799999999999999999999999999999999999999986       89999999999999999998

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.79  E-value=3.8e-20  Score=115.82  Aligned_cols=65  Identities=18%  Similarity=0.266  Sum_probs=61.1

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-----hhHhhHHHHHHHHHHHhcCCcc
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-----PQKIELKSKRDIHVEACRKSNL   92 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-----~y~~~a~~~k~~h~~a~p~yky   92 (113)
                      ++||||+||||||++++|..|+.+||++++.|||++||++|++     +|...+++.+..|..++++|+-
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~eK~~y~~~a~~~k~~y~~~~~~y~~   71 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6799999999999999999999999999999999999999985     7999999999999999998863

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.76  E-value=2.5e-19  Score=113.31  Aligned_cols=68  Identities=15%  Similarity=0.107  Sum_probs=63.2

Q ss_pred             CCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccCCC
Q psy15634         28 QHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLFDR   95 (113)
Q Consensus        28 ~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~pr   95 (113)
                      |.||||+||||||++++|..|+.+||+++++||+++||++|++       +|...+++.+..|.++++.|+..++
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~   75 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGK   75 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence            5799999999999999999999999999999999999999985       7999999999999999999976554

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=1.5e-18  Score=113.00  Aligned_cols=73  Identities=14%  Similarity=0.154  Sum_probs=64.1

Q ss_pred             CCCCCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCc
Q psy15634         19 DTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSN   91 (113)
Q Consensus        19 ~~~~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yk   91 (113)
                      ...+..+++++||||+||||||+++.|..|+.++|++++.||++.||++|++       +|...+++.+..|..+...|+
T Consensus        10 ~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~   89 (93)
T d1lwma_          10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYN   89 (93)
T ss_dssp             CCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445678999999999999999999999999999999999999999999986       677778887777877777765

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2e-18  Score=111.60  Aligned_cols=72  Identities=13%  Similarity=0.098  Sum_probs=66.9

Q ss_pred             CCCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         22 HLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        22 ~~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      +.+++++.|+||+||||||+++.|..|..+||+++++||+++||++|+.       +|...|++.+..|.++++.|.-.
T Consensus         3 k~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~   81 (91)
T d1k99a_           3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (91)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999999999999985       79999999999999999988754

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=3.2e-18  Score=110.43  Aligned_cols=72  Identities=18%  Similarity=0.256  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCChhHhhHHHHHHHHHHHhcCCccCCCCC
Q psy15634         23 LNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKSNLFDRDK   97 (113)
Q Consensus        23 ~~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~~y~~~a~~~k~~h~~a~p~yky~pr~k   97 (113)
                      ..+++++||||+||||||++++|..|..+||++++.||+++||++|+.   +.++++..|..++..+..-+.++.
T Consensus        14 ~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~---Ls~~eK~~Y~~~A~~~k~~y~~~~   85 (90)
T d1wgfa_          14 GKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWND---LSEKKKAKYKAREAALKAQSERKS   85 (90)
T ss_dssp             CSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHH---SCHHHHHHHHHHHHHHTTTTCCCC
T ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999999999999977   889999999888877666555443

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.72  E-value=7.3e-18  Score=104.41  Aligned_cols=62  Identities=8%  Similarity=0.037  Sum_probs=56.7

Q ss_pred             CCCCCCchHHHHHHHHHHHHHhhCCC--CChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCC
Q psy15634         29 HIKRPMNAFMVWSRIQRRKIALDNPK--MHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKS   90 (113)
Q Consensus        29 ~~KRPlNAFmlf~~~~R~~v~~~~P~--~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~y   90 (113)
                      +||||+||||||+++.|..|+.+||+  +++++|+++||++|++       +|...|++.+..|..+.++|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            58999999999999999999999997  5578999999999986       79999999999999988877

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=5e-15  Score=96.86  Aligned_cols=66  Identities=11%  Similarity=-0.100  Sum_probs=57.3

Q ss_pred             CCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        26 ~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      ....+|||+||||||++++|..+...+  +++.||+++||++|+.       +|...|++.+..|..+++.|+..
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~--~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~   77 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKS   77 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTT--SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344589999999999999999987655  5689999999999986       78899999999999999998765

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=2.6e-14  Score=94.77  Aligned_cols=66  Identities=6%  Similarity=-0.049  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCchHHHHHHHHHHHHHhhCCCCChHHHHHHhhhhcCC-------hhHhhHHHHHHHHHHHhcCCccC
Q psy15634         24 NLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLC-------PQKIELKSKRDIHVEACRKSNLF   93 (113)
Q Consensus        24 ~k~~~~~KRPlNAFmlf~~~~R~~v~~~~P~~~~~eISk~LG~~Wk~-------~y~~~a~~~k~~h~~a~p~yky~   93 (113)
                      ..++..+|||+||||||++++|..    +|++++.||+++||++|++       +|...|++.+..|..+++.|...
T Consensus        12 ~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~   84 (108)
T d1v64a_          12 KFDGRPTKPPPNSYSLYCAELMAN----MKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLES   84 (108)
T ss_dssp             CTTTSCCCCCSSHHHHHHHHHHHH----CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCcHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            356667799999999999998864    6899999999999999985       79999999999999999988753