Psyllid ID: psy5107

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70----
Protein Sequence
MGLYSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Secondary Structure (PSIPRED)
ccccccccccccccccccccccHHHHHHcHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mglyspmratkknnpnhikrpmnAFMVWSQMERRKIcevqpdmhNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Flexible Loop (DISEMBL)
mglyspmratkknnpnhikrpmNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Low Complexity Region (SEG)
MGLYSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Disordered region (IsUnstruct)
**********************NAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF**
Disordered Region (DISOPRED)
**********************NAFMVWSQMERR***********AEISKRLALLSLYKSNGFNWLLAEQLFSC
Disordered Region (DISEMBL)
MGLYSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Disordered Region (DISPRO)
*****************IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGLYSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFSC
Positional Conservation
no confident homologs detected

---

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	74	2.2.26 [Sep-21-2011]
P40656	669	Putative transcription fa	yes	N/A	0.675	0.074	0.76	1e-16
Q06831	440	Transcription factor SOX-	yes	N/A	0.567	0.095	0.785	2e-13
Q06945	474	Transcription factor SOX-	yes	N/A	0.567	0.088	0.785	4e-13
P35716	441	Transcription factor SOX-	no	N/A	0.567	0.095	0.761	2e-12
P40650	374	Transcription factor Sox-	N/A	N/A	0.567	0.112	0.761	2e-12
P48435	396	Transcription factor SOX-	no	N/A	0.567	0.106	0.761	2e-12
Q91731	382	Transcription factor Sox-	N/A	N/A	0.567	0.109	0.761	2e-12
P0C1G9	395	Transcription factor SOX-	no	N/A	0.567	0.106	0.761	2e-12
Q7M6Y2	395	Transcription factor SOX-	no	N/A	0.567	0.106	0.761	2e-12
Q66JF1	383	Transcription factor Sox-	no	N/A	0.567	0.109	0.761	3e-12

>sp|P40656|SOX14_DROME Putative transcription factor SOX-14 OS=Drosophila melanogaster GN=Sox14 PE=2 SV=3

 Score = 85.1 bits (209), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 38/50 (76%), Positives = 41/50 (82%)

Query: 4   YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           YS    TKK++P HIKRPMNAFMVWSQMERRKICE  PD+HNAEISK L 
Sbjct: 173 YSDATRTKKHSPGHIKRPMNAFMVWSQMERRKICERTPDLHNAEISKELG 222

Drosophila melanogaster (taxid: 7227)

>sp|Q06831|SOX4_MOUSE Transcription factor SOX-4 OS=Mus musculus GN=Sox4 PE=1 SV=2

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL 
Sbjct: 53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLG 94

Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.

Mus musculus (taxid: 10090)

>sp|Q06945|SOX4_HUMAN Transcription factor SOX-4 OS=Homo sapiens GN=SOX4 PE=1 SV=1

 Score = 73.6 bits (179), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL 
Sbjct: 53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLG 94

Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.

Homo sapiens (taxid: 9606)

>sp|P35716|SOX11_HUMAN Transcription factor SOX-11 OS=Homo sapiens GN=SOX11 PE=1 SV=2

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 43 KTASGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 84

Probably important in the developing nervous system. May also have a role in tissue modeling during development.

Homo sapiens (taxid: 9606)

>sp|P40650|SX11B_XENLA Transcription factor Sox-11-B OS=Xenopus laevis GN=sox11-b PE=1 SV=2

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 39 KTATGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 80

Binds to the DNA sequence 5'-AACAAT-3'. Plays a role together with nlk in neural induction during early embryogenesis.

Xenopus laevis (taxid: 8355)

>sp|P48435|SOX11_CHICK Transcription factor SOX-11 OS=Gallus gallus GN=SOX11 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 43 KTASGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 84

May function as a switch in neuronal development.

Gallus gallus (taxid: 9031)

>sp|Q91731|SX11A_XENLA Transcription factor Sox-11-A OS=Xenopus laevis GN=sox11-a PE=1 SV=2

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 41 KTATGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 82

Binds to the DNA sequence 5'-AACAAT-3'. Plays a role together with nlk in neural induction during early embryogenesis.

Xenopus laevis (taxid: 8355)

>sp|P0C1G9|SOX11_RAT Transcription factor SOX-11 OS=Rattus norvegicus GN=Sox11 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 43 KTASGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 84

Probably important in the developing nervous system. May also have a role in tissue modeling during development.

Rattus norvegicus (taxid: 10116)

>sp|Q7M6Y2|SOX11_MOUSE Transcription factor SOX-11 OS=Mus musculus GN=Sox11 PE=1 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 43 KTASGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 84

Probably important in the developing nervous system. May also have a role in tissue modeling during development.

Mus musculus (taxid: 10090)

>sp|Q66JF1|SOX11_XENTR Transcription factor Sox-11 OS=Xenopus tropicalis GN=sox11 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 34/42 (80%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          K    HIKRPMNAFMVWS++ERRKI E  PDMHNAEISKRL 
Sbjct: 42 KTATGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLG 83

Binds to the DNA sequence 5'-AACAAT-3'. Plays a role together with nlk in neural induction during early embryogenesis.

Xenopus tropicalis (taxid: 8364)

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	74
328791162	558	PREDICTED: hypothetical protein LOC72691	0.675	0.089	0.86	8e-20
380025154	560	PREDICTED: uncharacterized protein LOC10	0.675	0.089	0.86	2e-19
340713694	609	PREDICTED: hypothetical protein LOC10064	0.675	0.082	0.86	2e-19
383863867	477	PREDICTED: uncharacterized protein LOC10	0.675	0.104	0.86	3e-19
350417431	567	PREDICTED: hypothetical protein LOC10074	0.675	0.088	0.86	3e-19
270009646	306	hypothetical protein TcasGA2_TC008936 [T	0.675	0.163	0.86	2e-18
91086963	312	PREDICTED: similar to Putative transcrip	0.675	0.160	0.86	2e-18
345495794	450	PREDICTED: hypothetical protein LOC10012	0.675	0.111	0.84	5e-18
242009279	455	transcription factor Sox-2, putative [Pe	0.608	0.098	0.911	1e-17
328717332	503	PREDICTED: hypothetical protein LOC10057	0.689	0.101	0.803	8e-17

>gi|328791162|ref|XP_001122631.2| PREDICTED: hypothetical protein LOC726914 [Apis mellifera]

 Score =  100 bits (250), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICE+QPDMHNAEISKRL 
Sbjct: 15 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEIQPDMHNAEISKRLG 64

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025154|ref|XP_003696344.1| PREDICTED: uncharacterized protein LOC100871310 [Apis florea]

 Score = 99.8 bits (247), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICE+QPDMHNAEISKRL 
Sbjct: 30 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEIQPDMHNAEISKRLG 79

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340713694|ref|XP_003395374.1| PREDICTED: hypothetical protein LOC100647727 [Bombus terrestris]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICE+QPDMHNAEISKRL 
Sbjct: 30 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEIQPDMHNAEISKRLG 79

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383863867|ref|XP_003707401.1| PREDICTED: uncharacterized protein LOC100875283 [Megachile rotundata]

 Score = 99.4 bits (246), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICE+QPDMHNAEISKRL 
Sbjct: 15 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEIQPDMHNAEISKRLG 64

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350417431|ref|XP_003491419.1| PREDICTED: hypothetical protein LOC100743868 [Bombus impatiens]

 Score = 99.0 bits (245), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICE+QPDMHNAEISKRL 
Sbjct: 15 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEIQPDMHNAEISKRLG 64

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270009646|gb|EFA06094.1| hypothetical protein TcasGA2_TC008936 [Tribolium castaneum]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICEVQPDMHNAEISK+L 
Sbjct: 30 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEVQPDMHNAEISKKLG 79

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91086963|ref|XP_973116.1| PREDICTED: similar to Putative transcription factor SOX-14 [Tribolium castaneum]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKICEVQPDMHNAEISK+L 
Sbjct: 36 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICEVQPDMHNAEISKKLG 85

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345495794|ref|XP_003427576.1| PREDICTED: hypothetical protein LOC100123293 [Nasonia vitripennis]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/50 (84%), Positives = 44/50 (88%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKIC +QPDMHNAEISKRL 
Sbjct: 30 YSDATQTKKNNPNHIKRPMNAFMVWSQIERRKICSIQPDMHNAEISKRLG 79

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242009279|ref|XP_002425417.1| transcription factor Sox-2, putative [Pediculus humanus corporis] gi|212509234|gb|EEB12679.1| transcription factor Sox-2, putative [Pediculus humanus corporis]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/45 (91%), Positives = 43/45 (95%)

Query: 9  ATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           TKK+NPNHIKRPMNAFMVWSQ+ERRKICEVQPDMHNAEISKRL 
Sbjct: 5  GTKKHNPNHIKRPMNAFMVWSQIERRKICEVQPDMHNAEISKRLG 49

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328717332|ref|XP_003246175.1| PREDICTED: hypothetical protein LOC100571300 [Acyrthosiphon pisum]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 43/51 (84%)

Query: 4  YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLAL 54
          YS    TKKNNPNHIKRPMNAFMVWSQ+ERRKIC  QPDMHNAEISK L +
Sbjct: 36 YSDATQTKKNNPNHIKRPMNAFMVWSQLERRKICNDQPDMHNAEISKMLGV 86

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

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	74
FB|FBgn0005612	669	Sox14 "Sox box protein 14" [Dr	0.662	0.073	0.775	2.1e-15
WB|WBGene00004771	404	sem-2 [Caenorhabditis elegans	0.648	0.118	0.795	4e-15
UNIPROTKB|I3LK63	261	SOX12 "Uncharacterized protein	0.567	0.160	0.809	7.1e-13
ZFIN|ZDB-GENE-040426-1274	342	sox4b "SRY-box containing gene	0.554	0.119	0.804	1.8e-12
UNIPROTKB|E2RLZ6	356	SOX4 "Uncharacterized protein"	0.554	0.115	0.804	2.1e-12
UNIPROTKB|G3MYL8	378	G3MYL8 "Uncharacterized protei	0.554	0.108	0.804	2.4e-12
MGI|MGI:98366	440	Sox4 "SRY-box containing gene	0.554	0.093	0.804	3.5e-12
RGD|1309488	440	Sox4 "SRY (sex determining reg	0.554	0.093	0.804	3.5e-12
UNIPROTKB|Q06945	474	SOX4 "Transcription factor SOX	0.554	0.086	0.804	4.1e-12
UNIPROTKB|F1RUF9	477	SOX4 "Uncharacterized protein"	0.554	0.085	0.804	4.1e-12

FB|FBgn0005612 Sox14 "Sox box protein 14" [Drosophila melanogaster (taxid:7227)]

 Score = 204 (76.9 bits), Expect = 2.1e-15, P = 2.1e-15
 Identities = 38/49 (77%), Positives = 41/49 (83%)

Query:     4 YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             YS    TKK++P HIKRPMNAFMVWSQMERRKICE  PD+HNAEISK L
Sbjct:   173 YSDATRTKKHSPGHIKRPMNAFMVWSQMERRKICERTPDLHNAEISKEL 221

GO:0005634 "nucleus" evidence=ISS;IMP;NAS

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

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

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

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

GO:0016322 "neuron remodeling" evidence=IGI

GO:0048813 "dendrite morphogenesis" evidence=IGI

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

GO:0007552 "metamorphosis" evidence=IMP

WB|WBGene00004771 sem-2 [Caenorhabditis elegans (taxid:6239)]

 Score = 197 (74.4 bits), Expect = 4.0e-15, P = 4.0e-15
 Identities = 39/49 (79%), Positives = 42/49 (85%)

Query:     4 YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             YS     KK++ NHIKRPMNAFMVWSQMERRKICE QPDMHNAEISK+L
Sbjct:    80 YSDATNCKKSS-NHIKRPMNAFMVWSQMERRKICEHQPDMHNAEISKQL 127

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|I3LK63 SOX12 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 34/42 (80%), Positives = 34/42 (80%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
             K    HIKRPMNAFMVWSQ ERRKI E  PDMHNAEISKRLA
Sbjct:    34 KTPSGHIKRPMNAFMVWSQHERRKIMEQWPDMHNAEISKRLA 75

GO:0065004 "protein-DNA complex assembly" evidence=IEA

GO:0045165 "cell fate commitment" evidence=IEA

GO:0032993 "protein-DNA complex" evidence=IEA

GO:0021510 "spinal cord development" evidence=IEA

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1274 sox4b "SRY-box containing gene 4b" [Danio rerio (taxid:7955)]

 Score = 171 (65.3 bits), Expect = 1.8e-12, P = 1.8e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    49 KTASGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 89

GO:0031018 "endocrine pancreas development" evidence=IMP

UNIPROTKB|E2RLZ6 SOX4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 171 (65.3 bits), Expect = 2.1e-12, P = 2.1e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 93

GO:2000761 "positive regulation of N-terminal peptidyl-lysine acetylation" evidence=IEA

GO:0090263 "positive regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0071333 "cellular response to glucose stimulus" evidence=IEA

GO:0060993 "kidney morphogenesis" evidence=IEA

GO:0060563 "neuroepithelial cell differentiation" evidence=IEA

GO:0060412 "ventricular septum morphogenesis" evidence=IEA

GO:0060174 "limb bud formation" evidence=IEA

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=IEA

GO:0050821 "protein stabilization" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IEA

GO:0046826 "negative regulation of protein export from nucleus" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0042769 "DNA damage response, detection of DNA damage" evidence=IEA

GO:0035910 "ascending aorta morphogenesis" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0032024 "positive regulation of insulin secretion" evidence=IEA

GO:0031397 "negative regulation of protein ubiquitination" evidence=IEA

GO:0031018 "endocrine pancreas development" evidence=IEA

GO:0030217 "T cell differentiation" evidence=IEA

GO:0021782 "glial cell development" evidence=IEA

GO:0021522 "spinal cord motor neuron differentiation" evidence=IEA

GO:0014009 "glial cell proliferation" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003357 "noradrenergic neuron differentiation" evidence=IEA

GO:0003289 "atrial septum primum morphogenesis" evidence=IEA

GO:0003215 "cardiac right ventricle morphogenesis" evidence=IEA

GO:0003211 "cardiac ventricle formation" evidence=IEA

GO:0003183 "mitral valve morphogenesis" evidence=IEA

GO:0002328 "pro-B cell differentiation" evidence=IEA

GO:0001841 "neural tube formation" evidence=IEA

GO:0001501 "skeletal system development" evidence=IEA

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0001046 "core promoter sequence-specific DNA binding" evidence=IEA

UNIPROTKB|G3MYL8 G3MYL8 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 171 (65.3 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 93

GO:2000761 "positive regulation of N-terminal peptidyl-lysine acetylation" evidence=IEA

GO:0090263 "positive regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0071333 "cellular response to glucose stimulus" evidence=IEA

GO:0060993 "kidney morphogenesis" evidence=IEA

GO:0060563 "neuroepithelial cell differentiation" evidence=IEA

GO:0060412 "ventricular septum morphogenesis" evidence=IEA

GO:0060174 "limb bud formation" evidence=IEA

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=IEA

GO:0050821 "protein stabilization" evidence=IEA

GO:0048485 "sympathetic nervous system development" evidence=IEA

GO:0046826 "negative regulation of protein export from nucleus" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0042769 "DNA damage response, detection of DNA damage" evidence=IEA

GO:0035910 "ascending aorta morphogenesis" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0032024 "positive regulation of insulin secretion" evidence=IEA

GO:0031397 "negative regulation of protein ubiquitination" evidence=IEA

GO:0031018 "endocrine pancreas development" evidence=IEA

GO:0030217 "T cell differentiation" evidence=IEA

GO:0021782 "glial cell development" evidence=IEA

GO:0021522 "spinal cord motor neuron differentiation" evidence=IEA

GO:0014009 "glial cell proliferation" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003357 "noradrenergic neuron differentiation" evidence=IEA

GO:0003289 "atrial septum primum morphogenesis" evidence=IEA

GO:0003215 "cardiac right ventricle morphogenesis" evidence=IEA

GO:0003211 "cardiac ventricle formation" evidence=IEA

GO:0003183 "mitral valve morphogenesis" evidence=IEA

GO:0002328 "pro-B cell differentiation" evidence=IEA

GO:0001841 "neural tube formation" evidence=IEA

GO:0001501 "skeletal system development" evidence=IEA

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

GO:0001046 "core promoter sequence-specific DNA binding" evidence=IEA

MGI|MGI:98366 Sox4 "SRY-box containing gene 4" [Mus musculus (taxid:10090)]

 Score = 171 (65.3 bits), Expect = 3.5e-12, P = 3.5e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 93

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IDA

GO:0001046 "core promoter sequence-specific DNA binding" evidence=ISO;IDA

GO:0001071 "nucleic acid binding transcription factor activity" evidence=ISO;IDA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=ISO;IDA

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=IDA

GO:0001501 "skeletal system development" evidence=IMP

GO:0001666 "response to hypoxia" evidence=ISO

GO:0001841 "neural tube formation" evidence=IMP

GO:0002328 "pro-B cell differentiation" evidence=IMP

GO:0003183 "mitral valve morphogenesis" evidence=IMP

GO:0003211 "cardiac ventricle formation" evidence=IMP

GO:0003215 "cardiac right ventricle morphogenesis" evidence=IMP

GO:0003289 "atrial septum primum morphogenesis" evidence=IMP

GO:0003357 "noradrenergic neuron differentiation" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO

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

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

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=ISO

GO:0007507 "heart development" evidence=IMP

GO:0008284 "positive regulation of cell proliferation" evidence=ISO;IMP

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0014009 "glial cell proliferation" evidence=IMP

GO:0021510 "spinal cord development" evidence=IMP

GO:0021522 "spinal cord motor neuron differentiation" evidence=IMP

GO:0021782 "glial cell development" evidence=IMP

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=IMP

GO:0030217 "T cell differentiation" evidence=IMP

GO:0031018 "endocrine pancreas development" evidence=IMP

GO:0031397 "negative regulation of protein ubiquitination" evidence=ISO

GO:0031647 "regulation of protein stability" evidence=ISO

GO:0032024 "positive regulation of insulin secretion" evidence=IMP

GO:0035019 "somatic stem cell maintenance" evidence=IDA

GO:0035910 "ascending aorta morphogenesis" evidence=IMP

GO:0042593 "glucose homeostasis" evidence=IMP

GO:0042769 "DNA damage response, detection of DNA damage" evidence=ISO

GO:0043065 "positive regulation of apoptotic process" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0045727 "positive regulation of translation" evidence=ISO

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

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

GO:0046826 "negative regulation of protein export from nucleus" evidence=ISO

GO:0048485 "sympathetic nervous system development" evidence=IMP

GO:0050821 "protein stabilization" evidence=ISO;IMP

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=IMP

GO:0060174 "limb bud formation" evidence=IMP

GO:0060412 "ventricular septum morphogenesis" evidence=IMP

GO:0060548 "negative regulation of cell death" evidence=IMP

GO:0060563 "neuroepithelial cell differentiation" evidence=IMP

GO:0060993 "kidney morphogenesis" evidence=IMP

GO:0071333 "cellular response to glucose stimulus" evidence=IMP

GO:0090263 "positive regulation of canonical Wnt receptor signaling pathway" evidence=IDA

GO:2000761 "positive regulation of N-terminal peptidyl-lysine acetylation" evidence=ISO

RGD|1309488 Sox4 "SRY (sex determining region Y)-box 4" [Rattus norvegicus (taxid:10116)]

 Score = 171 (65.3 bits), Expect = 3.5e-12, P = 3.5e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 93

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=ISO

GO:0001046 "core promoter sequence-specific DNA binding" evidence=ISO

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

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=ISO

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=ISO

GO:0001501 "skeletal system development" evidence=ISO

GO:0001666 "response to hypoxia" evidence=IDA

GO:0001841 "neural tube formation" evidence=ISO

GO:0002328 "pro-B cell differentiation" evidence=ISO

GO:0003183 "mitral valve morphogenesis" evidence=ISO

GO:0003211 "cardiac ventricle formation" evidence=ISO

GO:0003215 "cardiac right ventricle morphogenesis" evidence=ISO

GO:0003289 "atrial septum primum morphogenesis" evidence=ISO

GO:0003357 "noradrenergic neuron differentiation" evidence=ISO

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

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005739 "mitochondrion" evidence=ISO

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

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=ISO

GO:0007507 "heart development" evidence=ISO

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0014009 "glial cell proliferation" evidence=ISO

GO:0021510 "spinal cord development" evidence=ISO

GO:0021522 "spinal cord motor neuron differentiation" evidence=ISO

GO:0021782 "glial cell development" evidence=ISO

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=ISO

GO:0030217 "T cell differentiation" evidence=ISO

GO:0031018 "endocrine pancreas development" evidence=ISO

GO:0031397 "negative regulation of protein ubiquitination" evidence=ISO

GO:0031647 "regulation of protein stability" evidence=ISO

GO:0032024 "positive regulation of insulin secretion" evidence=ISO

GO:0035019 "somatic stem cell maintenance" evidence=ISO

GO:0035910 "ascending aorta morphogenesis" evidence=ISO

GO:0042593 "glucose homeostasis" evidence=ISO

GO:0042769 "DNA damage response, detection of DNA damage" evidence=ISO

GO:0043065 "positive regulation of apoptotic process" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0045727 "positive regulation of translation" evidence=ISO

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

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

GO:0046826 "negative regulation of protein export from nucleus" evidence=ISO

GO:0048485 "sympathetic nervous system development" evidence=ISO

GO:0050821 "protein stabilization" evidence=ISO

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=ISO

GO:0060174 "limb bud formation" evidence=ISO

GO:0060412 "ventricular septum morphogenesis" evidence=ISO

GO:0060548 "negative regulation of cell death" evidence=ISO

GO:0060563 "neuroepithelial cell differentiation" evidence=ISO

GO:0060993 "kidney morphogenesis" evidence=ISO

GO:0071333 "cellular response to glucose stimulus" evidence=ISO

GO:0090263 "positive regulation of canonical Wnt receptor signaling pathway" evidence=ISO

GO:2000761 "positive regulation of N-terminal peptidyl-lysine acetylation" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q06945 SOX4 "Transcription factor SOX-4" [Homo sapiens (taxid:9606)]

 Score = 171 (65.3 bits), Expect = 4.1e-12, P = 4.1e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 93

GO:0031018 "endocrine pancreas development" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0032024 "positive regulation of insulin secretion" evidence=ISS

GO:0071333 "cellular response to glucose stimulus" evidence=ISS

GO:0001046 "core promoter sequence-specific DNA binding" evidence=IDA

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

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

GO:0042593 "glucose homeostasis" evidence=ISS

GO:0090263 "positive regulation of canonical Wnt receptor signaling pathway" evidence=ISS

GO:0045727 "positive regulation of translation" evidence=IMP

GO:0042769 "DNA damage response, detection of DNA damage" evidence=IDA

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

GO:0001841 "neural tube formation" evidence=ISS

GO:0003357 "noradrenergic neuron differentiation" evidence=ISS

GO:0014009 "glial cell proliferation" evidence=ISS

GO:0021522 "spinal cord motor neuron differentiation" evidence=ISS

GO:0060174 "limb bud formation" evidence=ISS

GO:0060563 "neuroepithelial cell differentiation" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IDA

GO:0048485 "sympathetic nervous system development" evidence=ISS

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=ISS

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=ISS

GO:0031397 "negative regulation of protein ubiquitination" evidence=IMP

GO:0046826 "negative regulation of protein export from nucleus" evidence=IMP

GO:2000761 "positive regulation of N-terminal peptidyl-lysine acetylation" evidence=IDA

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=IMP

GO:0043065 "positive regulation of apoptotic process" evidence=IMP

GO:0008285 "negative regulation of cell proliferation" evidence=IMP

GO:0031647 "regulation of protein stability" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0001501 "skeletal system development" evidence=ISS

GO:0003211 "cardiac ventricle formation" evidence=ISS

GO:0021510 "spinal cord development" evidence=ISS

GO:0021782 "glial cell development" evidence=ISS

GO:0060548 "negative regulation of cell death" evidence=ISS

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

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

GO:0007507 "heart development" evidence=ISS

GO:0030217 "T cell differentiation" evidence=ISS

GO:0002328 "pro-B cell differentiation" evidence=ISS

GO:0005737 "cytoplasm" evidence=IDA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0050821 "protein stabilization" evidence=IMP

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=ISS

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=ISS

GO:0003289 "atrial septum primum morphogenesis" evidence=ISS

GO:0003183 "mitral valve morphogenesis" evidence=ISS

GO:0060412 "ventricular septum morphogenesis" evidence=ISS

GO:0003215 "cardiac right ventricle morphogenesis" evidence=ISS

GO:0060993 "kidney morphogenesis" evidence=ISS

GO:0035910 "ascending aorta morphogenesis" evidence=ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|F1RUF9 SOX4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 171 (65.3 bits), Expect = 4.1e-12, P = 4.1e-12
 Identities = 33/41 (80%), Positives = 34/41 (82%)

Query:    12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
             K    HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct:    53 KTPSGHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 93

GO:0060174 "limb bud formation" evidence=ISS

GO:0008284 "positive regulation of cell proliferation" evidence=ISS

GO:0002328 "pro-B cell differentiation" evidence=ISS

GO:0060563 "neuroepithelial cell differentiation" evidence=ISS

GO:0021522 "spinal cord motor neuron differentiation" evidence=ISS

GO:0014009 "glial cell proliferation" evidence=ISS

GO:0003357 "noradrenergic neuron differentiation" evidence=ISS

GO:0001841 "neural tube formation" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISS

GO:0046826 "negative regulation of protein export from nucleus" evidence=ISS

GO:0031647 "regulation of protein stability" evidence=ISS

GO:2000761 "positive regulation of N-terminal peptidyl-lysine acetylation" evidence=ISS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=ISS

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=ISS

GO:0007507 "heart development" evidence=ISS

GO:0030217 "T cell differentiation" evidence=ISS

GO:0090263 "positive regulation of canonical Wnt receptor signaling pathway" evidence=ISS

GO:0042593 "glucose homeostasis" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

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

GO:0001046 "core promoter sequence-specific DNA binding" evidence=ISS

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

GO:0060548 "negative regulation of cell death" evidence=ISS

GO:0021782 "glial cell development" evidence=ISS

GO:0021510 "spinal cord development" evidence=ISS

GO:0003211 "cardiac ventricle formation" evidence=ISS

GO:0001501 "skeletal system development" evidence=ISS

GO:0045727 "positive regulation of translation" evidence=ISS

GO:0042769 "DNA damage response, detection of DNA damage" evidence=ISS

GO:0031397 "negative regulation of protein ubiquitination" evidence=ISS

GO:0008285 "negative regulation of cell proliferation" evidence=ISS

GO:0001105 "RNA polymerase II transcription coactivator activity" evidence=ISS

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=ISS

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=ISS

GO:0048485 "sympathetic nervous system development" evidence=ISS

GO:0043066 "negative regulation of apoptotic process" evidence=ISS

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

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

GO:0050821 "protein stabilization" evidence=ISS

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

GO:0043065 "positive regulation of apoptotic process" evidence=ISS

GO:0030177 "positive regulation of Wnt receptor signaling pathway" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0071333 "cellular response to glucose stimulus" evidence=ISS

GO:0032024 "positive regulation of insulin secretion" evidence=ISS

GO:0060993 "kidney morphogenesis" evidence=IEA

GO:0060412 "ventricular septum morphogenesis" evidence=IEA

GO:0035910 "ascending aorta morphogenesis" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0031018 "endocrine pancreas development" evidence=IEA

GO:0003289 "atrial septum primum morphogenesis" evidence=IEA

GO:0003215 "cardiac right ventricle morphogenesis" evidence=IEA

GO:0003183 "mitral valve morphogenesis" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q06945	SOX4_HUMAN	No assigned EC number	0.7857	0.5675	0.0886	yes	N/A
P40656	SOX14_DROME	No assigned EC number	0.76	0.6756	0.0747	yes	N/A
Q06831	SOX4_MOUSE	No assigned EC number	0.7857	0.5675	0.0954	yes	N/A

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	74
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	9e-13
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	1e-09
smart00398	70	smart00398, HMG, high mobility group	1e-09
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-09
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	6e-06
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	4e-05
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	2e-04

>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 = 56.5 bits (137), Expect = 9e-13
 Identities = 20/37 (54%), Positives = 25/37 (67%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          HIKRPMNAFM++S+  RRK+ +  P   N  ISK L 
Sbjct: 1  HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILG 37

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 = 48.8 bits (117), Expect = 1e-09
 Identities = 17/36 (47%), Positives = 24/36 (66%)

Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           KRP++AF ++SQ +R K+    P + NAEISK L 
Sbjct: 1  PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILG 36

Length = 69

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

 Score = 48.5 bits (116), Expect = 1e-09
 Identities = 21/37 (56%), Positives = 26/37 (70%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
            KRPM+AFM++SQ  R KI    PD+ NAEISK+L 
Sbjct: 1  KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLG 37

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 = 47.2 bits (113), Expect = 4e-09
 Identities = 13/36 (36%), Positives = 21/36 (58%)

Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           KRP++A+ ++SQ  R ++    P +   EISK L 
Sbjct: 1  PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILG 36

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

>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

 Score = 39.1 bits (92), Expect = 6e-06
 Identities = 13/35 (37%), Positives = 23/35 (65%)

Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          KRP++A+ ++SQ +R K+ +  PD    E++K L 
Sbjct: 2  KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILG 36

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. Length = 66

>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 39.1 bits (91), Expect = 4e-05
 Identities = 16/49 (32%), Positives = 27/49 (55%)

Query: 5   SPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           S     KK +PN  KRP++A+ ++S   R +I +  P +   E+ K L+
Sbjct: 58  SKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLS 106

Length = 211

>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 35.3 bits (82), Expect = 2e-04
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           I RP NAF+++ Q +  ++    P + N EIS+ + 
Sbjct: 1  KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIG 37

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. Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	74
KOG0527|consensus	331		99.91
PTZ00199	94	high mobility group protein; Provisional	99.87
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.86
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.86
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.8
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.77
smart00398	70	HMG high mobility group.	99.76
KOG0528|consensus	511		99.76
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.76
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.76
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.66
KOG0381|consensus	96		99.64
KOG3248|consensus	421		99.47
KOG0526|consensus	615		99.4
KOG2746|consensus	683		99.16
KOG4715|consensus	410		98.8
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	98.05
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	97.33
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	96.93
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	96.93
COG5648	211	NHP6B Chromatin-associated proteins containing the	93.13
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	92.98
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	88.5
KOG3223|consensus	221		83.09

>KOG0527|consensus

Probab=99.91  E-value=3.5e-25  Score=163.48  Aligned_cols=62  Identities=45%  Similarity=0.651  Sum_probs=59.1

Q ss_pred             ccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHh
Q psy5107          10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQL   71 (74)
Q Consensus        10 ~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~   71 (74)
                      ..++..+||||||||||+|++++|++|.++||+|+|+||||+||.+|+.|+++||+||+|++
T Consensus        55 ~~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EA  116 (331)
T KOG0527|consen   55 KDKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEA  116 (331)
T ss_pred             cCCCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHH
Confidence            45667789999999999999999999999999999999999999999999999999999986

>PTZ00199 high mobility group protein; Provisional

Probab=99.87  E-value=6.9e-22  Score=122.93  Aligned_cols=66  Identities=21%  Similarity=0.251  Sum_probs=60.9

Q ss_pred             CccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           7 MRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMH--NAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         7 ~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~--~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+.++++||+.||||+||||+|++++|..|..+||+++  +++||++||++|+.||++||.+|.+.+.
T Consensus        12 ~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~   79 (94)
T PTZ00199         12 KNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQ   79 (94)
T ss_pred             ccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34566789999999999999999999999999999997  8999999999999999999999988764

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

Probab=99.86  E-value=8.2e-22  Score=117.63  Aligned_cols=56  Identities=25%  Similarity=0.316  Sum_probs=54.0

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +||||+||||+|+++.|..|+++||+++++|||++||++|+.|+++||.+|.+.+.
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~   56 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAE   56 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999998764

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=99.86  E-value=9.5e-22  Score=116.22  Aligned_cols=56  Identities=41%  Similarity=0.385  Sum_probs=54.2

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      |||||+||||+|++++|..|+++||++++.|||++||++|+.||++||.+|.+.+.
T Consensus         1 ~iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~   56 (72)
T cd01388           1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAK   56 (72)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999998875

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.

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

Probab=99.80  E-value=1.5e-19  Score=103.34  Aligned_cols=55  Identities=27%  Similarity=0.271  Sum_probs=53.1

Q ss_pred             CCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        18 pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ||||+||||+|++++|..++.+||++++.+|++.||++|+.||++||.+|.+.+.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~   55 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAE   55 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999999999999999998764

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.

>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=99.77  E-value=5.5e-19  Score=101.94  Aligned_cols=55  Identities=38%  Similarity=0.393  Sum_probs=51.0

Q ss_pred             CCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        18 pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ||||+||||+|+++++..++.+||++++.+|+++||.+|+.||++||.+|.+.+.
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~   55 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAE   55 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999999999999999988764

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=99.76  E-value=2.1e-18  Score=98.88  Aligned_cols=56  Identities=41%  Similarity=0.427  Sum_probs=53.4

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .||||+||||+|+++.|..+..+||++++++|+++||.+|+.||++||.+|.+.+.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~   56 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAK   56 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            48999999999999999999999999999999999999999999999999988753

>KOG0528|consensus

Probab=99.76  E-value=2.4e-19  Score=137.30  Aligned_cols=60  Identities=48%  Similarity=0.597  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQL   71 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~   71 (74)
                      -..+.||||||||||.|+++.|++|.+.+|+++|.+|||+||..|+.||.-||+||.|+-
T Consensus       320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQ  379 (511)
T KOG0528|consen  320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQ  379 (511)
T ss_pred             CCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHH
Confidence            345679999999999999999999999999999999999999999999999999999873

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

Probab=99.76  E-value=2.1e-18  Score=97.87  Aligned_cols=55  Identities=27%  Similarity=0.285  Sum_probs=52.9

Q ss_pred             CCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        18 pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ||||+||||+|+++.|..++.+||+++..+|++.+|.+|+.|+++||.+|.+.+.
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~   55 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAE   55 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999999999999999998763

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

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

Probab=99.76  E-value=1.2e-18  Score=122.24  Aligned_cols=64  Identities=23%  Similarity=0.288  Sum_probs=61.3

Q ss_pred             cccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           9 ATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         9 ~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .++++|||.||||++|||+|+.++|.+|++.+|++++.+|++++|++|+.|++.||.||-+.+.
T Consensus        62 ~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~  125 (211)
T COG5648          62 VRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEAN  125 (211)
T ss_pred             HHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHh
Confidence            5778999999999999999999999999999999999999999999999999999999988764

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

Probab=99.66  E-value=1.6e-16  Score=93.97  Aligned_cols=58  Identities=19%  Similarity=0.139  Sum_probs=50.5

Q ss_pred             CCCCCCCCchhHhHhHHHHHHHHHh-CCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          15 PNHIKRPMNAFMVWSQMERRKICEV-QPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        15 ~~~pKRP~nAfmlf~~~~R~~i~~~-~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      |++||||+|||++|+++++..++.. .+.....|+++.+|..|+.||++||.+|.+++.
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~   59 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAK   59 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            6789999999999999999999999 788889999999999999999999999999874

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 ....

>KOG0381|consensus

Probab=99.64  E-value=5.6e-16  Score=94.79  Aligned_cols=56  Identities=27%  Similarity=0.381  Sum_probs=53.1

Q ss_pred             CC--CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHH
Q psy5107          14 NP--NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAE   69 (74)
Q Consensus        14 ~~--~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e   69 (74)
                      ++  +.||||++||++|+++.|..++.+||++++.||++.+|++|..|+++||.+|-+
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~   74 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEE   74 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            66  499999999999999999999999999999999999999999999999999843

>KOG3248|consensus

Probab=99.47  E-value=4.4e-14  Score=105.62  Aligned_cols=67  Identities=22%  Similarity=0.175  Sum_probs=59.7

Q ss_pred             CCccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           6 PMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         6 ~~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.+++.+....|||.|+||||+|++++|++|.+++......+|.++||..|-.||.+|.-.|+|.++
T Consensus       180 ~~k~e~e~KkphiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElAr  246 (421)
T KOG3248|consen  180 ESKKEEEAKKPHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELAR  246 (421)
T ss_pred             hccccccccCccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHH
Confidence            3444445345699999999999999999999999998889999999999999999999999999876

>KOG0526|consensus

Probab=99.40  E-value=2.9e-13  Score=105.40  Aligned_cols=57  Identities=26%  Similarity=0.423  Sum_probs=53.5

Q ss_pred             CccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcch
Q psy5107           7 MRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNW   65 (74)
Q Consensus         7 ~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~   65 (74)
                      .+++|++|||+||||++|||+|.+..|..|+.+  +.+++||+|.+|++|+.||..|+|
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~k~~w  581 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSAKEEW  581 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcccchh
Confidence            466788999999999999999999999999998  999999999999999999997776

>KOG2746|consensus

Probab=99.16  E-value=1.7e-11  Score=97.08  Aligned_cols=66  Identities=29%  Similarity=0.429  Sum_probs=60.9

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHH--HHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhhc
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMER--RKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLFS   73 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R--~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~~   73 (74)
                      +...|.+..|++|||||||+|++.+|  ..+.+.||+.+|.-||++||+.|-.|-..||+.|--.++|
T Consensus       172 rspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Q  239 (683)
T KOG2746|consen  172 RSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQ  239 (683)
T ss_pred             CCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHH
Confidence            44566778899999999999999999  9999999999999999999999999999999999877765

>KOG4715|consensus

Probab=98.80  E-value=8.8e-09  Score=77.04  Aligned_cols=59  Identities=15%  Similarity=0.205  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHH
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQ   70 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~   70 (74)
                      .+.|..|-+|+-.||.|++..++.|++.||++.-=||+|+||.||+-|.|+||.-|+-+
T Consensus        59 pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~E  117 (410)
T KOG4715|consen   59 PKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNE  117 (410)
T ss_pred             CCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHH
Confidence            34566778999999999999999999999999999999999999999999999988743

>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=98.05  E-value=1.5e-05  Score=55.92  Aligned_cols=59  Identities=27%  Similarity=0.474  Sum_probs=48.2

Q ss_pred             ccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        10 ~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .++....+.+||+|+||.|    |.-.....|+....++|.+|+..|.......+|-+.-.+.
T Consensus        36 ~~~~~~~~~kr~lN~Fm~F----Rsyy~~~~~~~~Qk~~S~~l~~lW~~dp~k~~W~l~ak~y   94 (201)
T PF04769_consen   36 SRKRSPEKAKRPLNGFMAF----RSYYSPIFPPLPQKELSGILTKLWEKDPFKNKWSLMAKAY   94 (201)
T ss_pred             cccccccccccchhHHHHH----HHHHHhhcCCcCHHHHHHHHHHHHhCCccHhHHHHHhhhh
Confidence            3455667899999999999    5545577899999999999999999998888887765443

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=97.33  E-value=0.00054  Score=39.46  Aligned_cols=39  Identities=13%  Similarity=0.109  Sum_probs=35.2

Q ss_pred             CchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCC
Q psy5107          22 MNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKS   60 (74)
Q Consensus        22 ~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s   60 (74)
                      ++.|=+|.+..|+.|.+.||++..+.|-.+++.+||.-+
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~   51 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQ   51 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHH
Confidence            356778999999999999999999999999999998643

; 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

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

Probab=96.93  E-value=0.0014  Score=45.59  Aligned_cols=45  Identities=18%  Similarity=0.088  Sum_probs=41.3

Q ss_pred             CchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHH
Q psy5107          22 MNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQ   70 (74)
Q Consensus        22 ~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~   70 (74)
                      -|||+-|..+.|.+    |.+|+..|+...-+..|..|++.||..|.-+
T Consensus        83 nnaYLNFLReFRrk----h~~L~p~dlI~~AAraW~rLSe~eK~rYrr~  127 (183)
T PF06382_consen   83 NNAYLNFLREFRRK----HCGLSPQDLIQRAARAWCRLSEAEKNRYRRM  127 (183)
T ss_pred             chHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHHhCCHHHHHHHHhh
Confidence            58999998888774    8999999999999999999999999999874

The function of this family is unknown.

>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=96.93  E-value=0.003  Score=43.55  Aligned_cols=46  Identities=20%  Similarity=0.157  Sum_probs=40.6

Q ss_pred             CCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCC
Q psy5107          15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKS   60 (74)
Q Consensus        15 ~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s   60 (74)
                      |.+-.|-++||-.|.++.=++|++.||++++.|.=+..+..|...+
T Consensus       119 PEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  119 PEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             ccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            3344566999999999999999999999999999999999998654

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

Probab=93.13  E-value=0.048  Score=38.81  Aligned_cols=54  Identities=17%  Similarity=0.076  Sum_probs=50.3

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHH
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQ   70 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~   70 (74)
                      .+++|...|+-+....|+.+...+|+-.-.++++.+|..|+.++..-|.+|++.
T Consensus       143 ~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~  196 (211)
T COG5648         143 PNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDK  196 (211)
T ss_pred             CCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHH
Confidence            567889999999999999999999999999999999999999999999999864

>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function

Probab=92.98  E-value=0.28  Score=32.19  Aligned_cols=47  Identities=13%  Similarity=0.113  Sum_probs=40.4

Q ss_pred             CCCCC-CCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCC
Q psy5107          15 PNHIK-RPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSN   61 (74)
Q Consensus        15 ~~~pK-RP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~   61 (74)
                      ..||- |-.-||--|.-.+=+.|+++||+|.-+++-.+|-.+|..-++
T Consensus        69 drHPErR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   69 DRHPERRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             CCCcchhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCC
Confidence            34654 555899999999999999999999999999999999987654

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=88.50  E-value=2.1  Score=26.49  Aligned_cols=53  Identities=9%  Similarity=0.006  Sum_probs=41.3

Q ss_pred             CCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHh
Q psy5107          18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQL   71 (74)
Q Consensus        18 pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~   71 (74)
                      |.-|-++==+|-+.......+.++.-...+. +.++..|..|++.||-+.+--+
T Consensus         4 PE~PKt~qe~Wqq~vi~dYla~~~~dr~K~~-kam~~~W~~me~Kekl~WIkKA   56 (85)
T PF14887_consen    4 PETPKTAQEIWQQSVIGDYLAKFRNDRKKAL-KAMEAQWSQMEKKEKLKWIKKA   56 (85)
T ss_dssp             S----THHHHHHHHHHHHHHHHTTSTHHHHH-HHHHHHHHTTGGGHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhhHhHHHHH-HHHHHHHHHhhhhhhhHHHHHH
Confidence            4556777788999888888888998887774 4999999999999999887544

>KOG3223|consensus

Probab=83.09  E-value=0.99  Score=32.18  Aligned_cols=46  Identities=15%  Similarity=0.177  Sum_probs=40.7

Q ss_pred             CCC-CCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCC
Q psy5107          16 NHI-KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSN   61 (74)
Q Consensus        16 ~~p-KRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~   61 (74)
                      .|| ||-.-||--|-..+-++|+.+||++..++.-.+|-.+|..-+|
T Consensus       162 rHPEkRmrAA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPD  208 (221)
T KOG3223|consen  162 RHPEKRMRAAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPD  208 (221)
T ss_pred             cChHHHHHHHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCC
Confidence            454 6777889999999999999999999999999999999987665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	74
3u2b_C	79	Structure Of The Sox4 Hmg Domain Bound To Dna Lengt		2e-13
1o4x_B	88	Ternary Complex Of The Dna Binding Domains Of The O		4e-10
4euw_A	106	Crystal Structure Of A Hmg Domain Of Transcription		9e-10
1i11_A	81	Solution Structure Of The Dna Binding Domain, Sox-5		1e-09
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
2yul_A	82	Solution Structure Of The Hmg Box Of Human Transcri		2e-08
4a3n_A	71	Crystal Structure Of Hmg-Box Of Human Sox17 Length		5e-08
3f27_D	83	Structure Of Sox17 Bound To Dna Length = 83		5e-08
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		1e-06
1j46_A	85	3d Solution Nmr Structure Of The Wild Type Hmg-Box		1e-06
1hrz_A	76	The 3d Structure Of The Human Sry-Dna Complex Solve		2e-06
1j47_A	85	3d Solution Nmr Structure Of The M9i Mutant Of The		4e-06

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/38 (84%), Positives = 33/38 (86%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL 
Sbjct: 1  GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLG 38

>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 = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 32/39 (82%)
Query: 15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          P+ +KRPMNAFMVWS+ +RRK+ +  P MHN+EISKRL 
Sbjct: 5  PDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 43

>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 = 58.5 bits (140), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 27/46 (58%), Positives = 34/46 (73%), Gaps = 1/46 (2%)
Query: 10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
          + KN P H+KRPMNAFMVW+Q  RRK+ +  P +HNAE+SK L  L
Sbjct: 23 SSKNKP-HVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKL 67

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)
Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          HIKRPMNAFMVW++ ERRKI +  PDMHN+ ISK L 
Sbjct: 4  HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILG 40

>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 = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 31/38 (81%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAFMVWS+ +RRK+ +  P MHN+EISKRL 
Sbjct: 2  DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 39

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 31/38 (81%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAFMVWS+ +RRK+ +  P MHN+EISKRL 
Sbjct: 1  DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 38

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          I+RPMNAFMVW++ ER+++ +  PD+HNAE+SK L 
Sbjct: 8  IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 43

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          I+RPMNAFMVW++ ER+++ +  PD+HNAE+SK L 
Sbjct: 3  IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 38

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          I+RPMNAFMVW++ ER+++ +  PD+HNAE+SK L 
Sbjct: 7  IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 42

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L 
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40

>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 = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 9/52 (17%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLL 67
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L         G+ W +
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQL---------GYQWKM 45

>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 = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L 
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40

>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 = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 9/52 (17%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLL 67
          + +KRP+NAF+VWS+ +RRK+    P M N+EISK+L         G+ W +
Sbjct: 3  DRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQL---------GYQWKM 45

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	74
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	1e-20
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-20
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	9e-20
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	1e-19
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	1e-19
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	2e-19
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	2e-19
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	2e-19
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	5e-19
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	6e-19
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	2e-18
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-18
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	1e-15
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	6e-10
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-14
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	2e-13
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	3e-12
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	3e-12
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	9e-12
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	9e-12
2lhj_A	97	High mobility group protein homolog NHP1; structur	1e-11
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	1e-11
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	1e-10
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	1e-08
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	3e-08
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	4e-08
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-07
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-07
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	9e-07
1ckt_A	71	High mobility group 1 protein; high-mobility group	1e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-05

>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 = 76.7 bits (189), Expect = 1e-20
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
              +PN  KRPMNAFM++++  R +  ++ P   N  IS  L 
Sbjct: 10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILG 53

>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 = 76.3 bits (188), Expect = 2e-20
 Identities = 14/49 (28%), Positives = 30/49 (61%)

Query: 5  SPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           P +   K      KRP++A  ++S+ +RR++ E +P++  +E+++ LA
Sbjct: 8  KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLA 56

>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 = 74.2 bits (183), Expect = 9e-20
 Identities = 11/39 (28%), Positives = 21/39 (53%)

Query: 14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
            +  +RPMNAF+++ +  R  + +  P + N   +K L
Sbjct: 4  GSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKIL 42

>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 = 74.7 bits (184), Expect = 1e-19
 Identities = 24/44 (54%), Positives = 30/44 (68%)

Query: 9  ATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
               N  H+KRPMNAFMVW+Q  RRK+ +  P +HNAE+SK L
Sbjct: 21 FQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTL 64

>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 = 73.4 bits (181), Expect = 1e-19
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
           HIKRPMNAFMVW++ ERRKI +  PDMHN+ ISK L
Sbjct: 3  PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKIL 39

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

 Score = 73.0 bits (180), Expect = 2e-19
 Identities = 21/36 (58%), Positives = 30/36 (83%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
           I+RPMNAFMVW++ ER+++ +  PD+HNAE+SK L
Sbjct: 2  SIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKML 37

>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 = 73.0 bits (180), Expect = 2e-19
 Identities = 21/37 (56%), Positives = 29/37 (78%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQL 39

>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 = 73.0 bits (180), Expect = 2e-19
 Identities = 21/39 (53%), Positives = 31/39 (79%)

Query: 14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
            + I+RPMNAFMVW++ ER+++ +  PD+HNAE+SK L
Sbjct: 3  FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKML 41

>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 = 72.2 bits (178), Expect = 5e-19
 Identities = 24/37 (64%), Positives = 31/37 (83%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
          + +KRPMNAFMVWS+ +RRK+ +  P MHN+EISKRL
Sbjct: 1  DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRL 37

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

 Score = 71.8 bits (177), Expect = 6e-19
 Identities = 32/36 (88%), Positives = 33/36 (91%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
          HIKRPMNAFMVWSQ+ERRKI E  PDMHNAEISKRL
Sbjct: 2  HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRL 37

>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 = 70.7 bits (174), Expect = 2e-18
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
          HIK+P+NAFM++ +  R  +        +A I++ L
Sbjct: 2  HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQIL 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 = 70.7 bits (174), Expect = 2e-18
 Identities = 21/37 (56%), Positives = 29/37 (78%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQL 39

>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 = 65.6 bits (160), Expect = 1e-15
 Identities = 21/38 (55%), Positives = 29/38 (76%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L 
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40

>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 = 51.0 bits (122), Expect = 6e-10
 Identities = 14/49 (28%), Positives = 23/49 (46%)

Query: 4   YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
                  K  +PN  KRP +AF ++    R KI    P +   +++K+L
Sbjct: 75  RKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKL 123

>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 = 60.9 bits (148), Expect = 2e-14
 Identities = 10/42 (23%), Positives = 19/42 (45%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           +  +  K P+  ++ +    R +I    PD+   EI+K L 
Sbjct: 2  SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLG 43

>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 = 58.0 bits (141), Expect = 2e-13
 Identities = 13/39 (33%), Positives = 21/39 (53%)

Query: 15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          PN  KRP +AF ++    R KI    P +   +++K+L 
Sbjct: 4  PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLG 42

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

 Score = 55.5 bits (134), Expect = 3e-12
 Identities = 8/42 (19%), Positives = 19/42 (45%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           +  + IK+PM+A  ++ Q  R +     P     + + ++ 
Sbjct: 2  SSGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIE 43

>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 = 55.4 bits (134), Expect = 3e-12
 Identities = 13/46 (28%), Positives = 24/46 (52%)

Query: 8  RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
             KK +PN  KR ++A+M ++   R  +    PD+   ++ K+L 
Sbjct: 11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLG 56

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

 Score = 53.4 bits (129), Expect = 9e-12
 Identities = 12/38 (31%), Positives = 17/38 (44%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          +  KR   AFM+W    R  I    P +   EI+K+  
Sbjct: 2  HMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGG 39

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

 Score = 54.3 bits (131), Expect = 9e-12
 Identities = 12/46 (26%), Positives = 26/46 (56%)

Query: 8  RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          +  KK +PN  ++P++A+ ++ +  +  I    P+    E+SK +A
Sbjct: 8  KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVA 53

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

 Score = 53.9 bits (130), Expect = 1e-11
 Identities = 12/45 (26%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHN--AEISKRLA 53
           K +PN  KR ++++M +++ +R +I    P++    A I K + 
Sbjct: 16 AKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIG 60

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

 Score = 54.0 bits (130), Expect = 1e-11
 Identities = 11/43 (25%), Positives = 25/43 (58%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           K +P+  K+P+  +  +   +R K  ++ P+M N +++K L+
Sbjct: 4  LKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILS 46

>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 = 50.7 bits (122), Expect = 1e-10
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          +  KRP++A+ +W    R  I    P +   E++KR  
Sbjct: 2  DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGG 39

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 46.2 bits (110), Expect = 1e-08
 Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 8  RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHN--AEISKRLA 53
              K +P   K  M+A+  + Q  R +  +  P++    AE SK+ +
Sbjct: 6  SGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCS 53

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 45.0 bits (107), Expect = 3e-08
 Identities = 10/44 (22%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPD--MHNAEISKRLA 53
          K +P   +  M+++  + Q  R +  +  PD  ++ +E SK+ +
Sbjct: 2  KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCS 45

>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 = 44.4 bits (104), Expect = 4e-08
 Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 1/38 (2%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHN-AEISKRL 52
              RP   F +W +  R  I    PD  + A+I K  
Sbjct: 4  GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEG 41

>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 = 45.0 bits (106), Expect = 1e-07
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 4   YSPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
                  K  +PN  KRP +AF ++    R KI    P +   +++K+L 
Sbjct: 88  PKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLG 137

>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 = 44.6 bits (105), Expect = 2e-07
 Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 8  RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPD--MHNAEISKRLA 53
              K +P   +  M+++  + Q  R +  +  PD  ++ +E SK+ +
Sbjct: 6  SGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCS 53

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 43.3 bits (101), Expect = 9e-07
 Identities = 9/46 (19%), Positives = 23/46 (50%)

Query: 8  RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          R +     +  K+P+++++ +S+ +        PD    E+ +R+A
Sbjct: 32 RGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIA 77

>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 = 40.4 bits (95), Expect = 1e-06
 Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHN--AEISKRLA 53
          +  M+++  + Q  R +  +  PD     +E SK+ +
Sbjct: 3  RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCS 39

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 8/43 (18%), Positives = 21/43 (48%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
               +  K+P+++++ +S+ +        PD    E+ +R+A
Sbjct: 3  SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIA 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	74
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.91
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.91
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.91
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.9
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.9
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.9
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.9
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.9
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.89
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.89
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.89
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.88
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.88
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.88
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.88
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.88
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.88
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.88
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.87
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.87
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.87
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.87
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.87
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.86
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.86
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.84
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.84
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.82
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.82
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.81
2cto_A	93	Novel protein; high mobility group box domain, hel	99.8
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.78
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.76
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.75
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.75
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.75
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.74
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.63
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.63

>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=99.91  E-value=8.7e-25  Score=133.24  Aligned_cols=65  Identities=22%  Similarity=0.306  Sum_probs=61.3

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.++++||++||||+||||+|++++|..|+.+||++++.|||++||++|+.|+++||.+|.+++.
T Consensus        11 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~   75 (90)
T 1wgf_A           11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREA   75 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            45667799999999999999999999999999999999999999999999999999999998764

>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=1.2e-24  Score=131.69  Aligned_cols=65  Identities=26%  Similarity=0.280  Sum_probs=61.2

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ..++++|+++||||+||||+|++++|..|+.+||++++.|||++||++|+.|+++||.+|.+++.
T Consensus         8 ~~~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   72 (87)
T 2e6o_A            8 GTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAK   72 (87)
T ss_dssp             SSCCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence            34567899999999999999999999999999999999999999999999999999999998864

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

Probab=99.91  E-value=1.3e-24  Score=134.80  Aligned_cols=64  Identities=17%  Similarity=0.286  Sum_probs=61.0

Q ss_pred             cccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           9 ATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         9 ~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +++++||++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~   65 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQ   65 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4577899999999999999999999999999999999999999999999999999999998764

>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=99.90  E-value=3.2e-24  Score=126.54  Aligned_cols=61  Identities=21%  Similarity=0.272  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   61 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAA   61 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            5799999999999999999999999999999999999999999999999999999998764

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

Probab=99.90  E-value=4e-24  Score=132.98  Aligned_cols=68  Identities=19%  Similarity=0.220  Sum_probs=63.0

Q ss_pred             CCCccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           5 SPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         5 ~~~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ...+.++++||++||||+||||+|++++|..|+.+||++++.||+++||++|+.|+++||.+|.+++.
T Consensus         5 ~~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~   72 (102)
T 2co9_A            5 SSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTE   72 (102)
T ss_dssp             CCCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            34456677899999999999999999999999999999999999999999999999999999998764

>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=99.90  E-value=2.4e-24  Score=126.77  Aligned_cols=59  Identities=37%  Similarity=0.613  Sum_probs=55.4

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ||++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   59 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQ   59 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999998764

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

Probab=99.90  E-value=1.4e-23  Score=128.09  Aligned_cols=61  Identities=16%  Similarity=0.149  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+||++||||+||||+|++++|..|+.+||++++.|||++||++|+.||++||.+|.+.+.
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~   62 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAE   62 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999999999999998764

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

Probab=99.90  E-value=1.2e-23  Score=126.90  Aligned_cols=66  Identities=21%  Similarity=0.146  Sum_probs=61.1

Q ss_pred             CccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           7 MRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMH--NAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         7 ~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~--~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+.++++||++||||+||||+|++++|..|+.+||+++  +.|||++||++|+.||++||.+|.+.+.
T Consensus         5 ~~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   72 (86)
T 2eqz_A            5 SSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAK   72 (86)
T ss_dssp             CSSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            35566789999999999999999999999999999997  6999999999999999999999998764

>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=99.89  E-value=9.5e-24  Score=127.66  Aligned_cols=59  Identities=22%  Similarity=0.259  Sum_probs=56.8

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCC-HHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMH-NAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~-~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++++||||+||||+|++++|..|+.+||+++ ++|||++||++|+.|+++||.||.+.+.
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~   61 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAK   61 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            6789999999999999999999999999998 9999999999999999999999999864

>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=99.89  E-value=1.8e-23  Score=124.67  Aligned_cols=58  Identities=48%  Similarity=0.578  Sum_probs=55.2

Q ss_pred             CCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        15 ~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   59 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQA   59 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHH
Confidence            5799999999999999999999999999999999999999999999999999998764

>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=99.89  E-value=2.3e-23  Score=125.44  Aligned_cols=59  Identities=37%  Similarity=0.613  Sum_probs=56.6

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .|++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   59 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQ   59 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999998764

>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=99.88  E-value=4.5e-24  Score=130.72  Aligned_cols=67  Identities=19%  Similarity=0.240  Sum_probs=62.0

Q ss_pred             CCccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           6 PMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         6 ~~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ..+.++++|+++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         9 ~~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   75 (93)
T 1cg7_A            9 KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQ   75 (93)
T ss_dssp             CCCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3345567899999999999999999999999999999999999999999999999999999998864

>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=99.88  E-value=2.7e-23  Score=122.86  Aligned_cols=57  Identities=56%  Similarity=0.748  Sum_probs=55.0

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||||+||||+|++++|..|+.+||+++++|||++||++|+.|+++||.+|.+++.
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   57 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAE   57 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999998864

>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=99.88  E-value=3.3e-23  Score=123.72  Aligned_cols=61  Identities=20%  Similarity=0.234  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ..++++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         2 ~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   62 (82)
T 1wz6_A            2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAK   62 (82)
T ss_dssp             CSSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999999999999999999999998764

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

Probab=99.88  E-value=2.6e-23  Score=120.45  Aligned_cols=57  Identities=39%  Similarity=0.576  Sum_probs=51.6

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||||+||||+|++++|+.|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   57 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAE   57 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            479999999999999999999999999999999999999999999999999998764

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

Probab=99.88  E-value=5.6e-23  Score=125.45  Aligned_cols=61  Identities=18%  Similarity=0.156  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ..++++||||+||||+|++++|..|+.+||++++.|||++||++|+.|+++||.+|.+.+.
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   62 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKAT   62 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999999999999999998764

>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=99.88  E-value=3.9e-23  Score=123.33  Aligned_cols=59  Identities=37%  Similarity=0.547  Sum_probs=53.6

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+++||||+||||+|++++|..|+.+||+++++|||++||++|+.|+++||.+|.+++.
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   61 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAE   61 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            46799999999999999999999999999999999999999999999999999998764

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

Probab=99.88  E-value=2.6e-23  Score=124.41  Aligned_cols=61  Identities=18%  Similarity=0.165  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMH--NAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~--~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||++||||+||||+|++++|..|+.+||+++  +.|||++||++|+.||++||.+|.+.+.
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   64 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK   64 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            579999999999999999999999999999997  5999999999999999999999998764

>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=99.87  E-value=1.1e-22  Score=122.53  Aligned_cols=57  Identities=25%  Similarity=0.184  Sum_probs=54.8

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   57 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELAR   57 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            479999999999999999999999999999999999999999999999999998874

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

Probab=99.87  E-value=1.7e-23  Score=128.82  Aligned_cols=65  Identities=20%  Similarity=0.216  Sum_probs=60.5

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMH--NAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~--~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.++++||++||||+||||+|++++|..|+.+||+++  ++|||++||++|+.||++||.+|.+++.
T Consensus        13 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~   79 (97)
T 2lhj_A           13 PRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSD   79 (97)
T ss_dssp             TTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHH
T ss_pred             cccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3455679999999999999999999999999999999  9999999999999999999999988764

>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=99.87  E-value=1.1e-22  Score=120.76  Aligned_cols=57  Identities=44%  Similarity=0.637  Sum_probs=54.8

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||||+||||+|++++|..|+.+||+++++|||++||++|+.||++||.+|.+++.
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~   57 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAK   57 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999998764

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

Probab=99.87  E-value=1.5e-22  Score=126.79  Aligned_cols=63  Identities=41%  Similarity=0.618  Sum_probs=55.5

Q ss_pred             ccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        10 ~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ...+++++||||+||||+|++++|+.|+.+||+++++|||++||++|+.|+++||.+|.+.+.
T Consensus        22 ~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~   84 (106)
T 4euw_A           22 QSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAE   84 (106)
T ss_dssp             ------CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             hccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            456788999999999999999999999999999999999999999999999999999998764

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

Probab=99.87  E-value=4e-22  Score=116.93  Aligned_cols=56  Identities=21%  Similarity=0.207  Sum_probs=53.7

Q ss_pred             CCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        15 ~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      |++||||+||||+|++++|..|+.+||+++++|||++||++|+.|  +||.+|.+.+.
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~   56 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAA   56 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHH
Confidence            689999999999999999999999999999999999999999999  99999998764

>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=99.86  E-value=5.7e-22  Score=115.11  Aligned_cols=56  Identities=16%  Similarity=0.081  Sum_probs=53.1

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCH--HHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHN--AEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~--~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +||||+||||+|++++|..|+.+||++++  +|||++||++|+.||++||.||.+.+.
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   58 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK   58 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence            58999999999999999999999999975  999999999999999999999998764

>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=99.86  E-value=7.9e-22  Score=115.67  Aligned_cols=55  Identities=22%  Similarity=0.319  Sum_probs=52.7

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.||||+||||+|++++|+.|+.+||+++++||+++||++|+.|++  |.||.+.+.
T Consensus         2 ~~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~   56 (73)
T 3nm9_A            2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAA   56 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHH
Confidence            6899999999999999999999999999999999999999999998  999998764

>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=99.84  E-value=4.1e-21  Score=125.86  Aligned_cols=64  Identities=22%  Similarity=0.274  Sum_probs=60.2

Q ss_pred             cccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           9 ATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         9 ~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .++.+||++||||+||||+|++++|..|+.+||+++++||+++||++|+.||++||.+|.+.+.
T Consensus        80 kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~  143 (159)
T 2gzk_A           80 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAA  143 (159)
T ss_dssp             GGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             cccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4456799999999999999999999999999999999999999999999999999999998764

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

Probab=99.84  E-value=5.9e-21  Score=126.89  Aligned_cols=64  Identities=22%  Similarity=0.274  Sum_probs=60.2

Q ss_pred             cccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           9 ATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         9 ~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .++.+||++||||+||||+|++++|..|+.+||+++++||+++||++|+.||++||.+|.+++.
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~  156 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAA  156 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHH
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4456799999999999999999999999999999999999999999999999999999998764

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

Probab=99.82  E-value=1.5e-20  Score=124.90  Aligned_cols=66  Identities=17%  Similarity=0.141  Sum_probs=60.9

Q ss_pred             CccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCC--CCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           7 MRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPD--MHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         7 ~~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~--~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+...++||++||||+||||+|++++|..|+.+||+  +++.|||++||++|+.||++||.+|.+.+.
T Consensus         5 ~~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   72 (173)
T 2yrq_A            5 SSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK   72 (173)
T ss_dssp             SCSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            344567899999999999999999999999999999  689999999999999999999999998764

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

Probab=99.82  E-value=1.6e-22  Score=125.13  Aligned_cols=61  Identities=11%  Similarity=-0.019  Sum_probs=56.8

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMH--NAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~--~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.++++||+.||||+||||+||+++|++|+.+||+++  ++|||    ++|+.|+++||.||.+.+.
T Consensus        13 ~~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~   75 (90)
T 2yuk_A           13 TLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKAR   75 (90)
T ss_dssp             HHHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHH
T ss_pred             HhhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHH
Confidence            3455679999999999999999999999999999999  99999    9999999999999998875

>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=99.81  E-value=2.9e-20  Score=117.04  Aligned_cols=62  Identities=11%  Similarity=-0.050  Sum_probs=57.3

Q ss_pred             CccccCCCCCCC-CCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           7 MRATKKNNPNHI-KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         7 ~~~~kk~~~~~p-KRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+.++.+|+++| |||+||||+|++++|..|+    +++++||+++||++|+.|+++||.||.+.+.
T Consensus         6 ~~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~   68 (108)
T 1v64_A            6 SGQLKDKFDGRPTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCD   68 (108)
T ss_dssp             SCCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            456778899999 9999999999999999987    8999999999999999999999999998764

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

Probab=99.80  E-value=1.2e-20  Score=116.97  Aligned_cols=60  Identities=12%  Similarity=-0.006  Sum_probs=56.3

Q ss_pred             cCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHH---HHHhhcCCCCcchhHHHHhh
Q psy5107          11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL---ALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        11 kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~l---g~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ...++++||||+||||+|++++|++|+.+  +++++||+++|   |++|+.|+++||.||.+.+.
T Consensus         4 ~~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~   66 (93)
T 2cto_A            4 GSSGMPNRKASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALLREEEKEKYAEMAR   66 (93)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45678999999999999999999999998  89999999999   99999999999999998764

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

Probab=99.78  E-value=6.4e-20  Score=105.81  Aligned_cols=53  Identities=19%  Similarity=0.072  Sum_probs=49.2

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||||+||||+|++++|..|+..||    +||+++||++|+.||++||.+|.+.+.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~y~~~A~   53 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAK   53 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence            57999999999999999999988776    799999999999999999999998764

>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=99.76  E-value=6.5e-19  Score=115.35  Aligned_cols=59  Identities=37%  Similarity=0.613  Sum_probs=56.2

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+++||||+||||+|+++.|..|+.+||+++++|||++||++|+.||++||.+|.+.+.
T Consensus         1 g~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   59 (159)
T 2gzk_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQ   59 (159)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CcCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHH
Confidence            36899999999999999999999999999999999999999999999999999998764

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

Probab=99.75  E-value=2.8e-19  Score=124.88  Aligned_cols=61  Identities=13%  Similarity=0.164  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ..+|++||||+||||+|++++|..|+++||+++++|||++||++|+.|+++||.+|.+.+.
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~   96 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYR   96 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999999999999999999999999998764

>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=99.75  E-value=1.8e-18  Score=107.15  Aligned_cols=56  Identities=9%  Similarity=0.018  Sum_probs=53.5

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.||||++||++|+++.|..++.+||+ +++||||.||++|+.||+.||.||.+.+.
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~   58 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAA   58 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            689999999999999999999999999 99999999999999999999999988653

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

Probab=99.75  E-value=6.3e-19  Score=121.47  Aligned_cols=59  Identities=14%  Similarity=0.182  Sum_probs=56.3

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .|++||||+||||+|++++|..|+++||+++++|||++||++|+.||++||.+|.+.+.
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~   64 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYR   64 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHH
Confidence            46899999999999999999999999999999999999999999999999999998764

>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=99.74  E-value=2.7e-18  Score=106.84  Aligned_cols=58  Identities=14%  Similarity=-0.050  Sum_probs=50.1

Q ss_pred             CCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          13 NNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        13 ~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ....+||||+||||+|+++++.  ...++++++.||+++||++|+.|+++||.||.+.+.
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~   61 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAE   61 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3457899999999999999975  334566889999999999999999999999998764

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

Probab=99.63  E-value=1.7e-17  Score=115.87  Aligned_cols=57  Identities=18%  Similarity=0.033  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+|+++||||+||||+|++++|..|+.+||+    +|++.||++|+.|+++||.||.+++.
T Consensus       141 ~kdp~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls~~eK~~Y~~~A~  197 (238)
T 3tmm_A          141 LTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAK  197 (238)
T ss_dssp             HHHTTCCCCCCCHHHHHHHHHTTTSCCSSHH----HHHHHHHHHHHTCCTTTTHHHHHHHH
T ss_pred             hcccCCCCCCCcHHHHHHHHHHHHHhccCHH----HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4689999999999999999999998876664    99999999999999999999998764

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

Probab=99.63  E-value=9.9e-18  Score=115.48  Aligned_cols=57  Identities=18%  Similarity=0.033  Sum_probs=51.8

Q ss_pred             CCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        12 k~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .+|++.||||+||||+|++++|..|+.+||+    ||++.||++|+.|+++||.||.+++.
T Consensus       109 ~kdp~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls~~eK~~Y~~~A~  165 (214)
T 3tq6_A          109 LTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAK  165 (214)
T ss_dssp             HHHTTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hccccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3589999999999999999999998776664    99999999999999999999998764

---

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	74
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	8e-13
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-12
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	1e-11
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	2e-11
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	4e-11
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	3e-10
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-10
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	1e-09
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	8e-09
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-07
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	5e-07
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-06

>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 = 55.2 bits (133), Expect = 8e-13
 Identities = 24/38 (63%), Positives = 31/38 (81%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAFMVWS+ +RRK+ +  P MHN+EISKRL 
Sbjct: 1  DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 38

>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 = 54.2 bits (130), Expect = 3e-12
 Identities = 13/48 (27%), Positives = 29/48 (60%)

Query: 5  SPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
           P +   K      KRP++A  ++S+ +RR++ E +P++  +E+++ L
Sbjct: 8  KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLL 55

>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 = 52.6 bits (126), Expect = 1e-11
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          HIK+P+NAFM++ +  R  +        +A I++ L 
Sbjct: 2  HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILG 38

>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 = 51.7 bits (124), Expect = 2e-11
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          HIKRPMNAFMVW++ ERRKI +  PDMHN+ ISK L 
Sbjct: 2  HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILG 38

>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 = 51.0 bits (122), Expect = 4e-11
 Identities = 21/38 (55%), Positives = 29/38 (76%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          + +KRPMNAF+VWS+ +RRK+    P M N+EISK+L 
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40

>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 = 49.5 bits (118), Expect = 3e-10
 Identities = 13/42 (30%), Positives = 24/42 (57%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRL 52
          KK +PN  KR ++A+M ++   R  +    PD+   ++ K+L
Sbjct: 14 KKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKL 55

>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 = 49.2 bits (117), Expect = 3e-10
 Identities = 10/41 (24%), Positives = 23/41 (56%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKR 51
           K +P+  K+P+  +  +   +R K  ++ P+M N +++K 
Sbjct: 4  LKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKI 44

>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 = 47.1 bits (112), Expect = 1e-09
 Identities = 12/38 (31%), Positives = 20/38 (52%)

Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          +  KRP++A+M+W    R  I    P +   E++KR  
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGG 39

>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 = 45.2 bits (107), Expect = 8e-09
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
          KRP +AF ++    R KI    P +   +++K+L 
Sbjct: 4  KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLG 38

>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 = 41.4 bits (97), Expect = 4e-07
 Identities = 7/43 (16%), Positives = 12/43 (27%), Gaps = 2/43 (4%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
             +    K PMN +  +SQ            +   E    + 
Sbjct: 2  SSGSSGPKKPPMNGYQKFSQELLSNG--ELNHLPLKERMVEIG 42

>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 = 40.2 bits (94), Expect = 5e-07
 Identities = 8/37 (21%), Positives = 20/37 (54%), Gaps = 2/37 (5%)

Query: 19 KRPMNAFMVWSQMERRKICEVQPD--MHNAEISKRLA 53
          +  M+++  + Q  R +  +  PD  ++ +E SK+ +
Sbjct: 3  RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCS 39

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

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 = 40.3 bits (94), Expect = 1e-06
 Identities = 6/43 (13%), Positives = 15/43 (34%), Gaps = 4/43 (9%)

Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
           K +    K P N++ ++       +     D+ + E     +
Sbjct: 11 DKFDGRPTKPPPNSYSLYCAELMANM----KDVPSTERMVLCS 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	74
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.9
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.88
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.88
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.86
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.86
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.86
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.85
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.82
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.82
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.7
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.7

>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=99.90  E-value=5e-24  Score=123.74  Aligned_cols=56  Identities=50%  Similarity=0.602  Sum_probs=54.4

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +||||+||||+|++++|+.|+++||+++++|||++||++|+.||++||.||.+.+.
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~   57 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQA   57 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999998764

>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=99.88  E-value=2e-23  Score=125.04  Aligned_cols=58  Identities=38%  Similarity=0.636  Sum_probs=55.7

Q ss_pred             CCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        15 ~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      .|+||||+||||||++++|..|+.+||+++++|||++||++|+.||++||.+|.+.+.
T Consensus         2 ~~~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~   59 (85)
T d1j46a_           2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQ   59 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            3799999999999999999999999999999999999999999999999999999764

>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=99.88  E-value=1.7e-23  Score=124.64  Aligned_cols=57  Identities=44%  Similarity=0.637  Sum_probs=55.1

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ++||||+||||||++++|+.|+++||+++++|||++||++|+.|+++||.+|.+++.
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~   57 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAK   57 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999998875

>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=99.88  E-value=2.3e-23  Score=124.96  Aligned_cols=56  Identities=25%  Similarity=0.200  Sum_probs=54.5

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      |||||+||||||++++|+.|..+||++++++||++||.+|+.||++||.+|.+.+.
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~   57 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELAR   57 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999998764

>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=99.86  E-value=2.2e-22  Score=120.76  Aligned_cols=65  Identities=22%  Similarity=0.306  Sum_probs=60.6

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ....+.++++||||+||||||++++|..|+.+||++++.||+++||++|+.|+++||.+|.+.+.
T Consensus        11 ~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~   75 (90)
T d1wgfa_          11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREA   75 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            44567789999999999999999999999999999999999999999999999999999988764

>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=99.86  E-value=4.4e-22  Score=120.61  Aligned_cols=71  Identities=20%  Similarity=0.243  Sum_probs=62.8

Q ss_pred             CCCCCC--ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           2 GLYSPM--RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         2 ~p~~~~--~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +|....  ..+++++|++||||+||||+|++++|..|+.+||++++.+|++.||++|+.||++||.+|.+.+.
T Consensus         3 tp~~~~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~   75 (93)
T d1lwma_           3 TPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQ   75 (93)
T ss_dssp             CSCCTTSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            444444  44566789999999999999999999999999999999999999999999999999999987653

>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=99.86  E-value=3.3e-22  Score=120.21  Aligned_cols=63  Identities=17%  Similarity=0.293  Sum_probs=60.3

Q ss_pred             ccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        10 ~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.++||+.||||+||||+|++++|..|+.+||++++.+|+++||+.|+.||++||.+|.+++.
T Consensus         3 k~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~   65 (91)
T d1k99a_           3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQ   65 (91)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHH
Confidence            567899999999999999999999999999999999999999999999999999999999864

>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=99.85  E-value=4.5e-22  Score=117.12  Aligned_cols=57  Identities=21%  Similarity=0.248  Sum_probs=54.9

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      |.||||+||||+|++++|..|+.+||+++++||+++||++|+.||++||.+|.+.+.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~   57 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAA   57 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999999999999999998764

>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=99.82  E-value=1.2e-20  Score=108.78  Aligned_cols=56  Identities=16%  Similarity=0.098  Sum_probs=52.3

Q ss_pred             CCCCCCchhHhHhHHHHHHHHHhCCC--CCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          17 HIKRPMNAFMVWSQMERRKICEVQPD--MHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        17 ~pKRP~nAfmlf~~~~R~~i~~~~P~--~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +||||+||||+|++++|..|+.+||+  +++++|+++||++|+.||++||.+|.+++.
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~   58 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK   58 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            58999999999999999999999997  558999999999999999999999988764

>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=99.82  E-value=1.2e-20  Score=109.70  Aligned_cols=55  Identities=24%  Similarity=0.309  Sum_probs=50.9

Q ss_pred             CCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        16 ~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      |+||||+||||+|++++|+.|+++||++++.|||++||++|+.++  ||.+|.+.+.
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~   56 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAA   56 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHH
Confidence            689999999999999999999999999999999999999999764  6999988653

>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=99.70  E-value=6.6e-18  Score=102.59  Aligned_cols=57  Identities=14%  Similarity=-0.080  Sum_probs=50.7

Q ss_pred             CCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107          14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus        14 ~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      ....+|||+||||+|++++|..++..  ++++.||+++||++|+.|+++||.+|.+++.
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~--~~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~   61 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELN--HLPLKERMVEIGSRWQRISQSQKEHYKKLAE   61 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTT--TSCHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence            34568999999999999999998754  5679999999999999999999999998864

>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=99.70  E-value=1.3e-17  Score=102.79  Aligned_cols=61  Identities=11%  Similarity=-0.031  Sum_probs=53.3

Q ss_pred             ccccCCCCCCCCCCCchhHhHhHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCCCcchhHHHHhh
Q psy5107           8 RATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLLAEQLF   72 (74)
Q Consensus         8 ~~~kk~~~~~pKRP~nAfmlf~~~~R~~i~~~~P~~~~~eisk~lg~~W~~~s~~Ek~~~~e~~~   72 (74)
                      +.+.+.++..+|||+||||+|++++|..    +|++++.||+++||++|+.||++||.+|.+++.
T Consensus         8 ~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~   68 (108)
T d1v64a_           8 QLKDKFDGRPTKPPPNSYSLYCAELMAN----MKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCD   68 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCcHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            4445567777899999999999998865    689999999999999999999999999998763