Psyllid ID: psy2704

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250------
Protein Sequence
MDLKPLLEVTTDLHNIRLPIVTVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPHFSPPVCSTSSFYLGMEWGGFMSYQGASTPQPQKESSDIISTDDKI
Secondary Structure (PSIPRED)
cccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccHHHHcccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdlkpllevttdlhnirlpivtvpnnaysisgllntpnqngdpllsgftlpisqmppVIVTTLQQscsanfqpvmkynpstspqvspsspptlcfsptptpespptqqtgkrkqrryrttFSNFQLEELERAFhkthypdvfFREELALRIDLTEARVQVWFQNRRAKWRKQEKlvskqpqelfssplqspaspspdlnvisvpaaspvphfsppvcstssfylgmewggfmsyqgastpqpqkessdiistddki
Flexible Loop (DISEMBL)
MDLKPLLEVTtdlhnirlpivtVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFsptptpespptqqtgkrkqrryRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPHFSPPVCSTSSFYLGMEWGGFMSYQGastpqpqkessdiistddki
Low Complexity Region (SEG)
MDLKPLLEVTTDLHNIRLPIVTVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNpstspqvspssppTLCFsptptpespptqqtGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFssplqspaspspDLNVISVPAASPVPHFSPPVCSTSSFYLGMEWGGFMSYQGASTPQPQKESSDIISTDDKI
Disordered region (IsUnstruct)
*****LLEVTTDLHNIRLPIVTVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSAN************************************************TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW********************************************PPVCSTSSFYLGMEWGGFMSY**********************
Disordered Region (DISOPRED)
***********************************************************************************************************************TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK****************************************************************************************
Disordered Region (DISEMBL)
MDLKPLLEVTTDLHNIRLPIVTVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYN**************LCFS********************YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA****************************PDLNVISVPAASPVPHFSPPVCSTSSFYLGMEWGGFMSYQ*********************
Disordered Region (DISPRO)
*********************************************************************************************************************RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS*******SSPLQSPASPSPDLNVISVPAASPVPHFSPPVCSTSSFYLGMEWGG******A*******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDLKPLLEVTTDLHNIRLPIVTVPNNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPHFSPPVCSTSSFYLGMEWGGFMSYQGASTPQPQKESSDIISTDDKI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	256	2.2.26 [Sep-21-2011]
A6YP92	566	Homeobox protein ARX OS=R	yes	N/A	0.25	0.113	0.875	2e-29
Q96QS3	562	Homeobox protein ARX OS=H	yes	N/A	0.25	0.113	0.875	2e-29
O42115	453	Aristaless-related homeob	no	N/A	0.312	0.176	0.756	3e-29
O35085	564	Homeobox protein ARX OS=M	yes	N/A	0.25	0.113	0.875	3e-29
Q26657	327	Aristaless homeobox prote	no	N/A	0.351	0.275	0.702	3e-29
Q06453	408	Homeobox protein aristale	no	N/A	0.253	0.159	0.830	8e-29
Q4LAL6	397	Homeobox protein aristale	yes	N/A	0.316	0.204	0.629	3e-26
Q9H161	411	Homeobox protein aristale	no	N/A	0.328	0.204	0.619	4e-26
O97039	268	Retinal homeobox protein	N/A	N/A	0.703	0.671	0.388	6e-26
O35137	399	Homeobox protein aristale	no	N/A	0.316	0.203	0.629	7e-26

>sp|A6YP92|ARX_RAT Homeobox protein ARX OS=Rattus norvegicus GN=Arx PE=2 SV=1

 Score =  129 bits (325), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct: 329 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 388

Query: 171 KQEK 174
           K+EK
Sbjct: 389 KREK 392

Transcription factor required for normal brain development. May be important for maintenance of specific neuronal subtypes in the cerebral cortex and axonal guidance in the floor plate.
Rattus norvegicus (taxid: 10116)

>sp|Q96QS3|ARX_HUMAN Homeobox protein ARX OS=Homo sapiens GN=ARX PE=1 SV=1

 Score =  129 bits (324), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct: 325 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 384

Query: 171 KQEK 174
           K+EK
Sbjct: 385 KREK 388

Transcription factor required for normal brain development. May be important for maintenance of specific neuronal subtypes in the cerebral cortex and axonal guidance in the floor plate.

Homo sapiens (taxid: 9606)

>sp|O42115|ARX_DANRE Aristaless-related homeobox protein OS=Danio rerio GN=arx PE=2 SV=1

 Score =  129 bits (323), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 69/82 (84%), Gaps = 2/82 (2%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct: 212 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 271

Query: 171 KQEKL-VSKQPQEL-FSSPLQS 190
           K+EK  V   P  L F  PL +
Sbjct: 272 KREKAGVQAHPTGLPFPGPLAA 293

Appears to be indispensable for the central nervous system development. May have a role in the neuronal differentiation of the ganglionic eminence and ventral thalamus. May also be involved in axonal guidance in the floor plate.

Danio rerio (taxid: 7955)

>sp|O35085|ARX_MOUSE Homeobox protein ARX OS=Mus musculus GN=Arx PE=2 SV=3

 Score =  129 bits (323), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct: 327 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 386

Query: 171 KQEK 174
           K+EK
Sbjct: 387 KREK 390

Transcription factor required for normal brain development. May be important for maintenance of specific neuronal subtypes in the cerebral cortex and axonal guidance in the floor plate.

Mus musculus (taxid: 10090)

>sp|Q26657|ALX_STRPU Aristaless homeobox protein (Fragment) OS=Strongylocentrotus purpuratus GN=ALX PE=2 SV=2

 Score =  129 bits (323), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 66/94 (70%), Positives = 75/94 (79%), Gaps = 4/94 (4%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct: 209 KRKQRRYRTTFTSYQLEELERAFCKTHYPDVFTREELAMRVDLTEARVQVWFQNRRAKWR 268

Query: 171 KQEKLVSKQPQELFSSPLQSP--ASPSPDLNVIS 202
           K+EKL   QP+ L   P   P    P  D N++S
Sbjct: 269 KREKL-GLQPR-LHPHPHFGPILGGPISDSNLVS 300

Strongylocentrotus purpuratus (taxid: 7668)

>sp|Q06453|AL_DROME Homeobox protein aristaless OS=Drosophila melanogaster GN=al PE=1 SV=2

 Score =  127 bits (319), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 54/65 (83%), Positives = 62/65 (95%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWR
Sbjct: 82  KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 141

Query: 171 KQEKL 175
           KQEK+
Sbjct: 142 KQEKV 146

Involved in the morphogenesis of proximal and distal pattern elements in a subset of appendages. Also has a role in early imaginal disk development.

Drosophila melanogaster (taxid: 7227)

>sp|Q4LAL6|ALX4_BOVIN Homeobox protein aristaless-like 4 OS=Bos taurus GN=ALX4 PE=2 SV=1

 Score =  119 bits (297), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 64/81 (79%)

Query: 99  PTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARV 158
           P+P      ++ K K+RR RTTF+++QLEELE+ F KTHYPDV+ RE+LA+R DLTEARV
Sbjct: 185 PSPMEKADSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARV 244

Query: 159 QVWFQNRRAKWRKQEKLVSKQ 179
           QVWFQNRRAKWRK+E+    Q
Sbjct: 245 QVWFQNRRAKWRKRERFGQMQ 265

Transcription factor involved in skull and limb development.

Bos taurus (taxid: 9913)

>sp|Q9H161|ALX4_HUMAN Homeobox protein aristaless-like 4 OS=Homo sapiens GN=ALX4 PE=1 SV=2

 Score =  118 bits (295), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 52/84 (61%), Positives = 65/84 (77%)

Query: 96  SPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTE 155
           S  P+P      ++ K K+RR RTTF+++QLEELE+ F KTHYPDV+ RE+LA+R DLTE
Sbjct: 196 SDLPSPLEKADSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTE 255

Query: 156 ARVQVWFQNRRAKWRKQEKLVSKQ 179
           ARVQVWFQNRRAKWRK+E+    Q
Sbjct: 256 ARVQVWFQNRRAKWRKRERFGQMQ 279

Transcription factor involved in skull and limb development. Plays an essential role in craniofacial development, skin and hair follicle development.

Homo sapiens (taxid: 9606)

>sp|O97039|RX_DUGJA Retinal homeobox protein Rax (Fragment) OS=Dugesia japonica GN=RAX PE=2 SV=1

 Score =  117 bits (294), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 78/201 (38%), Positives = 111/201 (55%), Gaps = 21/201 (10%)

Query: 25  NNAYSISGLLNTPNQNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVM--KYNPSTS 82
           N  Y+I  +L  P+Q    +L+ +         +  +  ++  S N + ++  K  P  S
Sbjct: 2   NKRYNIDDILGIPDQKS-LMLNNYQHQSVVENEICDSYQKKDISVNNRELLMVKRCPKDS 60

Query: 83  PQVSPSSPPTLCFSPTPTPESPPTQQTG-KRKQRRYRTTFSNFQLEELERAFHKTHYPDV 141
            + SP+       S     ES P Q +   +K RR RTTF+ +QL ELERAF K+HYPDV
Sbjct: 61  SEQSPA------ISEADETESSPDQLSNCNKKHRRNRTTFTTYQLHELERAFEKSHYPDV 114

Query: 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQP----QELFSSPLQS------P 191
           + REELA++I L E RVQVWFQNRRAKWR+QEK+ +       QE+F +  +S      P
Sbjct: 115 YSREELAMKISLPEVRVQVWFQNRRAKWRRQEKIEAANHTHNLQEVFPNVGKSLTSSLFP 174

Query: 192 ASPSPDLNVISVPAASPVPHF 212
           A+P P LN +S+P+      F
Sbjct: 175 ANPYPFLN-MSLPSVESTSFF 194

Dugesia japonica (taxid: 6161)

>sp|O35137|ALX4_MOUSE Homeobox protein aristaless-like 4 OS=Mus musculus GN=Alx4 PE=1 SV=1

 Score =  117 bits (293), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 64/81 (79%)

Query: 99  PTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARV 158
           P+P      ++ K K+RR RTTF+++QLEELE+ F KTHYPDV+ RE+LA+R DLTEARV
Sbjct: 187 PSPLEKTDSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARV 246

Query: 159 QVWFQNRRAKWRKQEKLVSKQ 179
           QVWFQNRRAKWRK+E+    Q
Sbjct: 247 QVWFQNRRAKWRKRERFGQMQ 267

Transcription factor involved in skull and limb development.

Mus musculus (taxid: 10090)

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	256
383854569	250	PREDICTED: paired mesoderm homeobox prot	0.554	0.568	0.586	9e-38
345484335	250	PREDICTED: paired mesoderm homeobox prot	0.718	0.736	0.474	2e-37
110762829	250	PREDICTED: hypothetical protein LOC72550	0.542	0.556	0.585	1e-36
340724400	251	PREDICTED: hypothetical protein LOC10065	0.554	0.565	0.576	1e-36
332017817	248	Homeobox protein ARX [Acromyrmex echinat	0.519	0.536	0.561	8e-35
307175916	249	Homeobox protein ARX [Camponotus florida	0.546	0.562	0.556	1e-34
91087879	220	PREDICTED: similar to transcription fact	0.406	0.472	0.669	2e-34
307195645	271	Homeobox protein ARX [Harpegnathos salta	0.554	0.523	0.497	3e-33
322800741	247	hypothetical protein SINV_12341 [Solenop	0.449	0.465	0.625	2e-32
328718058	218	PREDICTED: retinal homeobox protein Rx-B	0.363	0.426	0.690	2e-30

>gi|383854569|ref|XP_003702793.1| PREDICTED: paired mesoderm homeobox protein 2-like [Megachile rotundata]

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 88/150 (58%), Positives = 95/150 (63%), Gaps = 8/150 (5%)

Query: 95  FSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLT 154
           FSP+P  E   +   GKRKQRRYRTTF+NFQLEELERAF KTHYPDVFFREELALRI LT
Sbjct: 75  FSPSPGSEDRQSSGVGKRKQRRYRTTFTNFQLEELERAFQKTHYPDVFFREELALRIQLT 134

Query: 155 EARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPH--F 212
           EARVQVWFQNRRAKWRKQEK      Q   ++ L S   PS    V          H   
Sbjct: 135 EARVQVWFQNRRAKWRKQEK------QCKVTTHLTSHLPPSECQEVQQQQQQQQSDHLLL 188

Query: 213 SPPVCSTSSFYLGMEWGGFMSYQGASTPQP 242
            PP+ S    YLGMEW GF  Y   +T  P
Sbjct: 189 EPPLGSPPPIYLGMEWAGFSPYSNTATASP 218

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345484335|ref|XP_001599456.2| PREDICTED: paired mesoderm homeobox protein 2-like [Nasonia vitripennis]

 Score =  161 bits (408), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 101/213 (47%), Positives = 114/213 (53%), Gaps = 29/213 (13%)

Query: 42  DPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPT- 100
           DPL+S   +  S      +T  + S   + QP        +   S   P    +  T T 
Sbjct: 25  DPLVSAGAIVASS-----ITADEMSPGGDLQPSALVGLIGAQSSSVCFPAKFTYDFTSTS 79

Query: 101 ---PESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEAR 157
               E PPT   GKRKQRRYRTTF+NFQLEELERAF KTHYPDVFFREELALRI LTEAR
Sbjct: 80  PGNEERPPTGAIGKRKQRRYRTTFTNFQLEELERAFQKTHYPDVFFREELALRIQLTEAR 139

Query: 158 VQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSP--------DLNVISVPAASPV 209
           VQVWFQNRRAKWRKQEK        L +S L S              D  ++  P  SP 
Sbjct: 140 VQVWFQNRRAKWRKQEKQCKTDNTHL-TSHLASDCQDMQQQQLSQQTDHLLLETPLGSP- 197

Query: 210 PHFSPPVCSTSSFYLGMEWGGFMSYQGASTPQP 242
               PP+      YLGMEW GF  Y  A+T  P
Sbjct: 198 ----PPI------YLGMEWAGFSPYNNATTASP 220

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110762829|ref|XP_001121339.1| PREDICTED: hypothetical protein LOC725502 [Apis mellifera]

 Score =  159 bits (401), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 86/147 (58%), Positives = 93/147 (63%), Gaps = 8/147 (5%)

Query: 95  FSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLT 154
           FS +P  E   +   GKRKQRRYRTTF+NFQLEELERAF KTHYPDVFFREELALRI LT
Sbjct: 75  FSSSPGSEDRQSTGVGKRKQRRYRTTFTNFQLEELERAFQKTHYPDVFFREELALRIQLT 134

Query: 155 EARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPH--F 212
           EARVQVWFQNRRAKWRKQEK      Q   ++ L S   PS    V          H   
Sbjct: 135 EARVQVWFQNRRAKWRKQEK------QCKVTTHLTSHLPPSECQEVQQQQQQQQSDHLLL 188

Query: 213 SPPVCSTSSFYLGMEWGGFMSYQGAST 239
            PP+ S    YLGMEW GF  Y   +T
Sbjct: 189 EPPLGSPPPIYLGMEWAGFSPYSNTAT 215

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340724400|ref|XP_003400570.1| PREDICTED: hypothetical protein LOC100651262 [Bombus terrestris] gi|350397686|ref|XP_003484956.1| PREDICTED: hypothetical protein LOC100748675 [Bombus impatiens]

 Score =  159 bits (401), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 87/151 (57%), Positives = 94/151 (62%), Gaps = 9/151 (5%)

Query: 95  FSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLT 154
           FSP+P  E   +   GKRKQRRYRTTF+NFQLEELERAF KTHYPDVFFREELALRI LT
Sbjct: 75  FSPSPGSEDRQSTGVGKRKQRRYRTTFTNFQLEELERAFQKTHYPDVFFREELALRIQLT 134

Query: 155 EARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPH--- 211
           EARVQVWFQNRRAKWRKQEK      Q   ++ L S   PS    V              
Sbjct: 135 EARVQVWFQNRRAKWRKQEK------QCKVTTHLTSHMPPSECQEVQQQQQQQQQSDHLL 188

Query: 212 FSPPVCSTSSFYLGMEWGGFMSYQGASTPQP 242
             PP+ S    YLGMEW GF  Y   +T  P
Sbjct: 189 LEPPLGSPPPIYLGMEWAGFSPYSNTATTSP 219

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332017817|gb|EGI58478.1| Homeobox protein ARX [Acromyrmex echinatior]

 Score =  153 bits (386), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 87/155 (56%), Positives = 94/155 (60%), Gaps = 22/155 (14%)

Query: 92  TLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRI 151
           T  FS  P  E  P+   GKRKQRRYRTTFSNFQLEELERAF KTHYPDVFFREELA+RI
Sbjct: 74  TYDFSTGPESEERPSCVIGKRKQRRYRTTFSNFQLEELERAFQKTHYPDVFFREELAVRI 133

Query: 152 DLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPL-------QSPASPSPDLNVISVP 204
            LTEARVQVWFQNRRAKWRKQEK   K    + SS L       Q   S   D  ++  P
Sbjct: 134 QLTEARVQVWFQNRRAKWRKQEKQC-KIATHMTSSHLPPNCQEVQQHQSQHSDHLLLESP 192

Query: 205 AASPVPHFSPPVCSTSSFYLGMEWGGFMSYQGAST 239
             SP+             YLGMEW GF  Y    +
Sbjct: 193 -CSPI-------------YLGMEWAGFSPYNNTDS 213

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307175916|gb|EFN65729.1| Homeobox protein ARX [Camponotus floridanus]

 Score =  152 bits (384), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 84/151 (55%), Positives = 91/151 (60%), Gaps = 11/151 (7%)

Query: 92  TLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRI 151
           T  FS +   E  P+   GKRKQRRYRTTFSNFQLEELERAF KTHYPDVFFREELA+RI
Sbjct: 75  TFDFSTSSESEERPSCVIGKRKQRRYRTTFSNFQLEELERAFQKTHYPDVFFREELAVRI 134

Query: 152 DLTEARVQVWFQNRRAKWRKQE---KLVSKQPQELFSSPLQSPASPSPDLNVISVPAASP 208
            LTEARVQVWFQNRRAKWRKQE   K+ +     L SS  Q             +   SP
Sbjct: 135 QLTEARVQVWFQNRRAKWRKQEKQCKIATHMTSHLPSSDCQDIQQHQSQQQSDHLLLESP 194

Query: 209 VPHFSPPVCSTSSFYLGMEWGGFMSYQGAST 239
                   CS    YLGMEW GF  Y    +
Sbjct: 195 --------CSPPPIYLGMEWAGFSPYNNTDS 217

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91087879|ref|XP_969925.1| PREDICTED: similar to transcription factor protein [Tribolium castaneum] gi|270012765|gb|EFA09213.1| munster [Tribolium castaneum]

 Score =  151 bits (382), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 79/118 (66%), Positives = 87/118 (73%), Gaps = 14/118 (11%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTFSN+QLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR
Sbjct: 43  KRKQRRYRTTFSNYQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 102

Query: 171 KQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPHFSPPVCSTSSFYLGMEW 228
           KQEK V            Q+   PS      S P  SP+ +F PP  S ++ +LG+EW
Sbjct: 103 KQEKSVKNA---------QNINIPS----ACSTPLESPLLNF-PPEQSPTNLFLGLEW 146

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307195645|gb|EFN77487.1| Homeobox protein ARX [Harpegnathos saltator]

 Score =  147 bits (372), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 84/169 (49%), Positives = 92/169 (54%), Gaps = 27/169 (15%)

Query: 92  TLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRI 151
           T  FS +P  E  P+   GKRKQRRYRTTFSNFQLEELERAF KTHYPDVFFREELA+RI
Sbjct: 74  TYDFSTSPESEERPSCVIGKRKQRRYRTTFSNFQLEELERAFQKTHYPDVFFREELAVRI 133

Query: 152 DLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPH 211
            LTEARVQVWFQNRRAKWRKQEK      Q   ++ + S   PS    V+          
Sbjct: 134 QLTEARVQVWFQNRRAKWRKQEK------QCKIATHMTSHLPPSDCTEVVQQQQQQQQQQ 187

Query: 212 FSPPV---------------------CSTSSFYLGMEWGGFMSYQGAST 239
                                     CS    YLGMEW GF  Y    +
Sbjct: 188 QQQQQQQQQQQQQPQQQPDHLLLESPCSPPPIYLGMEWAGFSPYNNTDS 236

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322800741|gb|EFZ21645.1| hypothetical protein SINV_12341 [Solenopsis invicta]

 Score =  145 bits (366), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 80/128 (62%), Positives = 86/128 (67%), Gaps = 13/128 (10%)

Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
           GKRKQRRYRTTFSNFQLEELERAF KTHYPDVFFREELA+RI LTEARVQVWFQNRRAKW
Sbjct: 90  GKRKQRRYRTTFSNFQLEELERAFQKTHYPDVFFREELAVRIQLTEARVQVWFQNRRAKW 149

Query: 170 RKQEKLVSKQPQELFSSPLQSPASPSPDLNVISVPAASPVPHFSPPVCS---TSSFYLGM 226
           RKQEK      Q   ++ + S   PS D   +     S   H S P+      S  YLGM
Sbjct: 150 RKQEK------QCKIATHMTSHLPPS-DCQEMQQQHQS---HHSDPLSLESPCSPIYLGM 199

Query: 227 EWGGFMSY 234
           EW G   Y
Sbjct: 200 EWAGLSPY 207

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328718058|ref|XP_003246373.1| PREDICTED: retinal homeobox protein Rx-B-like isoform 1 [Acyrthosiphon pisum] gi|328718060|ref|XP_003246374.1| PREDICTED: retinal homeobox protein Rx-B-like isoform 2 [Acyrthosiphon pisum] gi|328718062|ref|XP_003246375.1| PREDICTED: retinal homeobox protein Rx-B-like isoform 3 [Acyrthosiphon pisum] gi|328718064|ref|XP_003246376.1| PREDICTED: retinal homeobox protein Rx-B-like isoform 4 [Acyrthosiphon pisum]

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/97 (69%), Positives = 72/97 (74%), Gaps = 4/97 (4%)

Query: 89  SPPTLCFSPTPTPESPPTQQTG----KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFR 144
           SP   C     +  S  T Q      KRKQRRYRTTF+NFQLEELE +F KTHYPDVFFR
Sbjct: 46  SPSDRCDDNDQSSGSLSTDQNSNSNVKRKQRRYRTTFTNFQLEELENSFQKTHYPDVFFR 105

Query: 145 EELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQ 181
           EELA+RIDLTEARVQVWFQNRRAKWRKQEK +  Q Q
Sbjct: 106 EELAMRIDLTEARVQVWFQNRRAKWRKQEKTLVSQHQ 142

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	256
FB|FBgn0023489	357	Pph13 "PvuII-PstI homology 13"	0.253	0.182	0.876	2e-30
ZFIN|ZDB-GENE-990415-15	453	arxa "aristaless related homeo	0.285	0.161	0.797	3.2e-27
UNIPROTKB|I3LRI8	451	I3LRI8 "Uncharacterized protei	0.25	0.141	0.875	3.9e-27
UNIPROTKB|J9NW39	520	ARX "Uncharacterized protein"	0.25	0.123	0.875	1.1e-26
UNIPROTKB|Q96QS3	562	ARX "Homeobox protein ARX" [Ho	0.25	0.113	0.875	1.6e-26
UNIPROTKB|E2QVR4	564	ARX "Uncharacterized protein"	0.25	0.113	0.875	1.6e-26
MGI|MGI:1097716	564	Arx "aristaless related homeob	0.25	0.113	0.875	1.6e-26
RGD|1562672	566	Arx "aristaless related homeob	0.25	0.113	0.875	1.6e-26
UNIPROTKB|D4A5S8	566	Arx "Homeobox protein ARX" [Ra	0.25	0.113	0.875	1.6e-26
UNIPROTKB|F1LQW2	566	Arx "Homeobox protein ARX" [Ra	0.25	0.113	0.875	1.6e-26

FB|FBgn0023489 Pph13 "PvuII-PstI homology 13" [Drosophila melanogaster (taxid:7227)]

 Score = 310 (114.2 bits), Expect = 2.0e-30, Sum P(2) = 2.0e-30
 Identities = 57/65 (87%), Positives = 62/65 (95%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+  QL+ELERAF +THYPDVFFREELA+RIDLTEARVQVWFQNRRAKWR
Sbjct:     7 KRKQRRYRTTFNTLQLQELERAFQRTHYPDVFFREELAVRIDLTEARVQVWFQNRRAKWR 66

Query:   171 KQEKL 175
             KQEK+
Sbjct:    67 KQEKI 71

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

GO:0005634 "nucleus" evidence=ISS;IDA

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

GO:0042052 "rhabdomere development" evidence=IMP

GO:0042463 "ocellus photoreceptor cell development" evidence=IGI

GO:0042051 "compound eye photoreceptor development" evidence=IMP

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

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

GO:0042803 "protein homodimerization activity" evidence=IDA

ZFIN|ZDB-GENE-990415-15 arxa "aristaless related homeobox a" [Danio rerio (taxid:7955)]

 Score = 306 (112.8 bits), Expect = 3.2e-27, P = 3.2e-27
 Identities = 59/74 (79%), Positives = 65/74 (87%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   212 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 271

Query:   171 KQEKL-VSKQPQEL 183
             K+EK  V   P  L
Sbjct:   272 KREKAGVQAHPTGL 285

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|I3LRI8 I3LRI8 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 305 (112.4 bits), Expect = 3.9e-27, P = 3.9e-27
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   214 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 273

Query:   171 KQEK 174
             K+EK
Sbjct:   274 KREK 277

GO:0005634 "nucleus" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0042127 "regulation of cell proliferation" evidence=IEA

GO:0021853 "cerebral cortex GABAergic interneuron migration" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021831 "embryonic olfactory bulb interneuron precursor migration" evidence=IEA

GO:0021800 "cerebral cortex tangential migration" evidence=IEA

GO:0021759 "globus pallidus development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

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

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

UNIPROTKB|J9NW39 ARX "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 305 (112.4 bits), Expect = 1.1e-26, P = 1.1e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   283 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 342

Query:   171 KQEK 174
             K+EK
Sbjct:   343 KREK 346

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|Q96QS3 ARX "Homeobox protein ARX" [Homo sapiens (taxid:9606)]

 Score = 305 (112.4 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   325 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 384

Query:   171 KQEK 174
             K+EK
Sbjct:   385 KREK 388

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

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

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

GO:0001764 "neuron migration" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0021759 "globus pallidus development" evidence=IEA

GO:0021800 "cerebral cortex tangential migration" evidence=IEA

GO:0021831 "embryonic olfactory bulb interneuron precursor migration" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021853 "cerebral cortex GABAergic interneuron migration" evidence=IEA

GO:0042127 "regulation of cell proliferation" evidence=IEA

GO:0046622 "positive regulation of organ growth" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E2QVR4 ARX "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 305 (112.4 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   327 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 386

Query:   171 KQEK 174
             K+EK
Sbjct:   387 KREK 390

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

GO:0005634 "nucleus" evidence=IEA

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

MGI|MGI:1097716 Arx "aristaless related homeobox" [Mus musculus (taxid:10090)]

 Score = 305 (112.4 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   327 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 386

Query:   171 KQEK 174
             K+EK
Sbjct:   387 KREK 390

GO:0001764 "neuron migration" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IDA

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

GO:0005634 "nucleus" evidence=IC

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007399 "nervous system development" evidence=IEA

GO:0007411 "axon guidance" evidence=IMP

GO:0021759 "globus pallidus development" evidence=IMP

GO:0021772 "olfactory bulb development" evidence=IMP

GO:0021800 "cerebral cortex tangential migration" evidence=IMP

GO:0021831 "embryonic olfactory bulb interneuron precursor migration" evidence=IMP

GO:0021846 "cell proliferation in forebrain" evidence=IMP

GO:0021853 "cerebral cortex GABAergic interneuron migration" evidence=IMP

GO:0030154 "cell differentiation" evidence=IEA

GO:0030900 "forebrain development" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

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

GO:0046622 "positive regulation of organ growth" evidence=IMP

RGD|1562672 Arx "aristaless related homeobox" [Rattus norvegicus (taxid:10116)]

 Score = 305 (112.4 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   329 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 388

Query:   171 KQEK 174
             K+EK
Sbjct:   389 KREK 392

GO:0001764 "neuron migration" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003682 "chromatin binding" evidence=ISO

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007399 "nervous system development" evidence=IEA

GO:0007411 "axon guidance" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0021759 "globus pallidus development" evidence=ISO

GO:0021772 "olfactory bulb development" evidence=ISO

GO:0021800 "cerebral cortex tangential migration" evidence=ISO

GO:0021831 "embryonic olfactory bulb interneuron precursor migration" evidence=ISO

GO:0021846 "cell proliferation in forebrain" evidence=ISO

GO:0021853 "cerebral cortex GABAergic interneuron migration" evidence=ISO

GO:0030154 "cell differentiation" evidence=IEA

GO:0030900 "forebrain development" evidence=ISO

GO:0042127 "regulation of cell proliferation" evidence=ISO

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

GO:0046622 "positive regulation of organ growth" evidence=ISO

UNIPROTKB|D4A5S8 Arx "Homeobox protein ARX" [Rattus norvegicus (taxid:10116)]

 Score = 305 (112.4 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   329 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 388

Query:   171 KQEK 174
             K+EK
Sbjct:   389 KREK 392

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

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|F1LQW2 Arx "Homeobox protein ARX" [Rattus norvegicus (taxid:10116)]

 Score = 305 (112.4 bits), Expect = 1.6e-26, P = 1.6e-26
 Identities = 56/64 (87%), Positives = 62/64 (96%)

Query:   111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
             KRKQRRYRTTF+++QLEELERAF KTHYPDVF REELA+R+DLTEARVQVWFQNRRAKWR
Sbjct:   329 KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQVWFQNRRAKWR 388

Query:   171 KQEK 174
             K+EK
Sbjct:   389 KREK 392

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

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" 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

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	256
pfam00046	57	pfam00046, Homeobox, Homeobox domain	9e-30
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	4e-25
smart00389	57	smart00389, HOX, Homeodomain	5e-24
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	2e-13

>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain

 Score =  105 bits (265), Expect = 9e-30
 Identities = 35/57 (61%), Positives = 43/57 (75%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           RR RTTF+  QLEELE+ F K  YP    REELA ++ LTE +V+VWFQNRRAKW++
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

 Score = 93.8 bits (234), Expect = 4e-25
 Identities = 33/59 (55%), Positives = 41/59 (69%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           RR RT F+  QLEELE+ F K  YP    REELA  + LTE +V++WFQNRRAK ++ E
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 90.8 bits (226), Expect = 5e-24
 Identities = 33/57 (57%), Positives = 43/57 (75%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           +RR RT+F+  QLEELE+ F K  YP    REELA ++ L+E +V+VWFQNRRAKW+
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. Length = 57

>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription]

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 1/103 (0%)

Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
           G    +  R   ++ QL  LER F    YP    R +L+L +++    VQ+WFQN+RAK 
Sbjct: 47  GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106

Query: 170 RKQEKLVSKQPQELFSSPL-QSPASPSPDLNVISVPAASPVPH 211
           +K+     +Q      + L +  +  +  +++I     S   +
Sbjct: 107 KKKRSGKVEQRPGEEEADLAKIGSLSTGQISIIETLEFSRTSY 149

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	256
KOG0484|consensus	125		99.84
KOG2251|consensus	228		99.82
KOG0488|consensus	309		99.81
KOG0489|consensus	261		99.8
KOG0842|consensus	307		99.8
KOG0850|consensus	245		99.78
KOG0487|consensus	308		99.76
KOG0491|consensus	194		99.76
KOG0494|consensus	332		99.74
KOG0848|consensus	317		99.72
KOG0843|consensus	197		99.71
KOG0485|consensus	268		99.69
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.68
KOG0492|consensus	246		99.66
KOG0844|consensus	408		99.62
KOG0486|consensus	351		99.61
KOG0493|consensus	342		99.58
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.56
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.55
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.55
KOG3802|consensus	398		99.55
COG5576	156	Homeodomain-containing transcription factor [Trans	99.49
KOG0483|consensus	198		99.47
KOG0847|consensus	288		99.39
KOG4577|consensus	383		99.37
KOG0490|consensus	235		99.36
KOG0849|consensus	354		99.24
KOG1168|consensus	385		99.07
KOG0775|consensus	304		99.0
KOG0774|consensus	334		98.97
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.42
KOG2252|consensus	558		98.2
KOG0490|consensus	235		98.2
KOG1146|consensus	1406		97.73
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.02
KOG0773|consensus	342		96.39
KOG3623|consensus	1007		95.91
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.09
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	86.33
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	81.12

>KOG0484|consensus

Probab=99.84  E-value=3.8e-21  Score=149.27  Aligned_cols=70  Identities=71%  Similarity=1.075  Sum_probs=65.7

Q ss_pred             CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhc
Q psy2704         109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK  178 (256)
Q Consensus       109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~  178 (256)
                      ..++|+||.||+|+..||.+||+.|...+||++..|++||..+.|++.+|||||||||+|.||+++...-
T Consensus        12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~   81 (125)
T KOG0484|consen   12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA   81 (125)
T ss_pred             hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            3468899999999999999999999999999999999999999999999999999999999999986643

>KOG2251|consensus

Probab=99.82  E-value=3.8e-20  Score=160.77  Aligned_cols=68  Identities=65%  Similarity=0.995  Sum_probs=65.1

Q ss_pred             CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      ...||+||.||+|+..|+++||..|.+++||+...|++||.+|+|.+.+|+|||+|||+|+|+++++.
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            55689999999999999999999999999999999999999999999999999999999999988865

>KOG0488|consensus

Probab=99.81  E-value=3.5e-19  Score=164.27  Aligned_cols=72  Identities=44%  Similarity=0.701  Sum_probs=65.7

Q ss_pred             cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704         108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ  179 (256)
Q Consensus       108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~  179 (256)
                      ....+|+||.||.||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+||||+.....+.
T Consensus       166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~  237 (309)
T KOG0488|consen  166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGEL  237 (309)
T ss_pred             cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence            344588889999999999999999999999999999999999999999999999999999999987764443

>KOG0489|consensus

Probab=99.80  E-value=8.8e-20  Score=164.85  Aligned_cols=68  Identities=46%  Similarity=0.762  Sum_probs=63.7

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ  179 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~  179 (256)
                      .+.||.||.||..|+.+||+.|..|+|+++..|.|||..|+|+|+|||||||||||||||.++.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            46789999999999999999999999999999999999999999999999999999999988766544

>KOG0842|consensus

Probab=99.80  E-value=3.7e-19  Score=162.68  Aligned_cols=78  Identities=45%  Similarity=0.599  Sum_probs=69.5

Q ss_pred             cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcCCcccCC
Q psy2704         108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFS  185 (256)
Q Consensus       108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~~~~~~~  185 (256)
                      .++.+++||.|..|+..|+.+||+.|..++|++..||++||..|+|++.||||||||||-|+||+++...........
T Consensus       147 ~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~  224 (307)
T KOG0842|consen  147 QTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLAS  224 (307)
T ss_pred             ccccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCC
Confidence            345678888899999999999999999999999999999999999999999999999999999998877665544443

>KOG0850|consensus

Probab=99.78  E-value=1e-18  Score=152.68  Aligned_cols=71  Identities=41%  Similarity=0.650  Sum_probs=65.6

Q ss_pred             ccCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         107 QQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       107 ~~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      ...+.+|.||.||.|+.-||..|.++|++++|+...||.+||..|||+..||||||||||.|.||..+...
T Consensus       115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~  185 (245)
T KOG0850|consen  115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS  185 (245)
T ss_pred             cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence            34566788888999999999999999999999999999999999999999999999999999999888443

>KOG0487|consensus

Probab=99.76  E-value=2.2e-18  Score=157.68  Aligned_cols=73  Identities=33%  Similarity=0.479  Sum_probs=65.5

Q ss_pred             ccCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704         107 QQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ  179 (256)
Q Consensus       107 ~~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~  179 (256)
                      .....+..||||--+|+.|+.+||+.|..|.|++++.|.||++.|+|+++||||||||||+|.||..+....+
T Consensus       228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~  300 (308)
T KOG0487|consen  228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK  300 (308)
T ss_pred             ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence            3344577888899999999999999999999999999999999999999999999999999999988755444

>KOG0491|consensus

Probab=99.76  E-value=2e-18  Score=144.08  Aligned_cols=138  Identities=25%  Similarity=0.272  Sum_probs=105.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCcccCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCccCCCCCCC
Q psy2704          39 QNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPP---TLCFSPTPTPESPPTQQTGKRKQR  115 (256)
Q Consensus        39 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~s~~~s~s~~~---~~~~s~~~~~~~~~~~~~~~~k~r  115 (256)
                      ....+...|.+.+++.++++-++.+..+...+.+..|...-..++..+....-   ..++...-...+-.......-++|
T Consensus        22 ~~pq~~gcGaeq~~psl~~sp~t~pptpt~gp~pss~lll~a~sp~~~hk~~~~~~kgv~p~lalglgn~~~~~~~~~r~  101 (194)
T KOG0491|consen   22 SSPQPVGCGAEQNYPSLQMSPATMPPTPTVGPLPSSMLLLIADSPDSSHKLLLASPKGVQPTLALGLGNKKTARLHCRRR  101 (194)
T ss_pred             cCCcccCcCcccCCCccccCCCCCCCCCCCCCCccccceeeccCCcccccccccCCCccchhHhhhcccchhhhHHHHhh
Confidence            34456777999999999999999999999999888888888887777663110   000000000000011112234567


Q ss_pred             CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      +.|++|+..|+..||+.|+..+|.+..+|.|||..|+|++.|||.||||||+|.||+++..
T Consensus       102 K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~  162 (194)
T KOG0491|consen  102 KARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN  162 (194)
T ss_pred             hhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            7899999999999999999999999999999999999999999999999999999987653

>KOG0494|consensus

Probab=99.74  E-value=2.5e-18  Score=152.45  Aligned_cols=66  Identities=61%  Similarity=1.036  Sum_probs=61.1

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhc
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK  178 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~  178 (256)
                      |+|+.||.||..|+++||+.|+..+||+...|+.||..+.|.|.+|+|||||||+||||.++.+..
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~  205 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG  205 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence            444449999999999999999999999999999999999999999999999999999999987653

>KOG0848|consensus

Probab=99.72  E-value=3.7e-18  Score=151.89  Aligned_cols=68  Identities=40%  Similarity=0.673  Sum_probs=63.1

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      +.|.+-|.|.++|..|+.+||++|..++|+++..+.|||..|||+|+||||||||||+|+||..+.+.
T Consensus       195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            44556677999999999999999999999999999999999999999999999999999999888774

>KOG0843|consensus

Probab=99.71  E-value=9.3e-18  Score=141.90  Aligned_cols=65  Identities=38%  Similarity=0.582  Sum_probs=61.5

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      .+.||.||.|+.+|+..||..|+.++|....+|++||+.|+|++.||||||||||.|.||.+...
T Consensus       100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            37889999999999999999999999999999999999999999999999999999999977653

>KOG0485|consensus

Probab=99.69  E-value=5.3e-17  Score=140.91  Aligned_cols=67  Identities=39%  Similarity=0.657  Sum_probs=62.4

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      +..++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|.||||||||||.||||+-...
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad  166 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD  166 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence            4567888899999999999999999999999999999999999999999999999999999976543

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.68  E-value=6.1e-17  Score=113.09  Aligned_cols=57  Identities=49%  Similarity=0.697  Sum_probs=55.1

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ||.|+.|+.+|+.+|+.+|..++||+..+++.||..|||+..+|++||+|||+++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            577999999999999999999999999999999999999999999999999999986

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>KOG0492|consensus

Probab=99.66  E-value=1.3e-16  Score=137.71  Aligned_cols=68  Identities=37%  Similarity=0.626  Sum_probs=62.1

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ  179 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~  179 (256)
                      +..|+.||.||..||..||+.|+..+|.++.+|.+++..|.|++.||||||||||+|.||.+...-+.
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek  209 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEK  209 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHH
Confidence            44567799999999999999999999999999999999999999999999999999999987765444

>KOG0844|consensus

Probab=99.62  E-value=3.2e-16  Score=141.85  Aligned_cols=67  Identities=39%  Similarity=0.625  Sum_probs=62.6

Q ss_pred             CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .....-||.||.||.+|+..||+.|-+..|.++..|.|||..|+|.|..|||||||||+|+||++..
T Consensus       176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            3456788999999999999999999999999999999999999999999999999999999998754

>KOG0486|consensus

Probab=99.61  E-value=3.8e-16  Score=141.83  Aligned_cols=66  Identities=58%  Similarity=0.943  Sum_probs=63.0

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      +|+||.||.|+..|+.+||..|++++||+...|++||...+|+|.+|+|||+|||+||||+++...
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            488999999999999999999999999999999999999999999999999999999999987654

>KOG0493|consensus

Probab=99.58  E-value=2e-15  Score=134.26  Aligned_cols=60  Identities=38%  Similarity=0.658  Sum_probs=56.9

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ||.||.|+.+||..|+..|+.|+|++.+.|++||.+|+|.|.||||||||+|+|.||...
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            577999999999999999999999999999999999999999999999999999998543

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.56  E-value=2.7e-15  Score=106.07  Aligned_cols=53  Identities=25%  Similarity=0.341  Sum_probs=50.8

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCccchhhhhhhhhh
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHY----PDVFFREELALRIDLTEARVQVWFQNRR  166 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~y----Ps~~~r~~LA~~lgLs~~qVqvWFQNRR  166 (256)
                      +||.||.||.+|+..||..|+.++|    |+..++++||..|||++.+|+|||||.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3788999999999999999999999    9999999999999999999999999965

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

Probab=99.55  E-value=8.5e-15  Score=102.06  Aligned_cols=57  Identities=54%  Similarity=0.817  Sum_probs=54.0

Q ss_pred             CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      +.|..|+..|+.+|+.+|..++||+..+++.||..+||++.+|++||+|||.+.|+.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            557889999999999999999999999999999999999999999999999998863

>smart00389 HOX Homeodomain

Probab=99.55  E-value=7.1e-15  Score=101.78  Aligned_cols=56  Identities=59%  Similarity=0.960  Sum_probs=52.4

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      ++.|+.|+.+|+.+|++.|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            35577899999999999999999999999999999999999999999999999864

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>KOG3802|consensus

Probab=99.55  E-value=2e-15  Score=141.15  Aligned_cols=63  Identities=29%  Similarity=0.389  Sum_probs=60.0

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .|+||+||.|+...+..||++|.+|+.|+.+|+.+||.+|+|.+.+|+|||||||+|.||...
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            478888999999999999999999999999999999999999999999999999999998665

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.49  E-value=3.7e-14  Score=119.11  Aligned_cols=68  Identities=34%  Similarity=0.515  Sum_probs=60.7

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      +.+..+++|++.+.+|+.+|++.|+.++||+...|..|+..|+|+++.|||||||||++.|+......
T Consensus        47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            33456667778889999999999999999999999999999999999999999999999998776543

>KOG0483|consensus

Probab=99.47  E-value=2.3e-14  Score=124.46  Aligned_cols=56  Identities=30%  Similarity=0.593  Sum_probs=53.0

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      +.+|+.+|...||+.|+.+.+....++..||+.|||..+||.|||||||||||.++
T Consensus        54 k~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   54 KRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            44599999999999999999999999999999999999999999999999999865

>KOG0847|consensus

Probab=99.39  E-value=1.7e-13  Score=119.35  Aligned_cols=65  Identities=42%  Similarity=0.741  Sum_probs=59.7

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      ..+++..|.+|+..|+..||+.|+..+|+-..+|.+||..+||++.+|+|||||||.||||+...
T Consensus       164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            35666678899999999999999999999999999999999999999999999999999997543

>KOG4577|consensus

Probab=99.37  E-value=1.5e-12  Score=117.46  Aligned_cols=67  Identities=40%  Similarity=0.568  Sum_probs=61.6

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      +....||.||+++..||+.|+..|+..+.|.+..|+.|+..+||.-++|||||||||+|+||.++..
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            3445678899999999999999999999999999999999999999999999999999999987643

>KOG0490|consensus

Probab=99.36  E-value=2.9e-13  Score=118.34  Aligned_cols=64  Identities=56%  Similarity=0.706  Sum_probs=61.5

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..++||.|+.|+..|+++||+.|+..+||+...|+.||..+++++..|+|||||||+|||++++
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            5688999999999999999999999999999999999999999999999999999999999875

>KOG0849|consensus

Probab=99.24  E-value=3e-11  Score=113.77  Aligned_cols=68  Identities=56%  Similarity=0.836  Sum_probs=63.5

Q ss_pred             cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      ...+++.||.|++|+..|+..||+.|++++||+...|++||.++++++..|+|||+|||+|+||....
T Consensus       170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            44567888889999999999999999999999999999999999999999999999999999998754

>KOG1168|consensus

Probab=99.07  E-value=4.5e-11  Score=108.04  Aligned_cols=63  Identities=27%  Similarity=0.408  Sum_probs=58.3

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..+||+||.+-.-+...||.+|..++.|+.+.+..||++|+|.+.+|+|||||+|+|.||...
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            356788999999999999999999999999999999999999999999999999999988553

>KOG0775|consensus

Probab=99.00  E-value=2.1e-09  Score=96.63  Aligned_cols=52  Identities=31%  Similarity=0.425  Sum_probs=47.9

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      |...-..+|.++|..++||+..++.+||+.+||+..||-+||+|||+|+|-.
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~  234 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA  234 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence            5556678999999999999999999999999999999999999999999943

>KOG0774|consensus

Probab=98.97  E-value=1.5e-09  Score=97.03  Aligned_cols=63  Identities=33%  Similarity=0.505  Sum_probs=57.3

Q ss_pred             CCCCccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         114 QRRYRTTFSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      .||+|..|++.-.++|..+|   ..++||+.+++++||+++|++..||..||.|+|-++||.....
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~  253 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN  253 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence            57788999999999999999   4788999999999999999999999999999999999865443

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=98.42  E-value=1.8e-07  Score=61.38  Aligned_cols=34  Identities=32%  Similarity=0.579  Sum_probs=29.0

Q ss_pred             hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704         135 KTHYPDVFFREELALRIDLTEARVQVWFQNRRAK  168 (256)
Q Consensus       135 ~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK  168 (256)
                      .++||+.+++++||.++||+..||..||-|.|.|
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            5789999999999999999999999999999875

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>KOG2252|consensus

Probab=98.20  E-value=1.9e-06  Score=84.15  Aligned_cols=57  Identities=21%  Similarity=0.395  Sum_probs=53.3

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW  169 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~  169 (256)
                      +.||.|.+|+..|+..|..+|+.+++|+.+..+.|+.+|||....|.+||-|-|.|.
T Consensus       419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            356779999999999999999999999999999999999999999999999988764

>KOG0490|consensus

Probab=98.20  E-value=1.5e-06  Score=75.90  Aligned_cols=66  Identities=52%  Similarity=0.704  Sum_probs=61.1

Q ss_pred             CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ....+.++.|+.|...|+..|+..|..+.+|+...++.|+..+|+.+..|++||+|+|++.++...
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            345677888999999999999999999999999999999999999999999999999999998765

>KOG1146|consensus

Probab=97.73  E-value=6e-05  Score=80.01  Aligned_cols=64  Identities=34%  Similarity=0.467  Sum_probs=59.1

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .-.+|+.|+.++..||..|...|....|+..++.+-|...+++..+.|++||||-|+|.||...
T Consensus       900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            3456778999999999999999999999999999999999999999999999999999988665

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A

Probab=97.02  E-value=0.00055  Score=48.06  Aligned_cols=43  Identities=21%  Similarity=0.299  Sum_probs=31.4

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704         126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK  168 (256)
Q Consensus       126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK  168 (256)
                      +..|+++|...+++...+...|+.+.+|+..||+.||--|+.+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e   52 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE   52 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence            4569999999999999999999999999999999999766543

>KOG0773|consensus

Probab=96.39  E-value=0.0024  Score=59.67  Aligned_cols=60  Identities=22%  Similarity=0.248  Sum_probs=49.8

Q ss_pred             CCCCccccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFH---KTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~---~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ++|.+..+......+|+.++.   ..+||+..++..||.++||+..||.+||-|.|-|..+-.
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence            445566788899999998753   346999999999999999999999999999998765533

>KOG3623|consensus

Probab=95.91  E-value=0.0092  Score=60.71  Aligned_cols=49  Identities=20%  Similarity=0.272  Sum_probs=45.9

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +.+|..+|..|..|+.++...+|.+.||..+.|+.||++++++.++.++
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r  616 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER  616 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence            7789999999999999999999999999999999999999999887664

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=95.09  E-value=0.055  Score=37.33  Aligned_cols=47  Identities=13%  Similarity=0.266  Sum_probs=35.2

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhh
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR  166 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRR  166 (256)
                      ||+|..+|-++...+-..++...     ....||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46788899988877777787765     577899999999999999999853

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=86.33  E-value=1.8  Score=28.75  Aligned_cols=46  Identities=17%  Similarity=0.250  Sum_probs=34.3

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      .++..+..+|...|...     ..-.++|..+|++...|+.+...-..|-|
T Consensus         4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            36778889999998333     34678999999999999988876555544

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=81.12  E-value=2.9  Score=26.69  Aligned_cols=44  Identities=16%  Similarity=0.174  Sum_probs=32.4

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704         120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK  168 (256)
Q Consensus       120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK  168 (256)
                      .++..+..++...|...     ....++|..+|++...|..|...-+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            35667777777776433     246778999999999999998765544

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	256
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		3e-27
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		7e-24
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		1e-23
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		3e-22
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-21
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		1e-20
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		3e-19
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		2e-16
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-15
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		2e-15
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		2e-14
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		7e-11
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		2e-09
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		2e-09
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		3e-09
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		4e-09
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		4e-09
1hom_A	68	Determination Of The Three-Dimensional Structure Of		4e-09
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		6e-09
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-08
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		5e-08
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		9e-08
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		9e-08
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		1e-07
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		2e-07
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		4e-07
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		9e-07
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-06
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		1e-06
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		2e-06
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		2e-06
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		2e-06
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		3e-06
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		5e-06
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		6e-06
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		7e-06
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		7e-06
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		1e-05
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-05
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		3e-05
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		3e-05
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		4e-05
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		5e-05
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		9e-05
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		1e-04
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-04
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		2e-04
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		3e-04
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		6e-04
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		7e-04

>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67

Iteration: 1
 Score =  118 bits (295), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 54/65 (83%), Positives = 62/65 (95%)
Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRRYRTTF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWR
Sbjct: 3   KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 171 KQEKL 175
           KQEK+
Sbjct: 63  KQEKV 67

>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58

Iteration: 1
 Score =  107 bits (267), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 48/58 (82%), Positives = 55/58 (94%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           RYRTTF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWRKQE
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4, Northeast Structural Genomics Consortium (Nesg) Target Hr4490c Length = 75

Iteration: 1
 Score =  106 bits (265), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/66 (72%), Positives = 58/66 (87%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
            K K+RR RTTF+++QLEELE+ F KTHYPDV+ RE+LA+R DLTEARVQVWFQNRRAKW
Sbjct: 5   NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKW 64
Query: 170 RKQEKL 175
           RK+E+ 
Sbjct: 65  RKRERF 70

>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain Length = 60

Iteration: 1
 Score =  102 bits (253), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 45/56 (80%), Positives = 53/56 (94%)
Query: 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175
           TF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWRKQEK+
Sbjct: 5   TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A Dna Oligonucleotide Length = 81

Iteration: 1
 Score = 99.8 bits (247), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 55/67 (82%)
Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           KRKQRR RTTFS  QL+ELERAF +T YPD++ REELA R +LTEAR+QVWFQNRRA+ R
Sbjct: 15  KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
Query: 171 KQEKLVS 177
           KQ   VS
Sbjct: 75  KQHTSVS 81

>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna Length = 61

Iteration: 1
 Score = 96.7 bits (239), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 45/59 (76%), Positives = 50/59 (84%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           QRR RTTF+  QLEELERAF +THYPD++ REELA R  LTEARVQVWF NRRA+WRKQ
Sbjct: 2   QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human Paired Box Protein Pax-6 Length = 80

Iteration: 1
 Score = 92.0 bits (227), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 53/66 (80%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175
           R RT+F+  Q+E LE+ F +THYPDVF RE LA +IDL EAR+QVWF NRRAKWR++EKL
Sbjct: 9   RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 68
Query: 176 VSKQPQ 181
            +++ Q
Sbjct: 69  RNQRRQ 74

>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant Length = 68

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 51/63 (80%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           QRR RT F++ QL+ELE  F + HYPD+  REE+A+  +LTEARV+VWF+NRRAKWRK+E
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 174 KLV 176
           + +
Sbjct: 63  EFI 65

>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Otx2 Length = 80

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 45/56 (80%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           RR RTTF+  QL+ LE  F KT YPD+F REE+AL+I+L E+RVQVWF+NRRAK R
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63

>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain Length = 68

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 50/63 (79%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           QRR RT F++ QL+ELE  F +  YPD+  REE+A+  +LTEARV+VWF+NRRAKWRK+E
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 174 KLV 176
           + +
Sbjct: 63  EFI 65

>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 33/57 (57%), Positives = 44/57 (77%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           RR+RT F++ QLE LE  F +T YPDV  RE+LA ++ L E +V+VWF+NRRAKWR+
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1 From Homo Sapiens Length = 71

Iteration: 1
 Score = 64.3 bits (155), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 28/59 (47%), Positives = 41/59 (69%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           K RR RT F++ QL ELE+ FH   Y  +  R ++A  + L+E +V++WFQNRRAKW++
Sbjct: 6   KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64

>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 93

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 41/60 (68%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           K+++ RT+F+  Q+ ELE+ FHK  Y     R  LA  + +T+A+V+ WFQNRR KWR+Q
Sbjct: 16  KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75

>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Dlx-5 Length = 70

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ RT +S+FQL  L+R F KT Y  +  R ELA  + LT+ +V++WFQN+R+K +K
Sbjct: 8   RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An Antennapedia Homeodomain-Dna Complex Length = 68

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 40/61 (65%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           ++R R T++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+ 
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 174 K 174
           K
Sbjct: 62  K 62

>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With Dna Length = 63

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           +R RT ++  QL ELE+ F    Y     R ELA+ ++LTE  +++WFQNRR KW+K+E
Sbjct: 4   KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62

>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 81

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 26/59 (44%), Positives = 39/59 (66%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           +RR R T++ +Q  ELE+ FH  HY     R E+A  + LTE ++++WFQNRR K +K+
Sbjct: 20  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78

>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The Antennapedia Homeodomain From Drosophila In Solution By 1h Nuclear Magnetic Resonance Spectroscopy Length = 68

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 40/61 (65%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           ++R R T++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+ 
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 174 K 174
           K
Sbjct: 62  K 62

>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex Length = 62

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 25/60 (41%), Positives = 40/60 (66%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           +++R R T++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+
Sbjct: 2   ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61

>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd Site Length = 88

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 40/60 (66%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           +R RT+++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+ K
Sbjct: 29  KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88

>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The Nmr Solution Structure And The Dna Binding Affinity With The Intact Antennapedia Homeodomain Length = 62

Iteration: 1
 Score = 54.7 bits (130), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 24/55 (43%), Positives = 36/55 (65%)
Query: 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           T++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+ K
Sbjct: 2   TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56

>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L Length = 67

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 38/60 (63%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           RR RT F+  Q+E LE  F    YP +   E+LA +++L   R+Q+WFQNRRAK ++  +
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Barh-Like 1 Length = 80

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 37/60 (61%)
Query: 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           +K RR RT F+  QL  LE+ F K  Y     R +LA  + L++ +V+ W+QNRR KW+K
Sbjct: 15  KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74

>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 97

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           RT F+  QL ELE+ FH   Y     R E+A  ++L E +V++WFQNRR K +K+E+
Sbjct: 38  RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94

>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna Length = 60

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 40/58 (68%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           RRYRT F+  QL  LE+ F+K +Y     R ELA +++L E+ ++VWFQNRR K ++Q
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain Length = 56

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 35/54 (64%)
Query: 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           T+FS  Q+ ELER F +  Y     R  LA  + +T+A+V+ WFQNRR KWR+Q
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex Length = 61

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 23/58 (39%), Positives = 40/58 (68%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WF+N+RAK +K
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant Length = 61

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/58 (39%), Positives = 39/58 (67%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL   +R F++  Y     R++L+  + L EA++++WFQN+RAK R+
Sbjct: 3   EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX Protein Lhx9 Length = 80

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           +R RT+F + QL  ++  F   H PD    ++LA +  LT+  +QVWFQN RAK+R+
Sbjct: 8   KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64

>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           R+ RT F+  QL  LER F +  Y  +  R E +  + LTE +V++WFQNRRAK
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK 54

>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex At 2.8 Angstroms Resolution: A Framework For Understanding Homeodomain-Dna Interactions Length = 61

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 40/58 (68%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WFQN+RAK +K
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex Length = 60

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 40/58 (68%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WFQN+RAK +K
Sbjct: 1   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From Human Cdna Length = 70

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 32/51 (62%)
Query: 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           FSN Q  ELE+ F    Y     R+ LA  + L+E +V+ WFQNRRAKWR+
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex Length = 57

Iteration: 1
 Score = 47.8 bits (112), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 23/56 (41%), Positives = 37/56 (66%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WF N+RAK +K
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e Length = 59

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WFQN RAK +K
Sbjct: 1   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a Length = 59

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WFQN RAK +K
Sbjct: 1   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain Length = 54

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 35/51 (68%)
Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WFQN+RAK
Sbjct: 3   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus Norvegicus) Length = 68

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 36/61 (59%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           +R+ R  FS  Q+ ELER F +  Y     RE LA  I LT  +V++WFQN R K ++Q 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 174 K 174
           K
Sbjct: 62  K 62

>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 77

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R  R+ R  ++  Q  ELE+ F    Y     R E+A  ++LTE +V++WFQNRR K +K
Sbjct: 11  RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
Query: 172 QEK 174
             K
Sbjct: 71  INK 73

>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex Length = 60

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ R  ++ +Q  ELE+ F    Y     R E+A  ++LTE +V++WFQNRR K +K
Sbjct: 2   RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna Length = 63

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA+V+ WF+N RAK +K
Sbjct: 4   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi Tarazu Homeodomain From Drosophila And Comparison With The Antennapedia Homeodomain Length = 70

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           +R R T++ +Q  ELE+ FH   Y     R ++A  + L+E ++++WFQNRR K +K   
Sbjct: 4   KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRT 63
Query: 175 LVS 177
           L S
Sbjct: 64  LDS 66

>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Length = 58

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 34/55 (61%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +R+ R  FS  Q+ ELER F +  Y     R++LA  + LT  +V++WFQNRR K
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56

>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES Length = 77

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 32/56 (57%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           K+R+ R  F+  Q  ELER F +  Y     RE LA  I LT  +V++WFQN R K
Sbjct: 8   KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63

>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna Binding Domain Bound To Dna Length = 67

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ R  ++  QL+ELER +    +     R  ++   +L+E +V +WFQNRR K +K
Sbjct: 2   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo Box B13 Length = 70

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ R  +S  QL ELER +    +     R +++    L+E ++ +WFQNRR K +K
Sbjct: 8   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective Protein) Length = 80

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 31/56 (55%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           K+R+ R  F+  Q  ELER F +  Y     RE L   I LT  +V++WFQN R K
Sbjct: 11  KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYK 66

>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To The Consensus Dna Binding Site Taatcc Length = 68

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 4/68 (5%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           RR RTTF++ Q+ ELE+ F +  Y       +L+ ++ L  A+V++WF+NR    R++ K
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNR----RRRHK 58
Query: 175 LVSKQPQE 182
           + S Q ++
Sbjct: 59  IQSDQHKD 66

>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox Protein Nkx-3.1 From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6470a Length = 69

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 125 QLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           Q+ ELER F    Y     R  LA  + LTE +V++WFQNRR K ++++
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain Length = 73

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ R  ++  QL+ELER +    +     R  ++   +L+E +V +WFQNRR K +K
Sbjct: 8   RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	256
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-48
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-48
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	6e-48
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-47
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	4e-47
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	4e-44
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	4e-44
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	8e-43
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-41
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	5e-40
1uhs_A	72	HOP, homeodomain only protein; structural genomics	7e-37
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-36
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-34
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-32
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	4e-31
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-27
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	3e-26
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-24
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	6e-24
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	7e-24
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	2e-23
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	4e-23
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	7e-23
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	8e-23
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-22
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-22
1e3o_C	160	Octamer-binding transcription factor 1; transcript	3e-22
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	8e-22
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-21
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	1e-21
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-21
1lfb_A	99	Liver transcription factor (LFB1); transcription r	2e-21
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-21
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	9e-21
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	2e-20
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	4e-20
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	4e-20
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	6e-20
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	1e-19
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	1e-19
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	2e-19
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	2e-19
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	3e-19
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-18
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	2e-18
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	2e-18
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	5e-18
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	7e-18
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-17
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	4e-17
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-16
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-16
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	6e-15
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	2e-14
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	4e-10
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	1e-09
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	3e-07
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	7e-07
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-06
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	1e-04

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80

 Score =  154 bits (391), Expect = 1e-48
 Identities = 43/78 (55%), Positives = 57/78 (73%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     +R RT+F+  Q+E LE+ F +THYPDVF RE LA +IDL EAR+QVWF NRRAK
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61

Query: 169 WRKQEKLVSKQPQELFSS 186
           WR++EKL +++ Q   SS
Sbjct: 62  WRREEKLRNQRRQSGPSS 79

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81

 Score =  154 bits (391), Expect = 1e-48
 Identities = 48/76 (63%), Positives = 55/76 (72%)

Query: 102 ESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVW 161
                    KRKQRR RTTFS  QL+ELERAF +T YPD++ REELA R +LTEAR+QVW
Sbjct: 6   CESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVW 65

Query: 162 FQNRRAKWRKQEKLVS 177
           FQNRRA+ RKQ   VS
Sbjct: 66  FQNRRARLRKQHTSVS 81

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score =  152 bits (385), Expect = 6e-48
 Identities = 33/66 (50%), Positives = 45/66 (68%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     RR+RT F++ QLE LE  F +T YPDV  RE+LA ++ L E +V+VWF+NRRAK
Sbjct: 2   SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61

Query: 169 WRKQEK 174
           WR+   
Sbjct: 62  WRRSGP 67

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80

 Score =  151 bits (383), Expect = 2e-47
 Identities = 41/78 (52%), Positives = 53/78 (67%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     RR RTTF+  QL+ LE  F KT YPD+F REE+AL+I+L E+RVQVWF+NRRAK
Sbjct: 2   SSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

Query: 169 WRKQEKLVSKQPQELFSS 186
            R+Q++      Q   SS
Sbjct: 62  CRQQQQQQQNGGQSGPSS 79

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68

 Score =  150 bits (380), Expect = 4e-47
 Identities = 36/64 (56%), Positives = 50/64 (78%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
            QRR RT F++ QL++LE  F +  YPD+  REE+A+  +LTEARV+VWF+NRRAKWRK+
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

Query: 173 EKLV 176
           E+ +
Sbjct: 62  EEFI 65

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67

 Score =  142 bits (360), Expect = 4e-44
 Identities = 26/65 (40%), Positives = 38/65 (58%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           RR RT F+  Q+E LE  F    YP +   E+LA +++L   R+Q+WFQNRRAK ++  +
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 175 LVSKQ 179
                
Sbjct: 62  ESQFL 66

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60

 Score =  141 bits (359), Expect = 4e-44
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175
             TF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWRKQEK+
Sbjct: 3   HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score =  139 bits (352), Expect = 8e-43
 Identities = 26/78 (33%), Positives = 39/78 (50%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     +R RT+F + QL  ++  F   H PD    ++LA +  LT+  +QVWFQN RAK
Sbjct: 2   SSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61

Query: 169 WRKQEKLVSKQPQELFSS 186
           +R+             SS
Sbjct: 62  FRRNLLRQENGGVSGPSS 79

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score =  136 bits (344), Expect = 1e-41
 Identities = 22/66 (33%), Positives = 32/66 (48%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     R  RT F+++QL  L+  F    YP     E+L+  ++L    + VWFQN R K
Sbjct: 2   SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61

Query: 169 WRKQEK 174
            RK   
Sbjct: 62  ARKSGP 67

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score =  132 bits (333), Expect = 5e-40
 Identities = 20/64 (31%), Positives = 32/64 (50%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           K  R RT  +  QL  L   +     PD   +E+L     L+   ++VWFQN+R K +K+
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 173 EKLV 176
             ++
Sbjct: 62  SIMM 65

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score =  124 bits (312), Expect = 7e-37
 Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 115 RRYRTTFSNFQLEELERAFHKTH-YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
                T +  Q+E LE  F+K + +PD      +A    LTE + Q WF+ R A+WR+ E
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 174 KLVSKQ 179
            L S+ 
Sbjct: 62  GLPSEC 67

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score =  123 bits (311), Expect = 1e-36
 Identities = 24/75 (32%), Positives = 36/75 (48%)

Query: 100 TPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQ 159
           +  S  T     ++ +R RTT +  QLE L + +     P     + +A  + L +  VQ
Sbjct: 3   SGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62

Query: 160 VWFQNRRAKWRKQEK 174
           VWFQN RA+ RK   
Sbjct: 63  VWFQNTRARERKSGP 77

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73

 Score =  116 bits (293), Expect = 5e-34
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 115 RRYRTTFSNFQLEELERAFHKTH-YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
            +  +  +  Q+E LE  F+K + +PD      +A    LTE + Q WF+ R A+WR+ E
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62

Query: 174 KLVSK 178
            L S+
Sbjct: 63  GLPSE 67

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score =  113 bits (284), Expect = 1e-32
 Identities = 16/65 (24%), Positives = 29/65 (44%)

Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
                +R RT  ++ QL  L + F   + P     +E+A +  L +  ++ WF+N   K 
Sbjct: 3   SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62

Query: 170 RKQEK 174
           R+   
Sbjct: 63  RQSGP 67

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95

 Score =  110 bits (275), Expect = 4e-31
 Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 15/93 (16%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------L 153
           +     R  R T+    L  +E  F++  YPD   REE+A   +               +
Sbjct: 2   SSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV 61

Query: 154 TEARVQVWFQNRRAKWRKQEKLVSKQPQELFSS 186
           T  +V  WF NRR + +++  + +       SS
Sbjct: 62  TSLKVYNWFANRRKEIKRRANIAAILESSGPSS 94

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 99.0 bits (247), Expect = 3e-27
 Identities = 17/67 (25%), Positives = 28/67 (41%)

Query: 108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167
            +G      Y+   S+ QL  L+ +F +  +P     E L     L+   V+ WF +RR 
Sbjct: 2   SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61

Query: 168 KWRKQEK 174
             R  + 
Sbjct: 62  HCRNLKG 68

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 98.9 bits (246), Expect = 3e-26
 Identities = 20/92 (21%), Positives = 32/92 (34%)

Query: 80  STSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYP 139
              P +          +                K+R+ RT+F+   +E L   F K   P
Sbjct: 59  KLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLP 118

Query: 140 DVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
                 E+A  ++     V+VWF NRR   + 
Sbjct: 119 TGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 93.9 bits (233), Expect = 4e-24
 Identities = 19/80 (23%), Positives = 32/80 (40%)

Query: 98  TPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEAR 157
           +    +   +   + ++R+ RT+        LE  F K   P       LA  + L +  
Sbjct: 83  SSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEV 142

Query: 158 VQVWFQNRRAKWRKQEKLVS 177
           V+VWF NRR K ++      
Sbjct: 143 VRVWFCNRRQKEKRMTPAAG 162

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 93.1 bits (231), Expect = 6e-24
 Identities = 24/110 (21%), Positives = 44/110 (40%), Gaps = 2/110 (1%)

Query: 62  TLQQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTF 121
              Q+    F+ +   +   + ++       L  +              +RK R+ RTT 
Sbjct: 37  EFSQTTICRFENLQL-SFKNACKLKAILSKWLEEAEQVGALYNEKVGANERK-RKRRTTI 94

Query: 122 SNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           S    + LER F +   P       +A  ++L +  V+VWF NRR + ++
Sbjct: 95  SIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 90.6 bits (225), Expect = 7e-24
 Identities = 28/73 (38%), Positives = 39/73 (53%)

Query: 102 ESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVW 161
            S     T  +K RR RT F+  QL  LE+ F K  Y     R +LA  + L++ +V+ W
Sbjct: 5   SSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTW 64

Query: 162 FQNRRAKWRKQEK 174
           +QNRR KW+K   
Sbjct: 65  YQNRRMKWKKSGP 77

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93

 Score = 89.9 bits (223), Expect = 2e-23
 Identities = 30/78 (38%), Positives = 46/78 (58%)

Query: 105 PTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQN 164
           P Q     K+++ RT+F+  Q+ ELE+ FHK  Y     R  LA  + +T+A+V+ WFQN
Sbjct: 8   PYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQN 67

Query: 165 RRAKWRKQEKLVSKQPQE 182
           RR KWR+Q     +  ++
Sbjct: 68  RRTKWRRQTAEEREAERQ 85

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155

 Score = 90.9 bits (225), Expect = 4e-23
 Identities = 20/78 (25%), Positives = 35/78 (44%)

Query: 94  CFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDL 153
                   +     +T  + ++R RT+  N     LE  F K+  P +     +A ++ L
Sbjct: 76  EADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGL 135

Query: 154 TEARVQVWFQNRRAKWRK 171
            +  V+VWF NRR K ++
Sbjct: 136 EKDVVRVWFSNRRQKGKR 153

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69

 Score = 87.8 bits (218), Expect = 7e-23
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
               + +  S+ Q+ ELER F    Y     R  LA  + LTE +V++WFQNRR K +++
Sbjct: 3   HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62

Query: 173 EK 174
           + 
Sbjct: 63  QL 64

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score = 87.5 bits (217), Expect = 8e-23
 Identities = 25/66 (37%), Positives = 35/66 (53%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     +  +  FSN Q  ELE+ F    Y     R+ LA  + L+E +V+ WFQNRRAK
Sbjct: 2   SSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61

Query: 169 WRKQEK 174
           WR+   
Sbjct: 62  WRRSGP 67

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 86.3 bits (214), Expect = 3e-22
 Identities = 27/66 (40%), Positives = 41/66 (62%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     R+ RT +S+FQL  L+R F KT Y  +  R ELA  + LT+ +V++WFQN+R+K
Sbjct: 2   SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61

Query: 169 WRKQEK 174
            +K   
Sbjct: 62  IKKSGP 67

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 86.0 bits (213), Expect = 3e-22
 Identities = 10/62 (16%), Positives = 25/62 (40%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
               +    +  Q+  L+ +F ++ +PD      L     L  + ++ WF + R + ++ 
Sbjct: 3   HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62

Query: 173 EK 174
             
Sbjct: 63  IV 64

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 88.9 bits (220), Expect = 3e-22
 Identities = 21/109 (19%), Positives = 50/109 (45%), Gaps = 1/109 (0%)

Query: 64  QQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPT-QQTGKRKQRRYRTTFS 122
            ++ + +F+ + K  P     ++ +       S   +P +  +    G  ++R+ RT+  
Sbjct: 50  FEALNLSFKNMSKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIE 109

Query: 123 NFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
                 LE++F +   P       +A ++++ +  ++VWF NRR K ++
Sbjct: 110 TNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84

 Score = 85.2 bits (211), Expect = 8e-22
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 96  SPTPTPESPPTQQTGK-RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLT 154
            PT    S   ++     K+++ RT FS+ QL  L   F +  Y  +   +EL+  ++L+
Sbjct: 3   QPTSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLS 62

Query: 155 EARVQVWFQNRRAKWRKQEK 174
             +V+ WFQN+R K ++ +K
Sbjct: 63  YKQVKTWFQNQRMKSKRWQK 82

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62

 Score = 84.3 bits (209), Expect = 1e-21
 Identities = 20/61 (32%), Positives = 36/61 (59%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
            +++ RT FS  QL  L+  F K  Y  +   +EL+  ++L+  +V+ WFQN+R K ++ 
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

Query: 173 E 173
           +
Sbjct: 62  Q 62

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68

 Score = 84.3 bits (209), Expect = 1e-21
 Identities = 27/61 (44%), Positives = 36/61 (59%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           +R+ R  FS  Q+ ELER F +  Y     RE LA  I LT  +V++WFQN R K ++Q 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 174 K 174
           K
Sbjct: 62  K 62

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77

 Score = 84.4 bits (209), Expect = 2e-21
 Identities = 25/68 (36%), Positives = 35/68 (51%)

Query: 107 QQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166
                 K+R+ R  F+  Q  ELER F +  Y     RE LA  I LT  +V++WFQN R
Sbjct: 2   SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61

Query: 167 AKWRKQEK 174
            K ++ + 
Sbjct: 62  YKTKRAQN 69

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99

 Score = 84.9 bits (209), Expect = 2e-21
 Identities = 21/88 (23%), Positives = 31/88 (35%), Gaps = 21/88 (23%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID------------------ 152
            +K RR R  +     + L +A+ +   P    RE L    +                  
Sbjct: 6   TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLG 65

Query: 153 ---LTEARVQVWFQNRRAKWRKQEKLVS 177
              +TE RV  WF NRR +   + KL  
Sbjct: 66  SNLVTEVRVYNWFANRRKEEAFRHKLAM 93

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61

 Score = 83.8 bits (208), Expect = 2e-21
 Identities = 16/60 (26%), Positives = 31/60 (51%)

Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           K K  + +++ S      LE  F +    +   +EE+A +  +T  +V+VWF N+R + +
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58

 Score = 81.9 bits (203), Expect = 9e-21
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ RT F+  QL  LER F +  Y  +  R E +  + LTE +V++WFQNRRAK ++
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68

 Score = 81.3 bits (201), Expect = 2e-20
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
            RR RTTF++ Q+ ELE+ F +  Y       +L+ ++ L  A+V++WF+NRR + + Q 
Sbjct: 2   PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

Query: 174 K 174
            
Sbjct: 62  D 62

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58

 Score = 80.0 bits (198), Expect = 4e-20
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           +R+ R  FS  Q+ ELER F +  Y     R++LA  + LT  +V++WFQNRR K +
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97

 Score = 81.5 bits (201), Expect = 4e-20
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 4/94 (4%)

Query: 85  VSPSSPPTLCF----SPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPD 140
           + P++P    F         P++    + G       RT F+  QL ELE+ FH   Y  
Sbjct: 1   MEPNTPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLS 60

Query: 141 VFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
              R E+A  ++L E +V++WFQNRR K +K+E+
Sbjct: 61  RARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60

 Score = 79.7 bits (197), Expect = 6e-20
 Identities = 28/59 (47%), Positives = 40/59 (67%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           RRYRT F+  QL  LE+ F+K +Y     R ELA +++L E+ ++VWFQNRR K ++Q 
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 83.5 bits (205), Expect = 1e-19
 Identities = 25/126 (19%), Positives = 39/126 (30%), Gaps = 21/126 (16%)

Query: 64  QQSCSANFQPVMKYNPSTSPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSN 123
           +Q            + S+  Q+    P     S  P        +   +K RR R  +  
Sbjct: 92  RQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGP 151

Query: 124 FQLEELERAFHKTHYPDVFFREELALRID---------------------LTEARVQVWF 162
              + L +A+ +   P    RE L    +                     +TE RV  WF
Sbjct: 152 ASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWF 211

Query: 163 QNRRAK 168
            NRR +
Sbjct: 212 ANRRKE 217

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56

 Score = 78.5 bits (194), Expect = 1e-19
 Identities = 26/54 (48%), Positives = 35/54 (64%)

Query: 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           T+FS  Q+ ELER F +  Y     R  LA  + +T+A+V+ WFQNRR KWR+Q
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194

 Score = 82.6 bits (203), Expect = 2e-19
 Identities = 21/94 (22%), Positives = 31/94 (32%), Gaps = 21/94 (22%)

Query: 96  SPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID--- 152
                 E P   +   +K RR R  +     + L +A+ +   P    RE L    +   
Sbjct: 97  GQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAE 156

Query: 153 ------------------LTEARVQVWFQNRRAK 168
                             +TE RV  WF NRR +
Sbjct: 157 CIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE 190

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61

 Score = 78.1 bits (193), Expect = 2e-19
 Identities = 23/58 (39%), Positives = 40/58 (68%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           ++R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WF+N+RAK +K
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 78.3 bits (193), Expect = 3e-19
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKT-HYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
              R RT  S   L  L+   H    YPD      L+ ++DL +  +  +FQN+R   + 
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 172 QEK 174
              
Sbjct: 66  SGP 68

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88

 Score = 76.8 bits (189), Expect = 1e-18
 Identities = 26/72 (36%), Positives = 42/72 (58%)

Query: 103 SPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWF 162
              +      + +R RT+++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WF
Sbjct: 17  LGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWF 76

Query: 163 QNRRAKWRKQEK 174
           QNRR KW+K+ K
Sbjct: 77  QNRRMKWKKEHK 88

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68

 Score = 75.9 bits (187), Expect = 2e-18
 Identities = 26/61 (42%), Positives = 40/61 (65%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           ++R R T++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+ 
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

Query: 174 K 174
           K
Sbjct: 62  K 62

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63

 Score = 75.9 bits (187), Expect = 2e-18
 Identities = 27/61 (44%), Positives = 39/61 (63%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
             +R RT ++  QL ELE+ F    Y     R ELA+ ++LTE  +++WFQNRR KW+K+
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

Query: 173 E 173
           E
Sbjct: 62  E 62

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score = 74.9 bits (184), Expect = 5e-18
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +     R+ R  +S  QL ELER +    +     R +++    L+E ++ +WFQNRR K
Sbjct: 2   SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61

Query: 169 WRKQEK 174
            +K   
Sbjct: 62  EKKSGP 67

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81

 Score = 74.8 bits (184), Expect = 7e-18
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 98  TPTPESPPTQQTGK-RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEA 156
           +     P     G    +RR R T++ +Q  ELE+ FH  HY     R E+A  + LTE 
Sbjct: 3   SNHTFYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTER 62

Query: 157 RVQVWFQNRRAKWRKQEK 174
           ++++WFQNRR K +K+ +
Sbjct: 63  QIKIWFQNRRMKLKKEIQ 80

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77

 Score = 73.7 bits (181), Expect = 2e-17
 Identities = 27/76 (35%), Positives = 40/76 (52%)

Query: 103 SPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWF 162
           +P       R  R+ R  ++  Q  ELE+ F    Y     R E+A  ++LTE +V++WF
Sbjct: 2   NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWF 61

Query: 163 QNRRAKWRKQEKLVSK 178
           QNRR K +K  K  +K
Sbjct: 62  QNRRMKMKKINKDRAK 77

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73

 Score = 73.0 bits (179), Expect = 4e-17
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
            + R+ R  ++  QL+ELER +    +     R  ++   +L+E +V +WFQNRR K +K
Sbjct: 5   LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

Query: 172 QEK 174
              
Sbjct: 65  VIN 67

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 74.1 bits (181), Expect = 1e-16
 Identities = 11/81 (13%), Positives = 27/81 (33%)

Query: 94  CFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDL 153
                   +     +      ++ R  F++ Q   L   F +   P    +  ++ ++ L
Sbjct: 77  LRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGL 136

Query: 154 TEARVQVWFQNRRAKWRKQEK 174
             + V  +F N R +   +  
Sbjct: 137 ELSTVSNFFMNARRRSLDKWL 157

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89

 Score = 71.2 bits (174), Expect = 2e-16
 Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 10/92 (10%)

Query: 96  SPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTE 155
           S    P+  P +   K +           Q++ LE +F K+ +P     + L +   L+ 
Sbjct: 5   SSGAYPDFAPQKFKEKTQG----------QVKILEDSFLKSSFPTQAELDRLRVETKLSR 54

Query: 156 ARVQVWFQNRRAKWRKQEKLVSKQPQELFSSP 187
             +  WF  RR      E+ V        S P
Sbjct: 55  REIDSWFSERRKLRDSMEQAVLDSMGSGKSGP 86

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 66.8 bits (163), Expect = 6e-15
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 106 TQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNR 165
           +  +G  K +      +  QL  LE +F +   P     + L     +T   +  WF  R
Sbjct: 3   SGSSGPTKYKE----RAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSER 58

Query: 166 RAKWRKQEK 174
           R K   +E 
Sbjct: 59  RKKVNAEET 67

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89

 Score = 66.2 bits (161), Expect = 2e-14
 Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 2/80 (2%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
            Q+    T    QL  L+ +F  +          L  +  LT   +  WF  ++     +
Sbjct: 12  PQKFKEKTAE--QLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK 69

Query: 173 EKLVSKQPQELFSSPLQSPA 192
           E+ +        SS   S  
Sbjct: 70  EEKMEIDESNAGSSSGPSSG 89

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 54.8 bits (131), Expect = 4e-10
 Identities = 20/90 (22%), Positives = 32/90 (35%), Gaps = 9/90 (10%)

Query: 82  SPQVSPSSPPTLCFSPTPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDV 141
           +      S         P P+S  T +  K+            QL  L+ AF +T +P  
Sbjct: 2   AHHHHHHSSGLEVLFQGPAPKSGSTGKICKKTPE---------QLHMLKSAFVRTQWPSP 52

Query: 142 FFREELALRIDLTEARVQVWFQNRRAKWRK 171
              ++LA    L    +  WF + R  W+ 
Sbjct: 53  EEYDKLAKESGLARTDIVSWFGDTRYAWKN 82

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 52.5 bits (126), Expect = 1e-09
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 110 GKRKQRRYRTTFSNFQLEELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           G +     +        + LE+ F   T YPD    + L+ ++D +  ++Q WF++RR +
Sbjct: 8   GIKDSPVNKVE----PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ 63

Query: 169 WRK 171
            + 
Sbjct: 64  DKP 66

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 9/54 (16%), Positives = 18/54 (33%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
               +  QL  L+  F +  +      ++L     L    +  WF + R   + 
Sbjct: 7   GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 45.3 bits (106), Expect = 7e-07
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHK----THYPDVFFREELALRIDLTEARVQVWFQN 164
           +G     + RT FS+  L  L++ +               E +A  +++    V+ W  N
Sbjct: 3   SGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGN 62

Query: 165 RRAKWRKQEK 174
           RR K+R    
Sbjct: 63  RRRKYRLMGI 72

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 125 QLEELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
               LE+ F   T +PD    E L+ ++D     +Q WF+ RR + + 
Sbjct: 11  PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Length = 80

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 98  TPTPESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHY----PDVFFREELALRIDL 153
           + +  S P+   G  K  R+RT F+  Q E++     +  +     D    E+      +
Sbjct: 3   SGSSGSNPSSSGGTTK--RFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGV 60

Query: 154 TEARVQVWFQNRRAKWRK 171
               +++W  N +     
Sbjct: 61  RRQVLKIWMHNNKNSGPS 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	256
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.83
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.83
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.83
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.82
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.82
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.81
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.81
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.81
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.81
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.81
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.81
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.81
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.81
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.81
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.8
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.8
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.8
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.8
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.8
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.8
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.8
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.79
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.79
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.79
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.79
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.79
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.79
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.79
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.79
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.79
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.79
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.78
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.78
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.78
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.78
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.78
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.78
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.77
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.77
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.77
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.77
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.77
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.76
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.76
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.76
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.75
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.75
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.75
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.74
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.74
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.74
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.74
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.73
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.72
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.72
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.72
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.72
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.71
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.71
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.71
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.71
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.7
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.7
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.7
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.69
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.67
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.67
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.67
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.64
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.59
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.54
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.46
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.46
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.44
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.36
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.76
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	95.58
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.56
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	84.68
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	84.06
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	82.21

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=6.2e-21  Score=141.84  Aligned_cols=64  Identities=41%  Similarity=0.691  Sum_probs=60.2

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ..++.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||..
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            3467788899999999999999999999999999999999999999999999999999999864

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.83  E-value=1.3e-20  Score=140.15  Aligned_cols=68  Identities=59%  Similarity=1.026  Sum_probs=63.4

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ  179 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~  179 (256)
                      .+.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.++.....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~~   72 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQR   72 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhcc
Confidence            46778899999999999999999999999999999999999999999999999999999988776543

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.83  E-value=7.1e-21  Score=142.48  Aligned_cols=65  Identities=32%  Similarity=0.482  Sum_probs=60.9

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ...+.||.|+.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.++
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            45677888999999999999999999999999999999999999999999999999999998654

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A

Probab=99.82  E-value=2.1e-20  Score=138.05  Aligned_cols=69  Identities=36%  Similarity=0.461  Sum_probs=63.5

Q ss_pred             cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      ..+.++.||.|+.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||..+..
T Consensus         7 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~~   75 (77)
T 1puf_A            7 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             SCCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhhc
Confidence            344567888999999999999999999999999999999999999999999999999999999987653

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.82  E-value=1.2e-20  Score=140.20  Aligned_cols=65  Identities=58%  Similarity=0.929  Sum_probs=60.8

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .++.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.++.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            35678889999999999999999999999999999999999999999999999999999997653

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A

Probab=99.82  E-value=2.6e-20  Score=137.53  Aligned_cols=66  Identities=38%  Similarity=0.526  Sum_probs=61.5

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      ..+++||.|+.|+..|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            345678889999999999999999999999999999999999999999999999999999997664

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.82  E-value=1.2e-20  Score=139.76  Aligned_cols=63  Identities=35%  Similarity=0.493  Sum_probs=59.7

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ..+.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.+
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            457788899999999999999999999999999999999999999999999999999999854

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=4.1e-20  Score=137.12  Aligned_cols=64  Identities=38%  Similarity=0.564  Sum_probs=60.2

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .+.||.|+.|+.+|+.+||.+|..++||+..++++||..|||++.+|+|||||||+|+||+...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            4677889999999999999999999999999999999999999999999999999999997653

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.81  E-value=4.7e-20  Score=141.07  Aligned_cols=69  Identities=41%  Similarity=0.691  Sum_probs=62.6

Q ss_pred             CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      ....++||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||......
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             SCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            344577888999999999999999999999999999999999999999999999999999999776443

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.2e-20  Score=134.47  Aligned_cols=63  Identities=52%  Similarity=0.878  Sum_probs=59.3

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .+.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            457788999999999999999999999999999999999999999999999999999998653

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.81  E-value=1.7e-20  Score=136.02  Aligned_cols=63  Identities=32%  Similarity=0.515  Sum_probs=59.3

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ..+.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            356778899999999999999999999999999999999999999999999999999999854

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.81  E-value=2e-20  Score=136.87  Aligned_cols=67  Identities=72%  Similarity=1.172  Sum_probs=62.0

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      .++++|.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.++.+.
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q   72 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQ   72 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhh
Confidence            4567888999999999999999999999999999999999999999999999999999999776543

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.81  E-value=2.9e-20  Score=132.09  Aligned_cols=61  Identities=44%  Similarity=0.748  Sum_probs=56.3

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      +.||.|+.|+..|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||.+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            4677899999999999999999999999999999999999999999999999999999864

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.81  E-value=3.1e-20  Score=133.99  Aligned_cols=63  Identities=43%  Similarity=0.602  Sum_probs=59.5

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      +||.|+.|+..|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~   64 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHh
Confidence            577899999999999999999999999999999999999999999999999999999977643

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.81  E-value=1.7e-20  Score=132.84  Aligned_cols=60  Identities=33%  Similarity=0.551  Sum_probs=53.1

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      +++|.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            467889999999999999999999999999999999999999999999999999999985

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.81  E-value=2.6e-20  Score=138.84  Aligned_cols=61  Identities=16%  Similarity=0.222  Sum_probs=57.9

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhh----CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHK----THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~----~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      .+++||.||.|+.+|+.+||..|+.    ++||+..+|++||..|||++.+|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4577888999999999999999999    999999999999999999999999999999999875

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.80  E-value=5e-20  Score=132.88  Aligned_cols=63  Identities=35%  Similarity=0.570  Sum_probs=59.6

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      .||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            577899999999999999999999999999999999999999999999999999999987654

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.80  E-value=2.6e-20  Score=134.82  Aligned_cols=64  Identities=34%  Similarity=0.491  Sum_probs=59.9

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..+.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||..+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            3567888999999999999999999999999999999999999999999999999999998643

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=99.80  E-value=6.2e-20  Score=136.62  Aligned_cols=65  Identities=71%  Similarity=1.048  Sum_probs=60.2

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .+++||.|+.|+..|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||+.+.
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~~   79 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   79 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhccc
Confidence            46778889999999999999999999999999999999999999999999999999999997753

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.80  E-value=2.7e-20  Score=134.77  Aligned_cols=64  Identities=25%  Similarity=0.310  Sum_probs=60.0

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .++.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||..+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            3567888999999999999999999999999999999999999999999999999999998653

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A

Probab=99.80  E-value=4e-20  Score=130.47  Aligned_cols=58  Identities=40%  Similarity=0.704  Sum_probs=53.3

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      .||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            5778999999999999999999999999999999999999999999999999999987

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.80  E-value=7.7e-20  Score=132.53  Aligned_cols=63  Identities=40%  Similarity=0.603  Sum_probs=58.7

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .+.+|.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+...
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            356677899999999999999999999999999999999999999999999999999998653

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.80  E-value=7.9e-20  Score=127.52  Aligned_cols=57  Identities=44%  Similarity=0.728  Sum_probs=55.3

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            577999999999999999999999999999999999999999999999999999987

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A

Probab=99.79  E-value=5e-20  Score=132.93  Aligned_cols=61  Identities=43%  Similarity=0.767  Sum_probs=58.3

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|+|||||||+|+||..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            5778999999999999999999999999999999999999999999999999999999764

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P

Probab=99.79  E-value=3.4e-20  Score=133.66  Aligned_cols=63  Identities=57%  Similarity=0.988  Sum_probs=59.8

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      ++||.|+.|+..|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||.++.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            567889999999999999999999999999999999999999999999999999999997654

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=6e-20  Score=133.10  Aligned_cols=63  Identities=43%  Similarity=0.700  Sum_probs=59.2

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ..+.||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            346778899999999999999999999999999999999999999999999999999998854

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.79  E-value=1.2e-19  Score=132.73  Aligned_cols=64  Identities=31%  Similarity=0.528  Sum_probs=60.0

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..+.||.|+.|+..|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            3567888999999999999999999999999999999999999999999999999999998653

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.79  E-value=1.1e-19  Score=127.84  Aligned_cols=58  Identities=48%  Similarity=0.739  Sum_probs=55.5

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      ||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5779999999999999999999999999999999999999999999999999999985

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=6.6e-20  Score=136.19  Aligned_cols=63  Identities=24%  Similarity=0.281  Sum_probs=59.3

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhC----CCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKT----HYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~----~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      .++.||.|+.|+.+|+.+||.+|..+    +||+..++++||..|||++.+|+|||||||+|+|+..
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            45778889999999999999999999    9999999999999999999999999999999999843

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*

Probab=99.79  E-value=6.8e-20  Score=136.64  Aligned_cols=63  Identities=41%  Similarity=0.676  Sum_probs=54.7

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .++||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||..+
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            456788999999999999999999999999999999999999999999999999999998643

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.79  E-value=5.9e-20  Score=131.59  Aligned_cols=62  Identities=32%  Similarity=0.539  Sum_probs=58.5

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +.||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.+.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            46788999999999999999999999999999999999999999999999999999998653

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.79  E-value=7.3e-20  Score=136.56  Aligned_cols=60  Identities=20%  Similarity=0.356  Sum_probs=56.6

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHK-----THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~-----~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ..++||.||.|+.+|+.+|| .|..     ++||+..+|++||..|||++.+|+|||||||+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            45678889999999999999 7999     999999999999999999999999999999999875

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.79  E-value=7.2e-20  Score=138.41  Aligned_cols=62  Identities=40%  Similarity=0.748  Sum_probs=55.5

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      .+.||.|+.|+.+|+.+||..|..++||+..+|++||..|||++.+|+|||||||+|+||.+
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            45778899999999999999999999999999999999999999999999999999999864

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.78  E-value=1.6e-19  Score=133.33  Aligned_cols=63  Identities=14%  Similarity=0.144  Sum_probs=57.3

Q ss_pred             CccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704         117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ  179 (256)
Q Consensus       117 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~  179 (256)
                      +|+.||.+|+.+||+.|..++||+..+|++||..+||++.+|+|||||||+|+|+.+..+..+
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w~~~   68 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRD   68 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSSTTC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHHHHH
Confidence            366799999999999999999999999999999999999999999999999999876554443

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.78  E-value=2.5e-19  Score=137.33  Aligned_cols=65  Identities=31%  Similarity=0.494  Sum_probs=61.6

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------CccchhhhhhhhhhHHHHHHHHh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------LTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lg---------------Ls~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .+++||.|+.|+.+|+.+||.+|..++||+..+|++||..||               |++.+|++||||||+|+||+.+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            457788999999999999999999999999999999999999               99999999999999999998765

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.78  E-value=2.5e-19  Score=130.93  Aligned_cols=61  Identities=34%  Similarity=0.465  Sum_probs=57.2

Q ss_pred             CCCccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         115 RRYRTTFSNFQLEELERAFHK-THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~-~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      ++.|+.|+.+|+.+||..|.. ++||+..++++||..+||++.+|++||||||+|+||.++.
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~   64 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   64 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccC
Confidence            466899999999999999995 9999999999999999999999999999999999997743

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*

Probab=99.78  E-value=1.4e-19  Score=127.53  Aligned_cols=60  Identities=27%  Similarity=0.403  Sum_probs=48.6

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      +++.+|.|+.|+.+|+.+||.+|..++||+..++++||..+||++.+|++||||||+|+|
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            356788899999999999999999999999999999999999999999999999999975

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.78  E-value=2.3e-19  Score=130.67  Aligned_cols=60  Identities=35%  Similarity=0.488  Sum_probs=56.7

Q ss_pred             CCCccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHK-THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~-~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .++|+.|+.+|+.+||..|.. ++||+..++++||..|||++.+|++||||||+|+||.++
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            456899999999999999996 999999999999999999999999999999999999764

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.78  E-value=1.8e-19  Score=126.78  Aligned_cols=58  Identities=78%  Similarity=1.254  Sum_probs=50.7

Q ss_pred             CccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       117 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||.++
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            4899999999999999999999999999999999999999999999999999999764

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.77  E-value=2.8e-19  Score=124.30  Aligned_cols=57  Identities=42%  Similarity=0.649  Sum_probs=54.6

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      +||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            467799999999999999999999999999999999999999999999999999975

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.77  E-value=1.8e-19  Score=129.47  Aligned_cols=61  Identities=43%  Similarity=0.745  Sum_probs=57.7

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+..+
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            3678999999999999999999999999999999999999999999999999999998654

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1

Probab=99.77  E-value=2.7e-19  Score=137.62  Aligned_cols=64  Identities=41%  Similarity=0.639  Sum_probs=56.9

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .+.+|.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||.++.
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            4677889999999999999999999999999999999999999999999999999999997653

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.77  E-value=2.6e-19  Score=134.80  Aligned_cols=64  Identities=31%  Similarity=0.502  Sum_probs=58.7

Q ss_pred             CCCccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhc
Q psy2704         115 RRYRTTFSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK  178 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~  178 (256)
                      ||.|+.|+.+|+.+||.+|   ..++||+..++++||..+||++.+|++||||||+|+|+.......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~~   68 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE   68 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccccc
Confidence            6779999999999999999   899999999999999999999999999999999999997765443

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.77  E-value=5.1e-19  Score=122.88  Aligned_cols=54  Identities=48%  Similarity=0.784  Sum_probs=51.0

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      |.|+.+|+.+||..|..++||+..+|++||..+||++.+|++||||||+|+||+
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            579999999999999999999999999999999999999999999999999985

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.76  E-value=4.8e-19  Score=134.68  Aligned_cols=56  Identities=18%  Similarity=0.223  Sum_probs=53.4

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .|+.+|+.+||+.|..++||+..+|++||..|||++.||+|||||||+|||++++.
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~   72 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   72 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999986654

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.76  E-value=4.5e-19  Score=136.23  Aligned_cols=66  Identities=23%  Similarity=0.315  Sum_probs=57.7

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      ....+|.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||.+...
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk~   87 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKW   87 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcccH
Confidence            345667899999999999999999999999999999999999999999999999999999975443

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.76  E-value=7e-19  Score=128.58  Aligned_cols=62  Identities=23%  Similarity=0.316  Sum_probs=58.2

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..++.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||.+.
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            45677999999999999999999999999999999999999999999999999999998654

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=8.2e-19  Score=128.93  Aligned_cols=58  Identities=24%  Similarity=0.306  Sum_probs=54.7

Q ss_pred             CccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       117 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +|+.||.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+|+.++
T Consensus        10 kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A           10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            4567999999999999999999999999999999999999999999999999999664

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=4.4e-19  Score=130.58  Aligned_cols=60  Identities=27%  Similarity=0.426  Sum_probs=56.3

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .+.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||.++
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            345899999999999999999999999999999999999999999999999999998654

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.75  E-value=2e-18  Score=125.92  Aligned_cols=62  Identities=18%  Similarity=0.299  Sum_probs=58.1

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ++.+|.|+.|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            467788999999999999999976   99999999999999999999999999999999999864

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=4.9e-18  Score=131.90  Aligned_cols=68  Identities=28%  Similarity=0.332  Sum_probs=62.7

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHh---------------------CCccchhhhhhhhhhHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRI---------------------DLTEARVQVWFQNRRAKW  169 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l---------------------gLs~~qVqvWFQNRRaK~  169 (256)
                      .+++||.|+.|+..|+.+||+.|..++||+..+|++||..|                     +|++.+|+|||||||+|+
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            35788899999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHHHHhhhc
Q psy2704         170 RKQEKLVSK  178 (256)
Q Consensus       170 rk~~~~~~~  178 (256)
                      |++++....
T Consensus        83 kr~~~~~~~   91 (102)
T 2da6_A           83 AFRQKLAMD   91 (102)
T ss_dssp             HHHHHHHHS
T ss_pred             HHhhHhhhc
Confidence            998776543

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=99.74  E-value=1.6e-18  Score=126.38  Aligned_cols=62  Identities=32%  Similarity=0.509  Sum_probs=57.9

Q ss_pred             CCCCccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         114 QRRYRTTFSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      .||.|+.|+.+|+.+||.+|   ..++||+..++++||..+||++.+|++||||||+|+|+....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            36779999999999999999   899999999999999999999999999999999999986553

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.74  E-value=4.5e-18  Score=127.40  Aligned_cols=63  Identities=16%  Similarity=0.248  Sum_probs=57.9

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .++||.|+.|+.+|+.+|+.+|..   ++||+..++++||..+||++.||++||||||+|+|+...
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~   70 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDML   70 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHH
Confidence            456778999999999999999987   699999999999999999999999999999999988644

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.74  E-value=9.9e-19  Score=124.35  Aligned_cols=59  Identities=27%  Similarity=0.427  Sum_probs=56.0

Q ss_pred             CCCCCccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ..+|.|+.|+.+|+.+||.+|   ..++||+..++++||..+||++.+|++||||||+|+||
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            356779999999999999999   89999999999999999999999999999999999986

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=5.4e-18  Score=128.62  Aligned_cols=57  Identities=25%  Similarity=0.401  Sum_probs=53.4

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      .||.+|+.+||..|..++||+..+|++||..+||++++|+|||||||+|+|+.++..
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            389999999999999999999999999999999999999999999999999876543

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=99.72  E-value=4.9e-18  Score=119.24  Aligned_cols=55  Identities=27%  Similarity=0.353  Sum_probs=53.0

Q ss_pred             ccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         118 RTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      |+.|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+||.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            688999999999999999   9999999999999999999999999999999999874

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.72  E-value=1.9e-18  Score=126.34  Aligned_cols=58  Identities=24%  Similarity=0.384  Sum_probs=53.0

Q ss_pred             CCCccccCHHHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F-~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      .+.|..++.+|+.+||+.| ..++||+..+|++||..|||++++|+|||||||+|+|+.
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            3445567788999999999 999999999999999999999999999999999999974

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.72  E-value=6.5e-18  Score=121.49  Aligned_cols=60  Identities=28%  Similarity=0.323  Sum_probs=56.1

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHK-THYPDVFFREELALRIDLTEARVQVWFQNRRAKW  169 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~-~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~  169 (256)
                      +.++.||.||.|+.+|+.+|+..|+. ++||+...|+.||.++||++++|+|||||||.-.
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            34578899999999999999999999 9999999999999999999999999999999754

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.72  E-value=3.1e-18  Score=143.02  Aligned_cols=62  Identities=24%  Similarity=0.404  Sum_probs=54.9

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      ..++||.|+.|+..|+.+||..|..++||+..+|++||..+||++++|+|||||||+|+||.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            35778889999999999999999999999999999999999999999999999999999985

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.71  E-value=3e-18  Score=143.84  Aligned_cols=64  Identities=30%  Similarity=0.376  Sum_probs=52.5

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .+++||.|+.|+..|+.+||+.|..++||+..+|++||..+||++++|+|||||||+|+||..+
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence            4577888999999999999999999999999999999999999999999999999999999654

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=99.71  E-value=4e-18  Score=140.47  Aligned_cols=62  Identities=31%  Similarity=0.457  Sum_probs=55.7

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      .+++||.|+.|+..|+.+||..|..++||+..+|++||..+||++++|+|||||||+|+||+
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            35677889999999999999999999999999999999999999999999999999999985

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.71  E-value=3e-18  Score=132.70  Aligned_cols=65  Identities=32%  Similarity=0.436  Sum_probs=54.1

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHH------------------hC---CccchhhhhhhhhhHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALR------------------ID---LTEARVQVWFQNRRAKW  169 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~------------------lg---Ls~~qVqvWFQNRRaK~  169 (256)
                      .+++||.|+.|+.+|+.+||..|..++||+..+|++||..                  ||   |++.+|+|||||||+|+
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4678889999999999999999999999999999999999                  88   99999999999999998


Q ss_pred             HHHHHh
Q psy2704         170 RKQEKL  175 (256)
Q Consensus       170 rk~~~~  175 (256)
                      |++++.
T Consensus        86 k~k~~~   91 (99)
T 1lfb_A           86 AFRHKL   91 (99)
T ss_dssp             SCCC--
T ss_pred             HHhchh
Confidence            876654

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.71  E-value=1e-17  Score=126.26  Aligned_cols=60  Identities=25%  Similarity=0.317  Sum_probs=55.9

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      .+++|.|+.|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+|.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            345666899999999999999999   999999999999999999999999999999999873

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.70  E-value=1.2e-17  Score=119.81  Aligned_cols=52  Identities=19%  Similarity=0.383  Sum_probs=49.9

Q ss_pred             CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         122 SNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       122 t~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      +.+|+.+||+.|..++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            5789999999999999999999999999999999999999999999999854

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=99.70  E-value=1.2e-17  Score=138.08  Aligned_cols=60  Identities=32%  Similarity=0.520  Sum_probs=57.7

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      +++||.|+.|+.+|+.+||.+|..++||+..+|++||..+||++++|+|||||||+|+||
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            467788999999999999999999999999999999999999999999999999999986

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.70  E-value=1.3e-17  Score=124.77  Aligned_cols=59  Identities=25%  Similarity=0.288  Sum_probs=54.3

Q ss_pred             CCccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         116 RYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ++|++|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            44666999999999999999   999999999999999999999999999999999998643

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.69  E-value=9.6e-18  Score=121.72  Aligned_cols=56  Identities=39%  Similarity=0.608  Sum_probs=52.4

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..++..|+.+||+.|..++||+..+|++||..|||++++|+|||||||+|+||.+.
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            35789999999999999999999999999999999999999999999999998653

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.67  E-value=2.1e-17  Score=118.20  Aligned_cols=48  Identities=29%  Similarity=0.387  Sum_probs=45.5

Q ss_pred             HHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         124 FQLEELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       124 ~Ql~~Le~~F-~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      .|+.+||+.| ..++||+..+|.+||.+|||+++||+|||||||+|+|+
T Consensus        10 ~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A           10 QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             CHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             hHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            3899999999 57999999999999999999999999999999999986

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.7e-17  Score=117.57  Aligned_cols=53  Identities=17%  Similarity=0.142  Sum_probs=49.7

Q ss_pred             cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ..++..|+.+||+.|..++||+..+|++||..|||++++|+|||||||+|.++
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            44668899999999999999999999999999999999999999999998765

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=99.67  E-value=2.9e-17  Score=136.50  Aligned_cols=61  Identities=31%  Similarity=0.457  Sum_probs=57.5

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      +++||.|+.|+..|+.+||..|..++||+..+|++||..+||++++|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            4667789999999999999999999999999999999999999999999999999999974

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.64  E-value=7e-17  Score=134.93  Aligned_cols=64  Identities=17%  Similarity=0.265  Sum_probs=54.9

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..+.||.|+.|+.+|+.+||..|..++||+..+|++||..|||++.+|+|||||||+|+|+...
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            3567888999999999999999999999999999999999999999999999999999988544

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.59  E-value=1.2e-15  Score=109.70  Aligned_cols=56  Identities=21%  Similarity=0.291  Sum_probs=50.3

Q ss_pred             cccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         119 TTFSNFQLEELERAFH---KTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       119 t~ft~~Ql~~Le~~F~---~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ..|+.+|+.+|+.+|.   .++||+..++++||..+||++.||++||||||+|+||...
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   61 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI   61 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHH
Confidence            3699999999999999   9999999999999999999999999999999999998543

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=99.54  E-value=1.2e-15  Score=131.30  Aligned_cols=62  Identities=31%  Similarity=0.390  Sum_probs=53.9

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CccchhhhhhhhhhHH
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------------LTEARVQVWFQNRRAK  168 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lg---------------------Ls~~qVqvWFQNRRaK  168 (256)
                      ..+++||.|+.|+..|+.+||+.|..++||+..+|++||..|+                     |++.+|++||||||+|
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4567889999999999999999999999999999999999999                     9999999999999999


Q ss_pred             HHH
Q psy2704         169 WRK  171 (256)
Q Consensus       169 ~rk  171 (256)
                      +|.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            764

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=5e-14  Score=101.80  Aligned_cols=46  Identities=15%  Similarity=0.298  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704         123 NFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK  168 (256)
Q Consensus       123 ~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK  168 (256)
                      .+|+.+|+.+|..+++|+.+++..||..+||++++|||||||||++
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            3589999999999999999999999999999999999999999973

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.46  E-value=3.7e-14  Score=123.68  Aligned_cols=61  Identities=31%  Similarity=0.432  Sum_probs=53.7

Q ss_pred             CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CccchhhhhhhhhhH
Q psy2704         109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------------LTEARVQVWFQNRRA  167 (256)
Q Consensus       109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lg---------------------Ls~~qVqvWFQNRRa  167 (256)
                      ...+++||.|+.|+..|+.+||+.|..++||+..+|++||..||                     |++.+|++||||||+
T Consensus       137 ~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             -----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            34577899999999999999999999999999999999999988                     899999999999998


Q ss_pred             HH
Q psy2704         168 KW  169 (256)
Q Consensus       168 K~  169 (256)
                      +.
T Consensus       217 ~~  218 (221)
T 2h8r_A          217 EE  218 (221)
T ss_dssp             TC
T ss_pred             hh
Confidence            64

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=99.44  E-value=1.5e-13  Score=104.09  Aligned_cols=58  Identities=17%  Similarity=0.209  Sum_probs=53.1

Q ss_pred             cccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         119 TTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       119 t~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      ..|+.++..+|+.+|..   ++||+..++++||..+||++.||++||+|||+|+++.....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            46889999999999977   89999999999999999999999999999999998876543

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.36  E-value=1.3e-13  Score=127.53  Aligned_cols=57  Identities=26%  Similarity=0.371  Sum_probs=53.7

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      .++.|+.|+.+|+..||+.|..++||+..+|++||.++||+++||+|||||||+|+|
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            456678899999999999999999999999999999999999999999999999976

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.76  E-value=1e-09  Score=69.78  Aligned_cols=21  Identities=43%  Similarity=0.931  Sum_probs=18.8

Q ss_pred             chhhhhhhhhhHHHHHHHHhh
Q psy2704         156 ARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       156 ~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      +||+|||||||+||||.+...
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            589999999999999988764

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.58  E-value=0.011  Score=42.30  Aligned_cols=39  Identities=21%  Similarity=0.281  Sum_probs=36.3

Q ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhh
Q psy2704         126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQN  164 (256)
Q Consensus       126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQN  164 (256)
                      .+.|+++|...+.+...+...|+.+.+|+..+|+.||-.
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            367999999999999999999999999999999999953

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=85.56  E-value=1.5  Score=31.57  Aligned_cols=45  Identities=13%  Similarity=0.196  Sum_probs=32.3

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ  163 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ  163 (256)
                      +|+.+..|+.++....-+.+... .    -..++|+.+|++...|..|.+
T Consensus        16 ~~~~~~~ys~e~k~~~v~~~~~g-~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           16 GKRPLRSLTPRDKIHAIQRIHDG-E----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CSSCCSSCCHHHHHHHHHHHHHT-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHHH
Confidence            34456678888865555555432 2    256889999999999999974

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=84.68  E-value=1.8  Score=31.17  Aligned_cols=50  Identities=12%  Similarity=0.167  Sum_probs=37.2

Q ss_pred             ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      .++..+..+|...|....     ...++|..+|++...|+.+...-|.|.|+.-.
T Consensus        37 ~L~~~~r~vl~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~   86 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRGW-----STAQIATDLGIAEGTVKSRLHYAVRALRLTLQ   86 (92)
T ss_dssp             TSCHHHHHHHHHHHTSCC-----CHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            366777777777653332     46789999999999999999877777766543

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=84.06  E-value=1.1  Score=29.73  Aligned_cols=46  Identities=13%  Similarity=0.200  Sum_probs=31.9

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhh
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQN  164 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQN  164 (256)
                      |..|+.+........+... ........++|..+|++...|..|.+.
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            4468888776665555433 221223678999999999999999753

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=82.21  E-value=2.3  Score=32.27  Aligned_cols=49  Identities=14%  Similarity=0.219  Sum_probs=37.8

Q ss_pred             CccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704         117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK  168 (256)
Q Consensus       117 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK  168 (256)
                      +|..|+.++...+-..+..+....   ..++|+.+|++...|..|.++++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~---~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCc---HHHHHHHhCCCHHHHHHHHhchhhh
Confidence            467899999877777775555443   3368999999999999999876654

---

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	256
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-31
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-30
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	5e-28
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	9e-28
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-27
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	5e-27
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-26
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-26
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-26
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-25
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	4e-25
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	7e-25
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-24
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-24
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-24
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	3e-24
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	9e-24
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	6e-23
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	7e-23
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-21
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	6e-21
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	4e-19
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	5e-19
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-19
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-18
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-18
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	5e-18
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	5e-18
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-17
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-16
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	9e-15
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-12

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (271), Expect = 3e-31
 Identities = 41/67 (61%), Positives = 54/67 (80%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           +R RT+F+  Q+E LE+ F +THYPDVF RE LA +IDL EAR+QVWF NRRAKWR++EK
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 175 LVSKQPQ 181
           L +++ Q
Sbjct: 62  LRNQRRQ 68

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  106 bits (267), Expect = 1e-30
 Identities = 27/76 (35%), Positives = 40/76 (52%)

Query: 103 SPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWF 162
           +P       R  R+ R  ++  Q  ELE+ F    Y     R E+A  ++LTE +V++WF
Sbjct: 2   NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWF 61

Query: 163 QNRRAKWRKQEKLVSK 178
           QNRR K +K  K  +K
Sbjct: 62  QNRRMKMKKINKDRAK 77

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =   99 bits (249), Expect = 5e-28
 Identities = 46/65 (70%), Positives = 53/65 (81%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           KQRR RTTFS  QL+ELERAF +T YPD++ REELA R +LTEAR+QVWFQNRRA+ RKQ
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

Query: 173 EKLVS 177
              VS
Sbjct: 61  HTSVS 65

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 99.1 bits (247), Expect = 9e-28
 Identities = 20/64 (31%), Positives = 32/64 (50%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           K  R RT  +  QL  L   +     PD   +E+L     L+   ++VWFQN+R K +K+
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 173 EKLV 176
             ++
Sbjct: 62  SIMM 65

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 98.7 bits (246), Expect = 1e-27
 Identities = 24/55 (43%), Positives = 36/55 (65%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           R T++ +Q  ELE+ FH   Y     R E+A  + LTE ++++WFQNRR KW+K+
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 97.3 bits (242), Expect = 5e-27
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ R  +S  QL ELER +    +     R +++    L+E ++ +WFQNRR K +K
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.6 bits (240), Expect = 2e-26
 Identities = 28/74 (37%), Positives = 42/74 (56%)

Query: 101 PESPPTQQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQV 160
           P++    + G       RT F+  QL ELE+ FH   Y     R E+A  ++L E +V++
Sbjct: 14  PKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 73

Query: 161 WFQNRRAKWRKQEK 174
           WFQNRR K +K+E+
Sbjct: 74  WFQNRRMKQKKRER 87

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 95.8 bits (238), Expect = 2e-26
 Identities = 36/60 (60%), Positives = 48/60 (80%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           QRR RT F++ QL++LE  F +  YPD+  REE+A+  +LTEARV+VWF+NRRAKWRK+E
Sbjct: 1   QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 60

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 95.3 bits (237), Expect = 2e-26
 Identities = 25/57 (43%), Positives = 34/57 (59%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           +  +  FSN Q  ELE+ F    Y     R+ LA  + L+E +V+ WFQNRRAKWR+
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 94.4 bits (234), Expect = 1e-25
 Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 15/80 (18%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRI---------------DLTEARVQ 159
           R  R T+    L  +E  F++  YPD   REE+A                   +T  +V 
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 160 VWFQNRRAKWRKQEKLVSKQ 179
            WF NRR + +++  + +  
Sbjct: 61  NWFANRRKEIKRRANIAAIL 80

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 92.3 bits (229), Expect = 4e-25
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           RYRT F+  QL  LE+ F+K +Y     R ELA +++L E+ ++VWFQNRR K ++Q
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 91.5 bits (227), Expect = 7e-25
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R+ RT F+  QL  LER F +  Y  +  R E +  + LTE +V++WFQNRRAK ++
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 91.5 bits (227), Expect = 1e-24
 Identities = 28/66 (42%), Positives = 38/66 (57%)

Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           +R+ R  FS  Q+ ELER F +  Y     RE LA  I LT  +V++WFQN R K ++Q 
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61

Query: 174 KLVSKQ 179
           K  + Q
Sbjct: 62  KDKAAQ 67

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 91.2 bits (226), Expect = 1e-24
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 115 RRYRTTFSNFQLEELERAFHKT-HYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
                T +  Q+E LE  F+K   +PD      +A    LTE + Q WF+ R A+WR+ E
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 174 KLVSK 178
            L S+
Sbjct: 62  GLPSE 66

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 90.0 bits (223), Expect = 3e-24
 Identities = 18/58 (31%), Positives = 30/58 (51%)

Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
           + RTT S    + LER F +   P       +A  ++L +  V+VWF NRR + ++ +
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 58

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 90.1 bits (223), Expect = 3e-24
 Identities = 20/65 (30%), Positives = 33/65 (50%)

Query: 108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167
           +T  + ++R RT+  N     LE  F K   P +     +A ++ L +  V+VWF NRR 
Sbjct: 2   ETLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 61

Query: 168 KWRKQ 172
           K ++ 
Sbjct: 62  KGKRS 66

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 88.8 bits (220), Expect = 9e-24
 Identities = 22/60 (36%), Positives = 37/60 (61%)

Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
           RR RTTF++ Q+ ELE+ F +  Y       +L+ ++ L  A+V++WF+NRR + + Q  
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 87.0 bits (215), Expect = 6e-23
 Identities = 25/63 (39%), Positives = 35/63 (55%)

Query: 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
            K+R+ R  F+  Q  ELER F +  Y     RE LA  I LT  +V++WFQN R K ++
Sbjct: 7   NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

Query: 172 QEK 174
            + 
Sbjct: 67  AQN 69

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 86.1 bits (213), Expect = 7e-23
 Identities = 23/53 (43%), Positives = 35/53 (66%)

Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           R RT FS+ QL  L+R F++  Y     R++L+  + L EA++++WFQN RAK
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.1 bits (205), Expect = 2e-21
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 115 RRYRTTFSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           RR R  F+    E L   F       YP    +EELA +  +T ++V  WF N+R +++K
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 172 QEK 174
              
Sbjct: 62  NIG 64

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 81.1 bits (200), Expect = 6e-21
 Identities = 14/53 (26%), Positives = 29/53 (54%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
           +++ S      LE+ F +    +   +EE+A +  +T  +V+VWF N+R + +
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.1 bits (189), Expect = 4e-19
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 113 KQRRYRTTFSNFQLEELERAFHKT-HYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
              R RT  S   L  L+   H    YPD      L+ ++DL +  +  +FQN+R   + 
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

Query: 172 QEK 174
              
Sbjct: 66  SGP 68

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 76.1 bits (187), Expect = 5e-19
 Identities = 11/49 (22%), Positives = 21/49 (42%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166
           R  F++ Q   L   F +   P    +  ++ ++ L  + V  +F N R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.7 bits (186), Expect = 7e-19
 Identities = 14/55 (25%), Positives = 28/55 (50%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
           RT+        LE++F +   P       +A ++++ +  ++VWF NRR K ++ 
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 56

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 75.2 bits (184), Expect = 2e-18
 Identities = 17/78 (21%), Positives = 26/78 (33%), Gaps = 21/78 (26%)

Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------------LTEA 156
           R  +     + L +A+ +   P    RE L    +                     +TE 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 157 RVQVWFQNRRAKWRKQEK 174
           RV  WF NRR +   + K
Sbjct: 61  RVYNWFANRRKEEAFRHK 78

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 74.4 bits (183), Expect = 2e-18
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 125 QLEELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
               LE+ F   T +PD    E L+ ++D     +Q WF+ RR + + 
Sbjct: 4   PNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 73.7 bits (181), Expect = 5e-18
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 5/60 (8%)

Query: 115 RRYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           R +R  F+   +  LE  F K     Y D    E L     L+  +++ W  NRR K + 
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 74.3 bits (182), Expect = 5e-18
 Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 103 SPPTQQTGKRKQRRYRTTFSNFQLEELERAFHK----THYPDVFFREELALRIDLTEARV 158
           S     +     +R+RT F+  Q E++     +        D    E+      +    +
Sbjct: 6   SGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVL 65

Query: 159 QVWFQNRRAKWRKQ 172
           ++W  N +      
Sbjct: 66  KIWMHNNKNSGPSS 79

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.0 bits (174), Expect = 5e-17
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 5/62 (8%)

Query: 110 GKRKQRRYRTTFSNFQLEELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           G +     +        + LE+ F   T YPD    + L+ ++D +  ++Q WF++RR +
Sbjct: 1   GIKDSPVNKVE----PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ 56

Query: 169 WR 170
            +
Sbjct: 57  DK 58

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (172), Expect = 1e-16
 Identities = 11/60 (18%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 115 RRYRTTFSNFQLEELERAFHKTH---YPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
           +  R          +     +     YP    ++++A + +LT  +V  WF N R +  +
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 9e-15
 Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 5/66 (7%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           T ++ + +     +  QL  L+ +F  +          L  +  LT   +  WF  ++  
Sbjct: 4   TPQKFKEK-----TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS 58

Query: 169 WRKQEK 174
              +E+
Sbjct: 59  KALKEE 64

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 1e-12
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 5/78 (6%)

Query: 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
           +G   +R      +  QL  L+  F +  +      ++L     L    +  WF + R  
Sbjct: 3   SGSSGKR-----KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYA 57

Query: 169 WRKQEKLVSKQPQELFSS 186
            +  +    +      SS
Sbjct: 58  LKHGQLKWFRDNASGPSS 75

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	256
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.84
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.84
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.84
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.83
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.83
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.83
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.83
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.83
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.82
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.82
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.82
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.82
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.81
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.81
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.81
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.79
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.78
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.78
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.77
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.76
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.76
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.75
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.74
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.72
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.7
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.69
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.66
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.65
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.63
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.6
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.59
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.75
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	82.75
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	81.73
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	80.61

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=1.4e-21  Score=143.10  Aligned_cols=66  Identities=38%  Similarity=0.509  Sum_probs=60.9

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704         111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV  176 (256)
Q Consensus       111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~  176 (256)
                      .+.+||.|+.|+.+|+.+||.+|..++||+..++++||..|||++++|+|||||||+|+|+..+..
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            345677899999999999999999999999999999999999999999999999999999977653

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.7e-22  Score=138.17  Aligned_cols=57  Identities=35%  Similarity=0.585  Sum_probs=55.0

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ||.|+.||.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            567899999999999999999999999999999999999999999999999999885

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=1.4e-21  Score=135.75  Aligned_cols=57  Identities=44%  Similarity=0.728  Sum_probs=55.4

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ||.|+.|+.+|+.+||+.|..++||+..++++||..|||++++|+|||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            567999999999999999999999999999999999999999999999999999997

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.83  E-value=2e-21  Score=138.70  Aligned_cols=61  Identities=36%  Similarity=0.601  Sum_probs=57.7

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      ||.|+.|+.+|+.+||..|..++||+..++.+||..|||++++|+|||||||+|+|++...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            5679999999999999999999999999999999999999999999999999999986654

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.83  E-value=1.8e-21  Score=134.67  Aligned_cols=57  Identities=47%  Similarity=0.725  Sum_probs=55.1

Q ss_pred             CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      |.|+.||.+|+.+||..|..++||+..++++||..|||++.+|+|||||||+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            579999999999999999999999999999999999999999999999999999973

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.83  E-value=2.9e-21  Score=137.03  Aligned_cols=63  Identities=70%  Similarity=1.040  Sum_probs=59.6

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL  175 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~  175 (256)
                      |+||.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||....
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            467889999999999999999999999999999999999999999999999999999987654

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.5e-21  Score=133.96  Aligned_cols=57  Identities=44%  Similarity=0.679  Sum_probs=55.0

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      |+.|+.||.+|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467899999999999999999999999999999999999999999999999999986

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=2.3e-21  Score=133.65  Aligned_cols=55  Identities=44%  Similarity=0.796  Sum_probs=53.6

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      ||.||.+|+.+||..|..++||+..++++||..|||++++|+|||||||+|+||+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7899999999999999999999999999999999999999999999999999984

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.82  E-value=1.4e-21  Score=143.15  Aligned_cols=64  Identities=39%  Similarity=0.553  Sum_probs=59.5

Q ss_pred             CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ...++||.|++|+.+|+.+||.+|..++||+..++++||..|||++.+|+|||||||+|+||.+
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            3456778899999999999999999999999999999999999999999999999999988754

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.6e-21  Score=143.74  Aligned_cols=62  Identities=42%  Similarity=0.680  Sum_probs=56.1

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +.+|.|+.|+.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|+||.++
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            45678999999999999999999999999999999999999999999999999999998754

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.6e-21  Score=136.02  Aligned_cols=63  Identities=63%  Similarity=1.097  Sum_probs=59.2

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      ||.||.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+..+...
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~~   64 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN   64 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhhh
Confidence            567999999999999999999999999999999999999999999999999999998776543

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.82  E-value=6.3e-21  Score=136.47  Aligned_cols=61  Identities=44%  Similarity=0.653  Sum_probs=57.8

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +||.|+.||..|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+..+
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            5678999999999999999999999999999999999999999999999999999998653

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.81  E-value=7.8e-21  Score=129.58  Aligned_cols=53  Identities=43%  Similarity=0.703  Sum_probs=51.5

Q ss_pred             CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704         116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK  168 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK  168 (256)
                      |.|+.|+.+|+.+||..|..++||+..+|++||..|||++++|+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            56999999999999999999999999999999999999999999999999986

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.7e-21  Score=133.85  Aligned_cols=60  Identities=60%  Similarity=1.019  Sum_probs=57.1

Q ss_pred             CCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       114 ~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      +||.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+||.+
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~~   60 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   60 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhcC
Confidence            467899999999999999999999999999999999999999999999999999999863

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=1.5e-20  Score=135.82  Aligned_cols=60  Identities=35%  Similarity=0.488  Sum_probs=56.2

Q ss_pred             CCCccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHK-THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~-~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ++.|++||.+|+.+||..|.. +.||+..+|++||..+||++++|+|||||||+|+||.+.
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            567999999999999999986 679999999999999999999999999999999998754

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=5.3e-20  Score=136.15  Aligned_cols=63  Identities=32%  Similarity=0.527  Sum_probs=58.4

Q ss_pred             CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------CccchhhhhhhhhhHHHHHHHHhhh
Q psy2704         115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------LTEARVQVWFQNRRAKWRKQEKLVS  177 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lg---------------Ls~~qVqvWFQNRRaK~rk~~~~~~  177 (256)
                      ||.|+.|+.+|+.+||.+|..++||+..+|++||..+|               |++.+|++||||||+|+||+.+...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            67899999999999999999999999999999999875               9999999999999999999776543

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=3.9e-20  Score=131.90  Aligned_cols=61  Identities=31%  Similarity=0.432  Sum_probs=57.3

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      ..+||.|+.|+.+|+.+|+..|..++||+..++++||..+||++.+|++||||||+|+||.
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            3456789999999999999999999999999999999999999999999999999999873

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.78  E-value=6.1e-20  Score=130.52  Aligned_cols=62  Identities=32%  Similarity=0.539  Sum_probs=58.3

Q ss_pred             CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +.+|.|+.|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            56788999999999999999999999999999999999999999999999999999987543

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.77  E-value=6.8e-20  Score=127.10  Aligned_cols=57  Identities=32%  Similarity=0.438  Sum_probs=54.9

Q ss_pred             CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      |+||.|+.+|+.+||..|..++||+..++.+||..|||++++|++||||||+|+||.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            569999999999999999999999999999999999999999999999999999874

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.76  E-value=1.9e-19  Score=122.65  Aligned_cols=53  Identities=26%  Similarity=0.433  Sum_probs=51.4

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      |+.|+++|+.+||..|..++||+..++++||..+||++++|++||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            78999999999999999999999999999999999999999999999999875

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.6e-19  Score=128.88  Aligned_cols=59  Identities=29%  Similarity=0.339  Sum_probs=55.0

Q ss_pred             CCCCCccccCHHHHHHHHHHHh-hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         113 KQRRYRTTFSNFQLEELERAFH-KTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       113 k~rR~Rt~ft~~Ql~~Le~~F~-~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ..+|.|+.|+.+|+.+||++|. .++||+..++++||.+|||++++|++||||||+|+|+
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            4567799999999999999997 5899999999999999999999999999999999886

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=5e-19  Score=122.23  Aligned_cols=56  Identities=25%  Similarity=0.392  Sum_probs=54.1

Q ss_pred             CccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704         117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ  172 (256)
Q Consensus       117 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~  172 (256)
                      +||.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999999874

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.74  E-value=5.6e-19  Score=129.96  Aligned_cols=60  Identities=17%  Similarity=0.296  Sum_probs=55.3

Q ss_pred             CCCCCCccccCHHHHHHHHHHHhh----CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         112 RKQRRYRTTFSNFQLEELERAFHK----THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       112 ~k~rR~Rt~ft~~Ql~~Le~~F~~----~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      .++||.||.||.+|+.+|+.+|++    ++||+..++++||..|||++.+|+|||||+|+++|+
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            456788999999999999999986    789999999999999999999999999999988764

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.6e-18  Score=125.17  Aligned_cols=54  Identities=19%  Similarity=0.244  Sum_probs=50.5

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      +|.+|+.+||..|..++||+..++++||..|||++++|++||||||+|.|+.++
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            489999999999999999999999999999999999999999999998776544

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=9e-18  Score=122.22  Aligned_cols=57  Identities=16%  Similarity=0.193  Sum_probs=53.0

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK  174 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~  174 (256)
                      ++.||.+|+.+||.+|..++||+..++++||..|||++.+|++||||||+|+|+.+.
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~   63 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchH
Confidence            345789999999999999999999999999999999999999999999999998543

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=4e-18  Score=114.51  Aligned_cols=49  Identities=22%  Similarity=0.388  Sum_probs=48.3

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhh
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR  166 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRR  166 (256)
                      |+.|+.+|+.+||+.|..++||+..++++||..|||++++|++||||||
T Consensus         2 Rt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           2 RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            8999999999999999999999999999999999999999999999998

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.8e-17  Score=119.72  Aligned_cols=59  Identities=34%  Similarity=0.552  Sum_probs=54.7

Q ss_pred             CCCccccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFH---KTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~---~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~  173 (256)
                      ||+|+.|+.+|+.+||.+|.   .++||+..++++||..+||++.||++||||+|+|+|+..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            56788999999999999997   488999999999999999999999999999999988754

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=1.3e-17  Score=112.93  Aligned_cols=50  Identities=28%  Similarity=0.395  Sum_probs=46.6

Q ss_pred             CHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         122 SNFQLEELERAFHK-THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       122 t~~Ql~~Le~~F~~-~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      |.+|..+||.+|.. ++||+..++++||..|||++++|++||||||+|+|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            45789999999986 689999999999999999999999999999999875

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.65  E-value=1.9e-17  Score=121.16  Aligned_cols=56  Identities=29%  Similarity=0.376  Sum_probs=52.6

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhC---------------------CccchhhhhhhhhhHHHHHHH
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRID---------------------LTEARVQVWFQNRRAKWRKQE  173 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lg---------------------Ls~~qVqvWFQNRRaK~rk~~  173 (256)
                      |++|+.+|+.+||++|+.++||+..+|++||..|+                     |++.+|++||||||+|.|++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999995                     899999999999999998753

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=4.2e-17  Score=113.21  Aligned_cols=55  Identities=25%  Similarity=0.422  Sum_probs=50.4

Q ss_pred             CCccccCHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         116 RYRTTFSNFQLEELERAFHK-THYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       116 R~Rt~ft~~Ql~~Le~~F~~-~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      |.++.++.++..+||++|.. ++||+..++++||.+|||++++|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45677888899999999976 68999999999999999999999999999999986

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.60  E-value=4.3e-16  Score=108.30  Aligned_cols=52  Identities=29%  Similarity=0.394  Sum_probs=48.4

Q ss_pred             ccCHHHHHHHHHHHhhC---CCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         120 TFSNFQLEELERAFHKT---HYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       120 ~ft~~Ql~~Le~~F~~~---~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      +|+.+|+.+|+.+|..+   +||+..++++||..+||++.+|++||||+|+|.|+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            39999999999999654   69999999999999999999999999999998875

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.1e-15  Score=106.92  Aligned_cols=56  Identities=20%  Similarity=0.332  Sum_probs=51.4

Q ss_pred             CCCccccCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704         115 RRYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWR  170 (256)
Q Consensus       115 rR~Rt~ft~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r  170 (256)
                      ||+|+.|+.+++.+|+.+|..   ++||+..++.+||..+||+..||++||+|+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            455788999999999999974   78999999999999999999999999999998854

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.75  E-value=0.16  Score=34.07  Aligned_cols=47  Identities=15%  Similarity=0.258  Sum_probs=37.9

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA  167 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa  167 (256)
                      |..+|-.+...+-+.|+.+....   ..+||+.+|+....|..|.+|+..
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHH
Confidence            44588888888888888876543   557999999999999999998544

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=82.75  E-value=0.73  Score=28.55  Aligned_cols=41  Identities=22%  Similarity=0.471  Sum_probs=34.4

Q ss_pred             ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704         118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ  163 (256)
Q Consensus       118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ  163 (256)
                      +..++.+|+....+.+.... +    +.+||..+|++...|-.||-
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-s----~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-P----RQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-C----HHHHHHHHTCCHHHHHHHSC
T ss_pred             CCcCCHHHHHHHHHHHHCCC-C----HHHHHHHHCcCHHHHHhhCC
Confidence            34689999999999997543 3    78899999999999999883

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=81.73  E-value=1.2  Score=28.86  Aligned_cols=46  Identities=13%  Similarity=-0.023  Sum_probs=34.3

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      +...+..++...|....     .-.++|..+|++...|+++++.-|.+-|+
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~   64 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAIDN   64 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            45566667766664443     36789999999999999999877766654

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=80.61  E-value=1.3  Score=28.56  Aligned_cols=46  Identities=13%  Similarity=0.104  Sum_probs=34.7

Q ss_pred             cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704         121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK  171 (256)
Q Consensus       121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk  171 (256)
                      ++..+..++...|....     ..+++|..+|+++..|+.....-|.+.|+
T Consensus        22 L~~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~~~ra~~~Lr~   67 (71)
T d1rp3a2          22 LPEREKLVIQLIFYEEL-----PAKEVAKILETSVSRVSQLKAKALERLRE   67 (71)
T ss_dssp             SCHHHHHHHHHHHTSCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhHhC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            56677777777765442     56789999999999999888766666554