Psyllid ID: psy15100

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-----
Protein Sequence
MTTSASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHGGLTHT
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHcccccHHHHHHHcccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccHHccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mttsastgtttmssatsaktppvrrnrgrspntqtpsedlvpesaFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRtkwkkqnpgmdvnsptvptcpggshsgpafpfhpalsgpgghysgtahyPYAAAAAAYFHHLgahhthggltht
Flexible Loop (DISEMBL)
mttsastgtttmssatsaktppvrrnrgrspntqtpsedlvpeSAFTYEQLVALENKFKTTRYLSVCERLNLALslsltetqvkiWFQNRRtkwkkqnpgmdvnSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHGGLTHT
Low Complexity Region (SEG)
MttsastgtttmssatsaktPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTahypyaaaaaayfhhlgahhthggltht
Disordered region (IsUnstruct)
********************************************AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW************************************GGHYSGTAHYPYAAAAAAYFHHLGAHHT*******
Disordered Region (DISOPRED)
*********************************************FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT*************************************************************************
Disordered Region (DISEMBL)
*************************************EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHH********
Disordered Region (DISPRO)
******************************************ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ************************PFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGA**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTTSASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHGGLTHT
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	165	2.2.26 [Sep-21-2011]
P22807	659	Homeobox protein slou OS=	yes	N/A	0.630	0.157	0.701	2e-35
P15858	74	Homeobox protein H40 (Fra	no	N/A	0.363	0.810	0.966	5e-29
Q15270	411	NK1 transcription factor-	yes	N/A	0.830	0.333	0.477	6e-29
P53547	132	Homeobox protein ceh-1 (F	yes	N/A	0.515	0.643	0.670	3e-28
Q9UD57	310	NK1 transcription factor-	yes	N/A	0.357	0.190	0.932	5e-28
P42580	305	NK1 transcription factor-	no	N/A	0.357	0.193	0.932	7e-28
P19601	232	Homeobox protein SAX-1 (F	no	N/A	0.333	0.237	0.927	6e-25
Q9BZE3	327	BarH-like 1 homeobox prot	no	N/A	0.436	0.220	0.481	8e-15
P63156	327	BarH-like 1 homeobox prot	no	N/A	0.436	0.220	0.481	1e-14
P63157	327	BarH-like 1 homeobox prot	no	N/A	0.436	0.220	0.481	1e-14

>sp|P22807|SLOU_DROME Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1

 Score =  148 bits (373), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 80/114 (70%), Positives = 84/114 (73%), Gaps = 10/114 (8%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 550 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 609

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHH 157
           NSPT+P   GGS    A+         G  YS    YP       YFH LGAHH
Sbjct: 610 NSPTIPPPGGGSFGPGAY-------ASGLLYSHAVPYP---PYGPYFHPLGAHH 653

May play a role in specifying the identity of particular somatic muscles and neurons of the CNS.
Drosophila melanogaster (taxid: 7227)

>sp|P15858|EMS_APIME Homeobox protein H40 (Fragment) OS=Apis mellifera PE=4 SV=1

 Score =  126 bits (317), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 58/60 (96%), Positives = 59/60 (98%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105
           FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG+DV S
Sbjct: 15  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGLDVIS 74

Apis mellifera (taxid: 7460)

>sp|Q15270|NKX11_HUMAN NK1 transcription factor-related protein 1 OS=Homo sapiens GN=NKX1-1 PE=2 SV=2

 Score =  126 bits (317), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 83/174 (47%), Positives = 97/174 (55%), Gaps = 37/174 (21%)

Query: 14  SATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLA 73
           +AT+AK  P R+  G    +  P       +AFTYEQLVALENKFK TRYLSVCERLNLA
Sbjct: 239 TATAAK--PKRKRTGSDSKSGKPRRA---RTAFTYEQLVALENKFKATRYLSVCERLNLA 293

Query: 74  LSLSLTETQVKIWFQNRRTKWKKQNPGMDVN-----------------------SPTVPT 110
           LSLSLTETQVKIWFQNRRTKWKKQNPG D +                       SP  P+
Sbjct: 294 LSLSLTETQVKIWFQNRRTKWKKQNPGADTSAPTGGGGGPGPGAGPGTGLPGGLSPLSPS 353

Query: 111 CPGGS---HSGPA-FPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHG 160
            P G+     GPA +P H    GPGG     A  P+ ++ A     +    T+G
Sbjct: 354 PPMGAPLGMHGPAGYPAH----GPGGLVC-AAQLPFLSSPAVLSPFVLGSQTYG 402

Homo sapiens (taxid: 9606)

>sp|P53547|HM01_CAEEL Homeobox protein ceh-1 (Fragment) OS=Caenorhabditis elegans GN=ceh-1 PE=4 SV=1

 Score =  124 bits (310), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 64/85 (75%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLVALENKFKT+RYLSV ERLNLA+ L L+ETQVKIWFQNRRTKWKK NPG D 
Sbjct: 6   TAFTYEQLVALENKFKTSRYLSVVERLNLAIQLQLSETQVKIWFQNRRTKWKKHNPGQDA 65

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALS 128
           N+P  P     +   P  P +P  S
Sbjct: 66  NTPQTPPSSDETQIQPILPANPITS 90

Caenorhabditis elegans (taxid: 6239)

>sp|Q9UD57|NKX12_HUMAN NK1 transcription factor-related protein 2 OS=Homo sapiens GN=NKX1-2 PE=2 SV=3

 Score =  123 bits (308), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 55/59 (93%), Positives = 57/59 (96%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD 102
           +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG D
Sbjct: 168 TAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGAD 226

May function in cell specification, particularly in the CNS.

Homo sapiens (taxid: 9606)

>sp|P42580|NKX12_MOUSE NK1 transcription factor-related protein 2 OS=Mus musculus GN=Nkx1-2 PE=1 SV=1

 Score =  122 bits (307), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 55/59 (93%), Positives = 57/59 (96%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD 102
           +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG D
Sbjct: 161 TAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGAD 219

May function in cell specification, particularly in the CNS.

Mus musculus (taxid: 10090)

>sp|P19601|SAX1_CHICK Homeobox protein SAX-1 (Fragment) OS=Gallus gallus GN=SAX1 PE=2 SV=2

 Score =  113 bits (282), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 51/55 (92%), Positives = 53/55 (96%)

Query: 43  ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
            +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ
Sbjct: 69  RTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 123

Gallus gallus (taxid: 9031)

>sp|Q9BZE3|BARH1_HUMAN BarH-like 1 homeobox protein OS=Homo sapiens GN=BARHL1 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 52/83 (62%), Gaps = 11/83 (13%)

Query: 15  ATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLAL 74
           ++S  +PPVR  + R   T           AFT  QL  LE  F+  +YLSV +R+ LA 
Sbjct: 165 SSSRDSPPVRLKKPRKART-----------AFTDHQLAQLERSFERQKYLSVQDRMELAA 213

Query: 75  SLSLTETQVKIWFQNRRTKWKKQ 97
           SL+LT+TQVK W+QNRRTKWK+Q
Sbjct: 214 SLNLTDTQVKTWYQNRRTKWKRQ 236

Homo sapiens (taxid: 9606)

>sp|P63156|BARH1_RAT BarH-like 1 homeobox protein OS=Rattus norvegicus GN=Barhl1 PE=2 SV=1

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 52/83 (62%), Gaps = 11/83 (13%)

Query: 15  ATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLAL 74
           ++S  +PPVR  + R   T           AFT  QL  LE  F+  +YLSV +R+ LA 
Sbjct: 165 SSSRDSPPVRLKKPRKART-----------AFTDHQLAQLERSFERQKYLSVQDRMELAA 213

Query: 75  SLSLTETQVKIWFQNRRTKWKKQ 97
           SL+LT+TQVK W+QNRRTKWK+Q
Sbjct: 214 SLNLTDTQVKTWYQNRRTKWKRQ 236

Rattus norvegicus (taxid: 10116)

>sp|P63157|BARH1_MOUSE BarH-like 1 homeobox protein OS=Mus musculus GN=Barhl1 PE=2 SV=1

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 52/83 (62%), Gaps = 11/83 (13%)

Query: 15  ATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLAL 74
           ++S  +PPVR  + R   T           AFT  QL  LE  F+  +YLSV +R+ LA 
Sbjct: 165 SSSRDSPPVRLKKPRKART-----------AFTDHQLAQLERSFERQKYLSVQDRMELAA 213

Query: 75  SLSLTETQVKIWFQNRRTKWKKQ 97
           SL+LT+TQVK W+QNRRTKWK+Q
Sbjct: 214 SLNLTDTQVKTWYQNRRTKWKRQ 236

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	165
328720395	463	PREDICTED: homeobox protein slou-like [A	0.715	0.254	0.758	7e-38
198450206	678	GA19667 [Drosophila pseudoobscura pseudo	0.612	0.148	0.692	2e-37
194745256	667	GF16414 [Drosophila ananassae] gi|190628	0.612	0.151	0.692	1e-36
195391550	699	GJ24446 [Drosophila virilis] gi|19415250	0.612	0.144	0.692	1e-36
195055979	719	GH13609 [Drosophila grimshawi] gi|193892	0.606	0.139	0.683	3e-36
195110715	754	GI24800 [Drosophila mojavensis] gi|19391	0.624	0.136	0.672	7e-36
357603885	165	nk homeobox protein [Danaus plexippus]	0.642	0.642	0.695	1e-35
170070126	209	nk homeobox protein [Culex quinquefascia	0.624	0.492	0.677	1e-35
157135796	184	nk homeobox protein [Aedes aegypti] gi|1	0.612	0.548	0.692	2e-35
347963914	688	AGAP000484-PA [Anopheles gambiae str. PE	0.618	0.148	0.675	4e-35

>gi|328720395|ref|XP_003247017.1| PREDICTED: homeobox protein slou-like [Acyrthosiphon pisum]

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 94/124 (75%), Positives = 100/124 (80%), Gaps = 6/124 (4%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG+DV
Sbjct: 340 TAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGLDV 399

Query: 104 NSPTV-PTCPGGSHS--GPAFPFHPALSGPGGHYSGTAHYPYAAAAAAYFHHLGAHHTHG 160
           NSPTV P  P GS +  GP F FHP L+    H+  T  Y  AAAAAAYFHHLGAHH+  
Sbjct: 400 NSPTVPPPGPAGSSATGGPPF-FHP-LAYSAAHHYQTQSY-SAAAAAAYFHHLGAHHSTI 456

Query: 161 GLTH 164
           G  H
Sbjct: 457 GGHH 460

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198450206|ref|XP_001357880.2| GA19667 [Drosophila pseudoobscura pseudoobscura] gi|198130935|gb|EAL27016.2| GA19667 [Drosophila pseudoobscura pseudoobscura]

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 81/117 (69%), Positives = 88/117 (75%), Gaps = 16/117 (13%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 569 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 628

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           NSPT+P   GGS+            GPG  Y+ +  YP+A        YFH LGAHH
Sbjct: 629 NSPTIPPPAGGSY------------GPGA-YASSLLYPHAVPYPPYGPYFHPLGAHH 672

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194745256|ref|XP_001955104.1| GF16414 [Drosophila ananassae] gi|190628141|gb|EDV43665.1| GF16414 [Drosophila ananassae]

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 81/117 (69%), Positives = 87/117 (74%), Gaps = 16/117 (13%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 558 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 617

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           NSPT+P   GGS             GPG  Y+ +  YP+A        YFH LGAHH
Sbjct: 618 NSPTIPPPTGGSF------------GPGA-YASSLLYPHAVPYPPYGPYFHPLGAHH 661

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195391550|ref|XP_002054423.1| GJ24446 [Drosophila virilis] gi|194152509|gb|EDW67943.1| GJ24446 [Drosophila virilis]

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 81/117 (69%), Positives = 87/117 (74%), Gaps = 16/117 (13%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 590 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 649

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           NSPT+P   GGS             GPG  Y+ +  YP+A        YFH LGAHH
Sbjct: 650 NSPTLPPPAGGSF------------GPGA-YASSLLYPHAVPYPPYGPYFHPLGAHH 693

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195055979|ref|XP_001994890.1| GH13609 [Drosophila grimshawi] gi|193892653|gb|EDV91519.1| GH13609 [Drosophila grimshawi]

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 80/117 (68%), Positives = 86/117 (73%), Gaps = 17/117 (14%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 611 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 670

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           NSPT+P  P G   GP            G Y+ +  YP+A        YFH LGAHH
Sbjct: 671 NSPTLP--PAGGSFGP------------GAYASSLLYPHAVPYPPYGPYFHPLGAHH 713

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195110715|ref|XP_001999925.1| GI24800 [Drosophila mojavensis] gi|193916519|gb|EDW15386.1| GI24800 [Drosophila mojavensis]

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 82/122 (67%), Positives = 89/122 (72%), Gaps = 19/122 (15%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 645 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 704

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAH---H 157
           NSPT+P   GGS             GPG  Y+ +  YP+A        YFH LGAH   H
Sbjct: 705 NSPTLPPPTGGSF------------GPGA-YASSLLYPHAVPYPPYGPYFHPLGAHQLSH 751

Query: 158 TH 159
           +H
Sbjct: 752 SH 753

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357603885|gb|EHJ63961.1| nk homeobox protein [Danaus plexippus]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 80/115 (69%), Positives = 86/115 (74%), Gaps = 9/115 (7%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 45  TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 104

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAAAA--AAYFHHLGAH 156
           NSPTVP  P G+    A+P        G  YS    YP+      A YFHHL A+
Sbjct: 105 NSPTVPPPPAGAFPSGAYPG-------GLLYSHGVPYPFTGPGPYAPYFHHLAAN 152

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170070126|ref|XP_001869473.1| nk homeobox protein [Culex quinquefasciatus] gi|167866042|gb|EDS29425.1| nk homeobox protein [Culex quinquefasciatus]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 80/118 (67%), Positives = 85/118 (72%), Gaps = 15/118 (12%)

Query: 43  ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD 102
            +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD
Sbjct: 98  RTAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD 157

Query: 103 VNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           VNSPTVP   GG   GP            G Y+ +  YP+A        YFH LG HH
Sbjct: 158 VNSPTVPPPNGGGAFGP------------GSYASSLLYPHAVPYPPYGPYFHPLGGHH 203

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157135796|ref|XP_001663597.1| nk homeobox protein [Aedes aegypti] gi|108870112|gb|EAT34337.1| AAEL013405-PA [Aedes aegypti]

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 81/117 (69%), Positives = 86/117 (73%), Gaps = 16/117 (13%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 75  TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 134

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           NSPTVP   GGS             GPG  Y+ +  YP+A        YFH LG HH
Sbjct: 135 NSPTVPPPNGGSF------------GPGS-YASSLLYPHAVPYPPYGPYFHPLGGHH 178

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347963914|ref|XP_310608.5| AGAP000484-PA [Anopheles gambiae str. PEST] gi|333466976|gb|EAA06450.5| AGAP000484-PA [Anopheles gambiae str. PEST]

 Score =  152 bits (385), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 79/117 (67%), Positives = 84/117 (71%), Gaps = 15/117 (12%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct: 578 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 637

Query: 104 NSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGTAHYPYAA---AAAAYFHHLGAHH 157
           NSPTVP    G   GP            G Y+ +  YP+A        YFH LG HH
Sbjct: 638 NSPTVPPPNSGGSFGP------------GSYASSLLYPHAMPYPPYGPYFHPLGGHH 682

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

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	165
FB|FBgn0002941	659	slou "slouch" [Drosophila mela	0.454	0.113	0.894	7.3e-32
UNIPROTKB|J9P324	413	NKX1-1 "Uncharacterized protei	0.618	0.246	0.630	4.4e-29
UNIPROTKB|Q15270	411	NKX1-1 "NK1 transcription fact	0.618	0.248	0.630	4.4e-29
ZFIN|ZDB-GENE-040615-2	373	nkx1.2lb "NK1 transcription fa	0.575	0.254	0.673	4.4e-29
RGD|1306744	268	Nkx1-2 "NK1 homeobox 2" [Rattu	0.642	0.395	0.615	2.2e-27
UNIPROTKB|F1NZL8	153	LOC100857765 "Uncharacterized	0.612	0.660	0.625	3.5e-27
UNIPROTKB|F1SDP4	320	NKX1-2 "Uncharacterized protei	0.648	0.334	0.6	3.5e-27
UNIPROTKB|J9P9C4	315	NKX1-2 "Uncharacterized protei	0.654	0.342	0.603	4.5e-27
UNIPROTKB|G3V2X8	332	NKX1-2 "NK1 transcription fact	0.618	0.307	0.608	4.5e-27
UNIPROTKB|Q9UD57	310	NKX1-2 "NK1 transcription fact	0.618	0.329	0.608	4.5e-27

FB|FBgn0002941 slou "slouch" [Drosophila melanogaster (taxid:7227)]

 Score = 356 (130.4 bits), Expect = 7.3e-32, P = 7.3e-32
 Identities = 68/76 (89%), Positives = 71/76 (93%)

Query:    44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
             +AFTYEQLV+LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV
Sbjct:   550 TAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 609

Query:   104 NSPTVPTCPGGSHSGP 119
             NSPT+P  PGG   GP
Sbjct:   610 NSPTIPP-PGGGSFGP 624

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

GO:0007521 "muscle cell fate determination" evidence=IEP;IMP

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

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

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

GO:0007525 "somatic muscle development" evidence=NAS

GO:0007399 "nervous system development" evidence=NAS

GO:0007517 "muscle organ development" evidence=TAS

GO:0007501 "mesodermal cell fate specification" evidence=NAS

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

UNIPROTKB|J9P324 NKX1-1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 70/111 (63%), Positives = 75/111 (67%)

Query:    22 PVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
             P R+  G    +  P       +AFTYEQLVALENKFK TRYLSVCERLNLALSLSLTET
Sbjct:   247 PKRKRTGSDSKSGKPRR---ARTAFTYEQLVALENKFKATRYLSVCERLNLALSLSLTET 303

Query:    82 QVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGG 132
             QVKIWFQNRRTKWKKQNPG D ++PT     GG   GP     P    PGG
Sbjct:   304 QVKIWFQNRRTKWKKQNPGADTSAPT----GGGGAPGPGAG--PGAGLPGG 348

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|Q15270 NKX1-1 "NK1 transcription factor-related protein 1" [Homo sapiens (taxid:9606)]

 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 70/111 (63%), Positives = 75/111 (67%)

Query:    22 PVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
             P R+  G    +  P       +AFTYEQLVALENKFK TRYLSVCERLNLALSLSLTET
Sbjct:   245 PKRKRTGSDSKSGKPRR---ARTAFTYEQLVALENKFKATRYLSVCERLNLALSLSLTET 301

Query:    82 QVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGG 132
             QVKIWFQNRRTKWKKQNPG D ++PT     GG   GP     P    PGG
Sbjct:   302 QVKIWFQNRRTKWKKQNPGADTSAPT----GGGGGPGPGAG--PGTGLPGG 346

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

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

GO:0043467 "regulation of generation of precursor metabolites and energy" evidence=IEA

GO:0050877 "neurological system process" evidence=IEA

GO:0003677 "DNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-040615-2 nkx1.2lb "NK1 transcription factor related 2-like,b" [Danio rerio (taxid:7955)]

 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 66/98 (67%), Positives = 75/98 (76%)

Query:    23 VRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQ 82
             V+  R RS +     +     +AFTYEQLVALENKFK+TRYLSVCERLNLALSLSLTETQ
Sbjct:   211 VKPKRKRSGSDSKSGKPRRARTAFTYEQLVALENKFKSTRYLSVCERLNLALSLSLTETQ 270

Query:    83 VKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPA 120
             VKIWFQNRRTKWKKQNPG D ++PT     GG  +GP+
Sbjct:   271 VKIWFQNRRTKWKKQNPGADTSAPT---SGGGGGNGPS 305

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

RGD|1306744 Nkx1-2 "NK1 homeobox 2" [Rattus norvegicus (taxid:10116)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 72/117 (61%), Positives = 79/117 (67%)

Query:    21 PPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTE 80
             P  RR R  S +   P       +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTE
Sbjct:   105 PRPRRRRAES-SCAKPRR---ARTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTE 160

Query:    81 TQVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSGT 137
             TQVKIWFQNRRTKWKKQNPG D     V    GGS   P  P   A++G GG  +G+
Sbjct:   161 TQVKIWFQNRRTKWKKQNPGAD---GAVQA--GGSAPQPGTP--NAVTGGGGSATGS 210

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

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|F1NZL8 LOC100857765 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 65/104 (62%), Positives = 72/104 (69%)

Query:    26 NRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKI 85
             NR R  N +   +     +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTETQVKI
Sbjct:     7 NR-RKKNRECYKKPRRARTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTETQVKI 65

Query:    86 WFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSG 129
             WFQNRRTKWKKQ+PG D      P  P  +   P+ P   AL G
Sbjct:    66 WFQNRRTKWKKQHPGAD--GAAAPAPPAAARCSPSPPRPAALPG 107

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1SDP4 NKX1-2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 69/115 (60%), Positives = 76/115 (66%)

Query:    22 PVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
             P  R R   P+   P       +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTET
Sbjct:   150 PRPRRRRSEPSCSKPRR---ARTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTET 206

Query:    82 QVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSG 136
             QVKIWFQNRRTKWKKQNPG +  +       GG+   P  P   A +G GG  SG
Sbjct:   207 QVKIWFQNRRTKWKKQNPGAEGTAQAA----GGAPQ-PVTPGAAAGAGGGGGGSG 256

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|J9P9C4 NKX1-2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 67/111 (60%), Positives = 70/111 (63%)

Query:    22 PVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
             P  R R   P    P       +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTET
Sbjct:   149 PRPRRRRAEPRCAKPRR---ARTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTET 205

Query:    82 QVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGG 132
             QVKIWFQNRRTKWKKQNPG D  +      P     GPA        G GG
Sbjct:   206 QVKIWFQNRRTKWKKQNPGADGAAQAGSGAPQPGAPGPAAGAGGGGGGAGG 256

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|G3V2X8 NKX1-2 "NK1 transcription factor-related protein 2" [Homo sapiens (taxid:9606)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 70/115 (60%), Positives = 73/115 (63%)

Query:    22 PVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
             P  R R   PN   P       +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTET
Sbjct:   171 PRPRRRRLEPNCAKPRR---ARTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTET 227

Query:    82 QVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSG 136
             QVKIWFQNRRTKWKKQNPG D          G +  G   P   A  G GG  SG
Sbjct:   228 QVKIWFQNRRTKWKKQNPGAD----------GAAQVGGGAPQPGAAGGGGGGGSG 272

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q9UD57 NKX1-2 "NK1 transcription factor-related protein 2" [Homo sapiens (taxid:9606)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 70/115 (60%), Positives = 73/115 (63%)

Query:    22 PVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
             P  R R   PN   P       +AFTYEQLVALENKF+ TRYLSVCERLNLALSLSLTET
Sbjct:   149 PRPRRRRLEPNCAKPRR---ARTAFTYEQLVALENKFRATRYLSVCERLNLALSLSLTET 205

Query:    82 QVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGSHSGPAFPFHPALSGPGGHYSG 136
             QVKIWFQNRRTKWKKQNPG D          G +  G   P   A  G GG  SG
Sbjct:   206 QVKIWFQNRRTKWKKQNPGAD----------GAAQVGGGAPQPGAAGGGGGGGSG 250

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P15858	EMS_APIME	No assigned EC number	0.9666	0.3636	0.8108	no	N/A
P53547	HM01_CAEEL	No assigned EC number	0.6705	0.5151	0.6439	yes	N/A
P22807	SLOU_DROME	No assigned EC number	0.7017	0.6303	0.1578	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	165
pfam00046	57	pfam00046, Homeobox, Homeobox domain	6e-25
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-21
smart00389	57	smart00389, HOX, Homeodomain	3e-20
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	4e-10

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

 Score = 90.6 bits (226), Expect = 6e-25
 Identities = 31/52 (59%), Positives = 35/52 (67%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
           FT EQL  LE +F+  RY S  ER  LA  L LTE QVK+WFQNRR KWK+
Sbjct: 6  TFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 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 = 81.9 bits (203), Expect = 1e-21
 Identities = 30/53 (56%), Positives = 33/53 (62%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          FT EQL  LE +F+   Y S  ER  LA  L LTE QVKIWFQNRR K K+  
Sbjct: 7  FTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 78.4 bits (194), Expect = 3e-20
 Identities = 29/51 (56%), Positives = 34/51 (66%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
          +FT EQL  LE +F+   Y S  ER  LA  L L+E QVK+WFQNRR KWK
Sbjct: 7  SFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 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 = 54.8 bits (132), Expect = 4e-10
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 47  TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           T EQL+ LE +F+   Y S   R+ L+L L++    V+IWFQN+R K KK+ 
Sbjct: 59  TDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	165
KOG0488|consensus	309		99.84
KOG0850|consensus	245		99.82
KOG0842|consensus	307		99.82
KOG0489|consensus	261		99.81
KOG0487|consensus	308		99.79
KOG0485|consensus	268		99.78
KOG0484|consensus	125		99.78
KOG2251|consensus	228		99.76
KOG0843|consensus	197		99.75
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.75
KOG0848|consensus	317		99.73
KOG0492|consensus	246		99.73
KOG0494|consensus	332		99.72
KOG0493|consensus	342		99.72
KOG0491|consensus	194		99.69
KOG3802|consensus	398		99.67
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.65
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.65
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.64
KOG0844|consensus	408		99.63
KOG0486|consensus	351		99.62
COG5576	156	Homeodomain-containing transcription factor [Trans	99.59
KOG0483|consensus	198		99.58
KOG4577|consensus	383		99.46
KOG0847|consensus	288		99.46
KOG0490|consensus	235		99.31
KOG0849|consensus	354		99.27
KOG0775|consensus	304		99.2
KOG1168|consensus	385		99.16
KOG0774|consensus	334		99.06
KOG2252|consensus	558		98.82
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.71
KOG0490|consensus	235		98.24
KOG1146|consensus	1406		98.0
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.57
KOG0773|consensus	342		97.17
KOG3623|consensus	1007		96.71
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.98
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	90.46
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	87.81
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	85.87
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	85.49
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	85.46
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	84.57
PRK03975	141	tfx putative transcriptional regulator; Provisiona	84.05
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	80.13

>KOG0488|consensus

Probab=99.84  E-value=4e-21  Score=158.76  Aligned_cols=74  Identities=46%  Similarity=0.775  Sum_probs=67.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         26 NRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        26 ~~~~~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..........++|.||.|++||..||..||+.|++.+|++..+|++||..|||++.||++||||||+||||+..
T Consensus       159 ~~~~~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a  232 (309)
T KOG0488|consen  159 QTNHPYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA  232 (309)
T ss_pred             ccCCCcccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence            33555556677999999999999999999999999999999999999999999999999999999999999754

>KOG0850|consensus

Probab=99.82  E-value=2.8e-20  Score=145.37  Aligned_cols=69  Identities=45%  Similarity=0.640  Sum_probs=64.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         33 TQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        33 ~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ..+.||.||.||.|+..||..|++.|++++|+...||.+||..|||+..||||||||||.|.||..+.+
T Consensus       116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g  184 (245)
T KOG0850|consen  116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG  184 (245)
T ss_pred             CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence            446788999999999999999999999999999999999999999999999999999999999987643

>KOG0842|consensus

Probab=99.82  E-value=2e-20  Score=153.10  Aligned_cols=70  Identities=44%  Similarity=0.596  Sum_probs=64.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS  105 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~  105 (165)
                      .+++||.|..|+..|+-+||+.|.+++|++..||+.||..|+|+++||||||||||-|+||++.+...+.
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            5678888999999999999999999999999999999999999999999999999999999887554443

>KOG0489|consensus

Probab=99.81  E-value=3.2e-20  Score=150.49  Aligned_cols=70  Identities=44%  Similarity=0.719  Sum_probs=64.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVN  104 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~  104 (165)
                      ...+.||.|+.||..|+.+||+.|..|+|++...|.+||..|+|+|+||||||||||+||||..+.....
T Consensus       155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            3456889999999999999999999999999999999999999999999999999999999988765544

>KOG0487|consensus

Probab=99.79  E-value=4.3e-20  Score=151.21  Aligned_cols=68  Identities=41%  Similarity=0.575  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         32 NTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        32 ~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +-...+..||||.-+|+.|+.+||+.|..|.|++.+.|.+|++.|+|+++||+|||||||+|+||..+
T Consensus       228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r  295 (308)
T KOG0487|consen  228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR  295 (308)
T ss_pred             ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence            44556788999999999999999999999999999999999999999999999999999999999875

>KOG0485|consensus

Probab=99.78  E-value=5.7e-19  Score=137.05  Aligned_cols=64  Identities=52%  Similarity=0.788  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++||.|++|+..|+..||..|+..+|++..||..||+.|.|+|.||||||||||.||||+..
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a  164 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA  164 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence            4478889999999999999999999999999999999999999999999999999999999854

>KOG0484|consensus

Probab=99.78  E-value=1.8e-19  Score=125.02  Aligned_cols=64  Identities=39%  Similarity=0.639  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .+|.++-|+.|+..||.+||+.|.+..||++-.|++||.++.|++..|+|||||||+|.||+++
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr   77 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER   77 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence            3567788999999999999999999999999999999999999999999999999999999865

>KOG2251|consensus

Probab=99.76  E-value=4.6e-19  Score=137.87  Aligned_cols=66  Identities=39%  Similarity=0.641  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++|.||+||.|+..|+++||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~   97 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ   97 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence            678999999999999999999999999999999999999999999999999999999999998765

>KOG0843|consensus

Probab=99.75  E-value=7.3e-19  Score=132.88  Aligned_cols=63  Identities=51%  Similarity=0.685  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      +.||.||.|+.+||..||..|+.+.|..-.||++||..|+|++.||+|||||||.|.||.+..
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e  163 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE  163 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence            788899999999999999999999999999999999999999999999999999999997654

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.75  E-value=1.8e-18  Score=109.03  Aligned_cols=57  Identities=53%  Similarity=0.609  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      |++|+.|+.+|+.+|+..|..++||+..+++.||.+|||+..+|++||+|||.++||
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            578899999999999999999999999999999999999999999999999999986

; 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 ....

>KOG0848|consensus

Probab=99.73  E-value=1e-18  Score=139.16  Aligned_cols=63  Identities=41%  Similarity=0.619  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      +-|-|.++|+.|+.+||+.|..++|+++..+.+||..|||+|+||||||||||+|+||..+..
T Consensus       199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            345588999999999999999999999999999999999999999999999999999976544

>KOG0492|consensus

Probab=99.73  E-value=2.3e-18  Score=132.84  Aligned_cols=62  Identities=53%  Similarity=0.811  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..||+|+.||..||..||+.|.+.+|.+++||.+++..|.|++.||+|||||||+|.||.++
T Consensus       143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            36788999999999999999999999999999999999999999999999999999999764

>KOG0494|consensus

Probab=99.72  E-value=1.4e-17  Score=132.40  Aligned_cols=61  Identities=39%  Similarity=0.602  Sum_probs=57.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +|.-||.||..|++.||+.|++..||+...|+.||.+++|.|..|+|||||||+||||.++
T Consensus       141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek  201 (332)
T KOG0494|consen  141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK  201 (332)
T ss_pred             cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence            3334999999999999999999999999999999999999999999999999999999875

>KOG0493|consensus

Probab=99.72  E-value=1e-17  Score=133.19  Aligned_cols=65  Identities=46%  Similarity=0.715  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..+..||+|+.|+.+||+.|+..|+.|+|++...|.+||.+|+|.+.||+|||||+|+|.||-..
T Consensus       242 ~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  242 SSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             ccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            34456788999999999999999999999999999999999999999999999999999998753

>KOG0491|consensus

Probab=99.69  E-value=1e-17  Score=125.07  Aligned_cols=66  Identities=48%  Similarity=0.648  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ..+++|.|++|+..|+..||+.|+..+|.+..|+.+||..|+|+++||+.||||||+|.||+.+..
T Consensus        97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~  162 (194)
T KOG0491|consen   97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN  162 (194)
T ss_pred             HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            345678899999999999999999999999999999999999999999999999999999987643

>KOG3802|consensus

Probab=99.67  E-value=1.1e-16  Score=133.93  Aligned_cols=62  Identities=29%  Similarity=0.369  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ++||+||.|....+..||++|.+|+.|+.+|+..||.+|+|.+++|+|||||||.|+||...
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            78899999999999999999999999999999999999999999999999999999999887

>smart00389 HOX Homeodomain

Probab=99.65  E-value=2.3e-16  Score=98.74  Aligned_cols=56  Identities=52%  Similarity=0.769  Sum_probs=52.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      ++.|+.|+.+|+.+|+..|..+.||+..++..||..+||+..+|++||+|||.+.+
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            35678899999999999999999999999999999999999999999999998864

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

>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=99.65  E-value=3.1e-16  Score=98.88  Aligned_cols=57  Identities=53%  Similarity=0.693  Sum_probs=54.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      +.|..|+.+|+.+||..|..++||+..+++.||.++||++.+|++||+|||.+.++.
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            567889999999999999999999999999999999999999999999999998864

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.64  E-value=2.9e-16  Score=99.35  Aligned_cols=53  Identities=17%  Similarity=0.245  Sum_probs=50.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRY----LSVCERLNLALSLSLTETQVKIWFQNRR   91 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~----p~~~~r~~La~~lgl~~~qV~~WFqNRR   91 (165)
                      ++|.||.|+.+|+..||..|+.++|    |+..++++||..|||++.+|++||||.+
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.

>KOG0844|consensus

Probab=99.63  E-value=5.1e-16  Score=125.92  Aligned_cols=71  Identities=41%  Similarity=0.554  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSP  106 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~~  106 (165)
                      ...-||-|+.||.+|+..||+.|-+..|.+...|.+||..|+|.|..||+||||||+|+||+.-.+....+
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhp  248 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHP  248 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCC
Confidence            34557789999999999999999999999999999999999999999999999999999999876666554

>KOG0486|consensus

Probab=99.62  E-value=2.3e-16  Score=128.28  Aligned_cols=64  Identities=38%  Similarity=0.694  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      +|+||.|+.|+..||.+||..|++++||+...|++||..++|++..|++||+|||+||||+++.
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN  173 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN  173 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence            4678889999999999999999999999999999999999999999999999999999998763

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.59  E-value=1.5e-15  Score=114.27  Aligned_cols=67  Identities=37%  Similarity=0.548  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ......+++|.+.+.+|+.+|+..|+.++||+..+|..|+..|+|+++.|+|||||||++.|+....
T Consensus        46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            3445677788899999999999999999999999999999999999999999999999999987664

>KOG0483|consensus

Probab=99.58  E-value=1.3e-15  Score=118.46  Aligned_cols=60  Identities=35%  Similarity=0.568  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ...++.+|+.+|+..||..|+.+.+....++..||++|||.++||.|||||||+|||.++
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            445567799999999999999999999999999999999999999999999999999865

>KOG4577|consensus

Probab=99.46  E-value=5.4e-14  Score=113.47  Aligned_cols=65  Identities=28%  Similarity=0.391  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .....||+|+.++..||+.|+..|+..+.|....|++|+.++||.-+.|+|||||||+|+||.++
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK  227 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK  227 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence            34557889999999999999999999999999999999999999999999999999999998754

>KOG0847|consensus

Probab=99.46  E-value=3.6e-14  Score=110.61  Aligned_cols=63  Identities=46%  Similarity=0.795  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .+++..|-.|+..|+..||..|+..+|+-.+++.+||..+|+++.+|+|||||||.||||+..
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            455666788999999999999999999999999999999999999999999999999999754

>KOG0490|consensus

Probab=99.31  E-value=8.6e-13  Score=104.16  Aligned_cols=64  Identities=34%  Similarity=0.438  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++++.|+.|+..|+++||+.|+...||+...++.||..+++++..|++||||||+||+++.+
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            4577889999999999999999999999999999999999999999999999999999999874

>KOG0849|consensus

Probab=99.27  E-value=1.4e-11  Score=103.87  Aligned_cols=71  Identities=35%  Similarity=0.591  Sum_probs=64.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         28 GRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        28 ~~~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      .........++.++.|+.|+..|++.||+.|+.++||++..|++||.+++|++..|++||+|||++++|..
T Consensus       165 ~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  165 EEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             cccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            33444555667778899999999999999999999999999999999999999999999999999999987

>KOG0775|consensus

Probab=99.20  E-value=6.5e-11  Score=95.08  Aligned_cols=53  Identities=32%  Similarity=0.399  Sum_probs=48.0

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      |...-..+|.++|..++||+..++.+||+.+||+..||-+||+|||+++|-..
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~  235 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA  235 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence            44445789999999999999999999999999999999999999999999543

>KOG1168|consensus

Probab=99.16  E-value=7.9e-12  Score=101.12  Aligned_cols=64  Identities=23%  Similarity=0.280  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++||+|+.+-.-+...||.+|...+.|+.+.+..||++|.|.+..|++||||.|+|.||...
T Consensus       306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            4578889999999999999999999999999999999999999999999999999999999653

>KOG0774|consensus

Probab=99.06  E-value=5.5e-10  Score=89.33  Aligned_cols=58  Identities=28%  Similarity=0.399  Sum_probs=54.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFK---TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      +|+|..|++.-.++|.++|-   .++||+.+++++||+++|++..||.+||.|+|-+.||.
T Consensus       189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~  249 (334)
T KOG0774|consen  189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN  249 (334)
T ss_pred             HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence            57788899999999999995   67899999999999999999999999999999999884

>KOG2252|consensus

Probab=98.82  E-value=1.9e-08  Score=87.72  Aligned_cols=66  Identities=23%  Similarity=0.213  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         30 SPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        30 ~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      .+....--..||.|.+|+..|++.|..+|+.+++|+.+..+.|+.+|+|....|.+||.|-|.|.+
T Consensus       411 ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl  476 (558)
T KOG2252|consen  411 EPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL  476 (558)
T ss_pred             CCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence            333444556778899999999999999999999999999999999999999999999999887753

>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=98.71  E-value=8.3e-09  Score=60.56  Aligned_cols=34  Identities=32%  Similarity=0.482  Sum_probs=28.8

Q ss_pred             hcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100         60 TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK   93 (165)
Q Consensus        60 ~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k   93 (165)
                      .++||+.+|+++|+.++||+..||..||-|.|.+
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            4789999999999999999999999999998864

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

>KOG0490|consensus

Probab=98.24  E-value=1.1e-06  Score=69.20  Aligned_cols=66  Identities=33%  Similarity=0.512  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ....+.++.|+.+...|+..|+..|....+|+...++.|+..+|+.+..|++||+|+|.+.++...
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            344567788999999999999999999999999999999999999999999999999999998765

>KOG1146|consensus

Probab=98.00  E-value=1.6e-05  Score=75.54  Aligned_cols=63  Identities=22%  Similarity=0.259  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      -.++..|+.++..||.+|..+|+...++..++.+.|...+++..+.|++||||-|.|.|+...
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            346778999999999999999999999999999999999999999999999999999998765

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

Probab=97.57  E-value=5.1e-05  Score=47.42  Aligned_cols=43  Identities=21%  Similarity=0.318  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100         51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK   93 (165)
Q Consensus        51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k   93 (165)
                      +..|+..|...+++...+...|..+.+|+..||+.||-.|+.+
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            4669999999999999999999999999999999999765443

>KOG0773|consensus

Probab=97.17  E-value=0.00042  Score=58.21  Aligned_cols=58  Identities=29%  Similarity=0.349  Sum_probs=49.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         39 DLVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      .++++..+......+|+.+...   .+||+..++..|+.++||+..||.+||-|.|.+..+
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~  299 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK  299 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence            5556668999999999988443   469999999999999999999999999999887554

>KOG3623|consensus

Probab=96.71  E-value=0.0034  Score=57.22  Aligned_cols=49  Identities=18%  Similarity=0.199  Sum_probs=46.3

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +.+|..+|..|..|..++...|+.+.||..+.|+.||+++++++...++
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            7899999999999999999999999999999999999999999888764

>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=95.98  E-value=0.019  Score=35.35  Aligned_cols=46  Identities=11%  Similarity=0.271  Sum_probs=35.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcc
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNR   90 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNR   90 (165)
                      +++|..+|-++...+-..++...     ....||.++|+...+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            46788899999888878887776     47789999999999999999884

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=90.46  E-value=0.48  Score=28.22  Aligned_cols=46  Identities=9%  Similarity=0.116  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      .+++.+..+|...|..+     ..-.++|..+|++...|+.+...-..|-|
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            46788999999999322     34678899999999999998765554443

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=87.81  E-value=0.96  Score=26.08  Aligned_cols=44  Identities=11%  Similarity=0.111  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK   93 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k   93 (165)
                      .++..+..+++..|..+     ....++|..+|++...|..|...-+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            36777888888777433     245678999999999999998754443

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

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=85.87  E-value=0.89  Score=29.19  Aligned_cols=44  Identities=7%  Similarity=0.092  Sum_probs=28.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ   88 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq   88 (165)
                      ++|..|+.++...+-..+...    ......||.++||+...|..|-+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence            456789999877766665222    24677899999999999999964

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=85.49  E-value=2.6  Score=21.65  Aligned_cols=38  Identities=13%  Similarity=0.157  Sum_probs=26.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWF   87 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WF   87 (165)
                      .++.++...+...|... .    ...+++..+|++...|..|.
T Consensus         5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence            35666666666666533 2    45678899999999988884

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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=85.46  E-value=1.5  Score=26.33  Aligned_cols=42  Identities=17%  Similarity=0.156  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT   92 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~   92 (165)
                      +++.+..++...|..+     ....++|..+|+++..|+.|.+.-|.
T Consensus        11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            4566666666655433     35778999999999999999975443

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 are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=84.57  E-value=1.8  Score=26.64  Aligned_cols=42  Identities=17%  Similarity=0.153  Sum_probs=33.4

Q ss_pred             CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCchhhhhhh
Q psy15100         46 FTYEQLVALENKFKTTRY--LSVCERLNLALSLSLTETQVKIWF   87 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~--p~~~~r~~La~~lgl~~~qV~~WF   87 (165)
                      +|+.|+++|...|+..=|  |-.....+||.+||++...|..-.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L   44 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL   44 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence            578899999999986543  666677899999999998765544

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=84.05  E-value=2.3  Score=31.60  Aligned_cols=50  Identities=20%  Similarity=0.125  Sum_probs=38.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ...+++.|+.+|+..+ ..     ....+||..||++...|..|.++.+.+.++..
T Consensus         4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~   53 (141)
T PRK03975          4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR   53 (141)
T ss_pred             ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3568999999998843 22     23567899999999999999998777766643

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=80.13  E-value=2.9  Score=25.57  Aligned_cols=44  Identities=20%  Similarity=0.149  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW   94 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~   94 (165)
                      .||..++++|.-...-.      ...++|..+++++..|+.+..+=+.|.
T Consensus         3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl   46 (58)
T PF00196_consen    3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKL   46 (58)
T ss_dssp             SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence            47888999887776543      367899999999999999988766554

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	165
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-13
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		5e-13
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		3e-12
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		6e-12
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-11
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		4e-11
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		6e-11
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		7e-11
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		8e-11
1hom_A	68	Determination Of The Three-Dimensional Structure Of		2e-10
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-10
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		3e-10
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		4e-10
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		4e-10
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		1e-09
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		1e-09
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		2e-09
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		5e-09
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		8e-09
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-08
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		1e-08
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		1e-08
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		2e-08
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-08
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		2e-08
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		2e-08
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-08
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		3e-08
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		3e-08
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		4e-08
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		5e-08
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-08
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		6e-08
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		8e-08
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-07
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		2e-07
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		2e-07
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		4e-07
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		6e-07
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		9e-07
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		9e-07
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-06
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		2e-06
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		3e-06
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		4e-06
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		7e-06
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		1e-05
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		1e-05
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		3e-05
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		4e-05
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		4e-05
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		4e-05

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 41/57 (71%)
Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
           +AFT EQL+ LE +F   +YLS+ ER  +A +L L+E QVKIWFQNRR KWK+   G
Sbjct: 12  TAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAG 68

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 41/55 (74%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P + FT  QL+ALE KF+  +YLS+ ER   + SLSLTETQVKIWFQNRR K K+
Sbjct: 3  PRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/58 (53%), Positives = 43/58 (74%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          P + ++  QL AL+ +F+ T+YL++ ER  LA SL LT+TQVKIWFQN+R+K KK  P
Sbjct: 10 PRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 30/64 (46%), Positives = 42/64 (65%)
Query: 34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
          +TP +   P ++FT  Q+  LE +F   +YL+  ER  LA  L +T+ QVK WFQNRRTK
Sbjct: 12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK 71
Query: 94 WKKQ 97
          W++Q
Sbjct: 72 WRRQ 75

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 40/56 (71%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          + FT  QL+ LE +F+  +YLS  +R++LA SL L++ QVK W+QNRR KWKK  P
Sbjct: 22 TVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 38/56 (67%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
            +T  Q + LE +F   RYL+   R+ +A +LSLTE Q+KIWFQNRR KWKK+N 
Sbjct: 7  QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62

>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 = 63.5 bits (153), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 38/54 (70%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          +T  Q + LE +F   RYL+   R+ +A +LSLTE Q+KIWFQNRR KWKK+N 
Sbjct: 3  YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 38/55 (69%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
            +T  Q + LE +F   RYL+   R+ +A +LSLTE Q+KIWFQNRR KWKK+N
Sbjct: 8  QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 40/56 (71%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          +++T  Q + LE +F   RYL+   R+ +A +LSLTE Q+KIWFQNRR KWKK++ 
Sbjct: 33 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88

>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 = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 37/56 (66%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
            +T  Q + LE +F   RYL+   R+ +A +L LTE Q+KIWFQNRR KWKK+N 
Sbjct: 7  QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 37/55 (67%)
Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
           F+ +Q + LE KF+T +YLS  ER  LA  L L+E QVK WFQNRR KW++  P 
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 39/54 (72%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          +A+T  QL+ LE +F   +Y+S   R+ LA+ L+LTE  +KIWFQNRR KWKK+
Sbjct: 8  TAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 39/54 (72%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          ++F+  Q++ LE +F   +YL+  ER  LA +L +T+ QVK WFQNRRTKW++Q
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 35/52 (67%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          FT  QL  LE +F   +YLS   R+ +A +L L ETQVKIWFQNRR K KK+
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92

>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 = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 38/54 (70%)
Query: 50  QLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           Q++ LE KF   +YLS  ER +LA +L LTETQVKIWFQNRR K K++    ++
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL 68

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 36/54 (66%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          FT EQL ALEN F+ T+Y  V  R  LA  + L E +V++WF+NRR KW++  P
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 33/52 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
          P   F+  Q+  LE +FK  RYLS  ER  LA  L LT TQVKIWFQNRR K
Sbjct: 5  PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 36/52 (69%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          +T  Q + LE +F T  YL+   R+ +A +LSLTE Q+KIWFQNRR K KK+
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78

>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 = 56.2 bits (134), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 35/55 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWFQN+R K KK
Sbjct: 6  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 35/55 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWFQN+R K KK
Sbjct: 4  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 40/68 (58%)
Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
           ++FT EQ+ ALE +F+ T Y  V  R  LA  + L E ++++WF NRR KW+++    + 
Sbjct: 12  TSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ 71
Query: 104 NSPTVPTC 111
              + P+ 
Sbjct: 72  RRQSGPSS 79

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 33/54 (61%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          FT  QL  LE  F  T Y  V  R  LA+ + LTE ++++WFQNRR KW+KQ  
Sbjct: 6  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 34/56 (60%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          + FT  QL  LE  F  T Y  V  R  LA+ + LTE ++++WFQNRR KW+KQ  
Sbjct: 11 TTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWFQN R K KK
Sbjct: 4  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 35/52 (67%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          F+  Q+  LE +FK  +YLS  ER +LA  + LT TQVKIWFQN R K K+Q
Sbjct: 9  FSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 34/55 (61%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          + FT  QL  LE  F  T Y  V  R  LA+ + LTE ++++WFQNRR KW+KQ 
Sbjct: 4  TTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWFQN R K KK
Sbjct: 4  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 35/55 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWF+N+R K KK
Sbjct: 6  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          +T  Q + LE +F   RY++   R+++A +LSL+E Q+KIWFQNRR K KK
Sbjct: 10 YTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60

>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 = 53.9 bits (128), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          + FT  QL  LE  F+ T Y  V  R  LA+   LTE +V++WFQNRR KW+K+
Sbjct: 14 TTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 25/52 (48%), Positives = 33/52 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWFQN+R K
Sbjct: 2  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWF N+R K KK
Sbjct: 2  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 33/51 (64%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          FT  Q   LE +F+  RYLS  ER +LA  + LT TQVKIWFQN R K K+
Sbjct: 16 FTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 33/54 (61%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          + FT EQL  LE  F+ T Y  +  R  LA    LTE +V++WF NRR +W+KQ
Sbjct: 7  TTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL   + +F   RYL+   R  L+  L L E Q+KIWFQN+R K ++
Sbjct: 6  PRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 36/60 (60%)
Query: 37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          S++  P +AF+ EQL  L+ +F   RYL+   R  L+  L L E QVK WF+N R K KK
Sbjct: 2  SDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 32/51 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          FT  Q   LE +F+  RYLS  ER +L   + LT TQVKIWFQN R K K+
Sbjct: 19 FTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
           FT +QL  LE  F+  RY  +  R  +A+  +LTE +V++WF+NRR KW+K+   +
Sbjct: 10  FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI 65

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 33/55 (60%)
Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
           +T  Q + LE +F    YL+   R  +A  L+LTE QVKIWFQNRR K KK N  
Sbjct: 20  YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD 74

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 33/53 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          +T  Q + LE +F    YL+   R  +A  L+LTE QVKIWFQNRR K KK N
Sbjct: 8  YTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 35/54 (64%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          +AFT +QL  LE +F    Y+S   R  LA  L+L E+ +K+WFQNRR K K+Q
Sbjct: 6  TAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
           + F+  QL  LE  F+ T+Y  +  R  LA   +LTE ++++WFQNRR + +KQ+  +
Sbjct: 23  TTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTSV 80

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
           FT +QL  LE  F+   Y  +  R  +A+  +LTE +V++WF+NRR KW+K+   +
Sbjct: 10  FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI 65

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          ++  QL  LE ++   ++++  +R  ++ + SL+E Q+ IWFQNRR K KK  P
Sbjct: 14 YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
          + FT  QL  LE  F  TRY  +  R  +AL ++L E++V++WF+NRR K
Sbjct: 12 TTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor Nanog Homeodomain Fragment Length = 84

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 9/78 (11%)
Query: 30 SPNTQTPSEDLVP------ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQV 83
          + N+    ED VP       + F+  QL  L ++F+  +YLS+ +   L+  L+L+  QV
Sbjct: 7  AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66
Query: 84 KIWFQNRRTK---WKKQN 98
          K WFQN+R K   W+K N
Sbjct: 67 KTWFQNQRMKSKRWQKNN 84

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 42 PESAFTYEQLVALENKFKTTRY--LSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AFT  Q+  LEN F+   Y  + + E  +LA  L+L   +++IWFQNRR K K+
Sbjct: 4  PRTAFTQNQIEVLENVFRVNCYPGIDILE--DLAQKLNLELDRIQIWFQNRRAKLKR 58

>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 = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          + FT  Q+  LE  F   RYL+     +L+  L+L   QVKIWF+NRR + K Q+
Sbjct: 7  TTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain Length = 62

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 36/53 (67%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          + F+  QL AL+++F+  +YLS+ +   L+  L+L+  QVK WFQN+R K K+
Sbjct: 8  TVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 34/51 (66%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          +T  QL  LE ++ T ++++  +R  ++ + +L+E QV IWFQNRR K KK
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif Length = 44

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 20/42 (47%), Positives = 26/42 (61%)
Query: 55 ENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          + +F   RYL+   R  L+  L L E Q+KIWFQN+R K KK
Sbjct: 2  KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 34/51 (66%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          +T  QL  LE ++ T ++++  +R  ++ + +L+E QV IWFQNRR K KK
Sbjct: 8  YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	165
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	9e-33
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-32
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	4e-32
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	4e-31
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	5e-31
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	7e-31
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	9e-31
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-30
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	4e-30
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	6e-30
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	7e-30
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	5e-29
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-25
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	1e-24
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	3e-24
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-24
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	4e-22
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	3e-21
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	7e-21
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-20
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	4e-20
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	6e-20
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	2e-19
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	3e-19
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-19
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-18
1e3o_C	160	Octamer-binding transcription factor 1; transcript	3e-18
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	3e-18
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-18
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-17
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	2e-17
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-17
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	3e-17
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	6e-17
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	7e-17
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	9e-17
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-16
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	5e-16
1uhs_A	72	HOP, homeodomain only protein; structural genomics	6e-16
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-15
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-15
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	4e-15
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	6e-15
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	6e-15
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	9e-15
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-13
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	8e-13
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-12
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-12
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	1e-12
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-12
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	9e-09
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	5e-08
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	4e-07
1lfb_A	99	Liver transcription factor (LFB1); transcription r	4e-07
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	1e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-06
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	3e-06
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	6e-06
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	5e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	8e-04

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

 Score =  110 bits (277), Expect = 9e-33
 Identities = 31/59 (52%), Positives = 43/59 (72%)

Query: 42  PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
           P + ++  QL AL+ +F+ T+YL++ ER  LA SL LT+TQVKIWFQN+R+K KK  P 
Sbjct: 10  PRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPS 68

>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 =  110 bits (276), Expect = 2e-32
 Identities = 36/88 (40%), Positives = 49/88 (55%), Gaps = 11/88 (12%)

Query: 13  SSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNL 72
           SS +S   P  +  +GR   T            FT  QL+ LE +F+  +YLS  +R++L
Sbjct: 2   SSGSSGGEPGTKAKKGRRSRT-----------VFTELQLMGLEKRFEKQKYLSTPDRIDL 50

Query: 73  ALSLSLTETQVKIWFQNRRTKWKKQNPG 100
           A SL L++ QVK W+QNRR KWKK  P 
Sbjct: 51  AESLGLSQLQVKTWYQNRRMKWKKSGPS 78

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

 Score =  108 bits (272), Expect = 4e-32
 Identities = 34/55 (61%), Positives = 41/55 (74%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P + FT  QL+ALE KF+  +YLS+ ER   + SLSLTETQVKIWFQNRR K K+
Sbjct: 3  PRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score =  106 bits (266), Expect = 4e-31
 Identities = 30/57 (52%), Positives = 39/57 (68%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
            S  ++ Q++ LE KF   +YLS  ER +LA +L LTETQVKIWFQNRR K K++ 
Sbjct: 7  HHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

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

 Score =  105 bits (264), Expect = 5e-31
 Identities = 26/53 (49%), Positives = 38/53 (71%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          +F+  Q++ LE +F   +YL+  ER  LA +L +T+ QVK WFQNRRTKW++Q
Sbjct: 3  SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score =  106 bits (265), Expect = 7e-31
 Identities = 25/79 (31%), Positives = 40/79 (50%)

Query: 19 KTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSL 78
          K P    N       + P +     + F+  QL  L ++F+  +YLS+ +   L+  L+L
Sbjct: 2  KQPTSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61

Query: 79 TETQVKIWFQNRRTKWKKQ 97
          +  QVK WFQN+R K K+ 
Sbjct: 62 SYKQVKTWFQNQRMKSKRW 80

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

 Score =  105 bits (263), Expect = 9e-31
 Identities = 22/56 (39%), Positives = 36/56 (64%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
            + F+  QL AL+++F+  +YLS+ +   L+  L+L+  QVK WFQN+R K K+ 
Sbjct: 6  MRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

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

 Score =  105 bits (264), Expect = 1e-30
 Identities = 32/76 (42%), Positives = 45/76 (59%)

Query: 23 VRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQ 82
          + R  G     +TP +   P ++FT  Q+  LE +F   +YL+  ER  LA  L +T+ Q
Sbjct: 1  MARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60

Query: 83 VKIWFQNRRTKWKKQN 98
          VK WFQNRRTKW++Q 
Sbjct: 61 VKTWFQNRRTKWRRQT 76

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

 Score =  103 bits (259), Expect = 4e-30
 Identities = 31/54 (57%), Positives = 34/54 (62%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
          P   F+  Q+  LE +FK  RYLS  ER  LA  L LT TQVKIWFQNRR K K
Sbjct: 5  PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>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 =  103 bits (258), Expect = 6e-30
 Identities = 29/56 (51%), Positives = 37/56 (66%)

Query: 45  AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
            F+ +Q + LE KF+T +YLS  ER  LA  L L+E QVK WFQNRR KW++  P 
Sbjct: 13  RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68

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

 Score =  103 bits (258), Expect = 7e-30
 Identities = 28/56 (50%), Positives = 35/56 (62%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
              F+  Q+  LE +FK  +YLS  ER +LA  + LT TQVKIWFQN R K K+Q
Sbjct: 5  RRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

>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 =  100 bits (252), Expect = 5e-29
 Identities = 28/57 (49%), Positives = 33/57 (57%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
              FT  Q   LE +F+  RYLS  ER +LA  + LT TQVKIWFQN R K K+  
Sbjct: 12 RRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

>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 = 91.1 bits (227), Expect = 3e-25
 Identities = 15/52 (28%), Positives = 28/52 (53%)

Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
          S+ + +    LE  F+  + L+  E+  +A    +T  QV++WF N+R + K
Sbjct: 10 SSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>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 = 89.7 bits (223), Expect = 1e-24
 Identities = 26/55 (47%), Positives = 35/55 (63%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWF+N+R K KK
Sbjct: 6  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 88.6 bits (220), Expect = 3e-24
 Identities = 23/54 (42%), Positives = 31/54 (57%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           FT  Q+  LE  F   RYL+     +L+  L+L   QVKIWF+NRR + K Q+
Sbjct: 8  TFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61

>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 = 87.8 bits (218), Expect = 5e-24
 Identities = 26/53 (49%), Positives = 34/53 (64%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          AFT +QL  LE +F    Y+S   R  LA  L+L E+ +K+WFQNRR K K+Q
Sbjct: 7  AFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

 Score = 82.8 bits (205), Expect = 4e-22
 Identities = 28/54 (51%), Positives = 38/54 (70%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          A+T  QL+ LE +F   +Y+S   R+ LA+ L+LTE  +KIWFQNRR KWKK+ 
Sbjct: 9  AYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62

>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 = 81.9 bits (202), Expect = 3e-21
 Identities = 29/54 (53%), Positives = 35/54 (64%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           FT  QL  LE +F   +YLS   R+ +A +L L ETQVKIWFQNRR K KK+ 
Sbjct: 40 NFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE 93

>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 = 80.2 bits (198), Expect = 7e-21
 Identities = 29/54 (53%), Positives = 38/54 (70%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           +T  Q + LE +F   RYL+   R+ +A +LSLTE Q+KIWFQNRR KWKK+N
Sbjct: 8  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

>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 = 78.7 bits (194), Expect = 3e-20
 Identities = 27/56 (48%), Positives = 36/56 (64%)

Query: 45  AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
            +T  Q + LE +F T  YL+   R+ +A +LSLTE Q+KIWFQNRR K KK+   
Sbjct: 26  TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQA 81

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

 Score = 78.7 bits (194), Expect = 4e-20
 Identities = 31/86 (36%), Positives = 46/86 (53%), Gaps = 4/86 (4%)

Query: 17 SAKTPPV----RRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNL 72
              P +    +R    +       E     +++T  Q + LE +F   RYL+   R+ +
Sbjct: 2  KKNPPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEI 61

Query: 73 ALSLSLTETQVKIWFQNRRTKWKKQN 98
          A +LSLTE Q+KIWFQNRR KWKK++
Sbjct: 62 AHALSLTERQIKIWFQNRRMKWKKEH 87

>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 = 77.6 bits (191), Expect = 6e-20
 Identities = 20/55 (36%), Positives = 34/55 (61%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
           ++  QL  LE ++   ++++  +R  ++ + SL+E Q+ IWFQNRR K KK  P
Sbjct: 13 PYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67

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

 Score = 76.4 bits (188), Expect = 2e-19
 Identities = 21/54 (38%), Positives = 34/54 (62%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           +T  QL  LE ++ T ++++  +R  ++ + +L+E QV IWFQNRR K KK  
Sbjct: 13 PYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66

>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 = 76.0 bits (187), Expect = 3e-19
 Identities = 27/54 (50%), Positives = 33/54 (61%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           +T  Q + LE +F    YL+   R  +A  L+LTE QVKIWFQNRR K KK N
Sbjct: 19 PYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72

>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 = 75.5 bits (186), Expect = 4e-19
 Identities = 19/54 (35%), Positives = 26/54 (48%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          FT  QL  L++ F    Y    E   L+  L+L    + +WFQN R K +K  P
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP 67

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

 Score = 76.6 bits (188), Expect = 2e-18
 Identities = 20/56 (35%), Positives = 27/56 (48%)

Query: 44  SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
           ++       ALE+ F      S  E   LA SL L +  V++WF NRR K K+  P
Sbjct: 104 TSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP 159

>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 = 76.2 bits (187), Expect = 3e-18
 Identities = 19/85 (22%), Positives = 37/85 (43%)

Query: 14  SATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLA 73
           +  S+ +     +   SP  +  S      ++      VALE  F   +  +  +   +A
Sbjct: 76  ANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIA 135

Query: 74  LSLSLTETQVKIWFQNRRTKWKKQN 98
             L++ +  +++WF NRR K K+ N
Sbjct: 136 EQLNMEKEVIRVWFSNRRQKEKRIN 160

>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 = 73.1 bits (180), Expect = 3e-18
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 16/74 (21%)

Query: 24 RRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQV 83
          RR R                +AFT  Q+  LEN F+   Y  +    +LA  L+L   ++
Sbjct: 2  RRPR----------------TAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRI 45

Query: 84 KIWFQNRRTKWKKQ 97
          +IWFQNRR K K+ 
Sbjct: 46 QIWFQNRRAKLKRS 59

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

 Score = 72.9 bits (179), Expect = 5e-18
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 44 SAFTYEQLVALENKF-KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          S  T +Q+  LE  F K  ++        +A    LTE Q + WF+ R  +W++ 
Sbjct: 7  SGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

>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 = 71.2 bits (175), Expect = 2e-17
 Identities = 23/52 (44%), Positives = 35/52 (67%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          FT +QL  LE  F+  RY  +  R  +A+  +LTE +V++WF+NRR KW+K+
Sbjct: 10 FTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>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 = 70.7 bits (174), Expect = 2e-17
 Identities = 26/52 (50%), Positives = 33/52 (63%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          FT  QL  LE  F  T Y  V  R  LA+ + LTE ++++WFQNRR KW+KQ
Sbjct: 6  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

 Score = 71.3 bits (175), Expect = 2e-17
 Identities = 14/52 (26%), Positives = 25/52 (48%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
           ++EQL AL+  F   ++    E  +L     L+  +V+ WF +RR   +  
Sbjct: 15 KSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL 66

>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 = 70.8 bits (174), Expect = 3e-17
 Identities = 26/52 (50%), Positives = 35/52 (67%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          FT EQL ALEN F+ T+Y  V  R  LA  + L E +V++WF+NRR KW++ 
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

>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 = 70.1 bits (172), Expect = 6e-17
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          F+  QL  LE  F+ T+Y  +  R  LA   +LTE ++++WFQNRR + +KQ
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76

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

 Score = 70.1 bits (172), Expect = 7e-17
 Identities = 24/65 (36%), Positives = 38/65 (58%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105
           FT EQ+ ALE +F+ T Y  V  R  LA  + L E ++++WF NRR KW+++    +   
Sbjct: 14  FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRR 73

Query: 106 PTVPT 110
            + P+
Sbjct: 74  QSGPS 78

>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 = 69.8 bits (171), Expect = 9e-17
 Identities = 24/65 (36%), Positives = 37/65 (56%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105
           FT  QL  LE  F  TRY  +  R  +AL ++L E++V++WF+NRR K ++Q        
Sbjct: 14  FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGG 73

Query: 106 PTVPT 110
            + P+
Sbjct: 74  QSGPS 78

>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 = 71.2 bits (174), Expect = 2e-16
 Identities = 20/105 (19%), Positives = 35/105 (33%), Gaps = 9/105 (8%)

Query: 1   MTTSASTGTTTMSSATSAKTPPV---------RRNRGRSPNTQTPSEDLVPESAFTYEQL 51
            TT        +S   + K   +         +     +             +  +    
Sbjct: 40  QTTICRFENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAK 99

Query: 52  VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
            ALE  F      S  E + +A  L+L +  V++WF NRR + K+
Sbjct: 100 DALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

>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 = 70.1 bits (171), Expect = 5e-16
 Identities = 15/51 (29%), Positives = 23/51 (45%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
           FT + + AL   F+     +  E   +A  L+     V++WF NRR   K 
Sbjct: 100 FTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 67.4 bits (165), Expect = 6e-16
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 42 PESAFTYEQLVALENKF-KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
            +  T +Q+  LE  F K  ++        +A    LTE Q + WF+ R  +W++ 
Sbjct: 4  GAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 66.4 bits (162), Expect = 2e-15
 Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 17/93 (18%)

Query: 8  GTTTMSSATSAKTPP-VRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSV 66
          G++  S  T  + P   +R R                +  T EQL  L  K+      + 
Sbjct: 1  GSSGSSGGTGGEEPQRDKRLR----------------TTITPEQLEILYQKYLLDSNPTR 44

Query: 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
              ++A  + L +  V++WFQN R + +K  P
Sbjct: 45 KMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP 77

>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 = 66.2 bits (162), Expect = 2e-15
 Identities = 15/58 (25%), Positives = 24/58 (41%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          P +  T +QL  L   F      S  +   +A    L +  +K WF+N   K ++  P
Sbjct: 10 PRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP 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 = 65.1 bits (159), Expect = 4e-15
 Identities = 13/53 (24%), Positives = 23/53 (43%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
             +QL  L   +          +  L     L+   +++WFQN+R K KK++
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

>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 = 64.8 bits (158), Expect = 6e-15
 Identities = 12/52 (23%), Positives = 24/52 (46%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
           T EQ+  L+  F  +++    E   L     L  +++K WF + R + ++ 
Sbjct: 11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62

>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 = 65.2 bits (159), Expect = 6e-15
 Identities = 15/65 (23%), Positives = 30/65 (46%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105
           F + QL  +++ F         +   LA    LT+  +++WFQN R K+++     +   
Sbjct: 14  FKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGG 73

Query: 106 PTVPT 110
            + P+
Sbjct: 74  VSGPS 78

>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 = 66.7 bits (162), Expect = 9e-15
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
                  +LE  F  +   S+ +  ++A  L L +  V++WF NRR K K+ +
Sbjct: 103 IENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS 155

>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 = 61.9 bits (150), Expect = 1e-13
 Identities = 16/69 (23%), Positives = 28/69 (40%)

Query: 47  TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSP 106
           T EQL  L+  F  +  L+  E   L     LT  ++  WF  ++     +   M+++  
Sbjct: 19  TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDES 78

Query: 107 TVPTCPGGS 115
              +  G S
Sbjct: 79  NAGSSSGPS 87

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

 Score = 61.8 bits (149), Expect = 8e-13
 Identities = 14/56 (25%), Positives = 23/56 (41%)

Query: 42  PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
           P   FT  Q   L   FK  +  S   ++ ++  L L  + V  +F N R +   +
Sbjct: 100 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK 155

>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 = 59.1 bits (143), Expect = 1e-12
 Identities = 15/53 (28%), Positives = 20/53 (37%)

Query: 47 TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
            EQL ALE+ F         E   L     +T  ++  WF  RR K   +  
Sbjct: 15 APEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET 67

>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 = 59.2 bits (143), Expect = 1e-12
 Identities = 13/67 (19%), Positives = 26/67 (38%)

Query: 47  TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSP 106
           T  Q+  LE+ F  + + +  E   L +   L+  ++  WF  RR         +  +  
Sbjct: 21  TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLDSMG 80

Query: 107 TVPTCPG 113
           +  + P 
Sbjct: 81  SGKSGPS 87

>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 = 59.7 bits (144), Expect = 1e-12
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 15/80 (18%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------LTETQVKIWFQNR 90
           +  E L  +E+ F   +Y    +R  +A + +               +T  +V  WF NR
Sbjct: 14  WRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANR 73

Query: 91  RTKWKKQNPGMDVNSPTVPT 110
           R + K++     +   + P+
Sbjct: 74  RKEIKRRANIAAILESSGPS 93

>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 = 58.3 bits (141), Expect = 2e-12
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 42 PESAFTYEQLVALENKFK-TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
            +  + E L  L++       Y        L+  L L +  +  +FQN+R   K   P
Sbjct: 10 SRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSGP 68

>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 = 48.6 bits (116), Expect = 9e-09
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 49 EQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          E    LE  F + T+Y        L+  L  +  +++ WF++RR + K   P
Sbjct: 18 EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP 69

>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 = 47.5 bits (112), Expect = 5e-08
 Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 29 RSPNTQTPSEDLVPESA-------FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81
           S   +   +   P+S         T EQL  L++ F  T++ S  E   LA    L  T
Sbjct: 8  HSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLART 67

Query: 82 QVKIWFQNRRTKWKKQN 98
           +  WF + R  WK  N
Sbjct: 68 DIVSWFGDTRYAWKNGN 84

>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 = 46.8 bits (110), Expect = 4e-07
 Identities = 21/117 (17%), Positives = 31/117 (26%), Gaps = 37/117 (31%)

Query: 2   TTSASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTT 61
           T +   G     +     T   RRNR                  +       L   ++  
Sbjct: 94  THAGQGGLIEEPTGDELPTKKGRRNR----------------FKWGPASQQILFQAYERQ 137

Query: 62  RYLSVCERLNLAL---------------------SLSLTETQVKIWFQNRRTKWKKQ 97
           +  S  ER  L                       S  +TE +V  WF NRR +   +
Sbjct: 138 KNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR 194

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

 Score = 45.2 bits (106), Expect = 4e-07
 Identities = 13/73 (17%), Positives = 22/73 (30%), Gaps = 21/73 (28%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------------LTETQVK 84
          +       L   ++  +  S  ER  L    +                     +TE +V 
Sbjct: 16 WGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVY 75

Query: 85 IWFQNRRTKWKKQ 97
           WF NRR +   +
Sbjct: 76 NWFANRRKEEAFR 88

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 12/53 (22%), Positives = 20/53 (37%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           T EQL  L++ F   ++    +   L     L   ++  WF + R   K   
Sbjct: 10 KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ 62

>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 = 42.9 bits (101), Expect = 1e-06
 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 54 LENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
          LE  F   T++        L+  L      ++ WF+ RR + K   P
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGP 61

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

 Score = 44.6 bits (104), Expect = 3e-06
 Identities = 18/118 (15%), Positives = 31/118 (26%), Gaps = 37/118 (31%)

Query: 1   MTTSASTGTTTMSSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKT 60
            +  +     +  + +      +RRNR                  +       L   +  
Sbjct: 120 FSQQSHGPGQSDDACSEPTNKKMRRNR----------------FKWGPASQQILYQAYDR 163

Query: 61  TRYLSVCERLNLAL---------------------SLSLTETQVKIWFQNRRTKWKKQ 97
            +  S  ER  L                       S  +TE +V  WF NRR +   +
Sbjct: 164 QKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFR 221

>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 Length = 37

 Score = 40.4 bits (94), Expect = 6e-06
 Identities = 15/24 (62%), Positives = 18/24 (75%), Gaps = 2/24 (8%)

Query: 82  QVKIWFQNRRTKWKKQ--NPGMDV 103
           Q+KIWFQNRR KWKK+  N   D+
Sbjct: 2   QIKIWFQNRRMKWKKRVFNDARDI 25

>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 = 39.2 bits (90), Expect = 5e-05
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 42 PESAFTYEQLVAL----ENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
            + F+   L  L    +N   +   +   +   +A  L++    V+ W  NRR K++  
Sbjct: 11 DRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM 70

Query: 98 N 98
           
Sbjct: 71 G 71

>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* Length = 83

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 5/53 (9%)

Query: 63  YLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSPTVPTCPGGS 115
           YL      NL  + SL+  Q+K W   RR K K         +P +     G 
Sbjct: 29  YLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI-----APELADLLSGE 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	165
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.87
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.87
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.86
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.86
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.85
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.85
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.85
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.85
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.85
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.85
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.85
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.84
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.84
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.84
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.84
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.84
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.84
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.84
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.84
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.84
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.84
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.84
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.84
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.84
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.83
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.83
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.83
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.83
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.83
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.83
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.83
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.83
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.83
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.83
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.82
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.82
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.82
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.82
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.82
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.82
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.82
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.81
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.81
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.81
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.81
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.81
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.81
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.79
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.79
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.79
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.79
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.78
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.78
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.77
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.77
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.77
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.77
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.77
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.77
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.77
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.77
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.76
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.76
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.76
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.75
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.74
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.72
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.72
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.69
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.6
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.56
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.55
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.54
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.43
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.78
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.73
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	90.92
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	89.42
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	89.17
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	87.24
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	86.32
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	85.79
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	85.14
3c57_A	95	Two component transcriptional regulatory protein;	84.3
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	82.91
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	82.43

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

Probab=99.87  E-value=3e-22  Score=135.16  Aligned_cols=68  Identities=32%  Similarity=0.535  Sum_probs=63.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         33 TQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        33 ~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ...+++.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+..+.
T Consensus        16 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~   83 (84)
T 2kt0_A           16 DKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN   83 (84)
T ss_dssp             CCCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            34566788899999999999999999999999999999999999999999999999999999998753

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

Probab=99.87  E-value=5.2e-22  Score=132.95  Aligned_cols=68  Identities=35%  Similarity=0.550  Sum_probs=63.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV  103 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~  103 (165)
                      .++.++.|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+|++......
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~   71 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQN   71 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCC
Confidence            45678899999999999999999999999999999999999999999999999999999998865443

>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=99.86  E-value=6.5e-22  Score=132.52  Aligned_cols=65  Identities=45%  Similarity=0.767  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+||...
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            45677888999999999999999999999999999999999999999999999999999999865

>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=99.86  E-value=8.3e-22  Score=128.77  Aligned_cols=64  Identities=33%  Similarity=0.544  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..+.+++|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            4567788999999999999999999999999999999999999999999999999999999864

>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=99.86  E-value=7.4e-22  Score=131.98  Aligned_cols=67  Identities=27%  Similarity=0.364  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         33 TQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        33 ~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ...+++.++.|+.|+.+|+.+||..|..++||+..++++||.+|||++.+|++||||||+|+||...
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           11 GEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            3445678889999999999999999999999999999999999999999999999999999999864

>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=99.85  E-value=1.2e-21  Score=131.04  Aligned_cols=65  Identities=23%  Similarity=0.342  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      .++.++.|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+|++...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            35678889999999999999999999999999999999999999999999999999999997543

>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=99.85  E-value=1.2e-21  Score=127.93  Aligned_cols=66  Identities=30%  Similarity=0.394  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ...+.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+....
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            345678889999999999999999999999999999999999999999999999999999997653

>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=99.85  E-value=7.7e-22  Score=131.25  Aligned_cols=67  Identities=43%  Similarity=0.567  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ..+++.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+....
T Consensus         4 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            4567778889999999999999999999999999999999999999999999999999999987543

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

Probab=99.85  E-value=1.7e-21  Score=127.22  Aligned_cols=64  Identities=44%  Similarity=0.713  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..+.++.|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             TTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            3456788999999999999999999999999999999999999999999999999999999865

>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=99.85  E-value=1e-21  Score=128.20  Aligned_cols=66  Identities=24%  Similarity=0.300  Sum_probs=61.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ..++.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+..++
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            345678899999999999999999999999999999999999999999999999999999998753

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

Probab=99.85  E-value=9.5e-22  Score=125.55  Aligned_cols=61  Identities=36%  Similarity=0.568  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      +.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+.+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~q   62 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ   62 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGGC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhcC
Confidence            4578899999999999999999999999999999999999999999999999999999864

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

Probab=99.85  E-value=3e-21  Score=127.14  Aligned_cols=66  Identities=33%  Similarity=0.470  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ..+.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+.....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKL   69 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhccc
Confidence            356788899999999999999999999999999999999999999999999999999999986544

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

Probab=99.85  E-value=3.1e-21  Score=132.78  Aligned_cols=71  Identities=42%  Similarity=0.749  Sum_probs=64.3

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         30 SPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        30 ~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      +.....+.+.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+....
T Consensus         8 p~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~   78 (93)
T 3a01_A            8 PYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE   78 (93)
T ss_dssp             CSTTSCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CcCCCCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHH
Confidence            33345567788899999999999999999999999999999999999999999999999999999997653

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

Probab=99.85  E-value=1.6e-21  Score=127.45  Aligned_cols=64  Identities=50%  Similarity=0.755  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..+.++.|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            4567788999999999999999999999999999999999999999999999999999998764

>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=99.84  E-value=3.2e-21  Score=125.98  Aligned_cols=63  Identities=48%  Similarity=0.761  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .+.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+...
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            456678899999999999999999999999999999999999999999999999999999865

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

Probab=99.84  E-value=1.5e-21  Score=130.64  Aligned_cols=66  Identities=20%  Similarity=0.275  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhc----CCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTT----RYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~----~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ..++.++.|+.|+.+|+.+||..|+.+    +||+..++++||.+|||++.+|++||||||+|+|+....
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~~~   73 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIE   73 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhccCC
Confidence            456778899999999999999999999    999999999999999999999999999999999997643

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

Probab=99.84  E-value=1.9e-21  Score=124.62  Aligned_cols=61  Identities=46%  Similarity=0.787  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      +.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+.+
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            3578899999999999999999999999999999999999999999999999999999975

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

Probab=99.84  E-value=1.4e-20  Score=128.45  Aligned_cols=61  Identities=23%  Similarity=0.341  Sum_probs=56.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCC
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS  105 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~  105 (165)
                      .|+.+|+.+||..|..++||+..++++||..|||+++||+|||||||+|+|++++....+.
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~~~   77 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDE   77 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhccc
Confidence            7999999999999999999999999999999999999999999999999999876655443

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

Probab=99.84  E-value=5.1e-21  Score=126.33  Aligned_cols=68  Identities=38%  Similarity=0.599  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD  102 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~  102 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+.++.+.
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q   72 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQ   72 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhh
Confidence            34567788999999999999999999999999999999999999999999999999999999877543

>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=99.84  E-value=3.9e-21  Score=128.88  Aligned_cols=61  Identities=11%  Similarity=0.071  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKT----TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~----~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      .++.++.|+.|+.+|+.+||..|+.    ++||+..++++||.+|||++.+|+|||||||+|+|+
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            3567888999999999999999999    999999999999999999999999999999999875

>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=99.84  E-value=2.3e-21  Score=123.41  Aligned_cols=58  Identities=45%  Similarity=0.756  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      .++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+||
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            4678999999999999999999999999999999999999999999999999999987

>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=99.84  E-value=3.1e-21  Score=125.45  Aligned_cols=63  Identities=46%  Similarity=0.719  Sum_probs=59.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      +++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~   64 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK   64 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcccc
Confidence            467899999999999999999999999999999999999999999999999999999987644

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

Probab=99.84  E-value=3.8e-21  Score=128.76  Aligned_cols=63  Identities=38%  Similarity=0.720  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .+.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+..+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   67 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhh
Confidence            466788999999999999999999999999999999999999999999999999999999764

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

Probab=99.84  E-value=3.8e-21  Score=121.07  Aligned_cols=58  Identities=59%  Similarity=0.858  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   58 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhccC
Confidence            5788999999999999999999999999999999999999999999999999999873

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

Probab=99.84  E-value=5.6e-21  Score=124.16  Aligned_cols=63  Identities=44%  Similarity=0.590  Sum_probs=59.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      .++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+..+..
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            567899999999999999999999999999999999999999999999999999999987654

>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=99.84  E-value=4.2e-21  Score=128.87  Aligned_cols=64  Identities=42%  Similarity=0.596  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .++.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+||..+
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            4567788999999999999999999999999999999999999999999999999999999754

>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=99.84  E-value=3.9e-21  Score=124.13  Aligned_cols=62  Identities=21%  Similarity=0.297  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +.++.|+.|+.+|+.+||..|+.++||+..++++||..+||++.+|++||||||+|+|++..
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            45788999999999999999999999999999999999999999999999999999998764

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

Probab=99.83  E-value=5.3e-21  Score=130.22  Aligned_cols=66  Identities=44%  Similarity=0.725  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ...++.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+..+
T Consensus        23 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   88 (88)
T 2r5y_A           23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK   88 (88)
T ss_dssp             --------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhcC
Confidence            345677889999999999999999999999999999999999999999999999999999998753

>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=99.83  E-value=1.4e-20  Score=124.58  Aligned_cols=61  Identities=25%  Similarity=0.255  Sum_probs=56.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ++|..|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|++....
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~   69 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK   69 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcc
Confidence            4566799999999999999999999999999999999999999999999999999987643

>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=99.83  E-value=2.1e-21  Score=126.18  Aligned_cols=64  Identities=36%  Similarity=0.662  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      +.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+..+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            4678899999999999999999999999999999999999999999999999999999987654

>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=99.83  E-value=7.1e-21  Score=127.56  Aligned_cols=61  Identities=15%  Similarity=0.163  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKT-----TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~-----~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      ...+.++.|+.|+.+|+.+|| .|..     ++||+..++++||.+|||++.+|+|||||||+|+|+
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            345678889999999999999 7999     999999999999999999999999999999999876

>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=99.83  E-value=9e-21  Score=126.05  Aligned_cols=65  Identities=42%  Similarity=0.539  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+..+
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k   73 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhh
Confidence            34567788999999999999999999999999999999999999999999999999999998653

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

Probab=99.83  E-value=4.5e-21  Score=124.61  Aligned_cols=62  Identities=37%  Similarity=0.562  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      .++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            46789999999999999999999999999999999999999999999999999999997543

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

Probab=99.83  E-value=8.8e-21  Score=125.79  Aligned_cols=65  Identities=22%  Similarity=0.305  Sum_probs=59.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCC
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVN  104 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~  104 (165)
                      .+.|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+|+........
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~~~~   73 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRSGP   73 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSSCCC
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccCCCC
Confidence            34478999999999999999999999999999999999999999999999999999987654443

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

Probab=99.83  E-value=6.2e-21  Score=120.98  Aligned_cols=58  Identities=45%  Similarity=0.622  Sum_probs=55.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|++
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            5789999999999999999999999999999999999999999999999999999985

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

Probab=99.83  E-value=1.1e-20  Score=122.33  Aligned_cols=63  Identities=37%  Similarity=0.553  Sum_probs=59.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCC
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD  102 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~  102 (165)
                      ++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+......
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~~q   64 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ   64 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCTTC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchhcc
Confidence            678999999999999999999999999999999999999999999999999999999876543

>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=99.83  E-value=9.5e-21  Score=127.06  Aligned_cols=63  Identities=35%  Similarity=0.607  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      .++.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|++.
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~   77 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   77 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhc
Confidence            456788999999999999999999999999999999999999999999999999999999874

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

Probab=99.82  E-value=1.6e-20  Score=129.63  Aligned_cols=65  Identities=25%  Similarity=0.337  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------CCchhhhhhhhcchhhhhhhCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------LTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------l~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      .++.++.|+.|+.+|+.+||..|+.++||+..++++||.+|+               |++.+|++||||||+|+|++...
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            456788999999999999999999999999999999999999               99999999999999999998765

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

Probab=99.82  E-value=9.2e-21  Score=120.18  Aligned_cols=58  Identities=45%  Similarity=0.771  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+..+
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            4789999999999999999999999999999999999999999999999999998753

>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=99.82  E-value=1.4e-20  Score=124.53  Aligned_cols=58  Identities=21%  Similarity=0.246  Sum_probs=54.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +|..|+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+..-
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l   63 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHH
Confidence            4566999999999999999999999999999999999999999999999999998753

>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=99.82  E-value=2.2e-20  Score=122.60  Aligned_cols=61  Identities=23%  Similarity=0.356  Sum_probs=57.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         40 LVPESAFTYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      .++|+.|+.+|+.+||..|+. ++||+..++++||.+|||++.+|++||||||+|+|+....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~   63 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   63 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccC
Confidence            467899999999999999996 9999999999999999999999999999999999998753

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

Probab=99.82  E-value=2.7e-20  Score=122.49  Aligned_cols=61  Identities=25%  Similarity=0.338  Sum_probs=57.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         40 LVPESAFTYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      .+.|+.|+.+|+.+||..|+. ++||+..++++||..|||++.+|++||||||+|+|+....
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            467899999999999999995 9999999999999999999999999999999999998753

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

Probab=99.82  E-value=1.6e-20  Score=117.97  Aligned_cols=57  Identities=54%  Similarity=0.711  Sum_probs=54.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      +++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|
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            467899999999999999999999999999999999999999999999999999986

>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=99.82  E-value=1.1e-20  Score=120.02  Aligned_cols=59  Identities=25%  Similarity=0.384  Sum_probs=48.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      ++.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            45678899999999999999999999999999999999999999999999999999975

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

Probab=99.81  E-value=1.8e-20  Score=117.30  Aligned_cols=54  Identities=48%  Similarity=0.892  Sum_probs=51.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      +.|+.+|+.+||..|+.++||+..++++||..+||++.+|++||||||+|+||+
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            579999999999999999999999999999999999999999999999999986

>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=99.81  E-value=1.3e-20  Score=130.55  Aligned_cols=66  Identities=44%  Similarity=0.613  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ...+.++.|+.|+.+|+.+||..|..++||+..++++||..|||++.+|++||||||+|+|+..+.
T Consensus        30 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            345678889999999999999999999999999999999999999999999999999999998654

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

Probab=99.81  E-value=6.4e-20  Score=120.87  Aligned_cols=64  Identities=20%  Similarity=0.313  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ..++.|+.|+.+|+.+||..|+.++||+..++++||.++||++.+|++||||||+|+|+.....
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   68 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQ   68 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCC
Confidence            3467789999999999999999999999999999999999999999999999999999987543

>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=99.81  E-value=8.8e-20  Score=123.00  Aligned_cols=70  Identities=20%  Similarity=0.174  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS  105 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~  105 (165)
                      ..+.+++|+.|+.+|+.+||.+|..   ++||+..++++||..+||++.||++||||||+|+|+.........
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~~~~   76 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRND   76 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCCCCC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhccCC
Confidence            4567788999999999999999987   599999999999999999999999999999999998765544443

>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=99.81  E-value=6.9e-20  Score=120.48  Aligned_cols=65  Identities=20%  Similarity=0.237  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ..++.++.|+.|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            34567788999999999999999987   999999999999999999999999999999999998764

>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=99.81  E-value=2.4e-19  Score=122.38  Aligned_cols=58  Identities=21%  Similarity=0.322  Sum_probs=54.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCC
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD  102 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~  102 (165)
                      .|+.+|+.+||..|..++||+..++++||.+|||++.+|++||||||+|+|+......
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~   76 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL   76 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhh
Confidence            4899999999999999999999999999999999999999999999999999876543

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

Probab=99.79  E-value=4.9e-20  Score=118.22  Aligned_cols=59  Identities=25%  Similarity=0.375  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         39 DLVPESAFTYEQLVALENKF---KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F---~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      .++.|+.|+.+|+.+||.+|   ..++||+..++++||..+||++.+|++||+|||+|+||.
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   64 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   64 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSCC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhccC
Confidence            46788999999999999999   899999999999999999999999999999999999873

>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=99.79  E-value=1.3e-19  Score=119.18  Aligned_cols=62  Identities=26%  Similarity=0.344  Sum_probs=58.4

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         40 LVPESAFTYEQLVALENKF---KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F---~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      +++|+.|+.+|+.+||.+|   ..++||+..+++.||..+||++.+|++||||||+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   66 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccc
Confidence            6788999999999999999   8999999999999999999999999999999999999976543

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

Probab=99.79  E-value=1e-19  Score=125.85  Aligned_cols=62  Identities=32%  Similarity=0.358  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ...+++|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+|+..
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            34557889999999999999999999999999999999999999999999999999999875

>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=99.79  E-value=1.4e-19  Score=114.65  Aligned_cols=56  Identities=36%  Similarity=0.414  Sum_probs=53.6

Q ss_pred             CCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         42 PESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      +|+.|+.+|+.+||..|..   ++||+..++++||.++||++.+|++||+|||+|+|+.
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            3678999999999999999   9999999999999999999999999999999999985

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

Probab=99.78  E-value=2.6e-19  Score=116.69  Aligned_cols=59  Identities=51%  Similarity=0.719  Sum_probs=54.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCC
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMD  102 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~  102 (165)
                      ..++..|+.+||..|+.++||+..++++||..|||++++|++||||||+|+|++....+
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~~~   67 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE   67 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSSCC
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhhhh
Confidence            45899999999999999999999999999999999999999999999999999875443

>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=99.78  E-value=2.2e-19  Score=121.76  Aligned_cols=60  Identities=27%  Similarity=0.352  Sum_probs=56.6

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         40 LVPESAFTYEQLVALENKF---KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F---~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +++|+.|+.+|+.+||.+|   ..++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   64 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccc
Confidence            6788999999999999999   89999999999999999999999999999999999999764

>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=99.77  E-value=4.4e-19  Score=123.40  Aligned_cols=64  Identities=20%  Similarity=0.162  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHh---------------------CCCchhhhhhhhcchhhh
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSL---------------------SLTETQVKIWFQNRRTKW   94 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~l---------------------gl~~~qV~~WFqNRR~k~   94 (165)
                      .++.++.|+.|+..|+.+||+.|+.++||+..+|++||.+|                     +|++.+|++||||||+|+
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            45678899999999999999999999999999999999999                     799999999999999999


Q ss_pred             hhhCC
Q psy15100         95 KKQNP   99 (165)
Q Consensus        95 kr~~~   99 (165)
                      |++.+
T Consensus        83 kr~~~   87 (102)
T 2da6_A           83 AFRQK   87 (102)
T ss_dssp             HHHHH
T ss_pred             HHhhH
Confidence            98764

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

Probab=99.77  E-value=1.1e-19  Score=119.46  Aligned_cols=59  Identities=22%  Similarity=0.321  Sum_probs=54.5

Q ss_pred             CCCCCCCCHHHHHHHHHHH-HhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         40 LVPESAFTYEQLVALENKF-KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F-~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      .+.|..++.+|+.+||..| +.++||+..++++||.+|||++++|++||||||+|+|+..
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            3456678889999999999 9999999999999999999999999999999999999865

>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=99.77  E-value=5.2e-19  Score=113.64  Aligned_cols=60  Identities=22%  Similarity=0.217  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      .++.+|.|+.|+.+||.+|+..|+. +.||+.++|+.||.++||++++|++||||||--.+
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            4578899999999999999999999 99999999999999999999999999999997643

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

Probab=99.77  E-value=2.6e-19  Score=134.99  Aligned_cols=66  Identities=30%  Similarity=0.356  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ..++++++|+.|+..|+.+||..|..++||+..+|++||..|||++++|++||||||+|+||..+.
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            356778899999999999999999999999999999999999999999999999999999998754

>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=99.77  E-value=3.2e-19  Score=132.12  Aligned_cols=64  Identities=25%  Similarity=0.344  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..++++||..|||++++|++||||||+|+||++
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~k  146 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK  146 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhccC
Confidence            3466788899999999999999999999999999999999999999999999999999999863

>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=99.77  E-value=4.8e-19  Score=119.34  Aligned_cols=60  Identities=32%  Similarity=0.335  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         40 LVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +++|++|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+|+...
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            455677999999999999999   999999999999999999999999999999999999764

>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=99.77  E-value=5.2e-19  Score=120.06  Aligned_cols=60  Identities=35%  Similarity=0.392  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      .+++++|+.|+.+|+.+||.+|..   ++||+..++++||..+||++.+|++||||||+|+|.
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            445667899999999999999999   999999999999999999999999999999999873

>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=99.77  E-value=3.6e-19  Score=133.67  Aligned_cols=63  Identities=25%  Similarity=0.346  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ..+.++.|+.|+..|+.+||..|..++||+..++++||..|||++.+|++||||||+|+||+.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  160 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN  160 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSCC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhccC
Confidence            357788999999999999999999999999999999999999999999999999999999863

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

Probab=99.76  E-value=2.9e-19  Score=124.18  Aligned_cols=66  Identities=21%  Similarity=0.191  Sum_probs=54.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH------------------hC---CCchhhhhhhhcchhh
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALS------------------LS---LTETQVKIWFQNRRTK   93 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~------------------lg---l~~~qV~~WFqNRR~k   93 (165)
                      ..++.++.|+.|+..|+.+||..|+.++||+..+|++||..                  ||   |++.+|++||||||++
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            45677889999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             hhhhCCC
Q psy15100         94 WKKQNPG  100 (165)
Q Consensus        94 ~kr~~~~  100 (165)
                      +|++...
T Consensus        85 ~k~k~~~   91 (99)
T 1lfb_A           85 EAFRHKL   91 (99)
T ss_dssp             TSCCC--
T ss_pred             HHHhchh
Confidence            9887643

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

Probab=99.76  E-value=4.2e-19  Score=113.96  Aligned_cols=52  Identities=23%  Similarity=0.411  Sum_probs=49.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      .+.+|+.+||..|..++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            4789999999999999999999999999999999999999999999999974

>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=99.76  E-value=7.3e-19  Score=130.78  Aligned_cols=62  Identities=27%  Similarity=0.430  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      .+++++|+|+.|+.+|+.+||..|..++||+..++++||.+|||++.+|++||||||+|+||
T Consensus        89 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           89 EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            34677889999999999999999999999999999999999999999999999999999987

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.5e-19  Score=112.92  Aligned_cols=55  Identities=20%  Similarity=0.146  Sum_probs=51.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ..++.+|+.+||..|..++||+..++++||.+|||++++|++||||||+|+++.+
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~~   62 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ   62 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCSS
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCCC
Confidence            4467899999999999999999999999999999999999999999999988753

>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=99.74  E-value=8.9e-19  Score=112.31  Aligned_cols=51  Identities=22%  Similarity=0.274  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHH-HhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         48 YEQLVALENKF-KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        48 ~~Ql~~Le~~F-~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ..|+.+||+.| ..++||+..+|++||.+|||+++||++||||||+|+|+..
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~   60 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG   60 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence            34899999999 5689999999999999999999999999999999998754

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

Probab=99.72  E-value=3.8e-18  Score=128.37  Aligned_cols=66  Identities=21%  Similarity=0.180  Sum_probs=55.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ...+.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+....
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            456778899999999999999999999999999999999999999999999999999999987653

>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=99.72  E-value=3.3e-18  Score=127.82  Aligned_cols=61  Identities=25%  Similarity=0.335  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ++.+++|+.|+..|+.+||..|..++||+..++++||..|||++++|++||||||+|+||.
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            5677889999999999999999999999999999999999999999999999999999985

>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=99.69  E-value=2.9e-17  Score=106.37  Aligned_cols=57  Identities=25%  Similarity=0.219  Sum_probs=50.6

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100         44 SAFTYEQLVALENKFK---TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      ..|+.+|+.+|+.+|.   .++||+..++++||..+||++.||++||+|||+|+|+....
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            4699999999999999   99999999999999999999999999999999999987543

>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=99.60  E-value=2.1e-16  Score=121.83  Aligned_cols=61  Identities=21%  Similarity=0.191  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------------CCchhhhhhhhcchhhh
Q psy15100         36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------------LTETQVKIWFQNRRTKW   94 (165)
Q Consensus        36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------------l~~~qV~~WFqNRR~k~   94 (165)
                      .++.||.|+.|+..|+.+||..|+.++||+..+|++||..|+                     |++.+|++||||||+++
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            467788999999999999999999999999999999999999                     99999999999999998


Q ss_pred             hh
Q psy15100         95 KK   96 (165)
Q Consensus        95 kr   96 (165)
                      |.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            75

>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=99.56  E-value=2.3e-15  Score=97.22  Aligned_cols=47  Identities=19%  Similarity=0.359  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100         48 YEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW   94 (165)
Q Consensus        48 ~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~   94 (165)
                      ++|+.+||..|..|.+|+.+++..||..+||.+++|++||||||+..
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~   60 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ   60 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccccc
Confidence            46899999999999999999999999999999999999999999853

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=99.55  E-value=4.1e-15  Score=100.93  Aligned_cols=55  Identities=24%  Similarity=0.259  Sum_probs=51.5

Q ss_pred             CCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         44 SAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      -.|+.+++.+|+.+|..   ++||+.+++++||.++||++.||++||+|+|.|+++..
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~   67 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDM   67 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHH
Confidence            45899999999999987   89999999999999999999999999999999998754

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

Probab=99.54  E-value=4.5e-15  Score=115.95  Aligned_cols=60  Identities=23%  Similarity=0.204  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------------CCchhhhhhhhcchhh
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------------LTETQVKIWFQNRRTK   93 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------------l~~~qV~~WFqNRR~k   93 (165)
                      ..++.||.|+.|+..|+.+||..|+.++||+..+|++||..||                     |++.+|++||+|||++
T Consensus       138 ~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             ccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            4567788999999999999999999999999999999999998                     8999999999999987


Q ss_pred             h
Q psy15100         94 W   94 (165)
Q Consensus        94 ~   94 (165)
                      +
T Consensus       218 ~  218 (221)
T 2h8r_A          218 E  218 (221)
T ss_dssp             C
T ss_pred             h
Confidence            5

>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=99.43  E-value=6.2e-14  Score=117.13  Aligned_cols=55  Identities=27%  Similarity=0.430  Sum_probs=51.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      +.++.|+.+|+..||+.|+.++||+..+|++||.+|||+++||++||||||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            3467799999999999999999999999999999999999999999999999976

>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=98.78  E-value=7.8e-10  Score=62.83  Aligned_cols=20  Identities=65%  Similarity=1.149  Sum_probs=17.6

Q ss_pred             hhhhhhhhcchhhhhhhCCC
Q psy15100         81 TQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        81 ~qV~~WFqNRR~k~kr~~~~  100 (165)
                      +||+|||||||+||||++..
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            58999999999999997654

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.73  E-value=0.0014  Score=41.87  Aligned_cols=39  Identities=23%  Similarity=0.358  Sum_probs=37.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100         51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQN   89 (165)
Q Consensus        51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN   89 (165)
                      .++|+.+|...+.+..++...|+.+.+|+..||+.||-.
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            589999999999999999999999999999999999964

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=90.92  E-value=0.29  Score=29.30  Aligned_cols=46  Identities=13%  Similarity=0.199  Sum_probs=32.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100         43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQN   89 (165)
Q Consensus        43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN   89 (165)
                      |..|+.+....+...++.. ........++|.++||+...|..|...
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            4568888877665555433 322223668999999999999999754

>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=89.42  E-value=0.82  Score=31.32  Aligned_cols=48  Identities=10%  Similarity=0.213  Sum_probs=37.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100         42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT   92 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~   92 (165)
                      +|..|+.++...+-..+..+.....   .+||..+||+...|..|..++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~   51 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRA   51 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhh
Confidence            5678999998877777755555543   35789999999999999987655

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=89.17  E-value=1.2  Score=28.65  Aligned_cols=45  Identities=13%  Similarity=0.268  Sum_probs=32.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQN   89 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN   89 (165)
                      ++.+..|+.++....-..+.. ..    -..+||.++||+...|..|...
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~~-g~----s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIHD-GE----SKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHHH-TC----CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHHHHHH
Confidence            445667999886555555543 22    2567899999999999999853

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=87.24  E-value=1.5  Score=23.99  Aligned_cols=40  Identities=8%  Similarity=0.149  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQN   89 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN   89 (165)
                      .++.++...+...+... .    ...+||..+|++...|..|...
T Consensus         5 ~l~~~~~~~i~~~~~~g-~----s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHhh
Confidence            46777765555555433 2    2567899999999999999864

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=86.32  E-value=0.78  Score=29.72  Aligned_cols=47  Identities=13%  Similarity=0.179  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ++..+..+|.-.|....     ...+||..||++...|+.+...-|.|.|+.
T Consensus        38 L~~~~r~vl~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~   84 (92)
T 3hug_A           38 LSAEHRAVIQRSYYRGW-----STAQIATDLGIAEGTVKSRLHYAVRALRLT   84 (92)
T ss_dssp             SCHHHHHHHHHHHTSCC-----CHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            56667777766553332     356789999999999999998777776654

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=85.79  E-value=0.55  Score=26.33  Aligned_cols=41  Identities=10%  Similarity=0.174  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR   91 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR   91 (165)
                      ++.++...+...+...  .   ...+||..+|++...|..|+....
T Consensus         6 ~~~~~~~~i~~l~~~g--~---s~~~ia~~lgvs~~Tv~r~l~~~~   46 (52)
T 1jko_C            6 INKHEQEQISRLLEKG--H---PRQQLAIIFGIGVSTLYRYFPASS   46 (52)
T ss_dssp             SCTTHHHHHHHHHHTT--C---CHHHHHHTTSCCHHHHHHHSCTTC
T ss_pred             CCHHHHHHHHHHHHcC--C---CHHHHHHHHCCCHHHHHHHHHHcc
Confidence            4455555555555433  2   356789999999999999996543

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=85.14  E-value=0.98  Score=27.17  Aligned_cols=49  Identities=12%  Similarity=-0.054  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      .++..+..+|...|....     ...++|..+|++...|+.+...-+.+.++..
T Consensus        15 ~L~~~~r~il~l~~~~g~-----s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l   63 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLGL-----SYADAAAVCGCPVGTIRSRVARARDALLADA   63 (70)
T ss_dssp             SSCHHHHHHHHHHHTSCC-----CHHHHHHHHTSCHHHHHHHHHHHHHHHHC--
T ss_pred             hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            477888889988764332     3567899999999999999987666666543

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=84.30  E-value=1.6  Score=28.54  Aligned_cols=49  Identities=18%  Similarity=0.093  Sum_probs=37.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ..++..+..+|.-.++..      ...+||..||++...|+.+..+-+.|.+...
T Consensus        26 ~~Lt~~e~~vl~l~~~g~------s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~   74 (95)
T 3c57_A           26 SGLTDQERTLLGLLSEGL------TNKQIADRMFLAEKTVKNYVSRLLAKLGMER   74 (95)
T ss_dssp             -CCCHHHHHHHHHHHTTC------CHHHHHHHHTCCHHHHHHHHHHHHHHHTCCC
T ss_pred             hcCCHHHHHHHHHHHcCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHcCCC
Confidence            358999999998864322      2467899999999999999987666665543

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=82.91  E-value=2.1  Score=28.47  Aligned_cols=44  Identities=9%  Similarity=-0.071  Sum_probs=34.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK   93 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k   93 (165)
                      ..++..++++|.-.++-.      ...+||..||+++..|+.+..+-+.|
T Consensus        33 ~~Lt~re~~Vl~l~~~G~------s~~EIA~~L~iS~~TV~~~l~ri~~K   76 (99)
T 1p4w_A           33 KRLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQKKSAMMK   76 (99)
T ss_dssp             SSCCHHHHHHHHHHHHTC------CHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHcCC------CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            458999999998865422      24789999999999999998765544

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=82.43  E-value=1.4  Score=28.03  Aligned_cols=47  Identities=21%  Similarity=0.130  Sum_probs=35.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      ..++..+.++|.-.+  ..    ....+||..+|++...|+.+..+-+.|.+.
T Consensus        20 ~~Lt~~e~~vl~l~~--~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   66 (82)
T 1je8_A           20 NQLTPRERDILKLIA--QG----LPNKMIARRLDITESTVKVHVKHMLKKMKL   66 (82)
T ss_dssp             GGSCHHHHHHHHHHT--TT----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             ccCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            458999999998843  22    235678999999999999998765555443

---

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	165
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	6e-25
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	8e-24
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-23
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-22
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	5e-22
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-21
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	4e-21
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	7e-21
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	4e-20
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-20
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	6e-20
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-19
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-19
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-19
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	3e-19
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-18
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-18
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	5e-18
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	5e-18
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	6e-18
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	9e-18
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	4e-17
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	5e-17
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	8e-17
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	7e-16
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-15
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-15
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	8e-15
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-14
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	5e-14
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	6e-11
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-10

>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 = 89.1 bits (221), Expect = 6e-25
 Identities = 29/54 (53%), Positives = 38/54 (70%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           +T  Q + LE +F   RYL+   R+ +A +LSLTE Q+KIWFQNRR KWKK+N
Sbjct: 3  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 86.4 bits (214), Expect = 8e-24
 Identities = 23/54 (42%), Positives = 35/54 (64%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          +FT EQ+ ALE +F+ T Y  V  R  LA  + L E ++++WF NRR KW+++ 
Sbjct: 7  SFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 60

>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 = 86.0 bits (213), Expect = 1e-23
 Identities = 27/54 (50%), Positives = 33/54 (61%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           +T  Q + LE +F    YL+   R  +A  L+LTE QVKIWFQNRR K KK N
Sbjct: 19 PYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72

>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 = 82.6 bits (204), Expect = 2e-22
 Identities = 28/52 (53%), Positives = 36/52 (69%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
           F+ +Q + LE KF+T +YLS  ER  LA  L L+E QVK WFQNRR KW++
Sbjct: 6  RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 81.8 bits (202), Expect = 5e-22
 Identities = 13/54 (24%), Positives = 23/54 (42%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
              +QL  L   +          +  L     L+   +++WFQN+R K KK++
Sbjct: 9  VLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62

>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 = 80.3 bits (198), Expect = 2e-21
 Identities = 19/52 (36%), Positives = 33/52 (63%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
           ++  QL  LE ++   ++++  +R  ++ + SL+E Q+ IWFQNRR K KK
Sbjct: 7  PYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 79.6 bits (196), Expect = 4e-21
 Identities = 28/55 (50%), Positives = 35/55 (63%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
           F+  Q+  LE +FK  +YLS  ER +LA  + LT TQVKIWFQN R K K+Q  
Sbjct: 8  LFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

>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 = 78.8 bits (194), Expect = 7e-21
 Identities = 26/53 (49%), Positives = 34/53 (64%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          AFT +QL  LE +F    Y+S   R  LA  L+L E+ +K+WFQNRR K K+Q
Sbjct: 5  AFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>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 = 76.9 bits (189), Expect = 4e-20
 Identities = 23/53 (43%), Positives = 35/53 (66%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
           FT +QL  LE  F+  RY  +  R  +A+  +LTE +V++WF+NRR KW+K+
Sbjct: 7  HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 76.5 bits (188), Expect = 4e-20
 Identities = 16/53 (30%), Positives = 25/53 (47%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
            +     ALE  F      S  E + +A  L+L +  V++WF NRR + K+ 
Sbjct: 5  TISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV 57

>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 = 76.5 bits (188), Expect = 6e-20
 Identities = 22/54 (40%), Positives = 34/54 (62%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           F+  QL  LE  F+ T+Y  +  R  LA   +LTE ++++WFQNRR + +KQ+
Sbjct: 8  TFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 61

>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 = 75.8 bits (186), Expect = 2e-19
 Identities = 35/86 (40%), Positives = 45/86 (52%), Gaps = 5/86 (5%)

Query: 18 AKTPPVRRNRGRSPNTQTPSEDLVPES-----AFTYEQLVALENKFKTTRYLSVCERLNL 72
          A+T    + +   P T   SE  +         FT  QL  LE +F   +YLS   R+ +
Sbjct: 1  ARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEI 60

Query: 73 ALSLSLTETQVKIWFQNRRTKWKKQN 98
          A +L L ETQVKIWFQNRR K KK+ 
Sbjct: 61 AATLELNETQVKIWFQNRRMKQKKRE 86

>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 = 75.0 bits (184), Expect = 2e-19
 Identities = 33/52 (63%), Positives = 39/52 (75%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
           FT  QL+ALE KF+  +YLS+ ER   + SLSLTETQVKIWFQNRR K K+
Sbjct: 6  PFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 74.5 bits (183), Expect = 2e-19
 Identities = 25/52 (48%), Positives = 32/52 (61%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
          P +AF+ EQL  L+ +F   RYL+   R  L+  L L E Q+KIWFQN R K
Sbjct: 2  PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 74.6 bits (183), Expect = 3e-19
 Identities = 23/54 (42%), Positives = 31/54 (57%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           FT  Q+  LE  F   RYL+     +L+  L+L   QVKIWF+NRR + K Q+
Sbjct: 7  TFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 60

>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 = 71.4 bits (175), Expect = 3e-18
 Identities = 14/50 (28%), Positives = 21/50 (42%)

Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91
          P   FT  Q   L   FK  +  S   ++ ++  L L  + V  +F N R
Sbjct: 1  PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 71.5 bits (175), Expect = 4e-18
 Identities = 15/52 (28%), Positives = 28/52 (53%)

Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
          S+ + +    LE  F+  + L+  E+  +A    +T  QV++WF N+R + K
Sbjct: 2  SSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 70.9 bits (174), Expect = 5e-18
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 47 TYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          T +    LE  F   T++        L+  L      ++ WF+ RR + K 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 72.0 bits (176), Expect = 5e-18
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 15/69 (21%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLAL---------------SLSLTETQVKIWFQN 89
           +  E L  +E+ F   +Y    +R  +A                   +T  +V  WF N
Sbjct: 6  TWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFAN 65

Query: 90 RRTKWKKQN 98
          RR + K++ 
Sbjct: 66 RRKEIKRRA 74

>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 = 71.6 bits (175), Expect = 6e-18
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          +       +LE  F      S+ +  ++A  L L +  V++WF NRR K K+ +
Sbjct: 14 SIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67

>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 = 70.7 bits (173), Expect = 9e-18
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
          +      VALE  F   +  +  +   +A  L++ +  +++WF NRR K K+ N
Sbjct: 4  SIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 57

>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 = 69.2 bits (169), Expect = 4e-17
 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 45  AFTYEQLVALENKFK---TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
            F  +    L   F    +  Y S   +  LA    +T +QV  WF N+R ++KK     
Sbjct: 7   NFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF 66

Query: 102 D 102
            
Sbjct: 67  Q 67

>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 = 68.7 bits (168), Expect = 5e-17
 Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 46 FTYEQLVALENKFKTTR---YLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
          FT E +  LE+ F       YL      NL  + SL+  Q+K W  NRR K K 
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 68.9 bits (168), Expect = 8e-17
 Identities = 28/54 (51%), Positives = 33/54 (61%)

Query: 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
           FT  Q   LE +F+  RYLS  ER +LA  + LT TQVKIWFQN R K K+  
Sbjct: 15 LFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

>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 = 66.2 bits (161), Expect = 7e-16
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 44 SAFTYEQLVALENKF-KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
          +  T +Q+  LE  F K  ++        +A    LTE Q + WF+ R  +W++ 
Sbjct: 6  ATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 65.6 bits (159), Expect = 1e-15
 Identities = 13/74 (17%), Positives = 23/74 (31%), Gaps = 21/74 (28%)

Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------------LTETQVK 84
          +       L   ++  +  S  ER  L    +                     +TE +V 
Sbjct: 4  WGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVY 63

Query: 85 IWFQNRRTKWKKQN 98
           WF NRR +   ++
Sbjct: 64 NWFANRRKEEAFRH 77

>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 = 64.0 bits (156), Expect = 3e-15
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 46 FTYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
             E    LE  F + T+Y        L+  L  +  +++ WF++RR + K
Sbjct: 8  NKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 63.6 bits (154), Expect = 8e-15
 Identities = 14/62 (22%), Positives = 25/62 (40%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105
            T EQL  L+  F  +  L+  E   L     LT  ++  WF  ++     +   M+++ 
Sbjct: 11  KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDE 70

Query: 106 PT 107
             
Sbjct: 71  SN 72

>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 = 62.8 bits (153), Expect = 1e-14
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 46 FTYEQLVALENKFKTTR---YLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
                  + +         Y +  E+  +A   +LT  QV  WF N R +  +
Sbjct: 9  LPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 61.3 bits (148), Expect = 5e-14
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 45 AFTYEQLVALENKF-KTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
            + E L  L++       Y        L+  L L +  +  +FQN+R   K   P
Sbjct: 13 KISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSGP 68

>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 = 53.6 bits (128), Expect = 6e-11
 Identities = 13/65 (20%), Positives = 25/65 (38%)

Query: 46  FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105
            T EQL  L++ F   ++    +   L     L   ++  WF + R   K        ++
Sbjct: 10  KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDN 69

Query: 106 PTVPT 110
            + P+
Sbjct: 70  ASGPS 74

>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 = 52.7 bits (126), Expect = 1e-10
 Identities = 13/86 (15%), Positives = 24/86 (27%), Gaps = 9/86 (10%)

Query: 13 SSATSAKTPPVRRNRGRSPNTQTPSEDLVPESAFTYEQLVA-LENKFKTTRYLSVCERLN 71
          SS +S   P       +   T+  +E          E+++A  E      +         
Sbjct: 2  SSGSSGSNPSSSGGTTKRFRTKFTAEQK--------EKMLAFAERLGWRIQKHDDVAVEQ 53

Query: 72 LALSLSLTETQVKIWFQNRRTKWKKQ 97
                +    +KIW  N +      
Sbjct: 54 FCAETGVRRQVLKIWMHNNKNSGPSS 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	165
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.88
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.88
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.88
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.87
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.87
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.87
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.87
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.87
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.86
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.86
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.86
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.86
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.84
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.84
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.84
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.84
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.84
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.84
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.83
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.82
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.82
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.81
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.81
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.79
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.78
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.78
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.75
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.74
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.71
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.71
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.68
d1hlva1	66	DNA-binding domain of centromere binding protein B	94.66
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	91.11
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	84.5
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	83.18

>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=99.88  E-value=1.1e-23  Score=131.43  Aligned_cols=57  Identities=33%  Similarity=0.558  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      +++|+.|+.+|+.+||..|+.++||+.+++++||..|||++.+|++||||||+|+||
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            577899999999999999999999999999999999999999999999999999986

>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=99.88  E-value=1.8e-23  Score=137.59  Aligned_cols=68  Identities=43%  Similarity=0.552  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ..+.++++.|++|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+|+.....
T Consensus         4 g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   71 (77)
T d1vnda_           4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhcc
Confidence            45677788999999999999999999999999999999999999999999999999999999876543

>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=99.88  E-value=2.9e-23  Score=129.61  Aligned_cols=58  Identities=59%  Similarity=0.858  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ||+|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+||.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   58 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhccC
Confidence            5688999999999999999999999999999999999999999999999999999973

>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=99.87  E-value=4.5e-23  Score=128.30  Aligned_cols=57  Identities=49%  Similarity=0.779  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      |+.|+.|+.+|+.+||..|+.|+||+.+++++||..|||++.+|++||||||+|+||
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            577899999999999999999999999999999999999999999999999999986

>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=99.87  E-value=4.4e-23  Score=128.35  Aligned_cols=57  Identities=46%  Similarity=0.646  Sum_probs=55.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      |.|+.||.+|+.+||..|+.++||+..++++||..|||++.+|++||||||+|+||+
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            578999999999999999999999999999999999999999999999999999974

>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=99.87  E-value=4e-23  Score=132.52  Aligned_cols=60  Identities=38%  Similarity=0.590  Sum_probs=57.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +|+|++|+.+|+.+||..|+.++||+..++.+||..|||++++|+|||||||+|+|+...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            567999999999999999999999999999999999999999999999999999998653

>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=99.87  E-value=4e-23  Score=127.82  Aligned_cols=55  Identities=51%  Similarity=0.855  Sum_probs=53.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      |+.||.+|+.+||..|+.++||+..++++||..|||++++|+|||||||+|+||+
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            7899999999999999999999999999999999999999999999999999986

>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=99.87  E-value=1.8e-22  Score=132.72  Aligned_cols=64  Identities=42%  Similarity=0.551  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ..+..+++|++|+.+|+.+||..|+.++||+..++++||..|||++++|+|||||||+|+|+..
T Consensus         9 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~   72 (77)
T d1pufa_           9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHH
Confidence            3445678899999999999999999999999999999999999999999999999999999864

>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=99.86  E-value=1.4e-22  Score=129.22  Aligned_cols=61  Identities=36%  Similarity=0.632  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      +.++.|+.|+.+|+.+||..|+.++||+..++++||..|||++.+|++||||+|+|+|++.
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~   61 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   61 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcc
Confidence            4678899999999999999999999999999999999999999999999999999999864

>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=99.86  E-value=1.4e-22  Score=124.30  Aligned_cols=53  Identities=47%  Similarity=0.781  Sum_probs=51.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK   93 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k   93 (165)
                      |+|+.|+.+|+.+||..|+.++||+..++++||..|||++++|++||||||+|
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            57899999999999999999999999999999999999999999999999986

>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=99.86  E-value=3e-22  Score=128.73  Aligned_cols=63  Identities=44%  Similarity=0.590  Sum_probs=59.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100         39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM  101 (165)
Q Consensus        39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~  101 (165)
                      ++|.|+.|+..|+.+||..|+.++||+..++.+||..|||++.+|++||||||+|+|+.....
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~   64 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccch
Confidence            467899999999999999999999999999999999999999999999999999999876543

>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=99.86  E-value=1.6e-22  Score=136.11  Aligned_cols=63  Identities=46%  Similarity=0.664  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      .+.++.|+.|+.+|+.+||..|+.++||+.+++++||..|||++++|+|||||||+|+||..+
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            445678999999999999999999999999999999999999999999999999999998754

>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=99.84  E-value=2.2e-22  Score=126.42  Aligned_cols=59  Identities=39%  Similarity=0.730  Sum_probs=56.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      |+.|+.|+.+|+.+||..|..++||+..+++.||.+|||++.+|++||+|||+|+|+++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~~   60 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   60 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhcC
Confidence            57899999999999999999999999999999999999999999999999999999864

>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=99.84  E-value=1e-21  Score=125.47  Aligned_cols=62  Identities=21%  Similarity=0.297  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +.+|.|+.|+.+|+.+||..|..|+||+..++++||.++||++.+|++||||||+|+|+...
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            46788999999999999999999999999999999999999999999999999999998764

>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=99.84  E-value=9.9e-22  Score=126.28  Aligned_cols=59  Identities=39%  Similarity=0.758  Sum_probs=56.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~   98 (165)
                      ++.|++|+.+|+.+||..|+.|+||+..++++||..|||++.+|++||||+|+|+|+..
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~   60 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE   60 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhh
Confidence            56799999999999999999999999999999999999999999999999999999853

>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=99.84  E-value=2e-21  Score=126.03  Aligned_cols=60  Identities=23%  Similarity=0.386  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         40 LVPESAFTYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ++.|+.||.+|+.+||..|+. ++||+..++++||.+|||++++|++||||||+|+||...
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            467899999999999999986 689999999999999999999999999999999998753

>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=99.84  E-value=1.1e-21  Score=125.63  Aligned_cols=61  Identities=25%  Similarity=0.310  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ..++++|+.|+.+|+.+||..|..++||+..++++||.+|||++.+|++||||+|+++||.
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            4457889999999999999999999999999999999999999999999999999999875

>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=99.84  E-value=1.5e-21  Score=121.74  Aligned_cols=57  Identities=28%  Similarity=0.390  Sum_probs=55.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      |+|+.|+.+|+++||..|..++||+..++.+||.+|||++.+|++||||||+++|+.
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            578999999999999999999999999999999999999999999999999999875

>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=99.83  E-value=2.2e-21  Score=118.87  Aligned_cols=53  Identities=28%  Similarity=0.449  Sum_probs=51.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      |+.|+++|+.+||..|+.++||+..++.+||.+|||++.+|++||||||+|+|
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            68899999999999999999999999999999999999999999999999975

>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=99.82  E-value=6.2e-21  Score=123.54  Aligned_cols=61  Identities=21%  Similarity=0.226  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHH-hcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         37 SEDLVPESAFTYEQLVALENKFK-TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~-~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      ...++.|++|+.+|+.+||.+|. .++||+.+++++||.+|||++++|++||||+|+|+|+.
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            34567899999999999999997 48999999999999999999999999999999998874

>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=99.82  E-value=7.5e-21  Score=118.08  Aligned_cols=56  Identities=25%  Similarity=0.390  Sum_probs=54.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      +|+.|+.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||+|+||.
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            58999999999999999999999999999999999999999999999999999985

>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=99.81  E-value=7.2e-21  Score=126.49  Aligned_cols=61  Identities=25%  Similarity=0.354  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------CCchhhhhhhhcchhhhhhhCCC
Q psy15100         40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------LTETQVKIWFQNRRTKWKKQNPG  100 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------l~~~qV~~WFqNRR~k~kr~~~~  100 (165)
                      |++|+.|+.+|+.+||.+|+.++||+..+|++||..||               |++.+|++||||||+|+|++...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~   76 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   76 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhH
Confidence            57899999999999999999999999999999999875               99999999999999999997653

>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=99.81  E-value=4.5e-20  Score=120.89  Aligned_cols=61  Identities=23%  Similarity=0.341  Sum_probs=55.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCC
Q psy15100         45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS  105 (165)
Q Consensus        45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~  105 (165)
                      .+|.+|+.+||..|+.++||+..++++||.+|||++.+|++||||||++.|+.....+.+.
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~~~   70 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDE   70 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhccc
Confidence            4589999999999999999999999999999999999999999999999888776655544

>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=99.79  E-value=7e-20  Score=121.07  Aligned_cols=60  Identities=13%  Similarity=0.106  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         37 SEDLVPESAFTYEQLVALENKFKT----TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        37 ~~~~~~R~~~s~~Ql~~Le~~F~~----~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      .+.||.|+.|+.+|+++|+.+|+.    ++||+.+++++||.+|||++.+|+|||||+|.+.|+
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            455678999999999999999986    789999999999999999999999999999988765

>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=99.78  E-value=3.9e-20  Score=111.91  Aligned_cols=50  Identities=28%  Similarity=0.323  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100         42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR   91 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR   91 (165)
                      +|+.|+.+|+.+||..|+.++||+..++.+||.+|||++++|++||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999999999999999999999999999999999997

>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=99.78  E-value=3.1e-19  Score=116.85  Aligned_cols=57  Identities=21%  Similarity=0.248  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      +.+||.+|+.+||..|..|+||+.+++++||..|||++.+|++||+|+|+++|+...
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            456899999999999999999999999999999999999999999999999998654

>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=99.76  E-value=4.9e-19  Score=115.05  Aligned_cols=60  Identities=27%  Similarity=0.352  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100         40 LVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP   99 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~   99 (165)
                      ||+|+.|+.+|+.+||.+|..   ++||+.+++++||.++||++.+|++||+|+|+|+|+...
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            567899999999999999984   789999999999999999999999999999999997653

>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=99.75  E-value=3.3e-19  Score=117.06  Aligned_cols=56  Identities=23%  Similarity=0.245  Sum_probs=53.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC---------------------CCchhhhhhhhcchhhhhhhC
Q psy15100         43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLS---------------------LTETQVKIWFQNRRTKWKKQN   98 (165)
Q Consensus        43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------------l~~~qV~~WFqNRR~k~kr~~   98 (165)
                      |++|+++|+.+||..|+.++||+..+|+.||.+|+                     |++.+|++||+|||+++|++.
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            67899999999999999999999999999999994                     899999999999999999875

>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=99.74  E-value=3.5e-19  Score=108.38  Aligned_cols=50  Identities=24%  Similarity=0.303  Sum_probs=46.7

Q ss_pred             CHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         47 TYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        47 s~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      |.+|+.+||..|.. ++||+..++++||.+|||++++|++||||||+|+|+
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            45799999999987 689999999999999999999999999999999885

>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=99.71  E-value=1.1e-18  Score=108.73  Aligned_cols=55  Identities=24%  Similarity=0.326  Sum_probs=50.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         41 VPESAFTYEQLVALENKFKT-TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        41 ~~R~~~s~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      |.+.+++.++..+||.+|.. ++||+..++++||.+|||++++|++||||||+++|
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            45677888999999999986 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=99.71  E-value=6.5e-18  Score=105.64  Aligned_cols=54  Identities=37%  Similarity=0.439  Sum_probs=49.8

Q ss_pred             CCCCHHHHHHHHHHHHhc---CCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         44 SAFTYEQLVALENKFKTT---RYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~---~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      .+|+.+|+.+|+.+|..+   +||+.+++++||.++||++.+|++||+|+|+|.|+.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~~   59 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccccccC
Confidence            349999999999999765   699999999999999999999999999999998864

>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=99.68  E-value=3.7e-17  Score=102.76  Aligned_cols=56  Identities=20%  Similarity=0.203  Sum_probs=51.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100         40 LVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK   95 (165)
Q Consensus        40 ~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k   95 (165)
                      +++|+.|+++++.+|+.+|..   ++||+.+++.+||.++||+..||++||+|+|.|..
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            456788999999999999985   78999999999999999999999999999998754

>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=94.66  E-value=0.041  Score=33.18  Aligned_cols=47  Identities=11%  Similarity=0.244  Sum_probs=38.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100         42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR   91 (165)
Q Consensus        42 ~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR   91 (165)
                      +|..+|.++...+-..|+.++...   ..+||..+||....|..|.+|+.
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHH
Confidence            355689998888888888887555   45689999999999999999854

>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=91.11  E-value=0.29  Score=27.13  Aligned_cols=40  Identities=13%  Similarity=0.223  Sum_probs=34.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100         44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ   88 (165)
Q Consensus        44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq   88 (165)
                      ..++++|++.+.+.+....     .+.+||..+|++...|-.||-
T Consensus         4 ~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           4 RAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhCC
Confidence            4599999999999997543     277899999999999999984

>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=84.50  E-value=0.56  Score=27.36  Aligned_cols=47  Identities=9%  Similarity=-0.004  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ   97 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~   97 (165)
                      +.+.+..+|.-.|-.+.     ...+||..+|++...|+.+.+.-|.+-|..
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            45666677766665444     356789999999999999998777666553

>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=83.18  E-value=0.64  Score=27.07  Aligned_cols=46  Identities=9%  Similarity=0.060  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100         46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK   96 (165)
Q Consensus        46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr   96 (165)
                      +++.+..+|...|-...     ...++|..+|++...|+.....-|.+.|+
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            66777888877775443     46788999999999999988766666554