Citrus Sinensis ID: 035661

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-
Protein Sequence
MDIADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSNSSGWERNLAGALS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccHHcccccHHHHHHHHHHHHHHccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccEEEcccccccccccHHHHHHHccc
Coil and Loop (DISEMBL)
mdiadtqqnqkhpppnklnikKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAItcnnnsnyssatscsaekagscssfsLLHEEYhvhgndhdhdqglQIDHELFACLigngghsnssgwERNLAGALS
Flexible Loop (DISEMBL)
mdiadtqqnqkhpppnklnikkrlnQEQVRVLERsfttkkkldtelklklanqlgvparqvAVWYQNKRARWktqsleldyNTIQVKLenaladkrRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNgghsnssgwernlagals
Low Complexity Region (SEG)
MDIADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFttkkkldtelklklANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALAdkrrlekdvkllkeelrQAQEILFAKLMTSNNNNNQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSNSSGWERNLAGALS
Disordered region (IsUnstruct)
***********************************FTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLK**L***QEILF******************************************FSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNG*****************
Disordered Region (DISOPRED)
***************************QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR**********************************************************************************************************************************************
Disordered Region (DISEMBL)
*************PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCNNNSNY*************CSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSNSSGWERNLAGALS
Disordered Region (DISPRO)
**********************RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAK**********************************************************QGLQIDHELFACLIGNG**SNSSGW*******L*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDIADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLFAKLMTSNNNNNQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSNSSGWERNLAGALS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	211	2.2.26 [Sep-21-2011]
Q9FN29	156	Homeobox-leucine zipper p	yes	no	0.691	0.935	0.423	2e-30
Q10QP3	311	Homeobox-leucine zipper p	yes	no	0.469	0.318	0.474	9e-19
A2XDD6	312	Homeobox-leucine zipper p	N/A	no	0.469	0.317	0.49	1e-18
Q6Z248	269	Homeobox-leucine zipper p	no	no	0.649	0.509	0.372	8e-18
A2YWC0	269	Homeobox-leucine zipper p	N/A	no	0.649	0.509	0.372	8e-18
Q02283	272	Homeobox-leucine zipper p	no	no	0.772	0.599	0.337	8e-18
Q00466	314	Homeobox-leucine zipper p	no	no	0.725	0.487	0.362	9e-18
O23208	216	Homeobox-leucine zipper p	no	no	0.464	0.453	0.489	1e-17
A3BYC1	320	Homeobox-leucine zipper p	no	no	0.483	0.318	0.462	2e-17
Q6K498	277	Homeobox-leucine zipper p	no	no	0.431	0.328	0.472	1e-16

>sp|Q9FN29|ATB52_ARATH Homeobox-leucine zipper protein ATHB-52 OS=Arabidopsis thaliana GN=ATHB-52 PE=2 SV=1

 Score =  132 bits (332), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/184 (42%), Positives = 108/184 (58%), Gaps = 38/184 (20%)

Query: 19  NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
           N KKRL Q+QVR LE+ FT  KKL+ +LKL+L+NQLG+P RQVAVW+QNKRAR+KTQSLE
Sbjct: 10  NKKKRLTQDQVRQLEKCFTMNKKLEPDLKLQLSNQLGLPQRQVAVWFQNKRARFKTQSLE 69

Query: 79  LDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCN 138
           + + T+Q K E AL+DK +LE  V+ L++EL++A+  L                 A+  N
Sbjct: 70  VQHCTLQSKHEAALSDKAKLEHQVQFLQDELKRARNQL-----------------ALFTN 112

Query: 139 NNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSN 198
            +S   ++        GSC               D DHD  + +  EL+AC + NG  S+
Sbjct: 113 QDSPVDNSN------LGSC---------------DEDHDDQVVVFDELYACFVSNGHGSS 151

Query: 199 SSGW 202
           S+ W
Sbjct: 152 STSW 155

Probable transcription factor.
Arabidopsis thaliana (taxid: 3702)

>sp|Q10QP3|HOX13_ORYSJ Homeobox-leucine zipper protein HOX13 OS=Oryza sativa subsp. japonica GN=HOX13 PE=2 SV=1

 Score = 93.6 bits (231), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 47/99 (47%), Positives = 64/99 (64%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K+RL  EQVR LERSF T  KLD + K ++A  LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct: 73  KRRLALEQVRALERSFDTDNKLDPDRKARIARDLGLQPRQVAVWFQNRRARWKTKQLERD 132

Query: 81  YNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAK 119
           +  ++ + +   AD   L +D   L  E+R+ +E L  K
Sbjct: 133 FAALRARHDALRADCDALRRDKDALAAEIRELREKLPTK 171

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2XDD6|HOX13_ORYSI Homeobox-leucine zipper protein HOX13 OS=Oryza sativa subsp. indica GN=HOX13 PE=2 SV=2

 Score = 93.2 bits (230), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 49/100 (49%), Positives = 66/100 (66%), Gaps = 1/100 (1%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K+RL  EQVR LERSF T  KLD + K ++A  LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct: 73  KRRLALEQVRALERSFDTDNKLDPDRKARIARDLGLQPRQVAVWFQNRRARWKTKQLERD 132

Query: 81  YNTIQVKLENAL-ADKRRLEKDVKLLKEELRQAQEILFAK 119
           +  ++ +  +AL AD   L +D   L  E+R+ +E L  K
Sbjct: 133 FAALRAQHNDALRADCDALRRDKDALAAEIRELREKLPTK 172

Probable transcription factor.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q6Z248|HOX20_ORYSJ Homeobox-leucine zipper protein HOX20 OS=Oryza sativa subsp. japonica GN=HOX20 PE=2 SV=1

 Score = 90.5 bits (223), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 51/137 (37%), Positives = 79/137 (57%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K+RL+ EQVR LERSF T+ KL+ E K +LA  LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct: 44  KRRLSVEQVRALERSFETENKLEPERKARLARDLGLQPRQVAVWFQNRRARWKTKQLERD 103

Query: 81  YNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCNNN 140
           Y  ++   +   AD   L +D   L  E+++ +  L  +   ++ ++ +E  +    + +
Sbjct: 104 YAALRQSYDALRADHDALRRDKDALLAEIKELKGKLGDEDAAASFSSVKEEEDPAASDAD 163

Query: 141 SNYSSATSCSAEKAGSC 157
              + A   S+E   S 
Sbjct: 164 PPATGAPQGSSESDSSA 180

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2YWC0|HOX20_ORYSI Homeobox-leucine zipper protein HOX20 OS=Oryza sativa subsp. indica GN=HOX20 PE=2 SV=1

 Score = 90.5 bits (223), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 51/137 (37%), Positives = 79/137 (57%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K+RL+ EQVR LERSF T+ KL+ E K +LA  LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct: 44  KRRLSVEQVRALERSFETENKLEPERKARLARDLGLQPRQVAVWFQNRRARWKTKQLERD 103

Query: 81  YNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCNNN 140
           Y  ++   +   AD   L +D   L  E+++ +  L  +   ++ ++ +E  +    + +
Sbjct: 104 YAALRQSYDALRADHDALRRDKDALLAEIKELKGKLGDEDAAASFSSVKEEEDPAASDAD 163

Query: 141 SNYSSATSCSAEKAGSC 157
              + A   S+E   S 
Sbjct: 164 PPATGAPQGSSESDSSA 180

Probable transcription factor.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q02283|HAT5_ARATH Homeobox-leucine zipper protein HAT5 OS=Arabidopsis thaliana GN=HAT5 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 61/181 (33%), Positives = 94/181 (51%), Gaps = 18/181 (9%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K+RL  EQV +LE+SF T+ KL+ E K +LA +LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct: 69  KRRLTTEQVHLLEKSFETENKLEPERKTQLAKKLGLQPRQVAVWFQNRRARWKTKQLERD 128

Query: 81  YNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEA--------- 131
           Y+ ++   +  L++   +  D   L+ E+    E L  K  T+N    Q           
Sbjct: 129 YDLLKSTYDQLLSNYDSIVMDNDKLRSEVTSLTEKLQGKQETANEPPGQVPEPNQLDPVY 188

Query: 132 VEAITCNNNSNYSSATSCSA-------EKAGSCSSF--SLLHEEYHVHGNDHDHDQGLQI 182
           + A         SS +  SA       +   SC S+  S++  + + + +DHD+D+    
Sbjct: 189 INAAAIKTEDRLSSGSVGSAVLDDDAPQLLDSCDSYFPSIVPIQDNSNASDHDNDRSCFA 248

Query: 183 D 183
           D
Sbjct: 249 D 249

Probable transcription activator involved in leaf development. Binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.

Arabidopsis thaliana (taxid: 3702)

>sp|Q00466|HAT7_ARATH Homeobox-leucine zipper protein HAT7 OS=Arabidopsis thaliana GN=HAT7 PE=2 SV=4

 Score = 90.1 bits (222), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 63/174 (36%), Positives = 92/174 (52%), Gaps = 21/174 (12%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           KKRLN EQVR LE+SF    KL+ E K++LA  LG+  RQ+A+W+QN+RARWKT+ LE D
Sbjct: 116 KKRLNLEQVRALEKSFELGNKLEPERKMQLAKALGLQPRQIAIWFQNRRARWKTKQLERD 175

Query: 81  YNTIQVKL-------ENALADKRRLEKDVKLLKEELRQAQEIL---FAKLMTSNNNNNQE 130
           Y++++ +        ++ LA  ++L  ++  LK+  R+    +   FA+   SNN + + 
Sbjct: 176 YDSLKKQFDVLKSDNDSLLAHNKKLHAELVALKKHDRKESAKIKREFAEASWSNNGSTEN 235

Query: 131 AVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDH----DHDQGL 180
                  N+N+N S A   S  K    SS             DH    D DQG 
Sbjct: 236 -------NHNNNSSDANHVSMIKDLFPSSIRSATATTTSTHIDHQIVQDQDQGF 282

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|O23208|ATB40_ARATH Homeobox-leucine zipper protein ATHB-40 OS=Arabidopsis thaliana GN=ATHB-40 PE=2 SV=3

 Score = 89.7 bits (221), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 48/98 (48%), Positives = 68/98 (69%)

Query: 16  NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           N L  K++L  EQV +LE SF  + KL++E K +LA +LG+  RQVAVW+QN+RARWK +
Sbjct: 51  NGLFRKRKLTDEQVNMLEMSFGDEHKLESERKDRLAAELGLDPRQVAVWFQNRRARWKNK 110

Query: 76  SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQ 113
            LE +YN ++   +N + DK RLE +V  LKE+L  A+
Sbjct: 111 RLEEEYNKLKNSHDNVVVDKCRLESEVIQLKEQLYDAE 148

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|A3BYC1|HOX25_ORYSJ Homeobox-leucine zipper protein HOX25 OS=Oryza sativa subsp. japonica GN=HOX25 PE=2 SV=2

 Score = 89.0 bits (219), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 50/108 (46%), Positives = 70/108 (64%), Gaps = 6/108 (5%)

Query: 21  KKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79
           K+RL  EQVR LERSF   K+KL+ E K +LA +LG+  RQVAVW+QN+RARWKT+ LEL
Sbjct: 83  KRRLTAEQVRALERSFEEEKRKLEPERKSELARRLGIAPRQVAVWFQNRRARWKTKQLEL 142

Query: 80  DYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNN 127
           D++ ++   +  LA +  L  D     E LR +Q IL  + + +N  +
Sbjct: 143 DFDRLRAAHDELLAGRTALAAD----NESLR-SQVILLTEKLQANGKS 185

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6K498|HOX4_ORYSJ Homeobox-leucine zipper protein HOX4 OS=Oryza sativa subsp. japonica GN=HOX4 PE=1 SV=1

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/91 (47%), Positives = 60/91 (65%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K+RL+ EQVR LERSF  + KL+ E K +LA  LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct: 52  KRRLSVEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWKTKQLERD 111

Query: 81  YNTIQVKLENALADKRRLEKDVKLLKEELRQ 111
           Y  ++   ++   D   L +D   L  E+++
Sbjct: 112 YAALRHSYDSLRLDHDALRRDKDALLAEIKE 142

Probable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. May be involved in the regulation of gibberellin signaling.

Oryza sativa subsp. japonica (taxid: 39947)

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	211
224121628	170	predicted protein [Populus trichocarpa]	0.796	0.988	0.538	9e-37
225443586	171	PREDICTED: homeobox-leucine zipper prote	0.715	0.883	0.443	3e-33
302142956	449	unnamed protein product [Vitis vinifera]	0.616	0.289	0.528	1e-29
225461543	161	PREDICTED: homeobox-leucine zipper prote	0.488	0.639	0.630	4e-29
356517080	200	PREDICTED: homeobox-leucine zipper prote	0.734	0.775	0.444	4e-29
15239522	156	homeobox-leucine zipper protein ATHB-52	0.691	0.935	0.423	9e-29
255639145	197	unknown [Glycine max]	0.658	0.705	0.486	1e-28
297792823	156	ATHB52 [Arabidopsis lyrata subsp. lyrata	0.691	0.935	0.445	2e-28
224117104	81	predicted protein [Populus trichocarpa]	0.374	0.975	0.759	4e-28
255564575	162	hypothetical protein RCOM_0651000 [Ricin	0.725	0.944	0.404	2e-23

>gi|224121628|ref|XP_002330748.1| predicted protein [Populus trichocarpa] gi|118486271|gb|ABK94977.1| unknown [Populus trichocarpa] gi|222872524|gb|EEF09655.1| predicted protein [Populus trichocarpa]

 Score =  159 bits (401), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 105/195 (53%), Positives = 134/195 (68%), Gaps = 27/195 (13%)

Query: 1   MDIADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQ 60
           MD  ++Q  QK     K N KKRL ++QVR+LER+FTT KKL+ ELK++LANQLGVP RQ
Sbjct: 1   MDFFNSQTQQKQQYLPKHNNKKRLTEDQVRLLERTFTTNKKLEPELKVQLANQLGVPPRQ 60

Query: 61  VAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL 120
           +A+WYQNKRARWKTQSLELDYNT+QV+LENALAD+RRLE++V  L+EEL QAQ+++FA  
Sbjct: 61  IAIWYQNKRARWKTQSLELDYNTLQVRLENALADRRRLEREVVRLQEELWQAQQMVFA-- 118

Query: 121 MTSNNNNNQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGL 180
             +     Q AV         N+S  +SC  +  GS S    LHE   V+G      + L
Sbjct: 119 -VNQETAAQPAV---------NFSCNSSC--DDRGSSS----LHE--GVNG------EVL 154

Query: 181 QIDHELFACLIGNGG 195
           Q++ EL+ACL G GG
Sbjct: 155 QLE-ELYACLYGAGG 168

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443586|ref|XP_002273463.1| PREDICTED: homeobox-leucine zipper protein ATHB-52 [Vitis vinifera] gi|147785778|emb|CAN64250.1| hypothetical protein VITISV_002432 [Vitis vinifera]

 Score =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 83/187 (44%), Positives = 113/187 (60%), Gaps = 36/187 (19%)

Query: 8   QNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67
           Q +KH P      KKRL ++QVR+LE SF    KLD++ KL+LA +LG+P RQVA+WYQN
Sbjct: 7   QARKHQPKFS---KKRLTKDQVRLLETSFDLNNKLDSDRKLQLAQELGIPPRQVAIWYQN 63

Query: 68  KRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNN 127
           KRARWK QSLEL+YN +Q++L+ AL DKR+LEK+V  LK+EL++AQE+L           
Sbjct: 64  KRARWKNQSLELEYNALQLRLDAALGDKRKLEKEVDRLKQELQKAQEVL----------- 112

Query: 128 NQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELF 187
                  ++CN   +  ++ S S ++ GS S                  D  L +D EL+
Sbjct: 113 -------LSCNVTYSTLTSLSTSCDEDGSSSLLG---------------DSKLGLDKELY 150

Query: 188 ACLIGNG 194
           ACLIG G
Sbjct: 151 ACLIGGG 157

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142956|emb|CBI20251.3| unnamed protein product [Vitis vinifera]

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 74/140 (52%), Positives = 95/140 (67%), Gaps = 10/140 (7%)

Query: 8   QNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67
           Q+QKH        KKRL Q+QVR+LE SF   KKL+ E KL LA +LGVP RQVA+WYQN
Sbjct: 7   QHQKH--------KKRLTQDQVRLLETSFDHGKKLEPERKLHLARELGVPPRQVAIWYQN 58

Query: 68  KRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNN 127
           KRARWKTQ+LELDYN I+V+LE+AL +KRRLE+DV  L+ EL +A E+L A  +   N N
Sbjct: 59  KRARWKTQNLELDYNVIRVRLEHALIEKRRLERDVIRLQGELEKAHEMLHA--LNYANPN 116

Query: 128 NQEAVEAITCNNNSNYSSAT 147
               V  +  + + +   +T
Sbjct: 117 PPPIVSTVLSSISCDEGGST 136

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461543|ref|XP_002282682.1| PREDICTED: homeobox-leucine zipper protein ATHB-52-like [Vitis vinifera]

 Score =  134 bits (336), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 70/111 (63%), Positives = 85/111 (76%), Gaps = 8/111 (7%)

Query: 8   QNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN 67
           Q+QKH        KKRL Q+QVR+LE SF   KKL+ E KL LA +LGVP RQVA+WYQN
Sbjct: 7   QHQKH--------KKRLTQDQVRLLETSFDHGKKLEPERKLHLARELGVPPRQVAIWYQN 58

Query: 68  KRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFA 118
           KRARWKTQ+LELDYN I+V+LE+AL +KRRLE+DV  L+ EL +A E+L A
Sbjct: 59  KRARWKTQNLELDYNVIRVRLEHALIEKRRLERDVIRLQGELEKAHEMLHA 109

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517080|ref|XP_003527218.1| PREDICTED: homeobox-leucine zipper protein ATHB-52-like [Glycine max]

 Score =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 80/180 (44%), Positives = 116/180 (64%), Gaps = 25/180 (13%)

Query: 19  NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
           N KKRL ++QV +LE+ F++  KL+ E K  LANQLG+P RQVA+WYQNKRARWKTQSLE
Sbjct: 26  NNKKRLTEDQVAILEKCFSSNMKLEPEQKFHLANQLGLPPRQVAIWYQNKRARWKTQSLE 85

Query: 79  LDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCN 138
           +D+  +Q +LEN +A+K++LEKDV+ LK EL++AQE+L   L+T++             +
Sbjct: 86  VDHGVLQARLENVVAEKKQLEKDVERLKAELKKAQEML---LITNSVKGG---------D 133

Query: 139 NNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHD------QGLQIDHELFACLIG 192
           +N+N +   S S E+ GS S   L    YH     H H+      + +Q++ EL+A  +G
Sbjct: 134 HNNNNACEFSTSFEEGGS-SGVVLDDATYH-----HHHECWQSGGEVMQVE-ELYAYFVG 186

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239522|ref|NP_200209.1| homeobox-leucine zipper protein ATHB-52 [Arabidopsis thaliana] gi|75262744|sp|Q9FN29.1|ATB52_ARATH RecName: Full=Homeobox-leucine zipper protein ATHB-52; AltName: Full=HD-ZIP protein ATHB-52; AltName: Full=Homeodomain transcription factor ATHB-52 gi|10177260|dbj|BAB10728.1| unnamed protein product [Arabidopsis thaliana] gi|54261707|gb|AAV31157.1| At5g53980 [Arabidopsis thaliana] gi|61656133|gb|AAX49369.1| At5g53980 [Arabidopsis thaliana] gi|110738303|dbj|BAF01080.1| hypothetical protein [Arabidopsis thaliana] gi|332009052|gb|AED96435.1| homeobox-leucine zipper protein ATHB-52 [Arabidopsis thaliana]

 Score =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 78/184 (42%), Positives = 108/184 (58%), Gaps = 38/184 (20%)

Query: 19  NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
           N KKRL Q+QVR LE+ FT  KKL+ +LKL+L+NQLG+P RQVAVW+QNKRAR+KTQSLE
Sbjct: 10  NKKKRLTQDQVRQLEKCFTMNKKLEPDLKLQLSNQLGLPQRQVAVWFQNKRARFKTQSLE 69

Query: 79  LDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCN 138
           + + T+Q K E AL+DK +LE  V+ L++EL++A+  L                 A+  N
Sbjct: 70  VQHCTLQSKHEAALSDKAKLEHQVQFLQDELKRARNQL-----------------ALFTN 112

Query: 139 NNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSN 198
            +S   ++        GSC               D DHD  + +  EL+AC + NG  S+
Sbjct: 113 QDSPVDNSN------LGSC---------------DEDHDDQVVVFDELYACFVSNGHGSS 151

Query: 199 SSGW 202
           S+ W
Sbjct: 152 STSW 155

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255639145|gb|ACU19872.1| unknown [Glycine max]

 Score =  132 bits (332), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 74/152 (48%), Positives = 102/152 (67%), Gaps = 13/152 (8%)

Query: 19  NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
           N KKRL ++QV +LE+ F++  KL+ E K  LANQLG+P RQVA+WYQNKRARWKTQ LE
Sbjct: 26  NNKKRLTEDQVAILEKCFSSNMKLEPEQKFHLANQLGLPPRQVAIWYQNKRARWKTQRLE 85

Query: 79  LDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCN 138
           +DY  +Q +LEN +A+K++LEKDV+ LK EL++AQE+L   L+T++             +
Sbjct: 86  VDYGVLQARLENVVAEKKQLEKDVERLKAELKKAQEML---LITNSVKGG---------D 133

Query: 139 NNSNYSSATSCSAEKAGSCSSFSLLHEEYHVH 170
           +N+N +   S S E+ GS S   L    YH H
Sbjct: 134 HNNNNACEFSTSFEEGGS-SGVVLDDATYHHH 164

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792823|ref|XP_002864296.1| ATHB52 [Arabidopsis lyrata subsp. lyrata] gi|297310131|gb|EFH40555.1| ATHB52 [Arabidopsis lyrata subsp. lyrata]

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 82/184 (44%), Positives = 109/184 (59%), Gaps = 38/184 (20%)

Query: 19  NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
           N KKRL QEQVR LE+ FT  KKL+ +LKL+L+NQLG+P RQVAVW+QNKRAR KTQSLE
Sbjct: 10  NKKKRLTQEQVRQLEKCFTVNKKLEPDLKLQLSNQLGLPQRQVAVWFQNKRARSKTQSLE 69

Query: 79  LDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKLMTSNNNNNQEAVEAITCN 138
           + + T+Q KLE AL+DK +LE  V+ L++E+++ +  L   L T     NQ++       
Sbjct: 70  VQHCTLQSKLEAALSDKAKLEHQVQFLQDEVKRTRNQL--ALFT-----NQDSPV----- 117

Query: 139 NNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGNDHDHDQGLQIDHELFACLIGNGGHSN 198
           NNSN            GSC               D  HD  + +  EL+AC + NG  S+
Sbjct: 118 NNSNL-----------GSC---------------DEGHDDQVVVFDELYACFVSNGHGSS 151

Query: 199 SSGW 202
           S+ W
Sbjct: 152 STSW 155

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224117104|ref|XP_002317477.1| predicted protein [Populus trichocarpa] gi|222860542|gb|EEE98089.1| predicted protein [Populus trichocarpa]

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 60/79 (75%), Positives = 72/79 (91%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
          KKRL  +QVR+LER+FTT KKL+ ELK++LANQLGVP RQ+A+WYQNKRARWKTQSLELD
Sbjct: 3  KKRLTHDQVRLLERTFTTTKKLEPELKVQLANQLGVPPRQIAIWYQNKRARWKTQSLELD 62

Query: 81 YNTIQVKLENALADKRRLE 99
          YN++  KLE+ALAD+RRLE
Sbjct: 63 YNSLHAKLEDALADRRRLE 81

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564575|ref|XP_002523283.1| hypothetical protein RCOM_0651000 [Ricinus communis] gi|223537496|gb|EEF39122.1| hypothetical protein RCOM_0651000 [Ricinus communis]

 Score =  115 bits (287), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/210 (40%), Positives = 112/210 (53%), Gaps = 57/210 (27%)

Query: 1   MDIADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQ 60
           MD   TQ  Q H P  K + KKRL Q+QV                               
Sbjct: 1   MDFFHTQTQQIHTP--KHSNKKRLTQDQV------------------------------- 27

Query: 61  VAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFA-- 118
            A+WYQNKRARWKTQSLEL+YNT+QVKLENAL DK+RLEK+V  L+EELR+AQE++FA  
Sbjct: 28  -AIWYQNKRARWKTQSLELEYNTLQVKLENALIDKKRLEKEVMQLREELRKAQEMVFAFN 86

Query: 119 ------KLMTSNNNNNQEAVEAITCNNNSNYSSATSCSAEKAGSCSSFSLLHEEYHVHGN 172
                       ++++          N +N S  +SC  ++ GS S    LHE+  V+G 
Sbjct: 87  QRVIIPHHQQQQHHHHHPLPLPPHSLNINNVSCNSSC--DEGGSTS----LHED--VNG- 137

Query: 173 DHDHDQGLQIDHELFACLIGNGGHSNSSGW 202
                + LQ+D EL+ACL+G+ G +  S W
Sbjct: 138 -----EVLQLD-ELYACLLGSSGGAAGSTW 161

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

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	211
TAIR|locus:2154724	156	HB52 "homeobox protein 52" [Ar	0.355	0.480	0.546	6e-22
TAIR|locus:2102107	286	HB20 "homeobox protein 20" [Ar	0.791	0.583	0.287	6.8e-13
TAIR|locus:2140055	294	HB16 "homeobox protein 16" [Ar	0.502	0.360	0.333	7.6e-13
TAIR|locus:2150901	314	HB-3 "homeobox 3" [Arabidopsis	0.720	0.484	0.317	1.1e-12
TAIR|locus:2079542	235	HB-12 "homeobox 12" [Arabidops	0.350	0.314	0.432	1.2e-12
TAIR|locus:2205075	294	ATHB13 [Arabidopsis thaliana (	0.559	0.401	0.349	1.7e-12
TAIR|locus:2084228	272	HB-1 "homeobox 1" [Arabidopsis	0.516	0.400	0.348	6e-12
TAIR|locus:2062754	258	HB-7 "homeobox 7" [Arabidopsis	0.398	0.325	0.376	1e-11
TAIR|locus:2115215	216	HB40 "homeobox protein 40" [Ar	0.364	0.356	0.415	4.5e-11
TAIR|locus:2168225	312	HB5 "homeobox protein 5" [Arab	0.308	0.208	0.446	8.4e-11

TAIR|locus:2154724 HB52 "homeobox protein 52" [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 6.0e-22, Sum P(2) = 6.0e-22
 Identities = 41/75 (54%), Positives = 51/75 (68%)

Query:    19 NIKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLE 78
             N KKRL Q+QVR LE+ F              +NQLG+P RQVAVW+QNKRAR+KTQSLE
Sbjct:    10 NKKKRLTQDQVRQLEKCFTMNKKLEPDLKLQLSNQLGLPQRQVAVWFQNKRARFKTQSLE 69

Query:    79 LDYNTIQVKLENALA 93
             + + T+Q K E AL+
Sbjct:    70 VQHCTLQSKHEAALS 84

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009637 "response to blue light" evidence=IEP

GO:0009646 "response to absence of light" evidence=IEP

TAIR|locus:2102107 HB20 "homeobox protein 20" [Arabidopsis thaliana (taxid:3702)]

 Score = 172 (65.6 bits), Expect = 6.8e-13, P = 6.8e-13
 Identities = 52/181 (28%), Positives = 82/181 (45%)

Query:    21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLELD 80
             KKRL  EQV+ LE+SF              A  LG+  RQ+A+W+QN+RARWKT+ LE D
Sbjct:    88 KKRLQLEQVKALEKSFELGNKLEPERKIQLAKALGMQPRQIAIWFQNRRARWKTRQLERD 147

Query:    81 YNTIQVKLENALAXXXXXXXXXXXXXXXXXQAQEILFAKLMTSNNNN--NQEAVEAITCN 138
             Y++++ + E+  +                    E++  K    N  N   +EA EA   N
Sbjct:   148 YDSLKKQFESLKSDNASLLAYNKKLLA------EVMALKNKECNEGNIVKREA-EASWSN 200

Query:   139 NNSNYSSAT-SCSAEKAGSCSSFSLLHEEY----HVHGNDHDHDQGLQIDHELFACLIGN 193
             N S  +S+  +    +    +  + + + +        +D DH Q  +I  E   C + N
Sbjct:   201 NGSTENSSDINLEMPRETITTHVNTIKDLFPSSIRSSAHDDDHHQNHEIVQEESLCNMFN 260

Query:   194 G 194
             G
Sbjct:   261 G 261

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

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009733 "response to auxin stimulus" evidence=IEP

GO:0000041 "transition metal ion transport" evidence=RCA

TAIR|locus:2140055 HB16 "homeobox protein 16" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 7.6e-13, Sum P(2) = 7.6e-13
 Identities = 38/114 (33%), Positives = 58/114 (50%)

Query:    21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLELD 80
             K+RL  +QV+ LE++F              A +LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct:    60 KRRLKVDQVKALEKNFELENKLEPERKTKLAQELGLQPRQVAVWFQNRRARWKTKQLEKD 119

Query:    81 YNTIQVKLENALAXXXXXXXXXXXXXXXXXQAQEI--LFAKLMTSNNNNNQEAV 132
             Y  ++ + ++                      QEI  + AK+    +NNN +A+
Sbjct:   120 YGVLKGQYDSL------RHNFDSLRRDNDSLLQEISKIKAKVNGEEDNNNNKAI 167

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009637 "response to blue light" evidence=IMP

GO:0030308 "negative regulation of cell growth" evidence=IMP

GO:0048510 "regulation of timing of transition from vegetative to reproductive phase" evidence=IMP

GO:0048573 "photoperiodism, flowering" evidence=RCA;IMP

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

TAIR|locus:2150901 HB-3 "homeobox 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 172 (65.6 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 55/173 (31%), Positives = 76/173 (43%)

Query:    21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLELD 80
             KKRLN EQVR LE+SF              A  LG+  RQ+A+W+QN+RARWKT+ LE D
Sbjct:   116 KKRLNLEQVRALEKSFELGNKLEPERKMQLAKALGLQPRQIAIWFQNRRARWKTKQLERD 175

Query:    81 YNTIQ-----VKLENALAXXXXXXXXXXXXXXXXXQAQEIL-----FAKLMTSNNNNNQE 130
             Y++++     +K +N                      +E       FA+   SNN + + 
Sbjct:   176 YDSLKKQFDVLKSDNDSLLAHNKKLHAELVALKKHDRKESAKIKREFAEASWSNNGSTEN 235

Query:   131 AVEAITCNNNSNYSSATSCSAEK---AGSCSSFSLLHEEYHV-HGNDHDHDQG 179
                    N+N+N S A   S  K     S  S +      H+ H    D DQG
Sbjct:   236 -------NHNNNSSDANHVSMIKDLFPSSIRSATATTTSTHIDHQIVQDQDQG 281

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

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

TAIR|locus:2079542 HB-12 "homeobox 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 32/74 (43%), Positives = 45/74 (60%)

Query:    17 KLNIKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQS 76
             K N +KR ++EQ++ LE  F              A +LG+  RQVA+W+QNKRARWKT+ 
Sbjct:    27 KSNNQKRFSEEQIKSLELIFESETRLEPRKKVQVARELGLQPRQVAIWFQNKRARWKTKQ 86

Query:    77 LELDYNTIQVKLEN 90
             LE +YNT++    N
Sbjct:    87 LEKEYNTLRANYNN 100

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA

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

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

GO:0009651 "response to salt stress" evidence=IGI;RCA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP;RCA;IMP

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

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009615 "response to virus" evidence=IEP

GO:0006970 "response to osmotic stress" evidence=IEP

TAIR|locus:2205075 ATHB13 [Arabidopsis thaliana (taxid:3702)]

 Score = 169 (64.5 bits), Expect = 1.7e-12, P = 1.7e-12
 Identities = 44/126 (34%), Positives = 67/126 (53%)

Query:    21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLELD 80
             K+RLN EQV+ LE++F              A  LG+  RQ+A+W+QN+RARWKT+ LE D
Sbjct:    86 KRRLNMEQVKTLEKNFELGNKLEPERKMQLARALGLQPRQIAIWFQNRRARWKTKQLEKD 145

Query:    81 YNTIQVKLENALAXXXXXXXXXXXXXXXXXQAQEI-LFAKLMTSNNNNNQEAVEAITCNN 139
             Y+T++ + +   A                 QA+ + L  +  T + N N+E  E  +C+N
Sbjct:   146 YDTLKRQFDTLKAENDLLQTHNQKL-----QAEIMGLKNREQTESINLNKET-EG-SCSN 198

Query:   140 NSNYSS 145
              S+ SS
Sbjct:   199 RSDNSS 204

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

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

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009744 "response to sucrose stimulus" evidence=IMP

GO:0009965 "leaf morphogenesis" evidence=IMP

GO:0048826 "cotyledon morphogenesis" evidence=IMP

TAIR|locus:2084228 HB-1 "homeobox 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 6.0e-12, P = 6.0e-12
 Identities = 38/109 (34%), Positives = 52/109 (47%)

Query:    21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLELD 80
             K+RL  EQV +LE+SF              A +LG+  RQVAVW+QN+RARWKT+ LE D
Sbjct:    69 KRRLTTEQVHLLEKSFETENKLEPERKTQLAKKLGLQPRQVAVWFQNRRARWKTKQLERD 128

Query:    81 YNTIQVKLENALAXXXXXXXXXXXXXXXXXQAQEILFAKLMTSNNNNNQ 129
             Y+ ++   +  L+                    E L  K  T+N    Q
Sbjct:   129 YDLLKSTYDQLLSNYDSIVMDNDKLRSEVTSLTEKLQGKQETANEPPGQ 177

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

GO:0003677 "DNA binding" evidence=IEA;IDA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009637 "response to blue light" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

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

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

GO:0015996 "chlorophyll catabolic process" evidence=RCA

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0009965 "leaf morphogenesis" evidence=IMP

TAIR|locus:2062754 HB-7 "homeobox 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 32/85 (37%), Positives = 48/85 (56%)

Query:     6 TQQNQKHPPPNKLNIKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWY 65
             T +  K    NK N ++R + EQ++ LE  F              A +LG+  RQVA+W+
Sbjct:    19 TMKKMKKSNHNKNN-QRRFSDEQIKSLEMMFESETRLEPRKKVQLARELGLQPRQVAIWF 77

Query:    66 QNKRARWKTQSLELDYNTIQVKLEN 90
             QNKRARWK++ LE +YN ++   +N
Sbjct:    78 QNKRARWKSKQLETEYNILRQNYDN 102

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

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

GO:0009409 "response to cold" evidence=RCA

GO:0009414 "response to water deprivation" evidence=IEP;RCA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP;RCA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=IGI;RCA

GO:0042538 "hyperosmotic salinity response" evidence=RCA

TAIR|locus:2115215 HB40 "homeobox protein 40" [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 32/77 (41%), Positives = 45/77 (58%)

Query:    16 NKLNIKKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQ 75
             N L  K++L  EQV +LE SF              A +LG+  RQVAVW+QN+RARWK +
Sbjct:    51 NGLFRKRKLTDEQVNMLEMSFGDEHKLESERKDRLAAELGLDPRQVAVWFQNRRARWKNK 110

Query:    76 SLELDYNTIQVKLENAL 92
              LE +YN ++   +N +
Sbjct:   111 RLEEEYNKLKNSHDNVV 127

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

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

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

GO:0009733 "response to auxin stimulus" evidence=IEP

TAIR|locus:2168225 HB5 "homeobox protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 8.4e-11, P = 8.4e-11
 Identities = 29/65 (44%), Positives = 41/65 (63%)

Query:    21 KKRLNQEQVRVLERSFXXXXXXXXXXXXXXANQLGVPARQVAVWYQNKRARWKTQSLELD 80
             K+RL  EQV+ LE++F              A +LG+  RQVA+W+QN+RARWKT+ LE D
Sbjct:    73 KRRLGVEQVKALEKNFEIDNKLEPERKVKLAQELGLQPRQVAIWFQNRRARWKTKQLERD 132

Query:    81 YNTIQ 85
             Y  ++
Sbjct:   133 YGVLK 137

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

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

GO:0009787 "regulation of abscisic acid mediated signaling pathway" evidence=NAS

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

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IMP;IDA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=TAS

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.146.127.1 SubName- Full=Putative uncharacterized protein; (79 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	211
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-13
smart00389	57	smart00389, HOX, Homeodomain	5e-13
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	5e-12
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	1e-06

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

 Score = 62.9 bits (154), Expect = 1e-13
 Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          +KR     EQ+  LE+ F   +    E + +LA +LG+  RQV VW+QN+RA+WK
Sbjct: 2  RKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWK 56

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 61.1 bits (149), Expect = 5e-13
 Identities = 21/53 (39%), Positives = 31/53 (58%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          +     EQ+  LE+ F        E + +LA +LG+  RQV VW+QN+RA+WK
Sbjct: 5  RTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. 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 = 58.4 bits (142), Expect = 5e-12
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          + R   EQ+  LE+ F        E + +LA +LG+  RQV +W+QN+RA+ K   
Sbjct: 4  RTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

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

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 20/56 (35%), Positives = 33/56 (58%)

Query: 21  KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
           ++R   EQ+ VLER F       +  ++KL+  L +P + V +W+QNKRA+ K + 
Sbjct: 55  RRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	211
KOG0483	198	consensus Transcription factor HEX, contains HOX a	99.83
KOG0489	261	consensus Transcription factor zerknullt and relat	99.76
KOG0488	309	consensus Transcription factor BarH and related HO	99.71
KOG0843	197	consensus Transcription factor EMX1 and related HO	99.7
KOG0842	307	consensus Transcription factor tinman/NKX2-3, cont	99.69
KOG2251	228	consensus Homeobox transcription factor [Transcrip	99.68
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.68
KOG0487	308	consensus Transcription factor Abd-B, contains HOX	99.67
KOG0484	125	consensus Transcription factor PHOX2/ARIX, contain	99.67
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.66
KOG0494	332	consensus Transcription factor CHX10 and related H	99.64
KOG0850	245	consensus Transcription factor DLX and related pro	99.63
KOG0485	268	consensus Transcription factor NKX-5.1/HMX1, conta	99.59
KOG0848	317	consensus Transcription factor Caudal, contains HO	99.59
KOG0492	246	consensus Transcription factor MSH, contains HOX d	99.58
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.57
KOG0493	342	consensus Transcription factor Engrailed, contains	99.57
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.54
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.54
KOG3802	398	consensus Transcription factor OCT-1, contains POU	99.51
COG5576	156	Homeodomain-containing transcription factor [Trans	99.47
KOG0844	408	consensus Transcription factor EVX1, contains HOX	99.42
KOG0491	194	consensus Transcription factor BSH, contains HOX d	99.4
KOG0847	288	consensus Transcription factor, contains HOX domai	99.26
KOG0486	351	consensus Transcription factor PTX1, contains HOX	99.2
KOG0490	235	consensus Transcription factor, contains HOX domai	99.16
KOG0849	354	consensus Transcription factor PRD and related pro	99.05
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	99.04
KOG0775	304	consensus Transcription factor SIX and related HOX	98.85
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.4
KOG2252	558	consensus CCAAT displacement protein and related h	98.39
KOG0774	334	consensus Transcription factor PBX and related HOX	98.25
KOG0490	235	consensus Transcription factor, contains HOX domai	98.12
KOG1146	1406	consensus Homeobox protein [General function predi	97.43
KOG0773	342	consensus Transcription factor MEIS1 and related H	96.68
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.54
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	95.76
PRK09413	121	IS2 repressor TnpA; Reviewed	94.75
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.72
KOG3623	1007	consensus Homeobox transcription factor SIP1 [Tran	94.28
smart00340	44	HALZ homeobox associated leucin zipper.	92.43
smart00338	65	BRLZ basic region leucin zipper.	88.22
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	87.26
KOG4571	294	consensus Activating transcription factor 4 [Trans	86.63
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	83.63
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	82.48
KOG3119	269	consensus Basic region leucine zipper transcriptio	82.14
PRK00888	105	ftsB cell division protein FtsB; Reviewed	81.37
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	80.48

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]

Probab=99.83  E-value=8.9e-21  Score=157.67  Aligned_cols=102  Identities=45%  Similarity=0.720  Sum_probs=95.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHH
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKR   96 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~   96 (211)
                      .++++.+||.+|+..||+.|+...++.+.++..||++|||.+|||+|||||||+|||.++.+.++..++..++.+..++.
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~  129 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND  129 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Q 035661           97 RLEKDVKLLKEELRQAQEILFA  118 (211)
Q Consensus        97 ~l~~e~~~l~~e~~~~~~~l~~  118 (211)
                      +|++++..|..++......++.
T Consensus       130 ~Lq~e~~eL~~~~~~~~~~~~~  151 (198)
T KOG0483|consen  130 RLQSEVQELVAELSSLKREMQK  151 (198)
T ss_pred             HHHHHHHHHHHHHhhhhhhhcc
Confidence            9999999999998877665554

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]

Probab=99.76  E-value=4.1e-19  Score=154.13  Aligned_cols=64  Identities=25%  Similarity=0.542  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ...+.||.||.||..|+.+||+.|+.++|+++.+|.+||..|+|++|||||||||||+||||..
T Consensus       155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~  218 (261)
T KOG0489|consen  155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN  218 (261)
T ss_pred             ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence            4456789999999999999999999999999999999999999999999999999999999865

>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]

Probab=99.71  E-value=7e-18  Score=149.38  Aligned_cols=69  Identities=32%  Similarity=0.625  Sum_probs=64.2

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ....++|+||.||.||..|+..||+.|++.+|++..+|.+||..|||+..||++||||||+|||+...+
T Consensus       165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             ccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            445668888899999999999999999999999999999999999999999999999999999997744

>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]

Probab=99.70  E-value=1.2e-17  Score=135.35  Aligned_cols=64  Identities=28%  Similarity=0.427  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL   79 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~   79 (211)
                      +.||.||.||.+|+..||..|+.|.|....+|++||..|+|++.||+|||||||.|.||++.+.
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            7788999999999999999999999999999999999999999999999999999999987553

>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]

Probab=99.69  E-value=1.1e-17  Score=146.83  Aligned_cols=71  Identities=28%  Similarity=0.397  Sum_probs=64.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHH
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNT   83 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~   83 (211)
                      .+++|||.|..|+..|+.+||+.|+..+|++..+|+.||..|.|+++||||||||||-|.||+..+.....
T Consensus       149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            46677788899999999999999999999999999999999999999999999999999999886655443

>KOG2251 consensus Homeobox transcription factor [Transcription]

Probab=99.68  E-value=3.4e-17  Score=136.63  Aligned_cols=69  Identities=26%  Similarity=0.483  Sum_probs=64.5

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      =...++|.||.||+||..|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|+++..
T Consensus        30 ~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q   98 (228)
T KOG2251|consen   30 YSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ   98 (228)
T ss_pred             cCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence            345788999999999999999999999999999999999999999999999999999999999987743

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]

Probab=99.68  E-value=8.7e-17  Score=138.76  Aligned_cols=78  Identities=19%  Similarity=0.336  Sum_probs=73.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHH
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALAD   94 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e   94 (211)
                      .||+||+||..|++.|+..|+..++|.+..|++|+.++||..|+|+|||||||+|+|+.++......|.+.+..+...
T Consensus       167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~s  244 (383)
T KOG4577|consen  167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRS  244 (383)
T ss_pred             cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhcc
Confidence            468999999999999999999999999999999999999999999999999999999999999999999999887553

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]

Probab=99.67  E-value=2e-17  Score=145.34  Aligned_cols=66  Identities=26%  Similarity=0.385  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL   79 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~   79 (211)
                      .++.||||.-||..|+..||+.|-.|.|++...|.+|++.|+|++|||||||||||.|+||...+.
T Consensus       232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            466778899999999999999999999999999999999999999999999999999999987543

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]

Probab=99.67  E-value=2.4e-17  Score=122.88  Aligned_cols=67  Identities=24%  Similarity=0.446  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +...++|.||-||+||..|+..||++|.+.+||++..|++||.++.|++..|+|||||||++-|++.
T Consensus        10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE   76 (125)
T KOG0484|consen   10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE   76 (125)
T ss_pred             ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence            4456788899999999999999999999999999999999999999999999999999999998754

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.66  E-value=1.2e-16  Score=107.36  Aligned_cols=57  Identities=35%  Similarity=0.568  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ||+|+.||.+|+..|+.+|..++||+..++..||.++||++.+|++||+|+|.++|+
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            578999999999999999999999999999999999999999999999999999885

; 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 ....

>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]

Probab=99.64  E-value=1.5e-16  Score=135.48  Aligned_cols=74  Identities=23%  Similarity=0.458  Sum_probs=66.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhH
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLE   89 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~   89 (211)
                      |+|+-||.||..|++.||+.|++.+||+..-|+-||.++.|.+.+|+|||||||+||||..++....++.+++.
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyg  213 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYG  213 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhc
Confidence            33344899999999999999999999999999999999999999999999999999999998887777776653

>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]

Probab=99.63  E-value=3e-16  Score=131.68  Aligned_cols=65  Identities=25%  Similarity=0.423  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      +.+|.||.||.|+.-||..|.+.|+++.|+.-.+|.+||..|||+.+|||+||||||.|-||..+
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            56677778999999999999999999999999999999999999999999999999999998764

>KOG0485 consensus Transcription factor NKX-5

Probab=99.59  E-value=5.4e-16  Score=129.21  Aligned_cols=61  Identities=33%  Similarity=0.566  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +|||.||+|+..|+-.||..|+...|++..+|..||.+|.|+++|||+||||||.|||++.
T Consensus       103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~  163 (268)
T KOG0485|consen  103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY  163 (268)
T ss_pred             ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence            6678999999999999999999999999999999999999999999999999999999864

1/HMX1, contains HOX domain [Transcription]

>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]

Probab=99.59  E-value=6.3e-16  Score=132.18  Aligned_cols=61  Identities=30%  Similarity=0.475  Sum_probs=56.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      -|-|.+||..|..+||+.|...+|.++.++.+||.-|||+|||||+||||||+|+||..++
T Consensus       200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK  260 (317)
T KOG0848|consen  200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK  260 (317)
T ss_pred             cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence            3457899999999999999999999999999999999999999999999999999987643

>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]

Probab=99.58  E-value=2e-15  Score=125.05  Aligned_cols=60  Identities=27%  Similarity=0.473  Sum_probs=57.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .|+.||-||..|+..||+.|.+.+|+++.+|.+++..|.|+++|||+||||||+|.||.+
T Consensus       144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ  203 (246)
T KOG0492|consen  144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ  203 (246)
T ss_pred             CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence            356799999999999999999999999999999999999999999999999999999866

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.57  E-value=2.2e-15  Score=102.11  Aligned_cols=53  Identities=17%  Similarity=0.259  Sum_probs=50.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCC----CCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKK----LDTELKLKLANQLGVPARQVAVWYQNKR   69 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~----p~~~~r~~La~~lgL~~rqVkvWFqNRR   69 (211)
                      +||.||.||.+|++.||.+|..++|    |+...+.+||.++||++++|+|||||-+
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            4789999999999999999999999    9999999999999999999999999964

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.

>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]

Probab=99.57  E-value=1.8e-15  Score=129.08  Aligned_cols=59  Identities=29%  Similarity=0.549  Sum_probs=56.8

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ||.||.||.+||..|+..|+.+.|++..+|++||.+|||.+.||++||||+|+|.||-.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            67899999999999999999999999999999999999999999999999999999864

>smart00389 HOX Homeodomain

Probab=99.54  E-value=7.8e-15  Score=97.71  Aligned_cols=55  Identities=38%  Similarity=0.698  Sum_probs=52.2

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      +.|+.|+.+|+..|+..|..++||+..++.+||..+||+.++|+.||+|||.+.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5678899999999999999999999999999999999999999999999998764

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=99.54  E-value=1.2e-14  Score=97.43  Aligned_cols=57  Identities=35%  Similarity=0.619  Sum_probs=54.3

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      +.+..|+.+|+..||.+|..++||+..++..||.++||++++|++||+|||.+.++.
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            567899999999999999999999999999999999999999999999999998763

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]

Probab=99.51  E-value=6e-15  Score=132.44  Aligned_cols=61  Identities=21%  Similarity=0.330  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ||||+||.|+...+..||++|.+|++|+..+...||.+|+|++.+|+|||||||.|+||..
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~  353 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT  353 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence            7788999999999999999999999999999999999999999999999999999999876

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.47  E-value=5.5e-14  Score=113.29  Aligned_cols=66  Identities=30%  Similarity=0.483  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ..+..+++|++.|.+|+.+|++.|..|+||+...|..|+..|+|+++-|++||||||++.|+....
T Consensus        47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            345566788999999999999999999999999999999999999999999999999999987643

>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]

Probab=99.42  E-value=4.2e-14  Score=123.05  Aligned_cols=63  Identities=27%  Similarity=0.487  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      .-||-||.||.+|+..||+.|-+..|-++.+|.+||..|+|.++-|||||||||.|+||+...
T Consensus       180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            346789999999999999999999999999999999999999999999999999999997654

>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]

Probab=99.40  E-value=5.6e-14  Score=112.70  Aligned_cols=65  Identities=28%  Similarity=0.452  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ..+++|-|++|...|+..||+.|+..+|++..+|.+||..|+|+++||+.||||||.|.||.++.
T Consensus        97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~  161 (194)
T KOG0491|consen   97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN  161 (194)
T ss_pred             HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence            45677889999999999999999999999999999999999999999999999999999987633

>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]

Probab=99.26  E-value=2.9e-12  Score=107.21  Aligned_cols=62  Identities=29%  Similarity=0.568  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .++|..|.+|+..|+..||+.|...+|+-...|.+||..+|+++.||+|||||||.|||++.
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh  226 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH  226 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence            45566788999999999999999999999999999999999999999999999999999865

>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]

Probab=99.20  E-value=6.4e-12  Score=109.85  Aligned_cols=61  Identities=21%  Similarity=0.510  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      |+||.|+-||..|+..||..|.++.||+-..|++||--.+|++..|+|||.|||++||++.
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE  171 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE  171 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence            6678899999999999999999999999999999999999999999999999999999876

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=99.16  E-value=1.8e-11  Score=102.95  Aligned_cols=63  Identities=25%  Similarity=0.261  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +.++||.|+.|+..|++.||+.|...+||+...|+.||..+++++..|++||||||++|++..
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            677889999999999999999999999999999999999999999999999999999999865

>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]

Probab=99.05  E-value=1.8e-10  Score=104.12  Aligned_cols=68  Identities=26%  Similarity=0.457  Sum_probs=63.2

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661            9 NQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus         9 ~~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .....+++.+|.|++|+..|++.||+.|+.++||+...|++||.++++.+..|+|||+|||+++++..
T Consensus       168 p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  168 PGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             ccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            34556778888899999999999999999999999999999999999999999999999999999865

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]

Probab=99.04  E-value=8.9e-11  Score=101.85  Aligned_cols=64  Identities=23%  Similarity=0.367  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +...|||+||.+-....+.||.+|...++|+.+....||.+|+|.+.+|+|||+|.|.|.||++
T Consensus       305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~  368 (385)
T KOG1168|consen  305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK  368 (385)
T ss_pred             CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence            3456789999999999999999999999999999999999999999999999999999999865

>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]

Probab=98.85  E-value=2.4e-09  Score=92.32  Aligned_cols=52  Identities=21%  Similarity=0.371  Sum_probs=48.5

Q ss_pred             CCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        23 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      .|...-..+|..+|..++||++.++.+||+.+||+..||-.||.|||.|+|.
T Consensus       182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            4666778899999999999999999999999999999999999999999994

>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=98.40  E-value=1.8e-07  Score=58.84  Aligned_cols=34  Identities=32%  Similarity=0.514  Sum_probs=29.0

Q ss_pred             cCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661           38 TKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR   71 (211)
Q Consensus        38 ~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r   71 (211)
                      .+|||+..++..||.++||+.+||..||-|.|.|
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            4699999999999999999999999999999875

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

>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]

Probab=98.39  E-value=4.3e-07  Score=85.02  Aligned_cols=61  Identities=20%  Similarity=0.242  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ..+.||.|.+||..|++.|..+|+.+++|+..+.+.|+.+|||..+-|.+||-|-|.|.+-
T Consensus       417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~  477 (558)
T KOG2252|consen  417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLD  477 (558)
T ss_pred             cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccc
Confidence            3455678999999999999999999999999999999999999999999999999888643

>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]

Probab=98.25  E-value=5.9e-07  Score=77.34  Aligned_cols=58  Identities=26%  Similarity=0.462  Sum_probs=53.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFT---TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ||+|+.|+..-.++|..+|.   .+|||+...+++||+++|++..||-.||.|+|.|.|+.
T Consensus       189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~  249 (334)
T KOG0774|consen  189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN  249 (334)
T ss_pred             HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence            57889999999999999995   57999999999999999999999999999999999874

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=98.12  E-value=2.7e-06  Score=71.43  Aligned_cols=63  Identities=27%  Similarity=0.517  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..+.++.|+.++..|+..|+..|...++|+...+.+|+..+|+.++.|++||+|+|.+.++..
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~  212 (235)
T KOG0490|consen  150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK  212 (235)
T ss_pred             ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence            456677899999999999999999999999999999999999999999999999999999865

>KOG1146 consensus Homeobox protein [General function prediction only]

Probab=97.43  E-value=0.0001  Score=75.21  Aligned_cols=65  Identities=20%  Similarity=0.419  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ..-+|+.|+.++..||..+..+|....+|...+.+.|...+++..++|.|||||-|.+.|+..+.
T Consensus       900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n  964 (1406)
T KOG1146|consen  900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN  964 (1406)
T ss_pred             hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence            34467789999999999999999999999999999999999999999999999999999988763

>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]

Probab=96.68  E-value=0.002  Score=57.86  Aligned_cols=62  Identities=27%  Similarity=0.356  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..++|++..+....+.+|+.+...   .+||+...+..||+++||+..||..||-|.|-|..+--
T Consensus       237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             cCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence            335566778999999999987433   47999999999999999999999999999988876544

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

Probab=96.54  E-value=0.0013  Score=44.20  Aligned_cols=41  Identities=22%  Similarity=0.383  Sum_probs=31.3

Q ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661           29 VRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR   69 (211)
Q Consensus        29 l~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR   69 (211)
                      +..|++.|...+++.......|+.+.+|+..||+.||-.|+
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            46699999999999999999999999999999999997653

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []

Probab=95.76  E-value=0.039  Score=35.45  Aligned_cols=42  Identities=26%  Similarity=0.435  Sum_probs=36.9

Q ss_pred             hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF  117 (211)
Q Consensus        76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~  117 (211)
                      +.+.++..++..++.+..++++|..|+..|..++..+...++
T Consensus         2 QlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~   43 (45)
T PF02183_consen    2 QLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ   43 (45)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            567899999999999999999999999999999988776543

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=94.75  E-value=0.16  Score=39.00  Aligned_cols=94  Identities=15%  Similarity=0.087  Sum_probs=51.8

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHH
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLE   99 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~   99 (211)
                      +|++||.++....-..+..+..    ...++|+++|+++..|..|.+--+.....................+.+++.+|+
T Consensus         9 ~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L~   84 (121)
T PRK09413          9 KRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKELQ   84 (121)
T ss_pred             CCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHHH
Confidence            4566888775443333333332    356789999999999999975432211000000000001112223456677788


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 035661          100 KDVKLLKEELRQAQEILF  117 (211)
Q Consensus       100 ~e~~~l~~e~~~~~~~l~  117 (211)
                      +++.+|..|+..+...+.
T Consensus        85 ~el~~L~~E~diLKKa~~  102 (121)
T PRK09413         85 RLLGKKTMENELLKEAVE  102 (121)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            888888887776665443

>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=94.72  E-value=0.069  Score=35.24  Aligned_cols=46  Identities=22%  Similarity=0.278  Sum_probs=34.9

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK   68 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR   68 (211)
                      ||+|+.+|-++...+=..++...     ....||+++|+...+|..|..|+
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            57889999998887777777666     57889999999999999999885

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.

>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]

Probab=94.28  E-value=0.05  Score=53.35  Aligned_cols=48  Identities=21%  Similarity=0.358  Sum_probs=45.0

Q ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           29 VRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        29 l~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +.+|...|..|..|+..+...+|.+.||..+.|+.||+++++......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            788999999999999999999999999999999999999998877655

>smart00340 HALZ homeobox associated leucin zipper

Probab=92.43  E-value=0.34  Score=30.59  Aligned_cols=32  Identities=28%  Similarity=0.432  Sum_probs=27.1

Q ss_pred             hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 035661           76 SLELDYNTIQVKLENALADKRRLEKDVKLLKE  107 (211)
Q Consensus        76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~  107 (211)
                      +.+.+..-++..++.+.+||++|++|+..|+.
T Consensus         2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLra   33 (44)
T smart00340        2 QTEVDCELLKRCCESLTEENRRLQKEVQELRA   33 (44)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45667888999999999999999999988764

>smart00338 BRLZ basic region leucin zipper

Probab=88.22  E-value=3.4  Score=27.96  Aligned_cols=39  Identities=26%  Similarity=0.456  Sum_probs=30.5

Q ss_pred             hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           78 ELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEIL  116 (211)
Q Consensus        78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l  116 (211)
                      ......+..+...+..+|..|..++..|..++..+...+
T Consensus        25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            335667777888888889999999988888888776644

>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization

Probab=87.26  E-value=4.8  Score=27.14  Aligned_cols=44  Identities=20%  Similarity=0.379  Sum_probs=28.9

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEI  115 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~  115 (211)
                      ++|.|++.   ....+...+..+..++..|..++..|..++..+...
T Consensus        19 ~~R~RKk~---~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e   62 (64)
T PF00170_consen   19 RSRQRKKQ---YIEELEEKVEELESENEELKKELEQLKKEIQSLKSE   62 (64)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh---hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            44444443   555666677777777777777777777777766543

; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=86.63  E-value=2.9  Score=37.06  Aligned_cols=44  Identities=14%  Similarity=0.231  Sum_probs=36.2

Q ss_pred             hhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 035661           76 SLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAK  119 (211)
Q Consensus        76 ~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~  119 (211)
                      +++.+...+--+++.|...|++|+.++++|..|+.++.+.+...
T Consensus       245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~  288 (294)
T KOG4571|consen  245 KKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEV  288 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33446667777888899999999999999999999999877643

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

Probab=83.63  E-value=0.42  Score=32.87  Aligned_cols=47  Identities=17%  Similarity=0.281  Sum_probs=31.2

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR   69 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR   69 (211)
                      ++|++||+++...+-..+..    ......++|+++||++..|..|-.--+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence            46789999988777666622    235678899999999999999986444

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.

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []

Probab=82.48  E-value=3.9  Score=26.14  Aligned_cols=32  Identities=22%  Similarity=0.510  Sum_probs=21.2

Q ss_pred             hhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 035661           78 ELDYNTIQVKLENALADKRRLEKDVKLLKEEL  109 (211)
Q Consensus        78 ~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~  109 (211)
                      +..+..+..+++.+..|+..|..++..|...+
T Consensus        11 K~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl   42 (45)
T PF02183_consen   11 KASYDSLKAEYDSLKKENEKLRAEVQELKEKL   42 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            44566667777777777777777776666544

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]

Probab=82.14  E-value=6.9  Score=34.27  Aligned_cols=49  Identities=18%  Similarity=0.293  Sum_probs=37.3

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL  120 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~  120 (211)
                      |.|.+++...   ..+..+...|..||..|..++.+|+.++..+...+..+.
T Consensus       208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~  256 (269)
T KOG3119|consen  208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLP  256 (269)
T ss_pred             HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            5555555544   455566677888999999999999999999988777654

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=81.37  E-value=14  Score=27.75  Aligned_cols=54  Identities=15%  Similarity=0.157  Sum_probs=34.8

Q ss_pred             chhhhhhhhHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           60 QVAVWYQNKRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQE  114 (211)
Q Consensus        60 qVkvWFqNRR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~  114 (211)
                      ++..||.+.-. .+-...+.+...++.+++.+..+|..|+.++..|+....++..
T Consensus        16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe   69 (105)
T PRK00888         16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEE   69 (105)
T ss_pred             HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHH
Confidence            45678865422 1223344566677788888888888888888888774444443

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=80.48  E-value=26  Score=27.54  Aligned_cols=38  Identities=16%  Similarity=0.251  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661           22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR   71 (211)
Q Consensus        22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r   71 (211)
                      ..|+.+++..|            ..|+.--+.-|++...|-.|=|.||.-
T Consensus        22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTL   59 (135)
T KOG4196|consen   22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTL   59 (135)
T ss_pred             CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence            67888877766            333332333489999999999988743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	211
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	2e-19
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-11
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	4e-11
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	1e-10
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-10
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-10
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	9e-10
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-09
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-09
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-09
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-09
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	3e-09
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-09
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	5e-09
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	7e-09
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-08
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-08
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-08
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	1e-08
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-08
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-08
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	1e-08
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-08
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-08
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-08
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-08
1e3o_C	160	Octamer-binding transcription factor 1; transcript	3e-08
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	5e-08
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	5e-08
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	6e-08
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	1e-07
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	2e-07
1uhs_A	72	HOP, homeodomain only protein; structural genomics	5e-07
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	1e-06
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-06
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	2e-06
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	2e-06
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	3e-06
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	3e-06
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	4e-06
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-06
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	6e-06
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	6e-06
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	6e-06
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	7e-06
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	9e-06
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-05
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-05
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-05
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-05
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	4e-05
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	5e-05
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	6e-05
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-04
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	3e-04
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	9e-04

>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 = 77.2 bits (191), Expect = 2e-19
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          K  ++ +    LE  F  K+ L+++ K ++A + G+   QV VW+ NKR R K
Sbjct: 9  KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

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

 Score = 57.4 bits (139), Expect = 1e-11
 Identities = 12/56 (21%), Positives = 23/56 (41%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          K + + EQ+  L+ SF   +         L    G+  R+V  W+ ++R   +   
Sbjct: 12 KNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK 67

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

 Score = 58.3 bits (140), Expect = 4e-11
 Identities = 18/78 (23%), Positives = 33/78 (42%)

Query: 5   DTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVW 64
             Q++ K         +      Q R L   F   K+   EL++ ++ QLG+    V+ +
Sbjct: 85  KEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNF 144

Query: 65  YQNKRARWKTQSLELDYN 82
           + N R R   + LE  ++
Sbjct: 145 FMNARRRSLDKWLEHHHH 162

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

 Score = 54.8 bits (132), Expect = 1e-10
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 21 KKRLNQEQVRVLERSFT-TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
               ++QV +LE +F    K  D      +A + G+   Q   W++ + A W+  
Sbjct: 6  VSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

>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 = 54.4 bits (131), Expect = 2e-10
 Identities = 14/54 (25%), Positives = 28/54 (51%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
           +  EQ+ +L + +        ++   +A+++G+  R V VW+QN RAR +   
Sbjct: 23 TITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG 76

>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 = 53.9 bits (130), Expect = 2e-10
 Identities = 12/54 (22%), Positives = 27/54 (50%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          R+  +Q+RVL + F        E   ++A++ G+P + +  W++N   + +   
Sbjct: 13 RITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG 66

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

 Score = 51.9 bits (125), Expect = 9e-10
 Identities = 19/51 (37%), Positives = 29/51 (56%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          + QV  LER F  +K L +  +  LA  L +   QV  W+QN+R +W+ Q+
Sbjct: 6  RSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56

>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 = 51.8 bits (124), Expect = 1e-09
 Identities = 13/54 (24%), Positives = 24/54 (44%)

Query: 22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
          K    EQ+R LE SF        E   +L ++  +  R++  W+  +R +   +
Sbjct: 12 KERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65

>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 = 51.3 bits (123), Expect = 2e-09
 Identities = 11/59 (18%), Positives = 26/59 (44%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79
           ++  +EQ+  L+ SF   +  D     +L    G+   ++  W+ + R R +   + +
Sbjct: 8  HRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIVHI 66

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

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 15/73 (20%), Positives = 25/73 (34%)

Query: 1   MDIADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQ 60
              + T  ++      K   +  +       LE  F    K        LA+ L +    
Sbjct: 83  SSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEV 142

Query: 61  VAVWYQNKRARWK 73
           V VW+ N+R + K
Sbjct: 143 VRVWFCNRRQKEK 155

>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 = 51.9 bits (124), Expect = 2e-09
 Identities = 12/55 (21%), Positives = 22/55 (40%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           K   Q QV++LE SF            +L  +  +  R++  W+  +R    + 
Sbjct: 17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSM 71

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 12 HPPPNKLNIK-KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRA 70
             P+    K K    EQ+RVL+ SF     L  E   +L  Q  +  R++  W+  K+ 
Sbjct: 5  SSGPDFTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKK 64

Query: 71 RWKTQ 75
              +
Sbjct: 65 SKALK 69

>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 = 50.4 bits (121), Expect = 4e-09
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
          R    Q+RVL+  F        +   +L+N L +P R + VW+QN R + +  
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65

>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 = 52.3 bits (125), Expect = 5e-09
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 1   MDIADTQQNQKHPPPNKLNIKKR----LNQEQVRVLERSFTTKKKLDTELKLKLANQLGV 56
           ++ A+      +        K++    ++      LER F    K  ++  +++A +L +
Sbjct: 67  LEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNL 126

Query: 57  PARQVAVWYQNKRARWK 73
               V VW+ N+R R K
Sbjct: 127 EKEVVRVWFCNRRQREK 143

>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 = 49.8 bits (119), Expect = 7e-09
 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 21 KKRLNQEQVRVLERSFT-TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          + +++ E + +L+          D E    L+ QL +P   +  ++QN+R   K
Sbjct: 11 RTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

>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 = 49.3 bits (118), Expect = 1e-08
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 24 LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79
          LN++Q+  L   +    + D  +K +L    G+  R + VW+QNKR + K +S+ +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMM 65

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

 Score = 49.2 bits (118), Expect = 1e-08
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
          Q Q+  L+  F  +K L  +   +L++ L +  +QV  W+QN+R + K  
Sbjct: 12 QAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

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

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          Q QV  LER F  ++ L    + +LA+ L + + QV +W+QN+R + K
Sbjct: 11 QAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 49.4 bits (118), Expect = 1e-08
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 4  ADTQQNQKHPPPNKLNIKKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQV 61
          A+    +K         K R   +  Q+ VL   F  +K L  +   +L+N L +  +QV
Sbjct: 7  AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66

Query: 62 AVWYQNKRARWKTQ 75
            W+QN+R + K  
Sbjct: 67 KTWFQNQRMKSKRW 80

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 20/49 (40%), Positives = 28/49 (57%)

Query: 27 EQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           Q+  LE+ F  +K L T  ++ LA  LG+   QV  WYQN+R +WK  
Sbjct: 27 LQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS 75

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

 Score = 48.9 bits (117), Expect = 1e-08
 Identities = 19/53 (35%), Positives = 28/53 (52%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
            QV  LER F+ +K L    +  LA  L +   QV +W+QN+R + K + L 
Sbjct: 13 HTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS 65

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

 Score = 48.4 bits (116), Expect = 1e-08
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
            Q+  LER F  K+ L    + + ++ L +   QV +W+QN+RA+ K
Sbjct: 9  TAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56

>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 = 49.0 bits (117), Expect = 2e-08
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
          + Q   LER F  ++ L    +  LA+ + +   QV +W+QN R + K    E
Sbjct: 18 KAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE 70

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

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 19/53 (35%), Positives = 29/53 (54%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
          Q QV  LER F  +K L    +  LA+ + +   QV +W+QN R + K Q+ +
Sbjct: 11 QAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63

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

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 12 HPPPNKLNIKKR-----LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ 66
          HP  N+   K++       + QV  LE+ F  +K L +  +  LA  L +   QV  W+Q
Sbjct: 7  HPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQ 66

Query: 67 NKRARWKTQSLE 78
          N+R +W+ Q+ E
Sbjct: 67 NRRTKWRRQTAE 78

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

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
            Q+  L+R F   + L    + +LA  LG+   QV +W+QNKR++ K  
Sbjct: 16 SFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65

>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 = 50.3 bits (120), Expect = 3e-08
 Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 5   DTQQNQKHPPPNKLNIKKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVA 62
            +  N           KKR  +       LE+SF   +K  +E    +A QL +    + 
Sbjct: 87  PSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR 146

Query: 63  VWYQNKRARWK 73
           VW+ N+R + K
Sbjct: 147 VWFSNRRQKEK 157

>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 = 48.3 bits (114), Expect = 5e-08
 Identities = 15/74 (20%), Positives = 28/74 (37%)

Query: 4  ADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAV 63
           +       P         +   EQ+ +L+ +F   +    E   KLA + G+    +  
Sbjct: 12 LEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVS 71

Query: 64 WYQNKRARWKTQSL 77
          W+ + R  WK  +L
Sbjct: 72 WFGDTRYAWKNGNL 85

>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 = 47.5 bits (113), Expect = 5e-08
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 21 KKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
                E    LE+ F +  K  D +    L+ QL    R++  W++++R + K
Sbjct: 12 SPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65

>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 = 49.3 bits (117), Expect = 6e-08
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 2   DIADTQQNQKHPPPNKLNIKKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPAR 59
           +  + Q+  K     +   +KR  +       LE  F    K   +    +ANQLG+   
Sbjct: 79  NNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKD 138

Query: 60  QVAVWYQNKRARWK 73
            V VW+ N+R + K
Sbjct: 139 VVRVWFSNRRQKGK 152

>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 = 46.7 bits (111), Expect = 1e-07
 Identities = 14/51 (27%), Positives = 26/51 (50%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
             Q+R ++  F      D +   +LA + G+  R + VW+QN RA+++  
Sbjct: 15 KHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65

>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 = 45.9 bits (109), Expect = 2e-07
 Identities = 19/53 (35%), Positives = 29/53 (54%)

Query: 26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
           +Q   LE+ F T+K L    + +LA  L +  RQV  W+QN+RA+W+     
Sbjct: 16 NDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68

>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 = 45.1 bits (107), Expect = 5e-07
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 24 LNQEQVRVLERSFT-TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
          + ++QV +LE +F    K  D      +A + G+   Q   W++ + A W+  
Sbjct: 8  MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 44.2 bits (104), Expect = 1e-06
 Identities = 15/58 (25%), Positives = 25/58 (43%)

Query: 20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL 77
            KR  +EQ+ +L+  F   +    E   KL    G+P  ++  W+ + R   K   L
Sbjct: 6  SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL 63

>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 = 45.4 bits (107), Expect = 1e-06
 Identities = 12/71 (16%), Positives = 23/71 (32%), Gaps = 1/71 (1%)

Query: 5   DTQQNQKHPPPNKLNIKK-RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAV 63
                     P+K   ++     + +  L   F        +   ++A +L      V V
Sbjct: 80  QNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRV 139

Query: 64  WYQNKRARWKT 74
           W+ N+R   K 
Sbjct: 140 WFSNRRQTLKN 150

>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 = 43.1 bits (102), Expect = 2e-06
 Identities = 16/47 (34%), Positives = 30/47 (63%)

Query: 27 EQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          EQ+  L+R F   + L    + +L+++LG+   Q+ +W++NKRA+ K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59

>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 = 42.7 bits (101), Expect = 2e-06
 Identities = 16/49 (32%), Positives = 28/49 (57%)

Query: 27 EQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
          +Q+  LE+ F  +  +    + +LA QL +P   + VW+QN+R + K Q
Sbjct: 11 DQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>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 = 42.7 bits (101), Expect = 3e-06
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           Q Q+ VLE  F        ++   LA +L +   ++ +W+QN+RA+ K  
Sbjct: 9  TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59

>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 = 42.5 bits (100), Expect = 3e-06
 Identities = 14/49 (28%), Positives = 27/49 (55%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          Q+R LER +   K +  + + K++    +  RQ+ +W+QN+R + K   
Sbjct: 18 QLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG 66

>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 = 42.4 bits (100), Expect = 4e-06
 Identities = 15/51 (29%), Positives = 31/51 (60%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           + Q+ VLE  F   +  D  ++ ++A ++ +P  +V VW++N+RA+ + Q
Sbjct: 15 TRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ 65

>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 = 42.0 bits (99), Expect = 4e-06
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 27 EQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
           Q+  LE+ F   + L       L+ +L +   QV +W++N+R R K QS
Sbjct: 12 SQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 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 = 41.5 bits (98), Expect = 6e-06
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
             Q+  LE++F+     D   + +LA ++G+   ++ VW+QN+RA+W+ Q
Sbjct: 7  TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>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 = 42.6 bits (100), Expect = 6e-06
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 1  MDIADTQQNQKHPPPNKLNIKKRLNQ----EQVRVLERSFTTKKKLDTELKLKLANQLGV 56
          M +              L     L       Q+  LE+ F   K L    ++++A  L +
Sbjct: 14 MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 73

Query: 57 PARQVAVWYQNKRARWK 73
             QV +W+QN+R + K
Sbjct: 74 NETQVKIWFQNRRMKQK 90

>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 = 42.0 bits (99), Expect = 6e-06
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 5  DTQQNQKHPPPNKLNIKKRLN-----QEQVRVLERSFTTKKKLDTELKLKLANQLGVPAR 59
          +   + +  P   L  K+R +       Q+  LER+F   +  D   + +LA +  +   
Sbjct: 1  EDISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEA 60

Query: 60 QVAVWYQNKRARWKTQ 75
          ++ VW+QN+RAR + Q
Sbjct: 61 RIQVWFQNRRARLRKQ 76

>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 = 41.6 bits (98), Expect = 7e-06
 Identities = 16/51 (31%), Positives = 28/51 (54%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
            EQ+  LE  F   K  D   + +LA ++ +   +V VW++N+RA+W+  
Sbjct: 15 TDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

>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 = 41.1 bits (97), Expect = 9e-06
 Identities = 13/51 (25%), Positives = 29/51 (56%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
            +Q++ LE +F   +  D   + ++A    +   +V VW++N+RA+W+ +
Sbjct: 11 TSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 14/46 (30%), Positives = 28/46 (60%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          Q++ LER + T K +  + + +++    +  RQV +W+QN+R + K
Sbjct: 18 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63

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

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 16/51 (31%), Positives = 30/51 (58%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           QEQ+  LE+ F      D   + +LA ++ +P  ++ VW+ N+RA+W+ +
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65

>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 = 40.6 bits (95), Expect = 2e-05
 Identities = 15/49 (30%), Positives = 26/49 (53%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          Q   LE+ F     L  + + ++A  L +  RQV +W+QN+R + K  +
Sbjct: 24 QTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 15/46 (32%), Positives = 27/46 (58%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          Q   LE+ F T   L    ++++A+ L +  RQ+ +W+QN+R + K
Sbjct: 31 QTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76

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

 Score = 40.2 bits (94), Expect = 4e-05
 Identities = 15/46 (32%), Positives = 28/46 (60%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          Q   LE+ F   + L    ++++A+ L +  RQ+ +W+QN+R +WK
Sbjct: 39 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84

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

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 15/46 (32%), Positives = 27/46 (58%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          Q+  LE+ F   K +    +++LA  L +  R + +W+QN+R +WK
Sbjct: 14 QLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59

>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 = 38.9 bits (91), Expect = 6e-05
 Identities = 15/46 (32%), Positives = 28/46 (60%)

Query: 28 QVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          Q   LE+ F   + L    ++++A+ L +  RQ+ +W+QN+R +WK
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58

>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 = 37.9 bits (88), Expect = 1e-04
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 21 KKRLNQEQVRVLERSFTTK-KKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
                +   +LE+ FT   K  D +    L+ QL    R +  W++ +R + K
Sbjct: 4  GSSGTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57

>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 = 37.2 bits (85), Expect = 3e-04
 Identities = 12/66 (18%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 17 KLNIKKRLNQEQVRVLERSF----TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARW 72
           L  + + +   +  L++ +    T+   +  E    +A +L V    V  W  N+R ++
Sbjct: 8  ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY 67

Query: 73 KTQSLE 78
          +   +E
Sbjct: 68 RLMGIE 73

>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 = 36.5 bits (84), Expect = 9e-04
 Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 17/78 (21%)

Query: 15 PNKLNIKKRLN--QEQVRVLERSFTTKKKLDTELKLKLANQLG---------------VP 57
                  R    +E + V+E  F   +  D   + ++AN                  V 
Sbjct: 3  SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62

Query: 58 ARQVAVWYQNKRARWKTQ 75
          + +V  W+ N+R   K +
Sbjct: 63 SLKVYNWFANRRKEIKRR 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	211
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.8
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.8
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.8
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.8
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.79
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.79
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.79
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.79
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.79
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.79
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.79
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.79
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.79
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.79
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.79
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.78
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.78
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.78
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.78
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.78
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.78
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.78
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.78
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.78
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.78
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.77
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.77
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.77
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.77
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.77
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.77
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.77
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.77
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.77
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.76
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.76
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.75
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.75
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.75
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.75
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.75
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.75
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.74
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.74
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.74
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.74
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.73
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.73
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.73
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.72
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.72
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.71
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.71
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.71
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.71
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.71
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.7
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.7
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.7
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.7
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.7
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.69
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.69
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.69
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.68
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.67
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.66
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.65
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.65
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.64
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.6
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.49
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.43
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.42
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.42
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.29
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.62
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	94.29
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	93.4
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.83
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	92.07
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	91.97
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	91.9
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	89.49
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	85.96
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	85.72
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.62
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	82.79
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	81.32

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

Probab=99.82  E-value=2.4e-20  Score=137.04  Aligned_cols=76  Identities=29%  Similarity=0.509  Sum_probs=64.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhhhhHHHHH
Q 035661           11 KHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELDYNTIQV   86 (211)
Q Consensus        11 ~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~~~~~~~~   86 (211)
                      ...++++||.|++||.+|+..||..|..++||+..++..||..+||+++||+|||||||+++|+...+.......+
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~~~~   86 (93)
T 3a01_A           11 NRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQA   86 (93)
T ss_dssp             TSCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-------
T ss_pred             CCCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHHHHHHH
Confidence            3455677789999999999999999999999999999999999999999999999999999999876655444443

>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=99.80  E-value=4.4e-20  Score=131.46  Aligned_cols=67  Identities=22%  Similarity=0.454  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ....++++||.|++||.+|+..||..|..++||+..++.+||.+|||+++||++||||||+++|+..
T Consensus        10 ~~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           10 GGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            3445677888999999999999999999999999999999999999999999999999999999865

>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=99.80  E-value=7.2e-20  Score=129.84  Aligned_cols=67  Identities=27%  Similarity=0.387  Sum_probs=61.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL   79 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~   79 (211)
                      .++++||.|++||.+|+..||..|..++||+..++.+||..|||+++||++||||||+++|+.....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            3556678899999999999999999999999999999999999999999999999999999876543

>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=99.80  E-value=6.3e-20  Score=131.05  Aligned_cols=64  Identities=31%  Similarity=0.546  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..++.||.|++||.+|+..||..|..++||+..++.+||..|||+++||++||||||+++|+..
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            4566778999999999999999999999999999999999999999999999999999999865

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

Probab=99.80  E-value=4.1e-20  Score=125.77  Aligned_cols=61  Identities=26%  Similarity=0.441  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ++||.|+.||.+|+..||..|..++||+..++.+||..+||++++|++||||||+++|+++
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            4568899999999999999999999999999999999999999999999999999999853

>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=99.79  E-value=6.7e-20  Score=127.67  Aligned_cols=63  Identities=22%  Similarity=0.450  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..+.||+|++||.+|+..||..|..++||+..++.+||..|||+++||++||||||+++|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            356678999999999999999999999999999999999999999999999999999999865

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

Probab=99.79  E-value=1.7e-19  Score=128.87  Aligned_cols=63  Identities=25%  Similarity=0.577  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .+.||.|++||.+|+..||..|..++||+..++..||..|||++++|++||||||+++|+...
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            456789999999999999999999999999999999999999999999999999999998763

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

Probab=99.79  E-value=9.4e-20  Score=124.44  Aligned_cols=60  Identities=25%  Similarity=0.561  Sum_probs=56.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .||.|++||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|+..
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            567899999999999999999999999999999999999999999999999999999853

>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=99.79  E-value=1.1e-19  Score=129.68  Aligned_cols=65  Identities=23%  Similarity=0.473  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ..+.||.|++||.+|+..||.+|..++||+..++..||.+|||++++|++||||||+++|++...
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            34567899999999999999999999999999999999999999999999999999999997644

>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=99.79  E-value=8.6e-20  Score=123.80  Aligned_cols=58  Identities=28%  Similarity=0.560  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      .||.|+.||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|+
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            4678999999999999999999999999999999999999999999999999999986

>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=99.79  E-value=2.9e-19  Score=126.74  Aligned_cols=65  Identities=23%  Similarity=0.373  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..++.||.|++||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+...
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            44566789999999999999999999999999999999999999999999999999999998764

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

Probab=99.79  E-value=1.3e-19  Score=129.33  Aligned_cols=64  Identities=23%  Similarity=0.452  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .++.||.|++||.+|+..||..|..++||+..++..||..|||++++|++||||||+++|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            4567789999999999999999999999999999999999999999999999999999998764

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

Probab=99.79  E-value=1.6e-19  Score=125.65  Aligned_cols=63  Identities=25%  Similarity=0.500  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .+.||.|++||.+|+..||..|..++||+..++.+||.+|||+++||++||||||+++|+...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            456788999999999999999999999999999999999999999999999999999998653

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

Probab=99.79  E-value=1.1e-19  Score=130.70  Aligned_cols=64  Identities=28%  Similarity=0.430  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .+.++||.|+.||.+|+..||..|..++||+..++..||..|||+++||++||||||+++|+..
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            4567778999999999999999999999999999999999999999999999999999999865

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

Probab=99.79  E-value=1.6e-19  Score=121.16  Aligned_cols=57  Identities=28%  Similarity=0.499  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ||+|+.||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            478999999999999999999999999999999999999999999999999999986

>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=99.79  E-value=1.1e-19  Score=126.42  Aligned_cols=64  Identities=25%  Similarity=0.417  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..+.||.|++||.+|+..||..|..++||+..++..||..|||+++||++||||||+++|+...
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            4566789999999999999999999999999999999999999999999999999999998653

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

Probab=99.78  E-value=2.2e-19  Score=126.21  Aligned_cols=64  Identities=22%  Similarity=0.383  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..+.||.|++||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            4556789999999999999999999999999999999999999999999999999999998653

>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=99.78  E-value=9.5e-20  Score=125.44  Aligned_cols=61  Identities=28%  Similarity=0.534  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ++||.|++||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|+..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            4578999999999999999999999999999999999999999999999999999999865

>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=99.78  E-value=2.1e-19  Score=125.14  Aligned_cols=63  Identities=32%  Similarity=0.558  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .+.|+.|++||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+...
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            456678999999999999999999999999999999999999999999999999999998653

>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=99.78  E-value=2.2e-19  Score=128.40  Aligned_cols=64  Identities=25%  Similarity=0.432  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .++++||.|++||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|++.
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~   77 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   77 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhc
Confidence            4667788999999999999999999999999999999999999999999999999999999865

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

Probab=99.78  E-value=2.4e-19  Score=124.27  Aligned_cols=62  Identities=26%  Similarity=0.427  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      +||.|++||.+|+..||..|..++||+..++..||..+||++++|++||||||+++|+....
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            46789999999999999999999999999999999999999999999999999999987643

>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=99.78  E-value=1.3e-19  Score=126.14  Aligned_cols=64  Identities=19%  Similarity=0.389  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..+.||.|++||.+|+.+||..|..++||+..++..||..+||+++||++||||||+++|+...
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            4566789999999999999999999999999999999999999999999999999999998653

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

Probab=99.78  E-value=1.2e-19  Score=129.59  Aligned_cols=65  Identities=15%  Similarity=0.320  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccC----CCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTK----KKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~----~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..+++||.|+.||.+|+..||.+|..+    +||+..++.+||.++||+++||+|||||||+|+|+...
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~~   72 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGI   72 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhccC
Confidence            456677899999999999999999999    99999999999999999999999999999999998653

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

Probab=99.78  E-value=1.8e-19  Score=125.47  Aligned_cols=63  Identities=27%  Similarity=0.433  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..+.||.|++||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            455678999999999999999999999999999999999999999999999999999999865

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

Probab=99.78  E-value=2.1e-19  Score=124.53  Aligned_cols=62  Identities=31%  Similarity=0.465  Sum_probs=58.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      +||.|++||.+|+..||..|..++||+..++..||..+||++++|++||||||+++|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~   63 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhH
Confidence            56889999999999999999999999999999999999999999999999999999987643

>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=99.78  E-value=1.5e-19  Score=125.35  Aligned_cols=61  Identities=25%  Similarity=0.560  Sum_probs=58.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      +||.|++||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            4688999999999999999999999999999999999999999999999999999998754

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

Probab=99.77  E-value=2.1e-19  Score=130.51  Aligned_cols=63  Identities=24%  Similarity=0.531  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..+.||.|++||.+|+..||..|..++||+..++.+||..|||++++|++||||||+++|+..
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            455678999999999999999999999999999999999999999999999999999999864

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

Probab=99.77  E-value=2.6e-19  Score=121.02  Aligned_cols=58  Identities=28%  Similarity=0.515  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ||.|+.||.+|+..||..|..++||+..++..||..+||++++|++||||||+++|+.
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            5789999999999999999999999999999999999999999999999999999874

>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=99.77  E-value=1.3e-19  Score=129.71  Aligned_cols=61  Identities=16%  Similarity=0.285  Sum_probs=57.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhcc----CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTT----KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~----~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ..++||.||.||.+|+..||.+|..    ++||+..+|.+||..|||+++||+|||||||+++|+
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            4567789999999999999999999    999999999999999999999999999999999875

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

Probab=99.77  E-value=2.6e-19  Score=123.63  Aligned_cols=62  Identities=26%  Similarity=0.445  Sum_probs=58.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      .||+|++||.+|+..||..|..++||+..++..||..+||++++|++||||||+++|+....
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            36789999999999999999999999999999999999999999999999999999987654

>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=99.77  E-value=1.5e-19  Score=125.28  Aligned_cols=63  Identities=21%  Similarity=0.461  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ++||.|+.||.+|+..||..|..++||+..++..||..+||++++|++||||||+++|+....
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            457889999999999999999999999999999999999999999999999999999987643

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

Probab=99.77  E-value=4.6e-19  Score=118.48  Aligned_cols=57  Identities=32%  Similarity=0.484  Sum_probs=54.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      +||.|+.||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|
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            457899999999999999999999999999999999999999999999999999975

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

Probab=99.77  E-value=4.9e-19  Score=124.46  Aligned_cols=65  Identities=25%  Similarity=0.439  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ...++||.|++||.+|+..||..|..++||+..++..||..+||++++|++||||||+++|+...
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            45566788999999999999999999999999999999999999999999999999999998754

>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=99.77  E-value=2.6e-19  Score=121.24  Aligned_cols=59  Identities=31%  Similarity=0.458  Sum_probs=48.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      .+.+|.|++||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|
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

>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=99.77  E-value=3.3e-19  Score=127.73  Aligned_cols=63  Identities=24%  Similarity=0.444  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ..++||.|++||.+|+..||..|..++||+..++.+||..|||++++|++||||||+++|+..
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            345678899999999999999999999999999999999999999999999999999999864

>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=99.76  E-value=1.1e-18  Score=122.13  Aligned_cols=59  Identities=22%  Similarity=0.464  Sum_probs=56.3

Q ss_pred             CCCCCCCCHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .++|++||.+|+..||..|.. ++||+..++..||..+||+++||++||||||+++|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            468899999999999999996 99999999999999999999999999999999999865

>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=99.76  E-value=6.6e-19  Score=124.78  Aligned_cols=59  Identities=25%  Similarity=0.359  Sum_probs=55.6

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ++|++||.+|+.+||+.|..++||+..+|.+||..+||+++||++||||||+++|+...
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l   63 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHH
Confidence            35678999999999999999999999999999999999999999999999999998754

>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=99.75  E-value=3e-19  Score=127.92  Aligned_cols=61  Identities=15%  Similarity=0.278  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhcc-----CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTT-----KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~-----~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ...++||.||.||.+|+..|| .|..     ++||+..+|.+||.+|||+++||+|||||||+++|+
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            456677899999999999999 7999     999999999999999999999999999999999875

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

Probab=99.75  E-value=1.4e-18  Score=121.98  Aligned_cols=59  Identities=22%  Similarity=0.452  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +++|++||.+|+..||..|.. ++||+..++..||..+||+++||++||||||+++|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            468899999999999999994 99999999999999999999999999999999999865

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

Probab=99.75  E-value=7.3e-19  Score=118.81  Aligned_cols=57  Identities=28%  Similarity=0.574  Sum_probs=50.7

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .|++||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|+..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            478999999999999999999999999999999999999999999999999999864

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

Probab=99.75  E-value=1.1e-18  Score=116.44  Aligned_cols=54  Identities=35%  Similarity=0.634  Sum_probs=51.0

Q ss_pred             CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      |.||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|++
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            689999999999999999999999999999999999999999999999999985

>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=99.75  E-value=1.2e-18  Score=128.67  Aligned_cols=63  Identities=24%  Similarity=0.455  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .+.||.|++||.+|+..||..|..++||+..++.+||..|||+++||++||||||+++|+...
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            456778999999999999999999999999999999999999999999999999999998764

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

Probab=99.75  E-value=1.8e-18  Score=121.50  Aligned_cols=62  Identities=15%  Similarity=0.326  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..++.|+.||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+...
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            44578999999999999999999999999999999999999999999999999999998653

>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=99.74  E-value=1.9e-18  Score=122.01  Aligned_cols=59  Identities=22%  Similarity=0.334  Sum_probs=55.9

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ++|++||.+|+..||..|..++||+..++..||..+||+++||++||||||+++|++..
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            46778999999999999999999999999999999999999999999999999998764

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

Probab=99.74  E-value=1.3e-18  Score=128.35  Aligned_cols=69  Identities=22%  Similarity=0.384  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           10 QKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        10 ~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      .+-..+..+|+|++||.+|+..||..|..++||+..++.+||.+|||+++||++||||||+++|+.+.+
T Consensus        18 ~p~~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk   86 (96)
T 3nar_A           18 GPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLK   86 (96)
T ss_dssp             ---------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCH
T ss_pred             CCCCCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhccc
Confidence            344566677899999999999999999999999999999999999999999999999999999997644

>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=99.74  E-value=2.3e-18  Score=120.76  Aligned_cols=64  Identities=19%  Similarity=0.192  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .++.||+|++|+.+|+..||.+|..   ++||+..++.+||..+||+++||++||||||+|+|+...
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            3456788999999999999999977   999999999999999999999999999999999998754

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

Probab=99.74  E-value=3.4e-18  Score=119.86  Aligned_cols=61  Identities=26%  Similarity=0.458  Sum_probs=57.9

Q ss_pred             CCCCCCCCHHHHHHHHHHh---ccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSF---TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F---~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ||+|++||.+|+.+||.+|   ..++||+..++..||..+||+++||++||||||+++|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            5789999999999999999   999999999999999999999999999999999999987654

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

Probab=99.73  E-value=2.2e-18  Score=121.90  Aligned_cols=60  Identities=20%  Similarity=0.309  Sum_probs=56.7

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .+.|++||.+|+..||..|..++||+..++.+||..+||+++||++||||||+++|+...
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            356899999999999999999999999999999999999999999999999999998654

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

Probab=99.73  E-value=1.7e-18  Score=118.41  Aligned_cols=59  Identities=27%  Similarity=0.463  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHh---ccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSF---TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F---~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ..+++|++|+.+|+.+||.+|   ..++||+..++.+||..+||+++||++||||||+++|+
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            356789999999999999999   99999999999999999999999999999999999986

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

Probab=99.73  E-value=3.2e-18  Score=126.00  Aligned_cols=64  Identities=20%  Similarity=0.293  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhC---------------CCccchhhhhhhhHHHHhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLG---------------VPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------L~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .+++||.|+.||++|+.+||..|..++||+..+|++||..||               |++++|++||||||+++|++..
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            456778999999999999999999999999999999999999               9999999999999999998764

>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=99.72  E-value=6.6e-18  Score=122.12  Aligned_cols=61  Identities=26%  Similarity=0.458  Sum_probs=57.1

Q ss_pred             CCCCCCCCHHHHHHHHHHh---ccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSF---TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F---~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ||+|++|+.+|+.+||.+|   ..++||+..++..||..+||+++||++||||||+|+|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   65 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccc
Confidence            5789999999999999999   899999999999999999999999999999999999987643

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

Probab=99.72  E-value=5.5e-18  Score=123.62  Aligned_cols=57  Identities=26%  Similarity=0.366  Sum_probs=53.9

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      +.+||.+|+..||+.|..++||+..+|.+||..|||+++||+|||||||+++|++..
T Consensus        15 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~   71 (89)
T 2ecb_A           15 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   71 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             hccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHH
Confidence            348999999999999999999999999999999999999999999999999998653

>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=99.71  E-value=8.9e-18  Score=113.33  Aligned_cols=56  Identities=30%  Similarity=0.403  Sum_probs=53.5

Q ss_pred             CCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           20 IKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      +|++||.+|+.+||..|..   ++||+..++..||.++||+++||++||||||+++|+.
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            3689999999999999999   9999999999999999999999999999999999873

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

Probab=99.71  E-value=4.2e-18  Score=119.54  Aligned_cols=63  Identities=21%  Similarity=0.312  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHh-ccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSF-TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F-~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .....++|++++.+|+..||..| ..++||+..+|.+||.++||+++||+|||||||+++|+..
T Consensus         5 ~~~g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            5 SSGGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             ccCCCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            34456778889999999999999 9999999999999999999999999999999999999754

>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=99.71  E-value=1e-17  Score=115.51  Aligned_cols=60  Identities=20%  Similarity=0.284  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      .+++||.||.|+.+|+..|+.+|.. ++||+...|++||.++||++++|+|||||||--.+
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            3467789999999999999999999 99999999999999999999999999999997554

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

Probab=99.71  E-value=5.7e-18  Score=133.98  Aligned_cols=63  Identities=24%  Similarity=0.386  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ..+++||+|++||.+|+..||..|..++||+..+|..||..+||+++||+|||||||+|+|++
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            345667889999999999999999999999999999999999999999999999999999985

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.71  E-value=1.1e-17  Score=121.21  Aligned_cols=60  Identities=30%  Similarity=0.389  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      .+++++|++|+.+|+..||.+|..   ++||+..++..||..+||+++||++||||||+|+|.
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            445667999999999999999999   999999999999999999999999999999999873

>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=99.70  E-value=1.5e-17  Score=119.59  Aligned_cols=65  Identities=23%  Similarity=0.282  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ..++||+|+.|+.+|+.+||.+|..   ++||+..+|.+||..+||+++||++||||||+|+|+...+
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~   71 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQ   71 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHH
Confidence            3456788999999999999999987   5999999999999999999999999999999999886544

>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=99.70  E-value=2e-17  Score=120.49  Aligned_cols=58  Identities=21%  Similarity=0.275  Sum_probs=54.2

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      +++.||.+|+.+||..|..++||+..+|.+||..+||++++|++||||||+|+|++..
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             ccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            4456999999999999999999999999999999999999999999999999998653

>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=99.70  E-value=7.9e-18  Score=135.01  Aligned_cols=62  Identities=23%  Similarity=0.352  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      .+++||+|++||..|+..||..|..++||+..+|..||..+||+++||+|||||||+|+|++
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            35778899999999999999999999999999999999999999999999999999999985

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.70  E-value=9.3e-18  Score=120.65  Aligned_cols=60  Identities=28%  Similarity=0.371  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      +++|++|+.+|+..||.+|..   ++||+..++..||..+||+++||++||||||+|+|+...
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            356677999999999999999   999999999999999999999999999999999998754

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

Probab=99.70  E-value=7.2e-18  Score=135.85  Aligned_cols=66  Identities=21%  Similarity=0.246  Sum_probs=52.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ..+++||+|++||..|+..||..|..++||+..+|.+||..+||+++||+|||||||+|+|+....
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            346677899999999999999999999999999999999999999999999999999999997643

>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=99.69  E-value=3.4e-17  Score=121.97  Aligned_cols=63  Identities=14%  Similarity=0.206  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHh---------------------CCCccchhhhhhhhHHHH
Q 035661           14 PPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQL---------------------GVPARQVAVWYQNKRARW   72 (211)
Q Consensus        14 ~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~l---------------------gL~~rqVkvWFqNRR~r~   72 (211)
                      .+++||.|++|++.|+.+||..|..++||+..+|++||..|                     +|++.+|++||||||+++
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            45677899999999999999999999999999999999999                     799999999999999999


Q ss_pred             hhhh
Q 035661           73 KTQS   76 (211)
Q Consensus        73 k~~~   76 (211)
                      |++.
T Consensus        83 kr~~   86 (102)
T 2da6_A           83 AFRQ   86 (102)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            8865

>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=99.69  E-value=1.8e-17  Score=131.65  Aligned_cols=62  Identities=19%  Similarity=0.359  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      .+.++||+|++||.+|+..||..|..++||+..++.+||.++||+++||++||||||+|+|+
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            34567789999999999999999999999999999999999999999999999999999986

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

Probab=99.69  E-value=8.9e-18  Score=124.81  Aligned_cols=65  Identities=18%  Similarity=0.314  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHH------------------hC---CCccchhhhhhhhHHH
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQ------------------LG---VPARQVAVWYQNKRAR   71 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~------------------lg---L~~rqVkvWFqNRR~r   71 (211)
                      +++++||.|+.||++|+..||..|..++||+..+|++||..                  ||   |++++|++||||||++
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             Hhhhhh
Q 035661           72 WKTQSL   77 (211)
Q Consensus        72 ~k~~~~   77 (211)
                      +|++..
T Consensus        85 ~k~k~~   90 (99)
T 1lfb_A           85 EAFRHK   90 (99)
T ss_dssp             TSCCC-
T ss_pred             HHHhch
Confidence            987763

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

Probab=99.68  E-value=1.2e-17  Score=116.36  Aligned_cols=58  Identities=33%  Similarity=0.534  Sum_probs=54.3

Q ss_pred             CCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661           22 KRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL   79 (211)
Q Consensus        22 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~   79 (211)
                      ..+|..|+..||..|..++||+..+|.+||..+||+++||++||||||+|+|+.....
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~~   66 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSS   66 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSSC
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhhh
Confidence            4689999999999999999999999999999999999999999999999999876543

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

Probab=99.67  E-value=5.2e-17  Score=111.70  Aligned_cols=52  Identities=21%  Similarity=0.380  Sum_probs=49.9

Q ss_pred             CHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        25 t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      |.+|+..||..|..++||+..++.+||..+||+++||++||||||.++|+..
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            6899999999999999999999999999999999999999999999999754

>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=99.66  E-value=6.3e-17  Score=129.14  Aligned_cols=61  Identities=25%  Similarity=0.375  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      .++||+|++|+..|+..||..|..++||+..++.+||..+||+++||+|||||||+|+|+.
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            4667889999999999999999999999999999999999999999999999999999974

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

Probab=99.65  E-value=8.3e-17  Score=110.44  Aligned_cols=55  Identities=15%  Similarity=0.256  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      +..++.+|+..||..|..++||+..+|.+||.++||++++|++||||||+|.++.
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            4556799999999999999999999999999999999999999999999988763

>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=99.65  E-value=5.4e-17  Score=111.35  Aligned_cols=51  Identities=24%  Similarity=0.408  Sum_probs=47.5

Q ss_pred             CHHHHHHHHHHh-ccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           25 NQEQVRVLERSF-TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        25 t~~Ql~~Le~~F-~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      .+.|+..||+.| ..++||+..+|.+||.+|||+++||++||||||+++|+.
T Consensus         8 ~~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            8 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             CchHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            357899999999 678999999999999999999999999999999999864

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

Probab=99.64  E-value=9e-17  Score=129.03  Aligned_cols=65  Identities=23%  Similarity=0.314  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..++.||.|++||.+|+..||..|..++||+..+|..||..+||+++||++||||||+|+|+...
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            34566789999999999999999999999999999999999999999999999999999998654

>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=99.60  E-value=7.1e-16  Score=106.57  Aligned_cols=58  Identities=21%  Similarity=0.271  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhhh
Q 035661           22 KRLNQEQVRVLERSFT---TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL   79 (211)
Q Consensus        22 t~~t~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~~   79 (211)
                      .+|+.+|+.+|+.+|.   .++||+..++.+||..+||+++||++||||||+|+|+...+.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   63 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQ   63 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC---
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHH
Confidence            4799999999999999   999999999999999999999999999999999999876543

>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=99.49  E-value=5.3e-15  Score=122.04  Aligned_cols=62  Identities=16%  Similarity=0.271  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhC---------------------CCccchhhhhhhhHHH
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLG---------------------VPARQVAVWYQNKRAR   71 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------------L~~rqVkvWFqNRR~r   71 (211)
                      ..+++||.|+.|++.|+..||+.|..++||+..+|++||..|+                     |++.+|++||||||++
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            3466788999999999999999999999999999999999999                     9999999999999999


Q ss_pred             Hhh
Q 035661           72 WKT   74 (211)
Q Consensus        72 ~k~   74 (211)
                      +|.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            874

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

Probab=99.43  E-value=6e-14  Score=117.42  Aligned_cols=61  Identities=15%  Similarity=0.240  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhC---------------------CCccchhhhhhhhHH
Q 035661           12 HPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLG---------------------VPARQVAVWYQNKRA   70 (211)
Q Consensus        12 ~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------------L~~rqVkvWFqNRR~   70 (211)
                      ..+++.||.|+.|++.|+..||..|..++||+..+|++||..||                     |++.+|++||+|||.
T Consensus       137 ~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             -----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            34677788999999999999999999999999999999999998                     899999999999998


Q ss_pred             HH
Q 035661           71 RW   72 (211)
Q Consensus        71 r~   72 (211)
                      ..
T Consensus       217 ~~  218 (221)
T 2h8r_A          217 EE  218 (221)
T ss_dssp             TC
T ss_pred             hh
Confidence            64

>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=99.42  E-value=1e-13  Score=95.98  Aligned_cols=46  Identities=17%  Similarity=0.492  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661           26 QEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR   71 (211)
Q Consensus        26 ~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r   71 (211)
                      .+|+..||..|..+++|+..++..||..+||++++|+|||||||++
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5799999999999999999999999999999999999999999974

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

Probab=99.42  E-value=1.6e-13  Score=99.77  Aligned_cols=56  Identities=25%  Similarity=0.314  Sum_probs=52.1

Q ss_pred             CCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           22 KRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        22 t~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      .-|+.+++.+|+.+|..   ++||+..+|.+||.++||+++||++||+|+|.|.++...
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~   68 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDML   68 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHH
Confidence            46899999999999987   999999999999999999999999999999999987643

>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=99.29  E-value=8.8e-13  Score=117.34  Aligned_cols=55  Identities=31%  Similarity=0.498  Sum_probs=52.1

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      +.++.|+..|+..||+.|..++||+..+|.+||.++||+++||++||||||+|+|
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            3467899999999999999999999999999999999999999999999999876

>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=98.62  E-value=6.2e-09  Score=63.41  Aligned_cols=22  Identities=36%  Similarity=0.984  Sum_probs=19.1

Q ss_pred             cchhhhhhhhHHHHhhhhhhhh
Q 035661           59 RQVAVWYQNKRARWKTQSLELD   80 (211)
Q Consensus        59 rqVkvWFqNRR~r~k~~~~~~~   80 (211)
                      +||+|||||||+|||++..+..
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            6999999999999999886543

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

Probab=94.29  E-value=0.028  Score=38.42  Aligned_cols=44  Identities=18%  Similarity=0.343  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661           24 LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQN   67 (211)
Q Consensus        24 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqN   67 (211)
                      .++.-.+.|+..|...+.+.......|+.+..|+..||+-||-.
T Consensus        13 ~~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           13 PPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            34445689999999999999999999999999999999999954

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=93.40  E-value=0.33  Score=34.52  Aligned_cols=49  Identities=24%  Similarity=0.250  Sum_probs=37.9

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILFAKL  120 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~~~~  120 (211)
                      |+|.+++.   ....+..+...|..+|..|+.++..|..|+..+...+...+
T Consensus        29 rSR~krk~---r~~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr~ll~~~p   77 (87)
T 1hjb_A           29 KSRDKAKM---RNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFKQLP   77 (87)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCc
Confidence            55655555   34556677788899999999999999999999998888655

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=92.83  E-value=0.52  Score=31.24  Aligned_cols=46  Identities=13%  Similarity=0.228  Sum_probs=36.5

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF  117 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~  117 (211)
                      |+|.|++.   ....+..+.+.+..+|..|+.++..|..|+..+.+.+.
T Consensus        16 R~R~KKk~---~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~ll~   61 (63)
T 1ci6_A           16 RYRQKKRA---EQEALTGECKELEKKNEALKERADSLAKEIQYLKDLIE   61 (63)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            55544443   56677888888999999999999999999998887664

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=92.07  E-value=0.85  Score=30.12  Aligned_cols=46  Identities=20%  Similarity=0.248  Sum_probs=34.5

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF  117 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~  117 (211)
                      |+|.|++.   ....+..+.+.+..+|..|..++..|..++..+...+.
T Consensus        16 rcR~rKk~---~~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~l~   61 (63)
T 2wt7_A           16 KCRNRRRE---LTDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFILA   61 (63)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444433   55677778888888999999999999988888776654

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=91.97  E-value=0.79  Score=29.98  Aligned_cols=45  Identities=27%  Similarity=0.392  Sum_probs=34.2

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEIL  116 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l  116 (211)
                      ++|.|++.   ....+..+.+.+..+|..|..++..|..++..+...+
T Consensus        15 k~R~rKk~---~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk~~l   59 (61)
T 1t2k_D           15 RSRQKRKV---WVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLL   59 (61)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44444433   5567777888888999999999999999988887665

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A

Probab=91.90  E-value=0.28  Score=34.18  Aligned_cols=47  Identities=26%  Similarity=0.312  Sum_probs=34.8

Q ss_pred             hHHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           68 KRARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEILF  117 (211)
Q Consensus        68 RR~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l~  117 (211)
                      +|+|.+++.   ....+......|..+|..|..++..|..|+..+...+.
T Consensus        28 krSR~krk~---r~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr~ll~   74 (78)
T 1gu4_A           28 RKSRDKAKM---RNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFK   74 (78)
T ss_dssp             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356666655   34456667778888999999999999999888876543

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=89.49  E-value=0.62  Score=30.64  Aligned_cols=45  Identities=16%  Similarity=0.302  Sum_probs=30.3

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEELRQAQEIL  116 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~~~~~~~l  116 (211)
                      ++|.|++.   ....+..+.+.+..+|..|..++..|..++..+.+.+
T Consensus        15 k~R~rKk~---~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~~l   59 (62)
T 1jnm_A           15 KSRKRKLE---RIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKV   59 (62)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC---
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45544443   5566777777888888888888888888877665544

>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D

Probab=85.96  E-value=1.5  Score=29.06  Aligned_cols=38  Identities=26%  Similarity=0.378  Sum_probs=22.0

Q ss_pred             HHHHhhhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 035661           69 RARWKTQSLELDYNTIQVKLENALADKRRLEKDVKLLKEEL  109 (211)
Q Consensus        69 R~r~k~~~~~~~~~~~~~~~~~l~~e~~~l~~e~~~l~~e~  109 (211)
                      |+|.|++.   ....+..+.+.|..+|..|..++..|..++
T Consensus        23 rsR~RK~~---~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l   60 (63)
T 2dgc_A           23 RSRARKLQ---RMKQLEDKVEELLSKNYHLENEVARLKKLV   60 (63)
T ss_dssp             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55544443   445556666666666666666666666544

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=85.72  E-value=0.29  Score=34.32  Aligned_cols=43  Identities=19%  Similarity=0.254  Sum_probs=31.4

Q ss_pred             CCCCCHHHHHHHHHHhccC-CCCCHHHHHHHHHHhCCCccchhhhhhh
Q 035661           21 KKRLNQEQVRVLERSFTTK-KKLDTELKLKLANQLGVPARQVAVWYQN   67 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~-~~p~~~~r~~La~~lgL~~rqVkvWFqN   67 (211)
                      |..||.++....-..|... ..    ...++|+.+|+++..|..|...
T Consensus         3 r~~ys~e~k~~~v~~~~~~~g~----s~~~ia~~~gIs~~tl~rW~~~   46 (97)
T 2jn6_A            3 TKTYSEEFKRDAVALYENSDGA----SLQQIANDLGINRVTLKNWIIK   46 (97)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGS----CHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCC----hHHHHHHHHCcCHHHHHHHHHH
Confidence            3578898876665555332 22    3568999999999999999853

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

Probab=85.62  E-value=1.6  Score=30.05  Aligned_cols=44  Identities=16%  Similarity=0.251  Sum_probs=32.4

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ   66 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq   66 (211)
                      |+.+..|+.++....-..|. ...    ...++|+++|+++..|..|..
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~-~g~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIH-DGE----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHH-HTC----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHH
Confidence            45677899998665555564 222    256889999999999999974

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

Probab=82.79  E-value=0.99  Score=28.73  Aligned_cols=45  Identities=13%  Similarity=0.181  Sum_probs=31.8

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ   66 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq   66 (211)
                      |..|+.+........+.. ..+......++|+++|+++..|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            457999888777554433 332122256899999999999999975

>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=81.32  E-value=2.5  Score=30.71  Aligned_cols=49  Identities=16%  Similarity=0.290  Sum_probs=38.0

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR   71 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r   71 (211)
                      +|+.||.++...+-..+...+.+..   .++|+.+|+++..|..|..++...
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhhh
Confidence            5788999998777777755555543   368999999999999999776543

---

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	211
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	8e-13
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	1e-12
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-12
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	3e-12
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	6e-12
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-11
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-11
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	3e-11
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	5e-11
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	1e-10
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-10
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-10
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-10
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-10
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	3e-10
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	4e-10
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	5e-10
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	5e-10
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	5e-10
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	9e-10
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-09
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	5e-09
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	6e-09
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	7e-09
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	8e-09
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-08
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	1e-08
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	7e-08
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	1e-07
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-07
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-07
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-05

>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 = 58.6 bits (142), Expect = 8e-13
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 21 KKRLNQEQVRVLERSFTTKKK---LDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
            R  +E VR+LE  F    +   LDT+    L     +   Q+  W  N+R + KT +
Sbjct: 2  GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTIT 60

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (141), Expect = 1e-12
 Identities = 20/51 (39%), Positives = 31/51 (60%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          R + +Q   LE+ F T+K L    + +LA  L +  RQV  W+QN+RA+W+
Sbjct: 6  RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 56

>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 = 57.5 bits (139), Expect = 3e-12
 Identities = 15/52 (28%), Positives = 31/52 (59%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
           + Q   LE+ F   + L    ++++A+ L +  RQ+ +W+QN+R +WK ++
Sbjct: 5  TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 57.5 bits (139), Expect = 3e-12
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79
           LN++Q+  L   +    + D  +K +L    G+  R + VW+QNKR + K +S+ +
Sbjct: 9  VLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMM 65

>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 = 56.8 bits (137), Expect = 6e-12
 Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          KKR   ++ Q+R LER +   K +  + + K++    +  RQ+ +W+QN+R + K
Sbjct: 3  KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 57

>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 = 54.9 bits (132), Expect = 2e-11
 Identities = 16/51 (31%), Positives = 29/51 (56%)

Query: 25 NQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
           ++Q+  LE+ F  +  +    + +LA QL +P   + VW+QN+R + K Q
Sbjct: 7  TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>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 = 55.6 bits (134), Expect = 2e-11
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 5  DTQQNQKHPPPNKLNIKKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVA 62
          +   N  H    +   KKR    + Q   LE+ F     L  + + ++A  L +  RQV 
Sbjct: 2  NPAANWLHARSTR---KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK 58

Query: 63 VWYQNKRARWKTQSLE 78
          +W+QN+R + K  + +
Sbjct: 59 IWFQNRRMKMKKINKD 74

>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 = 54.5 bits (131), Expect = 3e-11
 Identities = 18/53 (33%), Positives = 31/53 (58%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          K  ++ +    LE+ F  K+ L+++ K ++A + G+   QV VW+ NKR R K
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 54.4 bits (131), Expect = 5e-11
 Identities = 16/54 (29%), Positives = 30/54 (55%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
             QEQ+  LE+ F      D   + +LA ++ +P  ++ VW+ N+RA+W+ + 
Sbjct: 7  SFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 60

>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 = 53.0 bits (127), Expect = 1e-10
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          K R      Q+  LER F  K+ L    + + ++ L +   QV +W+QN+RA+ K
Sbjct: 2  KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56

>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 = 53.5 bits (128), Expect = 2e-10
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 1  MDIADTQQNQKHPPPNKLNIKKR----LNQEQVRVLERSFTTKKKLDTELKLKLANQLGV 56
          M +              L             Q+  LE+ F   K L    ++++A  L +
Sbjct: 7  MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 66

Query: 57 PARQVAVWYQNKRARWKTQSLE 78
             QV +W+QN+R + K +  E
Sbjct: 67 NETQVKIWFQNRRMKQKKRERE 88

>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 = 52.0 bits (125), Expect = 2e-10
 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 27 EQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          +   +LE+ FT   K  D +    L+ QL    R +  W++ +R + K
Sbjct: 3  QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 50

>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 = 52.6 bits (126), Expect = 2e-10
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE 78
          + R      Q+  LE+ F   + L       L+ +L +   QV +W++N+R R K QS +
Sbjct: 3  RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 62

>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 = 52.2 bits (125), Expect = 3e-10
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 20 IKKR----LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
          ++++     +Q QV  LER F  +K L    +  LA+ + +   QV +W+QN R + K Q
Sbjct: 1  MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

Query: 76 SLE 78
          + +
Sbjct: 61 AKD 63

>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 = 52.3 bits (125), Expect = 3e-10
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 21 KKRLNQEQVRVLERSF-TTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
             + ++QV +LE +F    K  D      +A + G+   Q   W++ + A W+  
Sbjct: 5  AATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 51.7 bits (124), Expect = 4e-10
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 21 KKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
                E    LE+ F +  K  D +    L+ QL    R++  W++++R + K
Sbjct: 5  SPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 51.4 bits (123), Expect = 5e-10
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR 71
          + R   + EQ+  L+R F   + L    + +L+++LG+   Q+ +W+QN RA+
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 51.5 bits (123), Expect = 5e-10
 Identities = 13/53 (24%), Positives = 29/53 (54%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
              +Q++ LE +F   +  D   + ++A    +   +V VW++N+RA+W+ +
Sbjct: 7  HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 51.5 bits (123), Expect = 5e-10
 Identities = 16/53 (30%), Positives = 29/53 (54%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ 75
            +  Q+  LER+F   +  D   + +LA +  +   ++ VW+QN+RAR + Q
Sbjct: 8  TFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

>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 = 51.2 bits (122), Expect = 9e-10
 Identities = 19/70 (27%), Positives = 30/70 (42%)

Query: 13 PPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARW 72
           P  K   +    + Q   LER F  ++ L    +  LA+ + +   QV +W+QN R + 
Sbjct: 5  LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64

Query: 73 KTQSLELDYN 82
          K    E  Y 
Sbjct: 65 KRAQNEKGYE 74

>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 = 50.7 bits (121), Expect = 1e-09
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          K+R  ++      LER F    K  ++  +++A +L +    V VW+ N+R R K
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 55

>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 = 49.2 bits (117), Expect = 5e-09
 Identities = 9/74 (12%), Positives = 20/74 (27%), Gaps = 4/74 (5%)

Query: 4  ADTQQNQKHPPPNKLNIKKRLNQEQVRVLERSFTTK----KKLDTELKLKLANQLGVPAR 59
            +  N           + +   EQ   +           +K D     +   + GV  +
Sbjct: 4  GSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQ 63

Query: 60 QVAVWYQNKRARWK 73
           + +W  N +    
Sbjct: 64 VLKIWMHNNKNSGP 77

>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 = 48.3 bits (115), Expect = 6e-09
 Identities = 13/47 (27%), Positives = 22/47 (46%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR 69
               Q R L   F   K+   EL++ ++ QLG+    V+ ++ N R
Sbjct: 4  VFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 48.2 bits (115), Expect = 7e-09
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 21 KKRLNQEQVRVLERSFTTKKK---LDTELKLKLANQLGVPARQVAVWYQNKRAR 71
          +  L +    V+               + K ++A Q  +   QV  W+ N R R
Sbjct: 6  RGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 59

>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 = 48.6 bits (115), Expect = 8e-09
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLELD 80
           K    EQ+RVL+ SF     L  E   +L  Q  +  R++  W+  K+     +  +++
Sbjct: 8  FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 67

Query: 81 YN 82
           +
Sbjct: 68 ID 69

>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 = 47.7 bits (113), Expect = 1e-08
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS 76
          +KR  +       LE  F    K   +    +ANQLG+    V VW+ N+R + K  S
Sbjct: 10 RKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67

>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 = 48.0 bits (114), Expect = 1e-08
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 21 KKRLNQEQVRVLERSFT---TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL 77
          ++  N++   +L   F    +      E K +LA + G+   QV+ W+ NKR R+K    
Sbjct: 5  RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG 64

Query: 78 ELD 80
          +  
Sbjct: 65 KFQ 67

>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 = 46.2 bits (109), Expect = 7e-08
 Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 17/73 (23%)

Query: 21 KKR--LNQEQVRVLERSFTTKKKLDTELKLKLANQL---------------GVPARQVAV 63
            R    +E + V+E  F   +  D   + ++AN                  V + +V  
Sbjct: 2  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 64 WYQNKRARWKTQS 76
          W+ N+R   K ++
Sbjct: 62 WFANRRKEIKRRA 74

>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 = 45.5 bits (107), Expect = 1e-07
 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 21 KKRLNQEQVRVLERSFT-TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
          + +++ E + +L+          D E    L+ QL +P   +  ++QN+R   K
Sbjct: 11 RTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 1e-07
 Identities = 15/59 (25%), Positives = 26/59 (44%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLEL 79
           KR  +EQ+ +L+  F   +    E   KL    G+P  ++  W+ + R   K   L+ 
Sbjct: 7  GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKW 65

>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 = 44.5 bits (105), Expect = 2e-07
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 23 RLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK 73
           +       LE+SF   +K  +E    +A QL +    + VW+ N+R + K
Sbjct: 4  SIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 54

>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 = 39.4 bits (91), Expect = 2e-05
 Identities = 9/77 (11%), Positives = 23/77 (29%), Gaps = 21/77 (27%)

Query: 21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQL---------------------GVPAR 59
          + +      ++L +++  +K    E +  L  +                       V   
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 60 QVAVWYQNKRARWKTQS 76
          +V  W+ N+R     + 
Sbjct: 61 RVYNWFANRRKEEAFRH 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	211
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.85
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.84
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.84
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.83
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.83
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.83
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.83
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.82
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.82
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.81
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.81
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.81
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.8
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.8
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.79
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.79
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.78
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.78
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.77
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.75
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.75
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.74
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.71
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.71
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.7
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.69
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.68
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.65
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.63
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.61
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.61
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.57
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	89.95
d1hlva1	66	DNA-binding domain of centromere binding protein B	88.6

>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=99.85  E-value=1.3e-21  Score=137.53  Aligned_cols=71  Identities=21%  Similarity=0.330  Sum_probs=63.4

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661            8 QNQKHPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus         8 ~~~~~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      .......+..||+|++||++|+.+||.+|..++||+..++..||..|||+++||++||||||+++|+....
T Consensus         4 ~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_           4 AANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             TTTSCCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            33444555667889999999999999999999999999999999999999999999999999999987643

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.7e-22  Score=132.20  Aligned_cols=57  Identities=25%  Similarity=0.502  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ||+|++||.+|+.+||..|..++||+..++.+||..|||+++||++||||||+++|+
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            678999999999999999999999999999999999999999999999999999885

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=1.3e-21  Score=130.40  Aligned_cols=58  Identities=28%  Similarity=0.481  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ||+|++||++|+.+||..|..++||+..++.+||..|||++++|++||||||+++|+.
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            5689999999999999999999999999999999999999999999999999999873

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.7e-21  Score=129.46  Aligned_cols=57  Identities=35%  Similarity=0.625  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      |+.|++||++|+.+||..|..|+||+..++.+||..|||+++||++||||||+++|+
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            578999999999999999999999999999999999999999999999999999985

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.83  E-value=2.3e-21  Score=132.86  Aligned_cols=61  Identities=26%  Similarity=0.437  Sum_probs=57.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ||.|++||.+|+.+||..|..++||+..++.+||..|||++++|++||||||+++|+....
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            4678999999999999999999999999999999999999999999999999999987643

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=2.8e-21  Score=127.84  Aligned_cols=55  Identities=27%  Similarity=0.649  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ||.||++|+..||..|..++||+..++.+||..|||++++|++||||||+|+|++
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            7899999999999999999999999999999999999999999999999999974

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.83  E-value=3e-21  Score=128.23  Aligned_cols=56  Identities=27%  Similarity=0.530  Sum_probs=54.6

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      |.|+.||++|+..||..|..++||+..++.+||..+||++++|++||||||+++|+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            57899999999999999999999999999999999999999999999999999986

>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=99.82  E-value=6.6e-21  Score=129.80  Aligned_cols=61  Identities=26%  Similarity=0.474  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      |+||.|++||++|+.+||..|..++||+..++..||..|||+++||++||||+|+++|+..
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            4678999999999999999999999999999999999999999999999999999999865

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.82  E-value=1.8e-21  Score=136.81  Aligned_cols=66  Identities=26%  Similarity=0.379  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           12 HPPPNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        12 ~~~~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ..++++||.|++||++|+.+||.+|..++||+..++.+||..|||+++||++||||||+++|+...
T Consensus         4 g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   69 (77)
T d1vnda_           4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhh
Confidence            455667789999999999999999999999999999999999999999999999999999997654

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.81  E-value=7.3e-21  Score=124.55  Aligned_cols=53  Identities=28%  Similarity=0.594  Sum_probs=51.4

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHH
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRAR   71 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r   71 (211)
                      |+|+.||++|+..||..|..++||+..+|.+||..|||+++||++||||||+|
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            57899999999999999999999999999999999999999999999999985

>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=99.81  E-value=1.8e-20  Score=128.68  Aligned_cols=60  Identities=27%  Similarity=0.604  Sum_probs=57.2

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ||.|++||++|+.+||..|..++||+..++..||..+||++++|++||||+|+++|+...
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            678999999999999999999999999999999999999999999999999999998653

>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=99.81  E-value=8.1e-21  Score=130.43  Aligned_cols=61  Identities=31%  Similarity=0.458  Sum_probs=58.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           17 KLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        17 ~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      +||.|++||+.|+.+||..|..++||+..++..||..|||++++|++||||||+++|+...
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            4678999999999999999999999999999999999999999999999999999998754

>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=99.80  E-value=2.2e-20  Score=134.35  Aligned_cols=62  Identities=24%  Similarity=0.474  Sum_probs=55.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           15 PNKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        15 ~~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      .+++|.|++||.+|+.+||..|..++||+..++++||..|||++++|+|||||||+++|+..
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            44567899999999999999999999999999999999999999999999999999999865

>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=99.80  E-value=1.1e-20  Score=126.65  Aligned_cols=58  Identities=22%  Similarity=0.524  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ||.|++||++|+.+||..|..++||+..++..||..+||++++|++||||+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            5789999999999999999999999999999999999999999999999999999975

>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=99.79  E-value=4.8e-20  Score=127.79  Aligned_cols=59  Identities=22%  Similarity=0.464  Sum_probs=55.6

Q ss_pred             CCCCCCCCHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      ++.|++||.+|+.+||..|.. ++||+..++++||.++||++++|++||||||+++|+..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            578999999999999999986 67999999999999999999999999999999998864

>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=99.79  E-value=3e-20  Score=126.87  Aligned_cols=61  Identities=28%  Similarity=0.534  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +.+|.|++||.+|+.+||..|..++||+..++.+||.++||++++|++||||||++.|+..
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999999999999999998865

>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=99.78  E-value=6.3e-20  Score=122.16  Aligned_cols=57  Identities=25%  Similarity=0.425  Sum_probs=55.1

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      |+|++|+.+|+.+||..|..++||+..++.+||.++||++++|++||||||+++|+.
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

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=8.3e-20  Score=124.97  Aligned_cols=60  Identities=25%  Similarity=0.351  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      .+||+|++||.+|+..||..|..++||+..++.+||.++||++++|++||||+|+++|+.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            345789999999999999999999999999999999999999999999999999999874

>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=99.77  E-value=1.3e-19  Score=118.52  Aligned_cols=53  Identities=34%  Similarity=0.552  Sum_probs=51.5

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      |++||++|+.+||..|..++||+..++.+||..+||+++||++||||||+|.|
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            68999999999999999999999999999999999999999999999999875

>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=99.75  E-value=4.6e-19  Score=125.78  Aligned_cols=60  Identities=22%  Similarity=0.320  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhC---------------CCccchhhhhhhhHHHHhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLG---------------VPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------L~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ||+|++||++|+.+||.+|..++||+..+|++||..+|               |++.+|++||||||+++|++..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            57899999999999999999999999999999999875               9999999999999999999763

>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=99.75  E-value=5.1e-19  Score=122.25  Aligned_cols=60  Identities=20%  Similarity=0.290  Sum_probs=55.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           16 NKLNIKKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        16 ~~kr~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      ..+|+|++||++|+.+||.+|.. ++||+..++++||.++||+++||++||||+|++.|+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            34578999999999999999974 8999999999999999999999999999999998864

>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=99.74  E-value=6.2e-19  Score=116.90  Aligned_cols=56  Identities=25%  Similarity=0.392  Sum_probs=54.1

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhh
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQ   75 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~   75 (211)
                      +||+|+.+|+..||..|..++||+..++.+||.++||+++||++||||||+++|+.
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            58999999999999999999999999999999999999999999999999999874

>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=99.71  E-value=1.6e-18  Score=111.88  Aligned_cols=50  Identities=26%  Similarity=0.433  Sum_probs=48.8

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhH
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKR   69 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR   69 (211)
                      +|++||++|+.+||..|..++||+..++.+||.++||++++|++||||||
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

>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=99.71  E-value=2.1e-18  Score=121.83  Aligned_cols=62  Identities=13%  Similarity=0.195  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHhcc----CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           13 PPPNKLNIKKRLNQEQVRVLERSFTT----KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        13 ~~~~~kr~Rt~~t~~Ql~~Le~~F~~----~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      ...++||.|++||.+|++.|+.+|..    ++||+..++++||.+|||++++|+|||||+|.+.|.
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            34556678999999999999888886    789999999999999999999999999999988764

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=6.7e-18  Score=118.03  Aligned_cols=58  Identities=26%  Similarity=0.366  Sum_probs=53.1

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSLE   78 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~~   78 (211)
                      ++++|++|+.+||.+|..++||+..++++||..+||++++|++||||||++.|+....
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~   65 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   65 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHh
Confidence            3446999999999999999999999999999999999999999999999998876544

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.2e-17  Score=115.78  Aligned_cols=60  Identities=27%  Similarity=0.456  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhhh
Q 035661           18 LNIKKRLNQEQVRVLERSFT---TKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQSL   77 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~~   77 (211)
                      ||+|+.||++|+.+||.+|.   .+|||+..++.+||.++||+++||++||+|+|.|.|+...
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            57889999999999999997   4899999999999999999999999999999999987553

>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=99.68  E-value=1.8e-17  Score=115.85  Aligned_cols=58  Identities=24%  Similarity=0.342  Sum_probs=54.3

Q ss_pred             CCCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhhhh
Q 035661           19 NIKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~~~   76 (211)
                      +.++++|.+|+.+||..|..|+||+..++..||..+||++++|++||+|+|+++|+..
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            3556789999999999999999999999999999999999999999999999999754

>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=99.65  E-value=2.7e-17  Score=106.86  Aligned_cols=50  Identities=26%  Similarity=0.435  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           25 NQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        25 t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      |.+|+.+||.+|.. ++||+..++..||.++||++++|++||||||+++|+
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            57899999999987 689999999999999999999999999999999875

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.63  E-value=5.7e-17  Score=113.74  Aligned_cols=56  Identities=16%  Similarity=0.295  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhC---------------------CCccchhhhhhhhHHHHhhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLG---------------------VPARQVAVWYQNKRARWKTQS   76 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg---------------------L~~rqVkvWFqNRR~r~k~~~   76 (211)
                      |++||++|+.+||.+|..++||+..+|+.||.+|+                     |++.+|++||+|||.+.|++.
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            68999999999999999999999999999999994                     899999999999999998764

>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=99.61  E-value=3.4e-16  Score=104.46  Aligned_cols=53  Identities=32%  Similarity=0.459  Sum_probs=49.3

Q ss_pred             CCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHhh
Q 035661           22 KRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWKT   74 (211)
Q Consensus        22 t~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k~   74 (211)
                      .+||.+|+.+|+.+|..   +|||+..++.+||.++||+++||++||+|+|.|.|.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            45999999999999965   579999999999999999999999999999998875

>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=99.61  E-value=1.1e-16  Score=106.60  Aligned_cols=55  Identities=24%  Similarity=0.335  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           19 NIKKRLNQEQVRVLERSFTT-KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        19 r~Rt~~t~~Ql~~Le~~F~~-~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      |.+++++.+|..+||.+|.. ++||+..++..||.++||+++||++||||||+++|
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            57788999999999999976 68999999999999999999999999999999986

>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=99.57  E-value=1.7e-15  Score=101.71  Aligned_cols=56  Identities=21%  Similarity=0.238  Sum_probs=51.7

Q ss_pred             CCCCCCCCHHHHHHHHHHhcc---CCCCCHHHHHHHHHHhCCCccchhhhhhhhHHHHh
Q 035661           18 LNIKKRLNQEQVRVLERSFTT---KKKLDTELKLKLANQLGVPARQVAVWYQNKRARWK   73 (211)
Q Consensus        18 kr~Rt~~t~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgL~~rqVkvWFqNRR~r~k   73 (211)
                      ||+|+.|+++|+.+|+.+|..   +|||+..++..||.++||+.+||++||+|+|.|..
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            467789999999999999985   79999999999999999999999999999998754

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=89.95  E-value=0.048  Score=36.72  Aligned_cols=43  Identities=19%  Similarity=0.254  Sum_probs=30.4

Q ss_pred             CCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhh
Q 035661           21 KKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQ   66 (211)
Q Consensus        21 Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFq   66 (211)
                      |+.|+++.....-+.+....   .....++|+++|+++..|..|.+
T Consensus         3 rk~Ys~EfK~~aV~l~~~~~---g~s~~~vA~~lGIs~~tl~~W~k   45 (89)
T d2jn6a1           3 TKTYSEEFKRDAVALYENSD---GASLQQIANDLGINRVTLKNWII   45 (89)
T ss_dssp             CCCCCHHHHHHHHHHHTTGG---GSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcC---CCcHHHHHHHHCCCHHHHHHHHH
Confidence            45699987766555553321   12256799999999999999975

>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=88.60  E-value=0.35  Score=30.92  Aligned_cols=46  Identities=15%  Similarity=0.297  Sum_probs=37.3

Q ss_pred             CCCCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 035661           20 IKKRLNQEQVRVLERSFTTKKKLDTELKLKLANQLGVPARQVAVWYQNK   68 (211)
Q Consensus        20 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~rqVkvWFqNR   68 (211)
                      +|..+|-++...+=+.|+..+...   ..+||+.+|+....|..|..|+
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHH
Confidence            355789888777777888877655   5579999999999999999884