Psyllid ID: psy4877

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSASMLDDSQSPRDAPG
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
HHHHHHHcccHHHHHHHHHHHHHcHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccHHHHHcccccccccccccccccccccccccccccccccHcccccccccccc
Coil and Loop (DISEMBL)
MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMvahnrptgfyfpgggplifgaqhgsptapyffsasmlddsqsprdapg
Flexible Loop (DISEMBL)
melskllnltevqiktwfqnrrtkwkYVDKYLSVSKRMElskllnltevqiktwfqnrrTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSASMLDDSQSPRDAPG
Low Complexity Region (SEG)
MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSASMLDDSQSPRDAPG
Disordered region (IsUnstruct)
*****LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFF****************
Disordered Region (DISOPRED)
*****************FQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK***********************************************************
Disordered Region (DISEMBL)
MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSASM************
Disordered Region (DISPRO)
MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSASMLDD**S******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSASMLDDSQSPRDAPG
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	120	2.2.26 [Sep-21-2011]
P26797	199	Homeobox protein ceh-19 O	no	N/A	0.441	0.266	0.660	2e-14
Q9BZE3	327	BarH-like 1 homeobox prot	yes	N/A	0.383	0.140	0.630	2e-11
P63156	327	BarH-like 1 homeobox prot	yes	N/A	0.383	0.140	0.630	2e-11
P63157	327	BarH-like 1 homeobox prot	yes	N/A	0.383	0.140	0.630	2e-11
Q8VIB5	384	BarH-like 2 homeobox prot	no	N/A	0.516	0.161	0.430	2e-11
O88181	384	BarH-like 2 homeobox prot	no	N/A	0.516	0.161	0.430	3e-11
Q9NY43	387	BarH-like 2 homeobox prot	no	N/A	0.516	0.160	0.430	3e-11
Q24256	645	Homeobox protein B-H2 OS=	no	N/A	0.375	0.069	0.6	2e-10
Q24255	544	Homeobox protein B-H1 OS=	no	N/A	0.375	0.082	0.577	3e-10
P22544	606	Homeobox protein B-H1 OS=	N/A	N/A	0.375	0.074	0.555	2e-09

>sp|P26797|HM19_CAEEL Homeobox protein ceh-19 OS=Caenorhabditis elegans GN=ceh-19 PE=2 SV=2

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/53 (66%), Positives = 43/53 (81%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTG 80
            DKYLSV+KR++LS+ LNLTE QIKTWFQNRRTKWKKQL S ++ +  + PT 
Sbjct: 115 TDKYLSVNKRIQLSQTLNLTETQIKTWFQNRRTKWKKQLTSSIRQMVKDAPTS 167

Caenorhabditis elegans (taxid: 6239)

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

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 37/46 (80%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAH 75
           KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A 
Sbjct: 201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLAE 246

Homo sapiens (taxid: 9606)

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

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 37/46 (80%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAH 75
           KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A 
Sbjct: 201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLAE 246

Rattus norvegicus (taxid: 10116)

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

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 37/46 (80%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAH 75
           KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A 
Sbjct: 201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLAE 246

Mus musculus (taxid: 10090)

>sp|Q8VIB5|BARH2_MOUSE BarH-like 2 homeobox protein OS=Mus musculus GN=Barhl2 PE=2 SV=2

 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 49/86 (56%), Gaps = 24/86 (27%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFY------F 83
           KYLSV  RM+L+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A     G Y      F
Sbjct: 252 KYLSVQDRMDLAAALNLTDTQVKTWYQNRRTKWKRQTAVGLELLAE---AGNYSALQRMF 308

Query: 84  PGGGPLIFGAQHGSPTAPYFFSASML 109
           P               +PYF+  S+L
Sbjct: 309 P---------------SPYFYHPSLL 319

Potential regulator of neural basic helix-loop-helix genes. It may down-regulate expression of ASCL1 and, within the thalamus, up-regulate NGN2, thereby regulating distinct patterns of neuronal differentiation.

Mus musculus (taxid: 10090)

>sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 49/86 (56%), Gaps = 24/86 (27%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFY------F 83
           KYLSV  RM+L+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A     G Y      F
Sbjct: 252 KYLSVQDRMDLAAALNLTDTQVKTWYQNRRTKWKRQTAVGLELLAE---AGNYSALQRMF 308

Query: 84  PGGGPLIFGAQHGSPTAPYFFSASML 109
           P               +PYF+  S+L
Sbjct: 309 P---------------SPYFYHPSLL 319

Potential regulator of neural basic helix-loop-helix genes. It may down-regulate expression of ASCL1 and, within the thalamus, up-regulate NGN2, thereby regulating distinct patterns of neuronal differentiation.

Rattus norvegicus (taxid: 10116)

>sp|Q9NY43|BARH2_HUMAN BarH-like 2 homeobox protein OS=Homo sapiens GN=BARHL2 PE=2 SV=2

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 49/86 (56%), Gaps = 24/86 (27%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFY------F 83
           KYLSV  RM+L+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A     G Y      F
Sbjct: 255 KYLSVQDRMDLAAALNLTDTQVKTWYQNRRTKWKRQTAVGLELLAE---AGNYSALQRMF 311

Query: 84  PGGGPLIFGAQHGSPTAPYFFSASML 109
           P               +PYF+  S+L
Sbjct: 312 P---------------SPYFYHPSLL 322

Potential regulator of neural basic helix-loop-helix genes.

Homo sapiens (taxid: 9606)

>sp|Q24256|BARH2_DROME Homeobox protein B-H2 OS=Drosophila melanogaster GN=B-H2 PE=1 SV=3

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 36/45 (80%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
           KYLSV  RMEL+  L L++ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct: 403 KYLSVQDRMELANKLELSDCQVKTWYQNRRTKWKRQTAVGLELLA 447

B-H1 and B-H2 are regulated by members of the wg signaling pathway; wg and dpp. B-H1 and B-H2 are coexpressed and functionally required in R1 and R6 receptor cells and primary pigment cells for normal eye development. Coexpression is also required for the fate determination of external sensory organs, formation of notal microchaetae, formation of presutural macrochaetae, antennal development and for distal leg morphogenesis; segmentation and specification of tarsal segments 3-5.

Drosophila melanogaster (taxid: 7227)

>sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 26/45 (57%), Positives = 37/45 (82%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
           KYLSV +R EL+  L+L++ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct: 322 KYLSVQERQELAHKLDLSDCQVKTWYQNRRTKWKRQTAVGLELLA 366

B-H1 and B-H2 are regulated by members of the wg signaling pathway; wg and dpp. B-H1 and B-H2 are coexpressed and functionally required in R1 and R6 receptor cells and primary pigment cells for normal eye development. Coexpression is also required for the fate determination of external sensory organs, formation of notal microchaetae, formation of presutural macrochaetae, antennal development and for distal leg morphogenesis; segmentation and specification of tarsal segments 3-5.

Drosophila melanogaster (taxid: 7227)

>sp|P22544|BARH1_DROAN Homeobox protein B-H1 OS=Drosophila ananassae GN=B-H1 PE=2 SV=1

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 36/45 (80%)

Query: 30  KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
           KYLSV +R EL+  L+L++ Q+KTW+QNRRTKW +Q A  L+++A
Sbjct: 354 KYLSVQERQELAHKLDLSDCQVKTWYQNRRTKWMRQTAVGLELLA 398

Functionally required in R1 and R6 receptor cells and primary pigment cells for normal eye development.

Drosophila ananassae (taxid: 7217)

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	120
322786583	305	hypothetical protein SINV_03332 [Solenop	0.533	0.209	0.641	5e-17
156549094	331	PREDICTED: homeobox protein MSX-1-like [	0.616	0.223	0.646	6e-17
328704025	320	PREDICTED: homeobox protein pv.1-like [A	0.45	0.168	0.807	2e-16
340725237	387	PREDICTED: hypothetical protein LOC10065	0.541	0.167	0.613	2e-16
332017372	307	Homeobox protein ceh-19 [Acromyrmex echi	0.525	0.205	0.636	2e-16
350403982	432	PREDICTED: hypothetical protein LOC10074	0.65	0.180	0.561	2e-16
307175871	308	Homeobox protein ceh-19 [Camponotus flor	0.533	0.207	0.628	2e-16
383862479	329	PREDICTED: homeobox protein engrailed-2b	0.525	0.191	0.636	3e-16
307191995	188	Homeobox protein ceh-19 [Harpegnathos sa	0.533	0.340	0.628	3e-16
110763697	208	PREDICTED: motor neuron and pancreas hom	0.641	0.370	0.579	5e-16

>gi|322786583|gb|EFZ12978.1| hypothetical protein SINV_03332 [Solenopsis invicta]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 50/78 (64%), Positives = 54/78 (69%), Gaps = 14/78 (17%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR---PTGFYFP 84
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+        PT  YFP
Sbjct: 208 IDKYLSVSKRMELSKCLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPPT--YFP 265

Query: 85  G---------GGPLIFGA 93
                       PL+FGA
Sbjct: 266 TTQYPLLPYYAAPLMFGA 283

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156549094|ref|XP_001607545.1| PREDICTED: homeobox protein MSX-1-like [Nasonia vitripennis]

 Score = 91.7 bits (226), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 53/82 (64%), Positives = 59/82 (71%), Gaps = 8/82 (9%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGG 87
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LKM AH +     FP   
Sbjct: 232 IDKYLSVSKRMELSKCLNLTEVQIKTWFQNRRTKWKKQLTSRLKM-AHRQ---GLFP--- 284

Query: 88  PLIFGAQHGSPTAPYFFSASML 109
           P  F A    P  PY+ +A+ L
Sbjct: 285 PAYFPATQ-YPLLPYYAAAAPL 305

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328704025|ref|XP_003242379.1| PREDICTED: homeobox protein pv.1-like [Acyrthosiphon pisum]

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 49/57 (85%), Gaps = 3/57 (5%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFP 84
            DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQLASKLK +AH    G++ P
Sbjct: 186 TDKYLSVSKRMELSKALNLTEVQIKTWFQNRRTKWKKQLASKLK-IAHRH--GYFQP 239

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725237|ref|XP_003400979.1| PREDICTED: hypothetical protein LOC100651502 [Bombus terrestris]

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/75 (61%), Positives = 53/75 (70%), Gaps = 10/75 (13%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR--PTGFYFPG 85
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+       P+ ++ P 
Sbjct: 287 IDKYLSVSKRMELSKSLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPSAYFPPA 346

Query: 86  --------GGPLIFG 92
                     PL+FG
Sbjct: 347 QYSLLPYYTTPLVFG 361

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332017372|gb|EGI58114.1| Homeobox protein ceh-19 [Acromyrmex echinatior]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 53/77 (68%), Gaps = 14/77 (18%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR---PTGFYFP 84
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+        PT  YFP
Sbjct: 210 IDKYLSVSKRMELSKCLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPPT--YFP 267

Query: 85  G---------GGPLIFG 92
                       PL+FG
Sbjct: 268 TTQYPLLPYYAAPLMFG 284

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350403982|ref|XP_003486970.1| PREDICTED: hypothetical protein LOC100748877 [Bombus impatiens]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 50/89 (56%), Positives = 58/89 (65%), Gaps = 11/89 (12%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR--PTGFYFPG 85
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+       P+ ++ P 
Sbjct: 332 IDKYLSVSKRMELSKSLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPSAYFPPA 391

Query: 86  GGPLIFGAQHGSP--TAPYFFSASMLDDS 112
              L+       P  T P  F  S  DD+
Sbjct: 392 QYSLL-------PYYTTPLVFGTSASDDA 413

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307175871|gb|EFN65686.1| Homeobox protein ceh-19 [Camponotus floridanus]

 Score = 89.4 bits (220), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/78 (62%), Positives = 53/78 (67%), Gaps = 14/78 (17%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR---PTGFYFP 84
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+        PT  YFP
Sbjct: 211 IDKYLSVSKRMELSKCLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPPT--YFP 268

Query: 85  G---------GGPLIFGA 93
                       PL+FG 
Sbjct: 269 TTQYPLLPYYAAPLMFGG 286

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862479|ref|XP_003706711.1| PREDICTED: homeobox protein engrailed-2b-like [Megachile rotundata]

 Score = 89.4 bits (220), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 53/77 (68%), Gaps = 14/77 (18%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHN---RPTGFYFP 84
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+        PT  YFP
Sbjct: 229 IDKYLSVSKRMELSKSLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPPT--YFP 286

Query: 85  GG---------GPLIFG 92
                       PL+FG
Sbjct: 287 PAQYPLLPYYTAPLVFG 303

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307191995|gb|EFN75385.1| Homeobox protein ceh-19 [Harpegnathos saltator]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 49/78 (62%), Positives = 54/78 (69%), Gaps = 14/78 (17%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHN---RPTGFYFP 84
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+        PT  YFP
Sbjct: 91  IDKYLSVSKRMELSKCLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPPT--YFP 148

Query: 85  G---------GGPLIFGA 93
                       PL+FG+
Sbjct: 149 TTQYPLLPYYAAPLMFGS 166

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110763697|ref|XP_001122544.1| PREDICTED: motor neuron and pancreas homeobox protein 1-like [Apis mellifera]

 Score = 88.6 bits (218), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 51/88 (57%), Positives = 57/88 (64%), Gaps = 11/88 (12%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR--PTGFYFPG 85
           +DKYLSVSKRMELSK LNLTEVQIKTWFQNRRTKWKKQL S+LK+       P  ++ P 
Sbjct: 109 IDKYLSVSKRMELSKSLNLTEVQIKTWFQNRRTKWKKQLTSRLKIAQRQGLFPPTYFPPA 168

Query: 86  GGPLIFGAQHGSP--TAPYFFSASMLDD 111
             PL+       P  TAP  F     DD
Sbjct: 169 QYPLL-------PYYTAPLVFGTPTSDD 189

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
WB|WBGene00000442	199	ceh-19 [Caenorhabditis elegans	0.425	0.256	0.686	2.6e-15
UNIPROTKB|F1NZL8	153	LOC100857765 "Uncharacterized	0.3	0.235	0.666	1.1e-12
ZFIN|ZDB-GENE-050417-212	299	barhl1a "BarH-like 1a" [Danio	0.375	0.150	0.644	3.4e-11
ZFIN|ZDB-GENE-060118-2	323	barhl1b "BarH-like 1b" [Danio	0.375	0.139	0.644	4.3e-11
UNIPROTKB|E2QSL9	327	BARHL1 "Uncharacterized protei	0.375	0.137	0.644	4.5e-11
UNIPROTKB|Q9BZE3	327	BARHL1 "BarH-like 1 homeobox p	0.375	0.137	0.644	4.5e-11
UNIPROTKB|F1S0T9	327	BARHL1 "Uncharacterized protei	0.375	0.137	0.644	4.5e-11
MGI|MGI:1859288	327	Barhl1 "BarH-like 1 (Drosophil	0.375	0.137	0.644	4.5e-11
RGD|620648	327	Barhl1 "BarH-like homeobox 1"	0.375	0.137	0.644	4.5e-11
UNIPROTKB|E1B9T6	337	BARHL1 "Uncharacterized protei	0.375	0.133	0.644	4.9e-11

WB|WBGene00000442 ceh-19 [Caenorhabditis elegans (taxid:6239)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 35/51 (68%), Positives = 43/51 (84%)

Query:    29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPT 79
             DKYLSV+KR++LS+ LNLTE QIKTWFQNRRTKWKKQL S ++ +  + PT
Sbjct:   116 DKYLSVNKRIQLSQTLNLTETQIKTWFQNRRTKWKKQLTSSIRQMVKDAPT 166

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

 Score = 134 (52.2 bits), Expect = 1.1e-12, Sum P(2) = 1.1e-12
 Identities = 24/36 (66%), Positives = 30/36 (83%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
             +YLSV +R+ L+  L+LTE Q+K WFQNRRTKWKKQ
Sbjct:    42 RYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 77

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

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

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-050417-212 barhl1a "BarH-like 1a" [Danio rerio (taxid:7955)]

 Score = 158 (60.7 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   178 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 222

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-060118-2 barhl1b "BarH-like 1b" [Danio rerio (taxid:7955)]

 Score = 158 (60.7 bits), Expect = 4.3e-11, P = 4.3e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   197 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 241

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|E2QSL9 BARHL1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 158 (60.7 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 245

GO:0005634 "nucleus" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

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

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

UNIPROTKB|Q9BZE3 BARHL1 "BarH-like 1 homeobox protein" [Homo sapiens (taxid:9606)]

 Score = 158 (60.7 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 245

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

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

GO:0001764 "neuron migration" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1S0T9 BARHL1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 158 (60.7 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 245

GO:0005634 "nucleus" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

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

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

MGI|MGI:1859288 Barhl1 "BarH-like 1 (Drosophila)" [Mus musculus (taxid:10090)]

 Score = 158 (60.7 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 245

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

GO:0001764 "neuron migration" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007605 "sensory perception of sound" evidence=IMP

GO:0030901 "midbrain development" evidence=IMP

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IMP

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

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

RGD|620648 Barhl1 "BarH-like homeobox 1" [Rattus norvegicus (taxid:10116)]

 Score = 158 (60.7 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   201 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 245

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

GO:0001764 "neuron migration" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0007605 "sensory perception of sound" evidence=IEA;ISO

GO:0030901 "midbrain development" evidence=IEA;ISO

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA;ISO

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

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

UNIPROTKB|E1B9T6 BARHL1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 158 (60.7 bits), Expect = 4.9e-11, P = 4.9e-11
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query:    30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
             KYLSV  RMEL+  LNLT+ Q+KTW+QNRRTKWK+Q A  L+++A
Sbjct:   211 KYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLA 255

GO:0005634 "nucleus" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	120
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-14
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-12
smart00389	57	smart00389, HOX, Homeodomain	6e-12
pfam00046	57	pfam00046, Homeobox, Homeobox domain	9e-10
smart00389	57	smart00389, HOX, Homeodomain	1e-08
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	3e-08
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	2e-04
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	7e-04

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

 Score = 62.1 bits (152), Expect = 2e-14
 Identities = 21/36 (58%), Positives = 27/36 (75%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++Y S  +R EL+K L LTE Q+K WFQNRR KWK+
Sbjct: 22 NRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

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

 Score = 57.6 bits (140), Expect = 1e-12
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 11/61 (18%)

Query: 8  NLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
            T  Q++     F+         + Y S  +R EL+K L LTE Q+K WFQNRR K K+
Sbjct: 6  RFTPEQLEELEKEFEK--------NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57

Query: 65 Q 65
           
Sbjct: 58 S 58

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 56.1 bits (136), Expect = 6e-12
 Identities = 21/40 (52%), Positives = 26/40 (65%)

Query: 24 KWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
          K    + Y S  +R EL+K L L+E Q+K WFQNRR KWK
Sbjct: 18 KEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 50.2 bits (121), Expect = 9e-10
 Identities = 18/25 (72%), Positives = 20/25 (80%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          EL+K L LTE Q+K WFQNRR KWK
Sbjct: 32 ELAKKLGLTERQVKVWFQNRRAKWK 56

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 47.6 bits (114), Expect = 1e-08
 Identities = 17/25 (68%), Positives = 20/25 (80%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          EL+K L L+E Q+K WFQNRR KWK
Sbjct: 33 ELAKKLGLSERQVKVWFQNRRAKWK 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 = 46.5 bits (111), Expect = 3e-08
 Identities = 17/25 (68%), Positives = 19/25 (76%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          EL+K L LTE Q+K WFQNRR K K
Sbjct: 32 ELAKELGLTERQVKIWFQNRRAKLK 56

Length = 59

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 16/38 (42%), Positives = 25/38 (65%)

Query: 28  VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           ++ Y S   R++LS LLN+    ++ WFQN+R K KK+
Sbjct: 72  INPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109

Length = 156

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 6/65 (9%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWK-----YVDKYLSVSKRMELSKLLNLTEVQIKTWFQ 56
           +LS LLN+    ++ WFQN+R K K      V++     +  +L+K+ +L+  QI     
Sbjct: 83  KLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGEEEA-DLAKIGSLSTGQISIIET 141

Query: 57  NRRTK 61
              ++
Sbjct: 142 LEFSR 146

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
KOG0484|consensus	125		99.82
KOG2251|consensus	228		99.71
KOG0489|consensus	261		99.68
KOG0488|consensus	309		99.67
KOG0842|consensus	307		99.67
KOG0848|consensus	317		99.65
KOG0492|consensus	246		99.65
KOG0494|consensus	332		99.64
KOG0843|consensus	197		99.63
KOG0487|consensus	308		99.62
KOG0485|consensus	268		99.58
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.57
KOG0850|consensus	245		99.55
KOG0491|consensus	194		99.53
KOG0493|consensus	342		99.51
KOG0844|consensus	408		99.44
KOG0483|consensus	198		99.42
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.41
KOG0486|consensus	351		99.4
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.4
COG5576	156	Homeodomain-containing transcription factor [Trans	99.39
KOG0490|consensus	235		99.39
KOG4577|consensus	383		99.37
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.32
KOG0775|consensus	304		99.25
KOG0488|consensus	309		99.2
KOG0489|consensus	261		99.18
KOG0490|consensus	235		99.18
KOG0847|consensus	288		99.17
KOG3802|consensus	398		99.14
KOG0849|consensus	354		99.08
KOG0494|consensus	332		99.06
KOG0484|consensus	125		99.01
KOG0848|consensus	317		98.89
KOG0487|consensus	308		98.89
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.88
KOG0843|consensus	197		98.85
KOG0774|consensus	334		98.79
KOG0483|consensus	198		98.75
KOG0485|consensus	268		98.69
KOG0847|consensus	288		98.69
KOG2251|consensus	228		98.58
KOG0850|consensus	245		98.55
KOG0491|consensus	194		98.5
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	98.49
KOG1168|consensus	385		98.49
KOG0844|consensus	408		98.34
KOG0842|consensus	307		98.23
KOG0492|consensus	246		98.22
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.2
KOG0493|consensus	342		98.2
COG5576	156	Homeodomain-containing transcription factor [Trans	98.17
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	98.08
KOG4577|consensus	383		97.93
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	97.85
KOG0486|consensus	351		97.82
KOG1146|consensus	1406		97.78
KOG0849|consensus	354		97.54
KOG0773|consensus	342		97.42
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.37
KOG2252|consensus	558		97.36
KOG3802|consensus	398		96.77
KOG0775|consensus	304		96.3
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	95.42
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	94.26
PHA01976	67	helix-turn-helix protein	94.2
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	93.57
TIGR02607	78	antidote_HigA addiction module antidote protein, H	93.46
KOG3623|consensus	1007		93.24
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	93.18
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	93.11
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	93.11
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	92.99
KOG3623|consensus	1007		92.77
TIGR00270	154	conserved hypothetical protein TIGR00270.	91.88
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	91.73
PRK06424	144	transcription factor; Provisional	91.59
PRK13890	120	conjugal transfer protein TrbA; Provisional	91.36
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	91.22
PRK09726	88	antitoxin HipB; Provisional	90.78
PRK10072	96	putative transcriptional regulator; Provisional	90.63
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	90.05
PRK08359	176	transcription factor; Validated	89.96
PHA01083	149	hypothetical protein	89.62
PRK09706	135	transcriptional repressor DicA; Reviewed	88.86
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	88.79
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	87.83
KOG1168|consensus	385		87.43
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	86.93
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	86.86
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	85.7
KOG3755|consensus	769		83.44
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	82.24
PRK02866	147	cyanate hydratase; Validated	82.13
PF10668	60	Phage_terminase: Phage terminase small subunit; In	82.08
PF10668	60	Phage_terminase: Phage terminase small subunit; In	81.85
KOG0774|consensus	334		81.22

>KOG0484|consensus

Probab=99.82  E-value=6.6e-20  Score=114.33  Aligned_cols=64  Identities=28%  Similarity=0.433  Sum_probs=57.8

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK   71 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~   71 (120)
                      ..-|+.||..||+.++..|-     ++|||++..|++||.++.|+|.+|||||||||||.|++.+....
T Consensus        18 RRIRTTFTS~QLkELErvF~-----ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~   81 (125)
T KOG0484|consen   18 RRIRTTFTSAQLKELERVFA-----ETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA   81 (125)
T ss_pred             hhhhhhhhHHHHHHHHHHHH-----hhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            34578999999999998887     69999999999999999999999999999999999998776554

>KOG2251|consensus

Probab=99.71  E-value=3.3e-17  Score=114.49  Aligned_cols=63  Identities=29%  Similarity=0.400  Sum_probs=58.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~   69 (120)
                      +..+||.|+-.|+.|++-.|.     +++|||...|++||.+++|.+.+|||||+|||+|+|+++...
T Consensus        37 qRRERTtFtr~QlevLe~LF~-----kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   37 QRRERTTFTRKQLEVLEALFA-----KTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             cccccceecHHHHHHHHHHHH-----hhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            356899999999999888887     699999999999999999999999999999999999987765

>KOG0489|consensus

Probab=99.68  E-value=1.5e-17  Score=121.04  Aligned_cols=63  Identities=43%  Similarity=0.651  Sum_probs=56.8

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK   71 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~   71 (120)
                      ..|+.||..|+..++..|-     .|+|.+...|.|||..|.|+|+||+|||||||+||||..+....
T Consensus       161 R~RtayT~~QllELEkEFh-----fN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~  223 (261)
T KOG0489|consen  161 RRRTAFTRYQLLELEKEFH-----FNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS  223 (261)
T ss_pred             CCCcccchhhhhhhhhhhc-----cccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence            4688999999999999888     69999999999999999999999999999999999996554443

>KOG0488|consensus

Probab=99.67  E-value=3.7e-17  Score=121.21  Aligned_cols=62  Identities=44%  Similarity=0.638  Sum_probs=57.0

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL   70 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~   70 (120)
                      ..|+-||+.||+.++..|.     +++|.+..+|.+||+.+||+..||++||||||+|||++.....
T Consensus       174 ksRTaFT~~Ql~~LEkrF~-----~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~  235 (309)
T KOG0488|consen  174 KSRTAFSDHQLFELEKRFE-----KQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG  235 (309)
T ss_pred             cchhhhhHHHHHHHHHHHH-----HhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence            4688999999999998888     5999999999999999999999999999999999999877644

>KOG0842|consensus

Probab=99.67  E-value=5.2e-17  Score=119.33  Aligned_cols=65  Identities=34%  Similarity=0.461  Sum_probs=57.0

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHHh
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMV   73 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~~   73 (120)
                      .-|+=|+..||=++++.|+     +++|++..+|++||..|.|+++||+|||||||-|.||+..++....
T Consensus       155 KrRVLFSqAQV~ELERRFr-----qQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~  219 (307)
T KOG0842|consen  155 KRRVLFSQAQVYELERRFR-----QQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA  219 (307)
T ss_pred             ccccccchhHHHHHHHHHH-----hhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence            4467788888888888777     7999999999999999999999999999999999999877766543

>KOG0848|consensus

Probab=99.65  E-value=3.3e-16  Score=112.19  Aligned_cols=59  Identities=32%  Similarity=0.489  Sum_probs=49.2

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~   69 (120)
                      |+-+|+.|-=.++.+|-     ..+|.++..+.|||.-|||+|+||+|||||||||+||..+.+
T Consensus       203 RvVYTDhQRLELEKEfh-----~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  203 RVVYTDHQRLELEKEFH-----TSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             eEEecchhhhhhhhhhc-----cccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            34456655555566665     589999999999999999999999999999999999987766

>KOG0492|consensus

Probab=99.65  E-value=3e-16  Score=108.84  Aligned_cols=61  Identities=39%  Similarity=0.548  Sum_probs=56.0

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL   70 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~   70 (120)
                      =||-||..||..++.+||     +.+|.++.+|.+++..+.|+++||+|||||||||.||.+....
T Consensus       147 PRtPFTtqQLlaLErkfr-----ekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~  207 (246)
T KOG0492|consen  147 PRTPFTTQQLLALERKFR-----EKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL  207 (246)
T ss_pred             CCCCCCHHHHHHHHHHHh-----HhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence            378899999999999998     6899999999999999999999999999999999999766544

>KOG0494|consensus

Probab=99.64  E-value=1.4e-16  Score=113.84  Aligned_cols=58  Identities=31%  Similarity=0.453  Sum_probs=53.5

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ||.||+.|+..++..|.     +-+|||...|+-||.+++|.|.+||||||||||||||..+.
T Consensus       145 RTiFT~~Qle~LEkaFk-----eaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~  202 (332)
T KOG0494|consen  145 RTIFTSYQLEELEKAFK-----EAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR  202 (332)
T ss_pred             cchhhHHHHHHHHHHHh-----hccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence            78999999988887776     79999999999999999999999999999999999997554

>KOG0843|consensus

Probab=99.63  E-value=4e-16  Score=106.05  Aligned_cols=60  Identities=32%  Similarity=0.443  Sum_probs=54.7

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~   69 (120)
                      .||-|+.+|+..++-.|.     .++|....+|++||+.|+|++.||+|||||||.|.||.....
T Consensus       105 ~RT~ft~~Ql~~LE~~F~-----~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  105 IRTAFTPEQLLKLEHAFE-----GNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             cccccCHHHHHHHHHHHh-----cCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            478999999999888887     599999999999999999999999999999999999975553

>KOG0487|consensus

Probab=99.62  E-value=2.8e-16  Score=115.56  Aligned_cols=62  Identities=40%  Similarity=0.463  Sum_probs=56.7

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~   69 (120)
                      .++|.-+|..|+..++.+|.     .|.|.+...|.||++.|+|+|+||+|||||||+|.||..++.
T Consensus       236 RKKRcPYTK~QtlELEkEFl-----fN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  236 RKKRCPYTKHQTLELEKEFL-----FNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             ccccCCchHHHHHHHHHHHH-----HHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            35778899999999999998     599999999999999999999999999999999999987633

>KOG0485|consensus

Probab=99.58  E-value=9.1e-15  Score=102.18  Aligned_cols=61  Identities=39%  Similarity=0.635  Sum_probs=54.0

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK   71 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~   71 (120)
                      ||-|+..||.-++-.|.     ..+|.+..+|.-||+++.|+|+||+|||||||.||||+......
T Consensus       108 RTvFSraQV~qLEs~Fe-----~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e  168 (268)
T KOG0485|consen  108 RTVFSRAQVFQLESTFE-----LKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE  168 (268)
T ss_pred             hhhhhHHHHHHHHHHHH-----HHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence            56789999988888887     47899999999999999999999999999999999998554443

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.57  E-value=3.2e-15  Score=85.04  Aligned_cols=55  Identities=45%  Similarity=0.544  Sum_probs=51.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .++.|+++|++++..-|.     .++||+..++++||..+||+..+|++||+|+|+++|+
T Consensus         3 ~r~~~t~~q~~~L~~~f~-----~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    3 KRTRFTKEQLKVLEEYFQ-----ENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSHHHHHHHHHHHH-----HSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHH-----HhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578899999999888887     4999999999999999999999999999999999886

; 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 ....

>KOG0850|consensus

Probab=99.55  E-value=1.3e-14  Score=102.00  Aligned_cols=61  Identities=33%  Similarity=0.507  Sum_probs=52.4

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL   70 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~   70 (120)
                      -||=++.-||+.+-+.|.     +++|.-..+|.+||+.|||+.+||+|||||||.|.||+.++..
T Consensus       125 PRTIYSS~QLqaL~rRFQ-----kTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~  185 (245)
T KOG0850|consen  125 PRTIYSSLQLQALNRRFQ-----QTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS  185 (245)
T ss_pred             CcccccHHHHHHHHHHHh-----hcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence            356677888888766665     5899999999999999999999999999999999999877433

>KOG0491|consensus

Probab=99.53  E-value=5e-15  Score=99.46  Aligned_cols=63  Identities=37%  Similarity=0.507  Sum_probs=53.8

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL   70 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~   70 (120)
                      ...|+-|.+.|+.++...|.     .++|.+..+|.|||..++|+++||+.||||||+|+||+.+...
T Consensus       101 ~K~Rtvfs~~ql~~l~~rFe-----~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  101 RKARTVFSDPQLSGLEKRFE-----RQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhcccccCccccccHHHHh-----hhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            34567777777777766665     4899999999999999999999999999999999999877665

>KOG0493|consensus

Probab=99.51  E-value=8.4e-15  Score=104.85  Aligned_cols=71  Identities=35%  Similarity=0.504  Sum_probs=57.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHHhhcCCCCC
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTG   80 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~~~~~~~~~   80 (120)
                      -||-||.+||+.+-..|+     +|+|.+...|.+||.+|+|+|.||+|||||+|+|.||....+.......+..+
T Consensus       249 PRTAFtaeQL~RLK~EF~-----enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqg  319 (342)
T KOG0493|consen  249 PRTAFTAEQLQRLKAEFQ-----ENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQG  319 (342)
T ss_pred             ccccccHHHHHHHHHHHh-----hhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhccc
Confidence            368899999999888877     49999999999999999999999999999999999995444333333333333

>KOG0844|consensus

Probab=99.44  E-value=3.1e-14  Score=103.91  Aligned_cols=55  Identities=44%  Similarity=0.599  Sum_probs=49.6

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ||-||.+||-.++.+|     +++.|-+...|.|||..++|+|+.|+|||||||+|+|||
T Consensus       185 RTAFTReQIaRLEKEF-----yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ  239 (408)
T KOG0844|consen  185 RTAFTREQIARLEKEF-----YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ  239 (408)
T ss_pred             HhhhhHHHHHHHHHHH-----HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence            6789999996666555     469999999999999999999999999999999999997

>KOG0483|consensus

Probab=99.42  E-value=7.9e-14  Score=97.34  Aligned_cols=56  Identities=36%  Similarity=0.552  Sum_probs=52.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ++.+|+.+|+..++..|.     .++|..-..+..||..+||.++||.||||||||+||..
T Consensus        53 kk~Rlt~eQ~~~LE~~F~-----~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k  108 (198)
T KOG0483|consen   53 KKRRLTSEQVKFLEKSFE-----SEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK  108 (198)
T ss_pred             ccccccHHHHHHhHHhhc-----cccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence            567899999999998887     59999999999999999999999999999999999975

>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=99.41  E-value=2.5e-13  Score=77.37  Aligned_cols=55  Identities=42%  Similarity=0.543  Sum_probs=49.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .+..++++++.++...|.     .++||+..++.+||..+||++.+|++||+|+|++.++
T Consensus         3 ~r~~~~~~~~~~Le~~f~-----~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           3 KRTRFTPEQLEELEKEFE-----KNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCcCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            456789999888777776     3999999999999999999999999999999999876

>KOG0486|consensus

Probab=99.40  E-value=3.4e-13  Score=98.65  Aligned_cols=65  Identities=28%  Similarity=0.502  Sum_probs=55.5

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKM   72 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~   72 (120)
                      ..+|+-|+..|+|.++--|+     +|+||+...|+|||--++|+|.+|.|||+|||+||||.++.....
T Consensus       113 rrQrthFtSqqlqele~tF~-----rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae  177 (351)
T KOG0486|consen  113 RRQRTHFTSQQLQELEATFQ-----RNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAE  177 (351)
T ss_pred             hhhhhhhHHHHHHHHHHHHh-----hccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHH
Confidence            46788899999888555544     399999999999999999999999999999999999977665533

>smart00389 HOX Homeodomain

Probab=99.40  E-value=2e-13  Score=77.10  Aligned_cols=53  Identities=40%  Similarity=0.610  Sum_probs=48.0

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW   62 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~   62 (120)
                      .++.++.+++.++.+.+.     .++||+..++.+||..+||+..+|++||+|+|++.
T Consensus         3 ~r~~~~~~~~~~L~~~f~-----~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~   55 (56)
T smart00389        3 KRTSFTPEQLEELEKEFQ-----KNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             CCCcCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence            356789999999888877     49999999999999999999999999999999875

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

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.39  E-value=3.3e-13  Score=91.28  Aligned_cols=61  Identities=33%  Similarity=0.444  Sum_probs=56.0

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ...++..+..|+-|+.+.|.     .++||+...|.+|+..++|+++-|||||||+|++.|+....
T Consensus        52 ~~~r~R~t~~Q~~vL~~~F~-----i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          52 KSKRRRTTDEQLMVLEREFE-----INPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             cccceechHHHHHHHHHHhc-----cCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            46788999999999999998     59999999999999999999999999999999999986444

>KOG0490|consensus

Probab=99.39  E-value=1.1e-13  Score=98.37  Aligned_cols=66  Identities=36%  Similarity=0.558  Sum_probs=58.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc----------------------------------------------------
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD----------------------------------------------------   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~----------------------------------------------------   29 (120)
                      +||.+++++|.+|||||||||+||+++.                                                    
T Consensus        92 ~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (235)
T KOG0490|consen   92 CLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETV  171 (235)
T ss_pred             HHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccccccccCCCccccCCCccccccchhHhhhhc
Confidence            5899999999999999999999999633                                                    


Q ss_pred             ----cccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877          30 ----KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus        30 ----~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                          .+|+...+++|+..+|+++..|++||+|+|++.++...
T Consensus       172 ~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  172 FRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             ccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence                35567889999999999999999999999999998544

>KOG4577|consensus

Probab=99.37  E-value=2.4e-13  Score=98.62  Aligned_cols=58  Identities=29%  Similarity=0.294  Sum_probs=51.8

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ||.+|..||+++-+.+.+     ...|-...|++|+..+||..++|||||||||||.||..++
T Consensus       171 RTTItAKqLETLK~AYn~-----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  171 RTTITAKQLETLKQAYNT-----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             cceeeHHHHHHHHHHhcC-----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            678899999998888764     6789999999999999999999999999999999987543

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.32  E-value=1.8e-12  Score=73.81  Aligned_cols=50  Identities=14%  Similarity=0.171  Sum_probs=46.3

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccc----cchhHHHHHhhhhcchhhhhhccccchh
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKY----LSVSKRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~y----p~~~~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      .||.||.+|++.....+.     .+.|    |+...+++||..+||++.+|+|||||-+
T Consensus         4 ~RT~Ft~~Q~~~Le~~fe-----~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         4 RRTKFTAEQKEKMRDFAE-----KLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCHHHHHHHHHHHH-----HcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            589999999999888887     4899    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.

>KOG0775|consensus

Probab=99.25  E-value=1.1e-11  Score=89.45  Aligned_cols=40  Identities=33%  Similarity=0.523  Sum_probs=36.9

Q ss_pred             cccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877          28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus        28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      ++.||+..++.+||+.+||+..||-+||+|||+++|....
T Consensus       197 ~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  197 QNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             cCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            3999999999999999999999999999999999995433

>KOG0488|consensus

Probab=99.20  E-value=4.4e-12  Score=94.26  Aligned_cols=30  Identities=60%  Similarity=1.004  Sum_probs=27.8

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      |+||++||||+.||++||||||||||++.-
T Consensus       203 ~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a  232 (309)
T KOG0488|consen  203 IELAASLGLTDAQVKTWFQNRRTKWKRQTA  232 (309)
T ss_pred             HHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence            689999999999999999999999998743

>KOG0489|consensus

Probab=99.18  E-value=6.6e-12  Score=91.51  Aligned_cols=34  Identities=59%  Similarity=0.882  Sum_probs=30.2

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhcccccch
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSV   34 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~   34 (120)
                      ||+|..|+|+|.||++|||||||||||+++-...
T Consensus       190 iEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~  223 (261)
T KOG0489|consen  190 IEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS  223 (261)
T ss_pred             HHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence            6899999999999999999999999998774443

>KOG0490|consensus

Probab=99.18  E-value=8.3e-12  Score=88.74  Aligned_cols=59  Identities=25%  Similarity=0.262  Sum_probs=53.7

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      -.+++|+..|++.+...|.     .+|||+...|+.||..+.++|..|+|||||+|+||+++..
T Consensus        62 r~rt~~~~~ql~~ler~f~-----~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   62 CARCKFTISQLDELERAFE-----KVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             ccCCCCCcCHHHHHHHhhc-----CCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            3578899999999888887     4899999999999999999999999999999999999764

>KOG0847|consensus

Probab=99.17  E-value=1.6e-11  Score=86.28  Aligned_cols=59  Identities=42%  Similarity=0.669  Sum_probs=49.0

Q ss_pred             CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877           8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK   71 (120)
Q Consensus         8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~   71 (120)
                      .|+-.||+.....+.     +.+|+-..+|.+||..+|+++.+|+|||||||.||||.......
T Consensus       173 Tf~g~qi~~le~~fe-----qtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma  231 (288)
T KOG0847|consen  173 TFTGHQIYQLERKFE-----QTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA  231 (288)
T ss_pred             Cccchhhhhhhhhhh-----hhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence            355667766665555     69999999999999999999999999999999999997554443

>KOG3802|consensus

Probab=99.14  E-value=2.2e-11  Score=91.83  Aligned_cols=59  Identities=17%  Similarity=0.166  Sum_probs=49.5

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      ..+||.|.....-.++..|.     .|..|+..++.+||.+|+|...+|+|||||||+|.||..
T Consensus       295 RKKRTSie~~vr~aLE~~F~-----~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~  353 (398)
T KOG3802|consen  295 RKKRTSIEVNVRGALEKHFL-----KNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT  353 (398)
T ss_pred             cccccceeHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence            35677777666556666665     499999999999999999999999999999999999943

>KOG0849|consensus

Probab=99.08  E-value=1.7e-10  Score=87.39  Aligned_cols=58  Identities=28%  Similarity=0.490  Sum_probs=51.8

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ||.|+..|+..+...|.     .++||++..|++||.++++++..|+|||+|||++++++...
T Consensus       180 rtsft~~Q~~~le~~f~-----rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  180 RTSFSPSQLEALEECFQ-----RTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             ccccccchHHHHHHHhc-----CCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            57799999988777666     48899999999999999999999999999999999997644

>KOG0494|consensus

Probab=99.06  E-value=5.5e-11  Score=85.35  Aligned_cols=37  Identities=41%  Similarity=0.679  Sum_probs=32.4

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRME   39 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~   39 (120)
                      ||.+|.|+|++||||||||||||||.++......++.
T Consensus       174 la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~ma  210 (332)
T KOG0494|consen  174 LADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMA  210 (332)
T ss_pred             HhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhh
Confidence            7889999999999999999999999888766665554

>KOG0484|consensus

Probab=99.01  E-value=9.6e-11  Score=73.42  Aligned_cols=29  Identities=38%  Similarity=0.846  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      |||.++-|||.+|||||||||||.+|+.+
T Consensus        49 EiA~kidLTEARVQVWFQNRRAKfRKQEr   77 (125)
T KOG0484|consen   49 EIALKIDLTEARVQVWFQNRRAKFRKQER   77 (125)
T ss_pred             HHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence            79999999999999999999999998754

>KOG0848|consensus

Probab=98.89  E-value=4.7e-10  Score=80.85  Aligned_cols=29  Identities=52%  Similarity=0.766  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      |||.-|||+|+||++||||||||-||.++
T Consensus       231 ELA~~LgLsERQVKIWFQNRRAKERK~nK  259 (317)
T KOG0848|consen  231 ELAATLGLSERQVKIWFQNRRAKERKDNK  259 (317)
T ss_pred             HHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence            89999999999999999999998887755

>KOG0487|consensus

Probab=98.89  E-value=2.2e-10  Score=84.56  Aligned_cols=30  Identities=63%  Similarity=0.923  Sum_probs=27.8

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      .|||..|+|||.||++||||||+|.||.++
T Consensus       266 ~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r  295 (308)
T KOG0487|consen  266 LELSRTLNLTERQVKIWFQNRRMKEKKVNR  295 (308)
T ss_pred             HHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence            389999999999999999999999999864

>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=98.88  E-value=1.1e-09  Score=57.90  Aligned_cols=34  Identities=35%  Similarity=0.572  Sum_probs=29.1

Q ss_pred             cccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877          28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK   61 (120)
Q Consensus        28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak   61 (120)
                      .+.||+..++++||..+||+..||..||-|.|.+
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            4899999999999999999999999999999864

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

>KOG0843|consensus

Probab=98.85  E-value=8e-10  Score=75.52  Aligned_cols=28  Identities=54%  Similarity=0.894  Sum_probs=25.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.|+|+|.||+|||||||+|-||..
T Consensus       134 ~LA~~L~LsetQVkvWFQNRRtk~kr~~  161 (197)
T KOG0843|consen  134 QLAQSLSLSETQVKVWFQNRRTKHKRMQ  161 (197)
T ss_pred             HHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence            6999999999999999999999888753

>KOG0774|consensus

Probab=98.79  E-value=2.2e-08  Score=72.16  Aligned_cols=60  Identities=27%  Similarity=0.490  Sum_probs=48.8

Q ss_pred             ccCCCH---HHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877           6 LLNLTE---VQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL   70 (120)
Q Consensus         6 ~~~~~~---~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~   70 (120)
                      |-+|+.   +-|+.||-..+     .|.||+...+++||.+++++..||..||.|.|-+.+|......
T Consensus       192 RRNFsK~aTeiLneyF~~h~-----~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~  254 (334)
T KOG0774|consen  192 RRNFSKQATEILNEYFYSHL-----SNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQ  254 (334)
T ss_pred             hcccchhHHHHHHHHHHHhc-----CCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhh
Confidence            335544   55666776665     6999999999999999999999999999999999998654443

>KOG0483|consensus

Probab=98.75  E-value=2.3e-09  Score=74.99  Aligned_cols=39  Identities=38%  Similarity=0.609  Sum_probs=29.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc-cccchhHHHHH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD-KYLSVSKRMEL   40 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~-~yp~~~~r~~L   40 (120)
                      .||+.+||...||.||||||||||+..+ -+.....+..+
T Consensus        82 ~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~  121 (198)
T KOG0483|consen   82 KLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQL  121 (198)
T ss_pred             HHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHH
Confidence            6999999999999999999999998732 23334444443

>KOG0485|consensus

Probab=98.69  E-value=5.2e-09  Score=73.58  Aligned_cols=27  Identities=59%  Similarity=0.986  Sum_probs=25.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      -||+.|-|||.||++||||||.|||++
T Consensus       136 ~LA~sLqLTETQVKIWFQNRRnKwKRq  162 (268)
T KOG0485|consen  136 GLAASLQLTETQVKIWFQNRRNKWKRQ  162 (268)
T ss_pred             HHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence            389999999999999999999999976

>KOG0847|consensus

Probab=98.69  E-value=6e-09  Score=73.39  Aligned_cols=28  Identities=57%  Similarity=1.016  Sum_probs=25.9

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      .|||..+|++|.||+|||||||+||||+
T Consensus       198 a~lA~~lgmteSqvkVWFQNRRTKWRKk  225 (288)
T KOG0847|consen  198 AQLAQELNMTESQVKVWFQNRRTKWRKK  225 (288)
T ss_pred             HHhhccccccHHHHHHHHhcchhhhhhh
Confidence            3788999999999999999999999984

>KOG2251|consensus

Probab=98.58  E-value=1.1e-08  Score=71.91  Aligned_cols=29  Identities=41%  Similarity=0.754  Sum_probs=27.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      |||.+|+|+|.+|||||.|||||++++.+
T Consensus        69 elAlklnLpeSrVqVWFKNRRAK~r~qq~   97 (228)
T KOG2251|consen   69 ELALKLNLPESRVQVWFKNRRAKCRRQQQ   97 (228)
T ss_pred             HHHHHhCCchhhhhhhhccccchhhHhhh
Confidence            79999999999999999999999998655

>KOG0850|consensus

Probab=98.55  E-value=2.2e-08  Score=70.85  Aligned_cols=30  Identities=53%  Similarity=0.872  Sum_probs=26.7

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +|||+-||||.+||++||||||-|.||.-+
T Consensus       153 AeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  153 AELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             HHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            489999999999999999999988887543

>KOG0491|consensus

Probab=98.50  E-value=4e-08  Score=66.42  Aligned_cols=30  Identities=53%  Similarity=0.832  Sum_probs=27.0

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +|||..++|++.||++||||||+|-+|+.+
T Consensus       131 ~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r  160 (194)
T KOG0491|consen  131 QELANALSLSETQVKTWFQNRRMKHKKQQR  160 (194)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence            489999999999999999999999888643

>PF00046 Homeobox: Homeobox domain not present here

Probab=98.49  E-value=7.5e-08  Score=54.34  Aligned_cols=26  Identities=65%  Similarity=0.872  Sum_probs=24.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||+..+|++||+|+|+|.++
T Consensus        32 ~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen   32 ELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             HHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccCHHHhHHHhCc
Confidence            69999999999999999999998774

; 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 ....

>KOG1168|consensus

Probab=98.49  E-value=2.5e-08  Score=72.88  Aligned_cols=38  Identities=29%  Similarity=0.436  Sum_probs=35.5

Q ss_pred             cccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877          28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus        28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ++..|+.+....||+++.|...+|.|||||+|+|-||.
T Consensus       330 vQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm  367 (385)
T KOG1168|consen  330 VQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM  367 (385)
T ss_pred             cCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence            57889999999999999999999999999999998883

>KOG0844|consensus

Probab=98.34  E-value=8.2e-08  Score=70.68  Aligned_cols=26  Identities=62%  Similarity=0.842  Sum_probs=25.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      |||+.|+|+|..|+|||||||+|-|+
T Consensus       213 ELAAaLNLPEtTIKVWFQNRRMKDKR  238 (408)
T KOG0844|consen  213 ELAAALNLPETTIKVWFQNRRMKDKR  238 (408)
T ss_pred             hHHHhhCCCcceeehhhhhchhhhhh
Confidence            89999999999999999999999887

>KOG0842|consensus

Probab=98.23  E-value=1.3e-07  Score=70.02  Aligned_cols=27  Identities=52%  Similarity=0.704  Sum_probs=25.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||.-|+||++||++||||||=|.||+
T Consensus       185 ~LA~~LrLT~TQVKIWFQNrRYK~KR~  211 (307)
T KOG0842|consen  185 HLASSLRLTPTQVKIWFQNRRYKTKRQ  211 (307)
T ss_pred             HHHHhcCCCchheeeeeecchhhhhhh
Confidence            699999999999999999999888875

>KOG0492|consensus

Probab=98.22  E-value=2.8e-07  Score=64.51  Aligned_cols=27  Identities=59%  Similarity=0.860  Sum_probs=23.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      |++.-+.|||.||++||||||||-||.
T Consensus       176 efSsSL~LTeTqVKIWFQNRRAKaKRl  202 (246)
T KOG0492|consen  176 EFSSSLELTETQVKIWFQNRRAKAKRL  202 (246)
T ss_pred             hhhhhhhhhhhheehhhhhhhHHHHHH
Confidence            567778999999999999999977643

>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=98.20  E-value=9.3e-07  Score=49.82  Aligned_cols=26  Identities=65%  Similarity=0.917  Sum_probs=23.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+|+++.+|+.||+|+|++.++
T Consensus        32 ~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086          32 ELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999986653

>KOG0493|consensus

Probab=98.20  E-value=6.3e-07  Score=64.80  Aligned_cols=26  Identities=58%  Similarity=0.851  Sum_probs=25.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||.+|||.|.||++||||.|+|.+|
T Consensus       278 ~La~ELgLNEsQIKIWFQNKRAKiKK  303 (342)
T KOG0493|consen  278 ELAQELGLNESQIKIWFQNKRAKIKK  303 (342)
T ss_pred             HHHHHhCcCHHHhhHHhhhhhhhhhh
Confidence            69999999999999999999999998

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=98.17  E-value=3.5e-07  Score=61.99  Aligned_cols=59  Identities=29%  Similarity=0.354  Sum_probs=45.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc-----ccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK-----YLSVSKRMELSKLLNLTEVQIKTWFQNRRTK   61 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~-----yp~~~~r~~La~~~~l~~~~vqvWFqNrRak   61 (120)
                      +|+..+++++.-||+||||+|++.++..+     ++.. +-..++....+.-..+-+||.+...+
T Consensus        83 ~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~~~~~-e~~~~~~~~~~~~~~~~~~~~~~~s~  146 (156)
T COG5576          83 KLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGE-EEADLAKIGSLSTGQISIIETLEFSR  146 (156)
T ss_pred             HHHHhcCCChhhhhhhhchHHHHHHHhcccchhccccc-ccccccccccccccchhhHHhhhccc
Confidence            68999999999999999999999988554     3333 44556777777777888888665433

>smart00389 HOX Homeodomain

Probab=98.08  E-value=1.8e-06  Score=48.29  Aligned_cols=24  Identities=63%  Similarity=1.135  Sum_probs=22.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKW   25 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~   25 (120)
                      +||+.+|++..+|+.||+|+|++.
T Consensus        32 ~la~~~~l~~~qV~~WF~nrR~~~   55 (56)
T smart00389       32 ELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             HHHHHHCcCHHHHHHhHHHHhhcc
Confidence            699999999999999999999753

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

>KOG4577|consensus

Probab=97.93  E-value=2.7e-06  Score=62.40  Aligned_cols=26  Identities=42%  Similarity=0.583  Sum_probs=24.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      ||+.+|||.-..|||||||||||.++
T Consensus       199 QLsseTGLDMRVVQVWFQNRRAKEKR  224 (383)
T KOG4577|consen  199 QLSSETGLDMRVVQVWFQNRRAKEKR  224 (383)
T ss_pred             HhhhccCcceeehhhhhhhhhHHHHh
Confidence            68999999999999999999998876

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=97.85  E-value=2.2e-06  Score=48.76  Aligned_cols=19  Identities=26%  Similarity=0.594  Sum_probs=18.4

Q ss_pred             cchhccCCCHHHHHHHHhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQN   20 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~   20 (120)
                      +||..|||++.+|+|||||
T Consensus        37 ~la~~lgl~~~vvKVWfqN   55 (58)
T TIGR01565        37 EFCEEIGVTRKVFKVWMHN   55 (58)
T ss_pred             HHHHHhCCCHHHeeeeccc
Confidence            6899999999999999999

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.

>KOG0486|consensus

Probab=97.82  E-value=4.6e-06  Score=61.72  Aligned_cols=29  Identities=41%  Similarity=0.953  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      |+|-.++|||.+|.|||.|||+||||.++
T Consensus       144 EIavwtNlTE~rvrvwfknrrakwrkrEr  172 (351)
T KOG0486|consen  144 EIAVWTNLTEARVRVWFKNRRAKWRKRER  172 (351)
T ss_pred             HHHhhccccchhhhhhcccchhhhhhhhh
Confidence            78999999999999999999999998655

>KOG1146|consensus

Probab=97.78  E-value=2e-05  Score=67.38  Aligned_cols=61  Identities=21%  Similarity=0.244  Sum_probs=56.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      ++|.+|-+++.||+..++=|++     ..||...+.|.|...+++..++|+|||||-|+|.++...
T Consensus       903 r~a~~~~~~d~qlk~i~~~~~~-----q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACYEA-----QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHHhh-----ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            4789999999999999999884     899999999999999999999999999999999998654

>KOG0849|consensus

Probab=97.54  E-value=4e-05  Score=58.33  Aligned_cols=32  Identities=41%  Similarity=0.750  Sum_probs=28.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLS   33 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~   33 (120)
                      +||.+++++|.+|+|||+|+|+||+|+..+.+
T Consensus       208 ~La~~i~l~e~riqvwf~nrra~~rr~~~~~s  239 (354)
T KOG0849|consen  208 TLAKETGLPEPRVQVWFQNRRAKWRRQHRDCS  239 (354)
T ss_pred             HHhhhccCCchHHHHHHhhhhhhhhhcccccc
Confidence            68999999999999999999999998765433

>KOG0773|consensus

Probab=97.42  E-value=5.2e-05  Score=57.22  Aligned_cols=56  Identities=23%  Similarity=0.413  Sum_probs=47.9

Q ss_pred             CCCHHHHHH----HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877           8 NLTEVQIKT----WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus         8 ~~~~~~~q~----~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~   69 (120)
                      +|++.-+.+    ||+++.      ..||+...+..||.++||+..+|-+||-|.|-+.-+.....
T Consensus       245 ~lP~~a~~ilr~Wl~~h~~------~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~  304 (342)
T KOG0773|consen  245 GLPKEAVSILRAWLFEHLL------HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE  304 (342)
T ss_pred             CCCHHHHHHHHHHHHHhcc------CCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence            888887777    777775      78999999999999999999999999999998877654433

>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=97.37  E-value=0.00013  Score=38.41  Aligned_cols=22  Identities=45%  Similarity=0.726  Sum_probs=19.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRT   23 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~   23 (120)
                      +||+.+|++..||..||-|.|.
T Consensus        18 ~L~~~tgls~~Qi~~WF~NaRr   39 (40)
T PF05920_consen   18 ELAKQTGLSRKQISNWFINARR   39 (40)
T ss_dssp             HHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHhHc
Confidence            6999999999999999999875

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

>KOG2252|consensus

Probab=97.36  E-value=0.00023  Score=56.36  Aligned_cols=52  Identities=25%  Similarity=0.243  Sum_probs=43.3

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW   62 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~   62 (120)
                      |+-||+.|-..+.--|+     +++||+....+.|+.+|+|..+.|.+||-|-|-+.
T Consensus       424 RlVfTd~QkrTL~aiFk-----e~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  424 RLVFTDIQKRTLQAIFK-----ENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             eeeecHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            66788866655444444     49999999999999999999999999999988774

>KOG3802|consensus

Probab=96.77  E-value=8.6e-05  Score=56.66  Aligned_cols=29  Identities=31%  Similarity=0.580  Sum_probs=27.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|+|..+.|.|||.|||-|.||.+.
T Consensus       326 ~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  326 HIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             HHHHHhccccceEEEEeeccccccccCCC
Confidence            68999999999999999999998888877

>KOG0775|consensus

Probab=96.30  E-value=0.0017  Score=47.60  Aligned_cols=21  Identities=48%  Similarity=0.855  Sum_probs=20.4

Q ss_pred             cchhccCCCHHHHHHHHhhhH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRR   22 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r   22 (120)
                      |||+.||||..||-.||.|||
T Consensus       208 eLA~aTgLt~tQVsNWFKNRR  228 (304)
T KOG0775|consen  208 ELAEATGLTITQVSNWFKNRR  228 (304)
T ss_pred             HHHHHhCCchhhhhhhhhhhh
Confidence            799999999999999999998

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

Probab=95.42  E-value=0.014  Score=32.89  Aligned_cols=31  Identities=26%  Similarity=0.404  Sum_probs=21.6

Q ss_pred             ccccchhHHHHHhhhhcchhhhhhccccchh
Q psy4877          29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        29 ~~yp~~~~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      .+++....-..|..+++|+..+|+.||-.+.
T Consensus        20 h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   20 HKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             T----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             cCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            5677778888999999999999999996554

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=94.26  E-value=0.072  Score=29.07  Aligned_cols=40  Identities=18%  Similarity=0.236  Sum_probs=32.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+.+|++...|..|+.+        ...|+...-..||..+|++..
T Consensus        14 ~la~~~gis~~~i~~~~~g--------~~~~~~~~~~~ia~~l~~~~~   53 (55)
T PF01381_consen   14 ELAEKLGISRSTISRIENG--------KRNPSLDTLKKIAKALGVSPE   53 (55)
T ss_dssp             HHHHHHTS-HHHHHHHHTT--------SSTSBHHHHHHHHHHHTSEHH
T ss_pred             HHHHHhCCCcchhHHHhcC--------CCCCCHHHHHHHHHHHCCCHH
Confidence            6888999999999988888        457888888888998888763

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PHA01976 helix-turn-helix protein

Probab=94.20  E-value=0.075  Score=30.31  Aligned_cols=40  Identities=18%  Similarity=0.208  Sum_probs=32.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+..        ...|+...-..||..++++..
T Consensus        20 ~lA~~~gvs~~~v~~~e~g--------~~~p~~~~l~~ia~~l~v~~~   59 (67)
T PHA01976         20 ELSRRAGVRHSLIYDFEAD--------KRLPNLKTLLRLADALGVTLD   59 (67)
T ss_pred             HHHHHhCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHHCcCHH
Confidence            6888888888888888877        346788888888888888774

>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A

Probab=93.57  E-value=0.091  Score=29.54  Aligned_cols=43  Identities=12%  Similarity=0.242  Sum_probs=25.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+.+.       ...++...-..||..++++...+
T Consensus        15 ~La~~~gis~~tl~~~~~~~-------~~~~~~~~l~~ia~~l~~~~~el   57 (63)
T PF13443_consen   15 DLARKTGISRSTLSRILNGK-------PSNPSLDTLEKIAKALNCSPEEL   57 (63)
T ss_dssp             HHHHHHT--HHHHHHHHTTT------------HHHHHHHHHHHT--HHHC
T ss_pred             HHHHHHCcCHHHHHHHHhcc-------cccccHHHHHHHHHHcCCCHHHH
Confidence            57778888888888777763       24666777777787777776554

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=93.46  E-value=0.1  Score=30.63  Aligned_cols=39  Identities=15%  Similarity=0.275  Sum_probs=32.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+..        ...++......|+..++++.
T Consensus        23 ~lA~~~gis~~tis~~~~g--------~~~~~~~~~~~l~~~l~v~~   61 (78)
T TIGR02607        23 ALAKALGVSRSTLSRIVNG--------RRGITADMALRLAKALGTSP   61 (78)
T ss_pred             HHHHHhCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHcCCCH
Confidence            6888999999999888877        34677788888999998876

Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.

>KOG3623|consensus

Probab=93.24  E-value=0.06  Score=44.64  Aligned_cols=62  Identities=15%  Similarity=0.253  Sum_probs=42.6

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccch---------------------------------hHHHHHhhhhcchhh
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSV---------------------------------SKRMELSKLLNLTEV   49 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~---------------------------------~~r~~La~~~~l~~~   49 (120)
                      +|..+|++-+.|++||++++++-...++-|+.                                 .+-.-++.++...+.
T Consensus       589 ia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~p  668 (1007)
T KOG3623|consen  589 IAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPP  668 (1007)
T ss_pred             HHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCc
Confidence            57788999999999999999988764433321                                 000012333455667


Q ss_pred             hhhccccchhHHHHH
Q psy4877          50 QIKTWFQNRRTKWKK   64 (120)
Q Consensus        50 ~vqvWFqNrRak~rr   64 (120)
                      +++|||++|+..-+.
T Consensus       669 v~ev~dhsrsstpsp  683 (1007)
T KOG3623|consen  669 VVEVWDHSRSSTPSP  683 (1007)
T ss_pred             chhhcccCCCCCCCC
Confidence            789999999887665

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=93.18  E-value=0.12  Score=28.10  Aligned_cols=37  Identities=16%  Similarity=0.200  Sum_probs=18.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNL   46 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l   46 (120)
                      +||+++|++...|..|+..+        ..|+......++..+|+
T Consensus        20 ~lA~~~gvs~~~vs~~e~g~--------~~~~~~~~~~i~~~lgv   56 (58)
T TIGR03070        20 DLADLAGVGLRFIRDVENGK--------PTVRLDKVLRVLDALGL   56 (58)
T ss_pred             HHHHHhCCCHHHHHHHHCCC--------CCCCHHHHHHHHHHcCC
Confidence            35555555555555555442        23444444555554443

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=93.11  E-value=0.15  Score=28.88  Aligned_cols=44  Identities=16%  Similarity=0.184  Sum_probs=30.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK   52 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq   52 (120)
                      ++|+++|++...|.-|+..++       ..|+...-..|+..++++...+.
T Consensus        19 ~lA~~~g~s~s~v~~iE~G~~-------~~p~~~~l~~l~~~l~~~~~~~~   62 (64)
T PF13560_consen   19 QLADRLGVSQSTVSRIERGRR-------PRPSPDTLQRLARALGVPPDERA   62 (64)
T ss_dssp             HHHHHHTS-HHHHHHHHTTSS-------SS-BHHHHHHHHHHTT--HHHHH
T ss_pred             HHHHHHCcCHHHHHHHHCCCC-------CCCCHHHHHHHHHHHCcCHHHHc
Confidence            578888888888888888843       14788888888888888876554

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

Probab=93.11  E-value=0.06  Score=30.29  Aligned_cols=21  Identities=29%  Similarity=0.601  Sum_probs=16.8

Q ss_pred             cchhccCCCHHHHHHHHhhhH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRR   22 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r   22 (120)
                      +|..+++|+..||..||-.++
T Consensus        30 ~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   30 ELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             HHHHHTT--HHHHHHHHHHHS
T ss_pred             HHHHHHCCCHHHHHHHHHHhc
Confidence            578899999999999999874

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=92.99  E-value=0.16  Score=28.66  Aligned_cols=43  Identities=16%  Similarity=0.203  Sum_probs=32.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK   52 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq   52 (120)
                      ++|+.+|++...|.-|+.+        ...|+......||..++++...+-
T Consensus        17 ~~a~~~~i~~~~i~~~e~g--------~~~~~~~~l~~i~~~~~v~~~~l~   59 (64)
T PF12844_consen   17 DLAEKLGISRSTISKIENG--------KRKPSVSTLKKIAEALGVSLDELF   59 (64)
T ss_dssp             HHHHHHTS-HHHHHHHHTT--------SS--BHHHHHHHHHHHTS-HHHHC
T ss_pred             HHHHHHCcCHHHHHHHHCC--------CcCCCHHHHHHHHHHhCCCHHHHh
Confidence            5788999999999999998        347888888999999999886543

>KOG3623|consensus

Probab=92.77  E-value=0.11  Score=43.18  Aligned_cols=38  Identities=13%  Similarity=0.284  Sum_probs=34.9

Q ss_pred             cccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877          28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus        28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .|..|+..+-..+|...||+...|++||++++++....
T Consensus       577 ln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv  614 (1007)
T KOG3623|consen  577 LNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV  614 (1007)
T ss_pred             hcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence            38899999999999999999999999999999997764

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=91.88  E-value=0.22  Score=33.77  Aligned_cols=41  Identities=22%  Similarity=0.143  Sum_probs=28.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|+.+        ...|+......||..++++...
T Consensus        87 eLA~~lgvs~s~IsriE~G--------~~~Ps~~~l~kLa~~Lgvsl~e  127 (154)
T TIGR00270        87 QLAKKIQEKESLIKKIENA--------EIEPEPKVVEKLEKLLKIKLRE  127 (154)
T ss_pred             HHHHHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence            5677777777777777766        4567777777777777766643

>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences

Probab=91.73  E-value=0.23  Score=28.60  Aligned_cols=38  Identities=11%  Similarity=0.237  Sum_probs=23.3

Q ss_pred             cchhccCCCHHHHH-HHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIK-TWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q-~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+.+|++..-|. .|...        +..| ...-..+|..+|++.
T Consensus        17 ~lA~~lgis~st~s~~~~~r--------~~~P-~~~l~~ia~~~gvsl   55 (66)
T PF07022_consen   17 ELAERLGISKSTLSNNWKKR--------GSIP-AEWLIKIALETGVSL   55 (66)
T ss_dssp             HHHCCTT--HHHHH-HHHHS--------SS---HHHHHHHHHHH---H
T ss_pred             HHHHHhCcCHHHhhHHHHhC--------CCCC-HHHHHHHHHHHCcCH
Confidence            68888888888887 66654        6777 667777788888776

The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.

>PRK06424 transcription factor; Provisional

Probab=91.59  E-value=0.21  Score=33.53  Aligned_cols=39  Identities=18%  Similarity=0.181  Sum_probs=23.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      |||+++|++...|..|+..        ...|+......||..+|++.
T Consensus       102 eLA~~iGvs~stIskiE~G--------~~~Ps~~~l~kLa~~Lgvsl  140 (144)
T PRK06424        102 DLAAKIFERKNVIASIERG--------DLLPDIKTARKLEKILGITL  140 (144)
T ss_pred             HHHHHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCC
Confidence            4666666666666666666        33556666666666665543

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=91.36  E-value=0.27  Score=31.82  Aligned_cols=42  Identities=12%  Similarity=0.045  Sum_probs=35.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      |||+++|++...+.-|++++        ..|+...-..||..++++...+
T Consensus        23 eLA~~~Gis~~~is~iE~g~--------~~ps~~~l~kIa~aL~v~~~~L   64 (120)
T PRK13890         23 ELSERSGVSISFLSDLTTGK--------ANPSLKVMEAIADALETPLPLL   64 (120)
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCCCHHHH
Confidence            68999999999999999884        4688999999999999887533

>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=91.22  E-value=0.32  Score=25.15  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=24.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+.+|++...|..|..+        ...++......++..+|++.
T Consensus        15 ~la~~~~i~~~~i~~~~~~--------~~~~~~~~~~~i~~~~~~~~   53 (56)
T smart00530       15 ELAEKLGVSRSTLSRIENG--------KRKPSLETLKKLAKALGVSL   53 (56)
T ss_pred             HHHHHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCh
Confidence            4666777777777666655        23445555666666666654

>PRK09726 antitoxin HipB; Provisional

Probab=90.78  E-value=0.29  Score=29.69  Aligned_cols=23  Identities=22%  Similarity=0.375  Sum_probs=14.6

Q ss_pred             HHHHHhhhhcchhhhhhccccch
Q psy4877          36 KRMELSKLLNLTEVQIKTWFQNR   58 (120)
Q Consensus        36 ~r~~La~~~~l~~~~vqvWFqNr   58 (120)
                      ..++||..+|++...|..|..++
T Consensus        27 tq~elA~~~gvs~~tis~~e~g~   49 (88)
T PRK09726         27 TQSELAKKIGIKQATISNFENNP   49 (88)
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCC
Confidence            35566666666666666666554

>PRK10072 putative transcriptional regulator; Provisional

Probab=90.63  E-value=0.37  Score=30.09  Aligned_cols=24  Identities=21%  Similarity=0.455  Sum_probs=14.5

Q ss_pred             HHHHHhhhhcchhhhhhccccchh
Q psy4877          36 KRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        36 ~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ...+||..+|++...|..|...+|
T Consensus        48 TQ~elA~~lGvS~~TVs~WE~G~r   71 (96)
T PRK10072         48 KIDDFARVLGVSVAMVKEWESRRV   71 (96)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCC
Confidence            355566666666666666665554

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=90.05  E-value=0.47  Score=24.63  Aligned_cols=39  Identities=21%  Similarity=0.233  Sum_probs=19.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      ++|..+|++...|..|+.+        ...++......++..++++.
T Consensus        17 ~~a~~~~~~~~~v~~~~~g--------~~~~~~~~~~~i~~~~~~~~   55 (58)
T cd00093          17 ELAEKLGVSRSTISRIENG--------KRNPSLETLEKLAKALGVSL   55 (58)
T ss_pred             HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCh
Confidence            3455555555555555554        22444444445555555443

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

>PRK08359 transcription factor; Validated

Probab=89.96  E-value=0.35  Score=33.49  Aligned_cols=39  Identities=13%  Similarity=0.219  Sum_probs=28.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      |||+.+|++...|..|+.+        ...|+......||..++++.
T Consensus       103 eLA~~lgvs~stI~~iE~G--------~~~Ps~~~l~kLak~l~VsL  141 (176)
T PRK08359        103 ELSHEVGLSVNDLRRIAHG--------EYEPTIKEAKKLERYFKIKL  141 (176)
T ss_pred             HHHHHhCCCHHHHHHHHCC--------CcCCCHHHHHHHHHHhCCcc
Confidence            5777778877777777777        34677777777777777763

>PHA01083 hypothetical protein

Probab=89.62  E-value=0.41  Score=32.19  Aligned_cols=44  Identities=11%  Similarity=0.123  Sum_probs=36.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK   52 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq   52 (120)
                      +||+++|++...|..|-...       .+|.+..+-..||+.+|++...+-
T Consensus        21 qLA~~LGVs~q~IS~~R~G~-------r~~i~de~A~~LAe~aGiDp~eal   64 (149)
T PHA01083         21 QIAHDLGVSPQKISKMRTGV-------RTYISDEEAIFLAESAGIDPEIAL   64 (149)
T ss_pred             HHHHHhCCCHHHHHHHHcCC-------CCCCCHHHHHHHHHHhCCCHHHHH
Confidence            69999999999998876661       358999999999999999975443

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=88.86  E-value=0.58  Score=30.59  Aligned_cols=39  Identities=21%  Similarity=0.348  Sum_probs=21.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++.
T Consensus        23 ~lA~~~gvs~~~is~~E~g~--------~~p~~~~l~~la~~l~vs~   61 (135)
T PRK09706         23 SLAKAVKVSHVSISQWERDE--------TEPTGKNLFALAKALQCSP   61 (135)
T ss_pred             HHHHHhCCCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCH
Confidence            45555666666665555552        2455555555555555554

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=88.79  E-value=0.39  Score=32.43  Aligned_cols=42  Identities=14%  Similarity=0.146  Sum_probs=34.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      |||+++|++...|..|+.+..      +..|+...-..||..+|++..
T Consensus        43 eLAerlGVS~~tIs~iE~G~~------~~~psl~~L~kIA~aLgv~~~   84 (150)
T TIGR02612        43 QLAGRLGVTPQRVEALEKSEL------SGTVTLKTLRAAAEALDCTFV   84 (150)
T ss_pred             HHHHHhCCCHHHHHHHHcCCC------CCCCCHHHHHHHHHHcCCCHH
Confidence            789999999999999998842      334778888899999998873

Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).

>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators

Probab=87.83  E-value=0.81  Score=24.46  Aligned_cols=39  Identities=8%  Similarity=0.211  Sum_probs=26.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHH---HHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKR---MELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r---~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..++...+   .+++..+|...
T Consensus         2 ~lA~~~gvs~~tvs~~l~g~--------~~vs~~~~~~i~~~~~~l~~~~   43 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGK--------PRVSEETRERVLAAAEELGYRP   43 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHHHhCCCC
Confidence            68999999999999988884        23333333   34567766544

HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre

>KOG1168|consensus

Probab=87.43  E-value=0.048  Score=40.55  Aligned_cols=26  Identities=31%  Similarity=0.607  Sum_probs=21.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      -+|+++-|....|.|||.|.|-|-+|
T Consensus       341 aIAekLDLKKNVVRVWFCNQRQKQKR  366 (385)
T KOG1168|consen  341 AIAEKLDLKKNVVRVWFCNQRQKQKR  366 (385)
T ss_pred             HHHHhhhhhhceEEEEeeccHHHHHH
Confidence            37899999999999999999865443

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=86.93  E-value=0.82  Score=31.41  Aligned_cols=41  Identities=24%  Similarity=0.206  Sum_probs=35.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|++.        ...|+...-..||..++++...
T Consensus        25 elA~~~gis~~~is~~E~g--------~~~p~~~~l~~ia~~l~v~~~~   65 (185)
T PRK09943         25 RAAELSGLTHSAISTIEQD--------KVSPAISTLQKLLKVYGLSLSE   65 (185)
T ss_pred             HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence            6899999999999999988        4588899999999999998754

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=86.86  E-value=0.81  Score=28.09  Aligned_cols=39  Identities=13%  Similarity=0.181  Sum_probs=23.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|-.|+.+        ...|+...-..++..+|++-
T Consensus        48 qLAe~~GIs~stLs~iE~g--------~~~Ps~~tL~kI~~aLgi~l   86 (89)
T TIGR02684        48 QLARKTGLSRESLYKALSG--------KGNPTFDTILKVTKALGLKL   86 (89)
T ss_pred             HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHcCCce
Confidence            3566666666666666655        34566666666666666543

gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=85.70  E-value=0.69  Score=27.44  Aligned_cols=46  Identities=15%  Similarity=0.124  Sum_probs=31.6

Q ss_pred             chhcc-CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccc
Q psy4877           3 LSKLL-NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQN   57 (120)
Q Consensus         3 la~~~-~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqN   57 (120)
                      ||+++ .+++..-++ |.=.|        |-......++|..+|+++..|+.|+.+
T Consensus         9 ~~~~l~~l~~~~r~a-f~L~R--------~~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         9 LAERLTWVDSLAEAA-AALAR--------EEAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             HHHHHhcCCHHHHHH-HHHHH--------HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            67777 444443333 33322        334667889999999999999999864

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>KOG3755|consensus

Probab=83.44  E-value=0.96  Score=37.02  Aligned_cols=63  Identities=27%  Similarity=0.333  Sum_probs=40.2

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhh----cccccchhHHHHHhhhh-------cchhhhhhccccchhHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKY----VDKYLSVSKRMELSKLL-------NLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~----~~~yp~~~~r~~La~~~-------~l~~~~vqvWFqNrRak~rr~   65 (120)
                      |+.-+.++...+..-|||.+.-.+.    .++-++.....+.-...       .....-|+-||+|||+++++.
T Consensus       684 LSa~~~~pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~  757 (769)
T KOG3755|consen  684 LSAQLDLPKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRL  757 (769)
T ss_pred             hhhhhcccHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhh
Confidence            5667788888888888887764433    33444443333322222       224467889999999999884

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=82.24  E-value=1.6  Score=32.58  Aligned_cols=42  Identities=10%  Similarity=0.090  Sum_probs=36.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+..        ...|+...-..||..+|++...+
T Consensus        46 ~lA~~~gvs~~~i~~~E~g--------~~~ps~~~l~~ia~~l~v~~~~l   87 (309)
T PRK08154         46 VLAQASGVSERYLAQLESG--------QGNVSILLLRRVARALGCSLADL   87 (309)
T ss_pred             HHHHHHCcCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCHHHH
Confidence            6899999999999999999        45789999999999999886433

>PRK02866 cyanate hydratase; Validated

Probab=82.13  E-value=2.2  Score=28.77  Aligned_cols=41  Identities=20%  Similarity=0.324  Sum_probs=30.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+.+|+++.-+-.+|..        ++.++...-+.|+..++|++..
T Consensus        23 ~IA~~iG~S~v~vaaa~lG--------Q~~ls~e~A~kla~~LgL~~~~   63 (147)
T PRK02866         23 DIAEAIGLSEVWVTAALLG--------QMTLPAEEAEKVAELLGLDEDA   63 (147)
T ss_pred             HHHHHhCCCHHHHHHHHhC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence            5777788888777777776        5566777777778888887753

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=82.08  E-value=0.86  Score=26.01  Aligned_cols=16  Identities=25%  Similarity=0.771  Sum_probs=8.9

Q ss_pred             cchhccCCCHHHHHHH
Q psy4877           2 ELSKLLNLTEVQIKTW   17 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~   17 (120)
                      ++|++||+++.+|..|
T Consensus        27 dIA~~Lgvs~~tIr~W   42 (60)
T PF10668_consen   27 DIAEKLGVSESTIRKW   42 (60)
T ss_pred             HHHHHHCCCHHHHHHH
Confidence            3555556665555544

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=81.85  E-value=0.83  Score=26.05  Aligned_cols=20  Identities=25%  Similarity=0.556  Sum_probs=17.5

Q ss_pred             HHHHHhhhhcchhhhhhccc
Q psy4877          36 KRMELSKLLNLTEVQIKTWF   55 (120)
Q Consensus        36 ~r~~La~~~~l~~~~vqvWF   55 (120)
                      .-.+||..+|+++.+|..|=
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK   43 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWK   43 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHh
Confidence            45678999999999999985

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>KOG0774|consensus

Probab=81.22  E-value=2.2  Score=31.51  Aligned_cols=25  Identities=44%  Similarity=0.829  Sum_probs=21.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWK   26 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~   26 (120)
                      |||+.-|++..||..||-|.|-+.+
T Consensus       223 eLAkqCnItvsQvsnwfgnkrIryk  247 (334)
T KOG0774|consen  223 ELAKQCNITVSQVSNWFGNKRIRYK  247 (334)
T ss_pred             HHHHHcCceehhhccccccceeehh
Confidence            7999999999999999999884443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		7e-08
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		8e-08
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		1e-07
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		2e-07
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		2e-07
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		2e-07
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		3e-07
1hom_A	68	Determination Of The Three-Dimensional Structure Of		3e-07
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		3e-07
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		9e-07
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-06
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		3e-06
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		3e-06
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		3e-06
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		3e-06
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		5e-06
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		7e-06
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		4e-05
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		4e-05
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		5e-05
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		8e-05
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		8e-05
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		1e-04
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		1e-04
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-04
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-04
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		1e-04
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		1e-04
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		2e-04
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-04
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		2e-04
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-04
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-04
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		3e-04
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		4e-04
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		4e-04
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		6e-04
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		6e-04
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-04
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		9e-04

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 33/43 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          +  KYL+ ++R  L++ L +T+ Q+KTWFQNRRTKW++Q A +
Sbjct: 37 HKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 79

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          KYL+ ++R  L+K L +T+ Q+KTWFQNRRTKW++Q
Sbjct: 20 KYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/37 (62%), Positives = 30/37 (81%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +KY+S  +R+EL+ +LNLTE  IK WFQNRR KWKK+
Sbjct: 25 NKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 20/38 (52%), Positives = 30/38 (78%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          +  KYLS+++R +++  L L+EVQ+K WFQNRR KWK+
Sbjct: 27 HCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 33/43 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          + ++YL+  +R+E++  L+LTE QIK WFQNRR KWKK+  +K
Sbjct: 22 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 64

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 33/43 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          + ++YL+  +R+E++  L+LTE QIK WFQNRR KWKK+  +K
Sbjct: 16 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 31/39 (79%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          + ++YL+  +R+E++  L+LTE QIK WFQNRR KWKK+
Sbjct: 48 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 32/43 (74%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          + ++YL+  +R+E++  L LTE QIK WFQNRR KWKK+  +K
Sbjct: 22 HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTK 64

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 31/39 (79%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          + ++YL+  +R+E++  L+LTE QIK WFQNRR KWKK+
Sbjct: 23 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 28/37 (75%)
Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
            KYLS  +R  L+K+L L+E Q+KTWFQNRR KW++
Sbjct: 28 TQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 29/35 (82%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          KYLS   R++L++ L L+++Q+KTW+QNRR KWKK
Sbjct: 40 KYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          YL+  +R E+++LLNLTE Q+K WFQNRR K KK
Sbjct: 37 YLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK-KQLASKL 70
           KYLS  +R  L+K L LTE Q+K WFQNRR K K KQL+S+L
Sbjct: 26 QKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL 68

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 31/42 (73%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68
          + + YL+  +R+E++  L+LTE QIK WFQNRR K KK++ +
Sbjct: 40 HTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQA 81

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 29/39 (74%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          + +KYLS ++R+E++  L L E Q+K WFQNRR K KK+
Sbjct: 54 HFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 27/35 (77%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          +YLS+++R E S  L+LTE Q+K WFQNRR K K+
Sbjct: 23 QYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 27/34 (79%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          YL+  +R E++++LNLTE Q+K WFQNRR K KK
Sbjct: 25 YLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 27/36 (75%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
           KYLS+ +  ELS +LNL+  Q+KTWFQN+R K K+
Sbjct: 25 QKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          +YL++ +R EL+  L LT+ Q+K WFQN+R+K KK
Sbjct: 30 QYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 26/39 (66%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y + Y+S  +R EL+  LNL E  IK WFQNRR K K+Q
Sbjct: 21 YKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  V  R EL+  + LTE +I+ WFQNRR KW+KQ
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 27/35 (77%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          KYLS+ +  ELS +LNL+  Q+KTWFQN+R K K+
Sbjct: 45 KYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  V  R EL+  + LTE +I+ WFQNRR KW+KQ
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  V  R EL+  + LTE +I+ WFQNRR KW+KQ
Sbjct: 30 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WFQN+R K KK
Sbjct: 23 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WFQN+R K KK
Sbjct: 25 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 29/38 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          + ++Y++  +R++++  L+L+E QIK WFQNRR K KK
Sbjct: 23 HFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WFQN+R K KK
Sbjct: 8  NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
           KYLS  +R  L+ +++LT  Q+K WFQN R K K+Q   K
Sbjct: 24 QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WFQN R K KK
Sbjct: 23 NRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 27/37 (72%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          ++Y  +S R E++   NLTE +++ WF+NRR KW+K+
Sbjct: 25 NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 26/39 (66%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68
          +Y  +  R EL++  NLTE +I+ WFQNRR + +KQ  S
Sbjct: 41 QYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS 79

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WFQN R K KK
Sbjct: 23 NRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WFQN+R K ++
Sbjct: 25 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 26/37 (70%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          + Y  +S R E++   NLTE +++ WF+NRR KW+K+
Sbjct: 25 NHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WF+N+R K KK
Sbjct: 25 NRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/35 (51%), Positives = 24/35 (68%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
           +YLS  +R +L+ +L LT  Q+K WFQNRR K K
Sbjct: 24 QRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61
          ++YL+  +R +LS  L L E QIK WFQN+R K
Sbjct: 21 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++YL+  +R +LS  L L E QIK WF N+R K KK
Sbjct: 21 NRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
          +K+++  KR  +S   NL+E Q+  WFQNRR K KK + +KLK  +
Sbjct: 23 NKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK-VINKLKTTS 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	3e-18
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	2e-11
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-17
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-10
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-17
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-11
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-17
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	6e-11
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-17
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-11
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	2e-17
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	2e-11
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	5e-17
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	1e-10
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	6e-17
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-10
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	6e-17
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-10
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	7e-17
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	8e-11
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	1e-16
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	1e-10
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-16
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-11
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	4e-14
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-10
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-14
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	3e-09
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	6e-14
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	3e-09
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	8e-14
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-09
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	1e-13
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	3e-09
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	1e-13
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	2e-09
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-13
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	1e-08
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	5e-13
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	8e-09
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	5e-13
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	5e-09
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	6e-13
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	2e-08
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	9e-13
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-08
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-12
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-08
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-11
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-07
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	5e-11
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	2e-06
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-10
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-07
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-10
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	5e-07
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-10
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-07
1uhs_A	72	HOP, homeodomain only protein; structural genomics	1e-09
1uhs_A	72	HOP, homeodomain only protein; structural genomics	1e-05
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-09
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	4e-07
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	9e-09
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	4e-06
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-08
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	8e-06
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	2e-08
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	6e-06
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	3e-08
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	9e-06
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	3e-08
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	9e-06
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	4e-08
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	9e-06
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	5e-08
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	9e-05
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	5e-08
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-05
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	7e-08
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-05
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	8e-08
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	3e-05
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-07
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	5e-05
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	1e-07
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-05
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-07
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	3e-05
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-07
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	4e-05
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-07
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	2e-05
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-07
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	6e-05
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	4e-07
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	4e-05
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	4e-07
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	5e-05
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-06
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-04
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	8e-05
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	4e-06
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	3e-04
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	1e-05
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	2e-04
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	5e-04

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

 Score = 71.6 bits (176), Expect = 3e-18
 Identities = 21/36 (58%), Positives = 30/36 (83%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          KYL+ ++R  L+K L +T+ Q+KTWFQNRRTKW++Q
Sbjct: 20 KYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

 Score = 53.9 bits (130), Expect = 2e-11
 Identities = 16/26 (61%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+K L +T+ Q+KTWFQNRRTKW+
Sbjct: 28 AALAKALRMTDAQVKTWFQNRRTKWR 53

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

 Score = 71.0 bits (174), Expect = 1e-17
 Identities = 21/46 (45%), Positives = 33/46 (71%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAH 75
          KYL+ ++R  L++ L +T+ Q+KTWFQNRRTKW++Q A + +    
Sbjct: 40 KYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQ 85

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

 Score = 53.3 bits (128), Expect = 1e-10
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN 45
            L++ L +T+ Q+KTWFQNRRTKW+        ++R   ++L+ 
Sbjct: 48 AALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQAANRLML 92

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

 Score = 70.0 bits (172), Expect = 1e-17
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          KYLS+ +  ELS +LNL+  Q+KTWFQN+R K K+ 
Sbjct: 26 KYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

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

 Score = 53.8 bits (130), Expect = 2e-11
 Identities = 16/26 (61%), Positives = 20/26 (76%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           ELS +LNL+  Q+KTWFQN+R K K
Sbjct: 34 QELSSILNLSYKQVKTWFQNQRMKCK 59

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

 Score = 70.1 bits (172), Expect = 1e-17
 Identities = 22/40 (55%), Positives = 27/40 (67%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          KYLS  +R  L+K L LTE Q+K WFQNRR K K++  S 
Sbjct: 27 KYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSS 66

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

 Score = 53.1 bits (128), Expect = 6e-11
 Identities = 16/26 (61%), Positives = 18/26 (69%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+K L LTE Q+K WFQNRR K K
Sbjct: 35 AHLAKNLKLTETQVKIWFQNRRYKTK 60

>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 = 70.6 bits (173), Expect = 1e-17
 Identities = 21/40 (52%), Positives = 30/40 (75%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          KYLS   R++L++ L L+++Q+KTW+QNRR KWKK   S 
Sbjct: 40 KYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPSS 79

>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 = 54.0 bits (130), Expect = 4e-11
 Identities = 14/26 (53%), Positives = 23/26 (88%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          ++L++ L L+++Q+KTW+QNRR KWK
Sbjct: 48 IDLAESLGLSQLQVKTWYQNRRMKWK 73

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

 Score = 69.2 bits (170), Expect = 2e-17
 Identities = 20/35 (57%), Positives = 27/35 (77%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          +YLS+++R E S  L+LTE Q+K WFQNRR K K+
Sbjct: 23 QYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 54.2 bits (131), Expect = 2e-11
 Identities = 16/26 (61%), Positives = 18/26 (69%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           E S  L+LTE Q+K WFQNRR K K
Sbjct: 31 AEFSSSLSLTETQVKIWFQNRRAKAK 56

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

 Score = 68.6 bits (168), Expect = 5e-17
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          +YL++ +R EL+  L LT+ Q+K WFQN+R+K KK   S 
Sbjct: 30 QYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPSS 69

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

 Score = 52.4 bits (126), Expect = 1e-10
 Identities = 14/26 (53%), Positives = 19/26 (73%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           EL+  L LT+ Q+K WFQN+R+K K
Sbjct: 38 AELAASLGLTQTQVKIWFQNKRSKIK 63

>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 = 68.6 bits (168), Expect = 6e-17
 Identities = 18/40 (45%), Positives = 24/40 (60%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          +YLS  +R  L+ L+ LT  Q+K WFQN R K K+    K
Sbjct: 32 RYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK 71

>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 = 52.1 bits (125), Expect = 2e-10
 Identities = 13/26 (50%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+ L+ LT  Q+K WFQN R K K
Sbjct: 40 EHLASLIRLTPTQVKIWFQNHRYKTK 65

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

 Score = 68.5 bits (168), Expect = 6e-17
 Identities = 19/40 (47%), Positives = 26/40 (65%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          KYLS  +R  L+ +++LT  Q+K WFQN R K K+Q   K
Sbjct: 25 KYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64

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

 Score = 51.6 bits (124), Expect = 2e-10
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+ +++LT  Q+K WFQN R K K
Sbjct: 33 EHLASMIHLTPTQVKIWFQNHRYKMK 58

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

 Score = 68.2 bits (167), Expect = 7e-17
 Identities = 22/40 (55%), Positives = 29/40 (72%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          KYLS  +R  L+K+L L+E Q+KTWFQNRR KW++   S 
Sbjct: 30 KYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPSS 69

>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 = 52.8 bits (127), Expect = 8e-11
 Identities = 16/26 (61%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+K+L L+E Q+KTWFQNRR KW+
Sbjct: 38 KRLAKMLQLSERQVKTWFQNRRAKWR 63

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

 Score = 68.3 bits (167), Expect = 1e-16
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          KYLS+ +  ELS +LNL+  Q+KTWFQN+R K K+ 
Sbjct: 45 KYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW 80

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

 Score = 52.9 bits (127), Expect = 1e-10
 Identities = 16/26 (61%), Positives = 20/26 (76%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           ELS +LNL+  Q+KTWFQN+R K K
Sbjct: 53 QELSNILNLSYKQVKTWFQNQRMKSK 78

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

 Score = 67.3 bits (165), Expect = 1e-16
 Identities = 18/34 (52%), Positives = 24/34 (70%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
          +YLS  +R +L+ +L LT  Q+K WFQNRR K K
Sbjct: 25 RYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 53.8 bits (130), Expect = 2e-11
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           +L+ +L LT  Q+K WFQNRR K K
Sbjct: 33 DQLASVLKLTSTQVKIWFQNRRYKSK 58

>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 = 61.1 bits (149), Expect = 4e-14
 Identities = 10/35 (28%), Positives = 22/35 (62%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
           + L+  ++ E++K   +T +Q++ WF N+R + K
Sbjct: 27 KQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>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 = 52.2 bits (126), Expect = 1e-10
 Identities = 9/26 (34%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           E++K   +T +Q++ WF N+R + K
Sbjct: 36 EEVAKKCGITPLQVRVWFINKRMRSK 61

>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 = 61.3 bits (149), Expect = 4e-14
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          +YL+  +  +LS  L L   Q+K WF+NRR + K Q    
Sbjct: 25 RYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH 64

>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 = 48.6 bits (116), Expect = 3e-09
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           +LS  L L   Q+K WF+NRR + K
Sbjct: 33 ADLSAKLALGTAQVKIWFKNRRRRHK 58

>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 = 60.4 bits (147), Expect = 6e-14
 Identities = 20/37 (54%), Positives = 25/37 (67%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          + Y+S  +R EL+  LNL E  IK WFQNRR K K+Q
Sbjct: 23 ENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 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 = 48.5 bits (116), Expect = 3e-09
 Identities = 16/26 (61%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           EL+  LNL E  IK WFQNRR K K
Sbjct: 32 CELAAQLNLPESTIKVWFQNRRMKDK 57

>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 = 60.4 bits (147), Expect = 8e-14
 Identities = 18/35 (51%), Positives = 24/35 (68%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          +YL+  +R +LS  L L E QIK WF+N+R K KK
Sbjct: 26 RYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 48.5 bits (116), Expect = 3e-09
 Identities = 14/25 (56%), Positives = 17/25 (68%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +LS  L L E QIK WF+N+R K K
Sbjct: 35 QLSSELGLNEAQIKIWFKNKRAKIK 59

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

 Score = 60.1 bits (146), Expect = 1e-13
 Identities = 23/37 (62%), Positives = 30/37 (81%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +KY+S  +R+EL+ +LNLTE  IK WFQNRR KWKK+
Sbjct: 25 NKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

 Score = 48.9 bits (117), Expect = 3e-09
 Identities = 18/26 (69%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +EL+ +LNLTE  IK WFQNRR KWK
Sbjct: 34 VELAVMLNLTERHIKIWFQNRRMKWK 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 = 60.1 bits (146), Expect = 1e-13
 Identities = 21/37 (56%), Positives = 30/37 (81%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          ++YL+  +R+E++  L+LTE QIK WFQNRR KWKK+
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60

>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 = 49.3 bits (118), Expect = 2e-09
 Identities = 17/26 (65%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +E++  L+LTE QIK WFQNRR KWK
Sbjct: 33 IEIAHALSLTERQIKIWFQNRRMKWK 58

>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 = 59.1 bits (143), Expect = 4e-13
 Identities = 22/42 (52%), Positives = 29/42 (69%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71
           YL+  +R E+++LLNLTE Q+K WFQNRR K KK    + K
Sbjct: 36 MYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAK 77

>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 = 47.5 bits (113), Expect = 1e-08
 Identities = 17/26 (65%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           E+++LLNLTE Q+K WFQNRR K K
Sbjct: 44 YEVARLLNLTERQVKIWFQNRRMKMK 69

>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 = 58.7 bits (142), Expect = 5e-13
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          K+++  KR ++S   +L+E QI  WFQNRR K KK   S 
Sbjct: 30 KFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPSS 69

>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 = 47.5 bits (113), Expect = 8e-09
 Identities = 13/26 (50%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           ++S   +L+E QI  WFQNRR K K
Sbjct: 38 RKISAATSLSERQITIWFQNRRVKEK 63

>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 = 58.7 bits (142), Expect = 5e-13
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           YL+  +R+E++  L+LTE QIK WFQNRR K KK+
Sbjct: 43 HYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78

>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 = 48.7 bits (116), Expect = 5e-09
 Identities = 16/26 (61%), Positives = 20/26 (76%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +E++  L+LTE QIK WFQNRR K K
Sbjct: 51 IEMAHALSLTERQIKIWFQNRRMKLK 76

>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 = 59.1 bits (143), Expect = 6e-13
 Identities = 20/40 (50%), Positives = 27/40 (67%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          KYLS ++R+E++  L L E Q+K WFQNRR K KK+    
Sbjct: 57 KYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREG 96

>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 = 47.2 bits (112), Expect = 2e-08
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +E++  L L E Q+K WFQNRR K K
Sbjct: 65 VEIAATLELNETQVKIWFQNRRMKQK 90

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

 Score = 57.9 bits (140), Expect = 9e-13
 Identities = 17/36 (47%), Positives = 23/36 (63%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          K+++  KR  +S   NL+E Q+  WFQNRR K KK 
Sbjct: 30 KFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 65

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

 Score = 47.2 bits (112), Expect = 1e-08
 Identities = 13/26 (50%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            +S   NL+E Q+  WFQNRR K K
Sbjct: 38 RRISATTNLSERQVTIWFQNRRVKEK 63

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

 Score = 57.9 bits (140), Expect = 1e-12
 Identities = 21/36 (58%), Positives = 29/36 (80%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +YL+  +R+E++  L+LTE QIK WFQNRR KWKK+
Sbjct: 51 RYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86

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

 Score = 47.5 bits (113), Expect = 1e-08
 Identities = 17/26 (65%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +E++  L+LTE QIK WFQNRR KWK
Sbjct: 59 IEIAHALSLTERQIKIWFQNRRMKWK 84

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

 Score = 54.3 bits (131), Expect = 3e-11
 Identities = 9/41 (21%), Positives = 22/41 (53%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
          +++   S+   L+K+  L+  +++ WF +RR   +    S+
Sbjct: 30 NQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSR 70

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

 Score = 44.7 bits (106), Expect = 1e-07
 Identities = 7/26 (26%), Positives = 15/26 (57%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+K+  L+  +++ WF +RR   +
Sbjct: 39 EHLTKVTGLSTREVRKWFSDRRYHCR 64

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

 Score = 53.2 bits (128), Expect = 5e-11
 Identities = 10/38 (26%), Positives = 20/38 (52%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          V+K+   +    ++    LTE Q + WF+ R  +W++ 
Sbjct: 24 VNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

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

 Score = 41.3 bits (97), Expect = 2e-06
 Identities = 8/26 (30%), Positives = 14/26 (53%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            ++    LTE Q + WF+ R  +W+
Sbjct: 34 CLIAAEAGLTEEQTQKWFKQRLAEWR 59

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 31  YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
             +      +++ LN+ +  I+ WF NRR K K+
Sbjct: 125 KPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

>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 = 46.5 bits (110), Expect = 1e-07
 Identities = 10/25 (40%), Positives = 16/25 (64%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWK 26
            +++ LN+ +  I+ WF NRR K K
Sbjct: 133 LIAEQLNMEKEVIRVWFSNRRQKEK 157

>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-10
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 29  DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
               S  +   L+  L L +  ++ WF NRR K K+ 
Sbjct: 121 CPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRM 157

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

 Score = 45.0 bits (106), Expect = 5e-07
 Identities = 10/29 (34%), Positives = 15/29 (51%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
            L+  L L +  ++ WF NRR K K +  
Sbjct: 131 GLADSLQLEKEVVRVWFCNRRQKEKRMTP 159

>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 = 51.2 bits (123), Expect = 3e-10
 Identities = 15/36 (41%), Positives = 18/36 (50%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           Y    +  +LS LLNL    I  WFQN R K +K 
Sbjct: 30 AYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65

>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 = 43.5 bits (103), Expect = 4e-07
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +LS LLNL    I  WFQN R K +
Sbjct: 39 QLSNLLNLPTRVIVVWFQNARQKAR 63

>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 = 50.1 bits (120), Expect = 1e-09
 Identities = 10/38 (26%), Positives = 20/38 (52%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          V+K+   +    ++    LTE Q + WF+ R  +W++ 
Sbjct: 23 VNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 39.7 bits (93), Expect = 1e-05
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKW 25
            ++    LTE Q + WF+ R  +W
Sbjct: 33 CLIAAEAGLTEEQTQKWFKQRLAEW 57

>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 = 51.6 bits (123), Expect = 1e-09
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 31  YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
             +  +  E++K LN     ++ WF NRR   K 
Sbjct: 117 LPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>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 = 45.0 bits (106), Expect = 4e-07
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWK 26
           E++K LN     ++ WF NRR   K
Sbjct: 125 EMAKELNYDREVVRVWFSNRRQTLK 149

>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 = 49.2 bits (117), Expect = 9e-09
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 16  TWFQNRRTKWKY-VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
           +       +  +      S  + M +++ LNL +  ++ WF NRR + K+
Sbjct: 95  SIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

>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 = 42.3 bits (99), Expect = 4e-06
 Identities = 9/25 (36%), Positives = 16/25 (64%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWK 26
            +++ LNL +  ++ WF NRR + K
Sbjct: 119 RMAEELNLEKEVVRVWFCNRRQREK 143

>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 = 47.9 bits (114), Expect = 1e-08
 Identities = 8/38 (21%), Positives = 18/38 (47%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +D   +      ++  + L +  ++ WFQN R + +K 
Sbjct: 38 LDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS 75

>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 = 40.2 bits (94), Expect = 8e-06
 Identities = 6/25 (24%), Positives = 14/25 (56%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           ++  + L +  ++ WFQN R + +
Sbjct: 49 HIAHEVGLKKRVVQVWFQNTRARER 73

>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 = 46.5 bits (111), Expect = 2e-08
 Identities = 14/35 (40%), Positives = 21/35 (60%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  +    +L++ LNL   +I+ WFQNRR K K+ 
Sbjct: 25 YPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 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 = 40.0 bits (94), Expect = 6e-06
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +L++ LNL   +I+ WFQNRR K K
Sbjct: 33 DLAQKLNLELDRIQIWFQNRRAKLK 57

>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 = 46.1 bits (110), Expect = 3e-08
 Identities = 19/35 (54%), Positives = 24/35 (68%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  V  R EL+  + LTE +I+ WFQNRR KW+KQ
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

>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 = 39.5 bits (93), Expect = 9e-06
 Identities = 14/25 (56%), Positives = 19/25 (76%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          EL+  + LTE +I+ WFQNRR KW+
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKWR 55

>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 = 46.1 bits (110), Expect = 3e-08
 Identities = 16/35 (45%), Positives = 25/35 (71%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  +S R E++   NLTE +++ WF+NRR KW+K+
Sbjct: 27 YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

 Score = 39.6 bits (93), Expect = 9e-06
 Identities = 12/31 (38%), Positives = 23/31 (74%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYL 32
          E++   NLTE +++ WF+NRR KW+  ++++
Sbjct: 35 EIAVWTNLTEARVRVWFKNRRAKWRKREEFI 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 = 45.6 bits (108), Expect = 4e-08
 Identities = 7/37 (18%), Positives = 18/37 (48%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           ++   ++   L ++  L   +IK WF + R + ++ 
Sbjct: 26 SQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62

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

 Score = 39.8 bits (93), Expect = 9e-06
 Identities = 7/25 (28%), Positives = 13/25 (52%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           L ++  L   +IK WF + R + +
Sbjct: 36 RLIEVTGLARSEIKKWFSDHRYRCQ 60

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

 Score = 47.9 bits (113), Expect = 5e-08
 Identities = 8/60 (13%), Positives = 19/60 (31%)

Query: 10  TEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
             +      +         +K  S   ++ +S+ L L    +  +F N R +   +    
Sbjct: 100 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEH 159

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

 Score = 38.7 bits (89), Expect = 9e-05
 Identities = 6/25 (24%), Positives = 11/25 (44%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWK 26
            +S+ L L    +  +F N R +  
Sbjct: 129 TISQQLGLELSTVSNFFMNARRRSL 153

>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 = 45.8 bits (109), Expect = 5e-08
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  +  R EL++  NLTE +I+ WFQNRR + +KQ
Sbjct: 42 YPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76

>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 = 39.7 bits (93), Expect = 1e-05
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLS 33
          EL++  NLTE +I+ WFQNRR + +     +S
Sbjct: 50 ELAQRTNLTEARIQVWFQNRRARLRKQHTSVS 81

>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 = 45.2 bits (107), Expect = 7e-08
 Identities = 12/38 (31%), Positives = 16/38 (42%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          V  Y        LS  L+L +  I  +FQN+R   K  
Sbjct: 29 VGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>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 = 39.0 bits (91), Expect = 2e-05
 Identities = 10/26 (38%), Positives = 14/26 (53%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            LS  L+L +  I  +FQN+R   K
Sbjct: 39 HTLSAQLDLPKHTIIKFFQNQRYHVK 64

>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 = 45.0 bits (107), Expect = 8e-08
 Identities = 13/35 (37%), Positives = 24/35 (68%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  V  R +L++ ++L E +++ WF+NRR KW++ 
Sbjct: 31 YPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

>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 = 38.5 bits (90), Expect = 3e-05
 Identities = 10/25 (40%), Positives = 20/25 (80%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +L++ ++L E +++ WF+NRR KW+
Sbjct: 39 QLARKVHLREEKVEVWFKNRRAKWR 63

>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 = 44.6 bits (106), Expect = 1e-07
 Identities = 9/38 (23%), Positives = 18/38 (47%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          ++   S  +  E++    L +  IK WF+N   K ++ 
Sbjct: 28 INNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS 65

>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 = 37.7 bits (88), Expect = 5e-05
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          E++    L +  IK WF+N   K +
Sbjct: 39 EMADKSGLPQKVIKHWFRNTLFKER 63

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 10/36 (27%), Positives = 18/36 (50%)

Query: 29  DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
               S+ +   ++  L L +  ++ WF NRR K K+
Sbjct: 118 SPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153

>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 = 40.1 bits (93), Expect = 2e-05
 Identities = 9/25 (36%), Positives = 14/25 (56%)

Query: 2   ELSKLLNLTEVQIKTWFQNRRTKWK 26
            ++  L L +  ++ WF NRR K K
Sbjct: 128 HIANQLGLEKDVVRVWFSNRRQKGK 152

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

 Score = 44.7 bits (106), Expect = 2e-07
 Identities = 14/35 (40%), Positives = 22/35 (62%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  V  R  L+  ++L E +I+ WF NRR KW+++
Sbjct: 31 YPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65

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

 Score = 38.5 bits (90), Expect = 3e-05
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKR 37
           L+  ++L E +I+ WF NRR KW+  +K  +  ++
Sbjct: 39 RLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRRQ 74

>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 = 44.3 bits (105), Expect = 2e-07
 Identities = 13/35 (37%), Positives = 23/35 (65%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          Y  +  R E++  +NL E +++ WF+NRR K ++Q
Sbjct: 31 YPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ 65

>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 = 38.2 bits (89), Expect = 4e-05
 Identities = 10/25 (40%), Positives = 18/25 (72%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          E++  +NL E +++ WF+NRR K +
Sbjct: 39 EVALKINLPESRVQVWFKNRRAKCR 63

>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 = 44.0 bits (104), Expect = 2e-07
 Identities = 12/35 (34%), Positives = 20/35 (57%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          KY    +   LSK L+ +  +I+ WF++RR + K 
Sbjct: 32 KYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP 66

>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 = 39.0 bits (91), Expect = 2e-05
 Identities = 10/26 (38%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            LSK L+ +  +I+ WF++RR + K
Sbjct: 40 KGLSKQLDWSVRKIQCWFRHRRNQDK 65

>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 = 43.6 bits (103), Expect = 4e-07
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTG 80
                  +L++   LT+  ++ WFQN R K+++ L  +         +G
Sbjct: 31 NPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGGVSGPSSG 80

>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 = 37.8 bits (88), Expect = 6e-05
 Identities = 9/25 (36%), Positives = 17/25 (68%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +L++   LT+  ++ WFQN R K++
Sbjct: 39 QLAQKTGLTKRVLQVWFQNARAKFR 63

>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 = 43.1 bits (102), Expect = 4e-07
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
                + +L ++  L+   I+ WFQN+R K KK+
Sbjct: 27 RPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 = 38.1 bits (89), Expect = 4e-05
 Identities = 10/25 (40%), Positives = 16/25 (64%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +L ++  L+   I+ WFQN+R K K
Sbjct: 35 QLVEMTGLSPRVIRVWFQNKRCKDK 59

>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 = 43.3 bits (102), Expect = 4e-07
 Identities = 8/37 (21%), Positives = 14/37 (37%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +      +   L     +T  +I +WF  RR K   +
Sbjct: 29 NPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65

>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 = 38.0 bits (88), Expect = 5e-05
 Identities = 8/30 (26%), Positives = 12/30 (40%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
            L     +T  +I +WF  RR K    + 
Sbjct: 38 DRLRSETKMTRREIDSWFSERRKKVNAEET 67

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

 Score = 42.3 bits (99), Expect = 2e-06
 Identities = 8/49 (16%), Positives = 18/49 (36%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNR 77
            + + ++   L     L+  +I +WF  RR        + L  +   +
Sbjct: 35 SSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLDSMGSGK 83

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 7/29 (24%), Positives = 13/29 (44%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
           L     L+  +I +WF  RR     +++
Sbjct: 45 RLRVETKLSRREIDSWFSERRKLRDSMEQ 73

>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 = 40.9 bits (96), Expect = 2e-06
 Identities = 11/35 (31%), Positives = 17/35 (48%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          K+    +   LSK L+     I+ WF+ RR + K 
Sbjct: 24 KHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 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 = 37.1 bits (86), Expect = 8e-05
 Identities = 10/26 (38%), Positives = 14/26 (53%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            LSK L+     I+ WF+ RR + K
Sbjct: 32 EGLSKQLDWDVRSIQRWFRQRRNQEK 57

>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 = 41.1 bits (96), Expect = 4e-06
 Identities = 7/37 (18%), Positives = 13/37 (35%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
             L+  +   L     LT  +I  WF  ++     +
Sbjct: 33 SSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK 69

>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 = 36.5 bits (84), Expect = 3e-04
 Identities = 6/29 (20%), Positives = 11/29 (37%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
           L     LT  +I  WF  ++      ++
Sbjct: 43 RLRAQTKLTRREIDAWFTEKKKSKALKEE 71

>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 = 40.0 bits (93), Expect = 1e-05
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 15/51 (29%)

Query: 30 KYLSVSKRMELSKLLN---------------LTEVQIKTWFQNRRTKWKKQ 65
          +Y   +KR E++   N               +T +++  WF NRR + K++
Sbjct: 30 QYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR 80

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWKY 27
          +LS L  +T +++  WF NRR + K 
Sbjct: 54 KLSDLERVTSLKVYNWFANRRKEIKR 79

>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 Length = 60

 Score = 35.0 bits (81), Expect = 5e-04
 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 5/50 (10%)

Query: 15 KTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++WF          + YL       L K  +L+ +QIK W  NRR K K 
Sbjct: 14 ESWFAKNIE-----NPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.79
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.77
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.76
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.76
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.75
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.75
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.75
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.75
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.75
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.75
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.75
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.75
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.74
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.74
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.74
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.74
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.73
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.73
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.73
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.73
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.73
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.73
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.73
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.73
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.73
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.72
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.72
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.72
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.72
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.72
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.72
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.72
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.72
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.71
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.71
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.71
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.71
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.71
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.71
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.71
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.71
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.71
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.71
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.7
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.7
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.7
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.7
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.7
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.69
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.69
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.69
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.69
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.68
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.67
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.66
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.66
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.66
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.66
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.66
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.65
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.65
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.64
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.63
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.61
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.61
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.61
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.6
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.59
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.59
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.57
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.57
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.53
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.52
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.41
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.39
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.31
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.27
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.18
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.14
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.14
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.13
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.11
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.09
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.07
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.07
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	99.06
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.05
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.05
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.05
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.04
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.04
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.03
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.03
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.03
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.02
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.02
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.01
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.01
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.01
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.01
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.01
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.01
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.01
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.01
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.0
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.0
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.0
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.0
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.0
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	98.99
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	98.99
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	98.99
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	98.99
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	98.98
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	98.98
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	98.97
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	98.97
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	98.97
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	98.97
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	98.96
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	98.96
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	98.96
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	98.96
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	98.96
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	98.96
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	98.95
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	98.94
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	98.92
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	98.92
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	98.91
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	98.91
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	98.91
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	98.9
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	98.88
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	98.88
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	98.85
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	98.84
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	98.8
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	98.78
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	98.63
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	98.63
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.62
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.5
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.47
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	98.45
1lfb_A	99	Liver transcription factor (LFB1); transcription r	98.44
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	95.07
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	94.75
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	94.54
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	94.49
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	94.41
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	94.36
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	94.32
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	94.27
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	94.24
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	94.11
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	93.92
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	93.8
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	93.76
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	93.74
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	93.63
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	93.44
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	93.42
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	93.07
3t76_A	88	VANU, transcriptional regulator vanug; structural	92.97
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	92.93
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	92.69
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	92.69
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	92.62
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	92.6
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	92.6
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	92.09
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	92.04
3ivp_A	126	Putative transposon-related DNA-binding protein; A	91.86
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	91.75
3mlf_A	111	Transcriptional regulator; structural genomics, he	91.73
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	91.72
3trb_A	104	Virulence-associated protein I; mobIle and extrach	91.04
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	90.93
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	90.86
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	90.8
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	90.62
2wus_R	112	RODZ, putative uncharacterized protein; structural	90.52
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	90.27
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	90.16
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	90.03
3cec_A	104	Putative antidote protein of plasmid maintenance;	89.88
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	89.66
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	89.52
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	88.63
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	88.52
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	88.49
1b0n_A	111	Protein (SINR protein); transcription regulator, a	88.46
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	88.45
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	87.0
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	84.47
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	83.93
1dw9_A	156	Cyanate lyase; cyanate degradation, structural gen	83.76
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	82.41
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	81.54
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	81.26
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	81.16

>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=1.8e-19  Score=108.67  Aligned_cols=63  Identities=27%  Similarity=0.478  Sum_probs=56.7

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKM   72 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~   72 (120)
                      .++.|+.+|+++++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+........
T Consensus        10 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~~   72 (80)
T 2cue_A           10 NRTSFTQEQIEALEKEFE-----RTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQR   72 (80)
T ss_dssp             CCCCSCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhcc
Confidence            578999999999888877     599999999999999999999999999999999999976665543

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

Probab=99.77  E-value=2.1e-19  Score=101.49  Aligned_cols=54  Identities=41%  Similarity=0.706  Sum_probs=49.0

Q ss_pred             cCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           7 LNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         7 ~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      +.|+.+|+.++...|.     .++||+..++.+||..+||++.+|+|||||||+|+|++
T Consensus         2 T~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFL-----RQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHH-----hcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            5689999999888877     49999999999999999999999999999999999985

>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=3.9e-19  Score=105.82  Aligned_cols=56  Identities=16%  Similarity=0.139  Sum_probs=51.7

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ++..||.+|+.++...|.     .++||+..+|++||..+||++.+|+|||||||+|+|+.
T Consensus         6 ~r~kfT~~Ql~~Le~~F~-----~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFL-----QCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            577899999999887777     49999999999999999999999999999999999984

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

Probab=99.76  E-value=3.2e-19  Score=102.07  Aligned_cols=57  Identities=37%  Similarity=0.589  Sum_probs=48.5

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      .++.||.+|+.++...|.     .++||+..++++||..+||++.+|++||||||+|+|+..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFS-----RTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHH-----cCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            368899999999888876     499999999999999999999999999999999999864

>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=99.75  E-value=5.2e-19  Score=101.46  Aligned_cols=56  Identities=34%  Similarity=0.522  Sum_probs=51.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus         5 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            5 RPRTAFSSEQLARLKREFN-----ENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             --CCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHH-----ccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4578999999999888887     4999999999999999999999999999999999986

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

Probab=99.75  E-value=7.9e-19  Score=101.34  Aligned_cols=56  Identities=45%  Similarity=0.692  Sum_probs=52.3

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         6 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            6 TRTAYTRAQLLELEKEFL-----FNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            578999999999888877     49999999999999999999999999999999999985

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

Probab=99.75  E-value=7.6e-19  Score=99.76  Aligned_cols=55  Identities=42%  Similarity=0.600  Sum_probs=51.4

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .++.|+.+|++++...|.     .++||+..++++||..+||++.+|++||||||+|+|+
T Consensus         3 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            3 PRTPFTTAQLLALERKFR-----QKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            578999999999888876     4999999999999999999999999999999999987

>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=99.75  E-value=8.8e-19  Score=102.62  Aligned_cols=59  Identities=39%  Similarity=0.590  Sum_probs=53.9

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      -..++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+..
T Consensus         3 rr~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            3 KRGRQTYTRYQTLELEKEFH-----FNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             SCTTCCCCHHHHHHHHHHHH-----HCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCcCHHHHHHHHHHHc-----cCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            45688999999999888877     499999999999999999999999999999999999953

>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=99.75  E-value=5.4e-19  Score=106.55  Aligned_cols=59  Identities=20%  Similarity=0.337  Sum_probs=53.4

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      ..++.|+.+|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (80)
T 2dmq_A            9 RMRTSFKHHQLRTMKSYFA-----INHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL   67 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHH
Confidence            3578999999999887776     4999999999999999999999999999999999999643

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

Probab=99.75  E-value=1.9e-19  Score=108.63  Aligned_cols=57  Identities=26%  Similarity=0.430  Sum_probs=52.9

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|+++++..|.     .++||+..++++||..++|++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~   65 (80)
T 2dms_A            9 RERTTFTRAQLDVLEALFA-----KTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ   65 (80)
T ss_dssp             CCCSSCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHH-----ccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHH
Confidence            3578999999999888887     49999999999999999999999999999999999994

>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=99.75  E-value=1.3e-18  Score=104.15  Aligned_cols=59  Identities=41%  Similarity=0.511  Sum_probs=54.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      .++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+....
T Consensus        16 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           16 KRCPYTKHQTLELEKEFL-----FNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            578899999999888887     49999999999999999999999999999999999997654

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

Probab=99.75  E-value=1.1e-18  Score=102.22  Aligned_cols=60  Identities=32%  Similarity=0.424  Sum_probs=54.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ..++.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+....
T Consensus         4 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            4 RTRTTFTSSQIAELEQHFL-----QGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CCSCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            3578999999999888887     59999999999999999999999999999999999996543

>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=99.74  E-value=1.6e-18  Score=103.83  Aligned_cols=58  Identities=34%  Similarity=0.495  Sum_probs=53.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      .++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus        12 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~   69 (77)
T 1nk2_P           12 RRVLFTKAQTYELERRFR-----QQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHh-----hcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhc
Confidence            478899999999888877     4999999999999999999999999999999999998644

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

Probab=99.74  E-value=1.6e-18  Score=99.09  Aligned_cols=56  Identities=39%  Similarity=0.496  Sum_probs=51.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+.+|+.++...|.     .++||+..++++||..+||++.+|++||||||+|+|++
T Consensus         4 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            4 YRTAFTRDQLGRLEKEFY-----KENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            578999999999888876     49999999999999999999999999999999999984

>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=99.74  E-value=1.9e-18  Score=102.18  Aligned_cols=58  Identities=22%  Similarity=0.314  Sum_probs=52.9

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhc-ccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYV-DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~-~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      ..++.|+..|+.++...|.     . ++||+..++++||..+||++.+|+|||||||+|+|+..
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~-----~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFN-----KVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----SSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHH-----ccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            3578999999999888775     4 89999999999999999999999999999999999954

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

Probab=99.74  E-value=1.6e-18  Score=102.05  Aligned_cols=57  Identities=28%  Similarity=0.546  Sum_probs=52.6

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2dmu_A            9 RHRTIFTDEQLEALENLFQ-----ETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS   65 (70)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHH-----ccCCCCHHHHHHHHHHHCCCHHHeehcccccccccccc
Confidence            3578999999999888877     49999999999999999999999999999999999984

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

Probab=99.73  E-value=2.3e-18  Score=102.15  Aligned_cols=59  Identities=24%  Similarity=0.327  Sum_probs=52.9

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      ..++.|+..|+.+++..|..    .++||+..++++||..+||++.+|+|||||||+|+|+..
T Consensus         4 k~Rt~ft~~Q~~~Le~~F~~----~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            4 QTVSGPTEDQVEILEYNFNK----VNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             SCCSSCCHHHHHHHHHHHHH----TTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHh----cCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            45789999999998877751    389999999999999999999999999999999999954

>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=99.73  E-value=2.3e-18  Score=101.38  Aligned_cols=57  Identities=39%  Similarity=0.660  Sum_probs=52.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|+++++..|.     .++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         9 r~R~~ft~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2e1o_A            9 GGQVRFSNDQTIELEKKFE-----TQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS   65 (70)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----cCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCC
Confidence            3578999999999888776     49999999999999999999999999999999999985

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

Probab=99.73  E-value=2.2e-18  Score=99.52  Aligned_cols=51  Identities=20%  Similarity=0.319  Sum_probs=47.4

Q ss_pred             CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      -|.+|++++...|.     .++||+..++++||..+||++++|++||||||+|+|+
T Consensus        11 ~~~~Ql~~LE~~F~-----~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kk   61 (66)
T 3nau_A           11 KTKEQIAHLKASFL-----QSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR   61 (66)
T ss_dssp             CCHHHHHHHHHHHH-----GGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhc
Confidence            36789999888887     5999999999999999999999999999999999997

>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=99.73  E-value=1e-18  Score=105.40  Aligned_cols=56  Identities=41%  Similarity=0.694  Sum_probs=52.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..||++++..|.     .++||+..++++||..++|++.+|+|||||||+|+|+.
T Consensus        20 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           20 SRTVFTELQLMGLEKRFE-----KQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             SCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            578899999999888887     49999999999999999999999999999999999984

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

Probab=99.73  E-value=2.6e-18  Score=100.59  Aligned_cols=59  Identities=32%  Similarity=0.517  Sum_probs=53.9

Q ss_pred             chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      ...++.|+..|+.++...|.     .++||+..++.+||..+||++.+|+|||||||+|+|+..
T Consensus         3 rr~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~   61 (68)
T 1ftt_A            3 RKRRVLFSQAQVYELERRFK-----QQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             SSSCSSCCHHHHHHHHHHHH-----HSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCccCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhh
Confidence            45688999999999888877     499999999999999999999999999999999999853

>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=99.73  E-value=7.2e-19  Score=103.53  Aligned_cols=57  Identities=33%  Similarity=0.503  Sum_probs=52.6

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+..|+++++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (70)
T 2cra_A            9 KKRIPYSKGQLRELEREYA-----ANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS   65 (70)
T ss_dssp             CSCCCSCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCcCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhccc
Confidence            3578999999999888887     49999999999999999999999999999999999884

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

Probab=99.73  E-value=8.9e-19  Score=100.80  Aligned_cols=57  Identities=37%  Similarity=0.504  Sum_probs=50.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         5 r~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            5 KMRTVFSQAQLCALKDRFQ-----KQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ---CCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            3578999999999888877     49999999999999999999999999999999999873

>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=99.73  E-value=3.9e-18  Score=103.01  Aligned_cols=59  Identities=31%  Similarity=0.472  Sum_probs=53.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      ..++.|+..|+.++...|.     .++||+..++.+||..+||++.+|++||||||+|+|++..
T Consensus        20 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           20 RSRTTFSASQLDELERAFE-----RTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            3578899999999888876     4999999999999999999999999999999999999653

>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=99.73  E-value=2.1e-18  Score=101.01  Aligned_cols=58  Identities=31%  Similarity=0.589  Sum_probs=53.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      ..++.|+..|++++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+..
T Consensus         5 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   62 (68)
T 1yz8_P            5 RQRTHFTSQQLQQLEATFQ-----RNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   62 (68)
T ss_dssp             CSCCCCCHHHHHHHHHHHT-----TCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHH-----ccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHh
Confidence            3578999999999888876     499999999999999999999999999999999999854

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

Probab=99.72  E-value=3.8e-18  Score=105.66  Aligned_cols=59  Identities=39%  Similarity=0.675  Sum_probs=53.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      .++.|+.+|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+....
T Consensus        20 ~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~   78 (93)
T 3a01_A           20 PRTSFTRIQVAELEKRFH-----KQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE   78 (93)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCcCCCHHHHHHHHHHHH-----cCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHH
Confidence            578999999999888877     59999999999999999999999999999999999997543

>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=99.72  E-value=2.3e-18  Score=101.25  Aligned_cols=57  Identities=21%  Similarity=0.248  Sum_probs=52.4

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|++++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da1_A            9 RPRTRITDDQLRVLRQYFD-----INNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS   65 (70)
T ss_dssp             SCSCCCCHHHHHHHHHHHH-----HCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhh
Confidence            3578999999999888876     49999999999999999999999999999999999984

>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=7.1e-19  Score=107.89  Aligned_cols=53  Identities=17%  Similarity=0.210  Sum_probs=49.2

Q ss_pred             CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .+|.+||.++...|.     .++||+..+|++||..+||++++|+|||||||+||++.
T Consensus        17 ~~t~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~   69 (89)
T 2ecb_A           17 EKTAEQLRVLQASFL-----NSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   69 (89)
T ss_dssp             CCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             cCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHH
Confidence            789999999887776     59999999999999999999999999999999999984

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

Probab=99.72  E-value=3.1e-18  Score=103.24  Aligned_cols=56  Identities=18%  Similarity=0.254  Sum_probs=51.6

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcc----cccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVD----KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~----~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..++.|+.+|++++...|.     .+    +||+..++++||..+||++.+|+|||||||+|+|+
T Consensus        10 r~Rt~ft~~Q~~~Le~~F~-----~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk   69 (80)
T 2da4_A           10 QDRTQFSDRDLATLKKYWD-----NGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRL   69 (80)
T ss_dssp             CSSCCCCHHHHHHHHHHHT-----TTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----hCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhh
Confidence            3578999999999877776     48    99999999999999999999999999999999998

>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=99.72  E-value=3.7e-18  Score=101.78  Aligned_cols=57  Identities=18%  Similarity=0.218  Sum_probs=52.6

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++..+|.+||.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFA-----QNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE   65 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHS
T ss_pred             CCCccCCHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHh
Confidence            3567899999999988887     49999999999999999999999999999999999984

>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=99.72  E-value=1.9e-18  Score=101.63  Aligned_cols=57  Identities=32%  Similarity=0.389  Sum_probs=52.4

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|+++++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da2_A            9 SSRTRFTDYQLRVLQDFFD-----ANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS   65 (70)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCHHHHHHHHHHHH-----cCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhc
Confidence            3578999999999888877     49999999999999999999999999999999999874

>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=99.72  E-value=3.5e-18  Score=103.27  Aligned_cols=57  Identities=39%  Similarity=0.541  Sum_probs=51.8

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        22 r~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           22 RGRQTYTRYQTLELEKEFH-----TNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             --CCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcccCHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            3578999999999888877     49999999999999999999999999999999999985

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

Probab=99.72  E-value=2.4e-18  Score=102.11  Aligned_cols=57  Identities=39%  Similarity=0.541  Sum_probs=52.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A            9 KKRVPYTKVQLKELEREYA-----TNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             CCCCCSCHHHHHHHHHHHH-----HTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHh-----hCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            3578999999999888887     49999999999999999999999999999999999984

>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=99.71  E-value=4.1e-18  Score=106.22  Aligned_cols=58  Identities=40%  Similarity=0.562  Sum_probs=53.5

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      .++.|+.+|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+...
T Consensus        37 ~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           37 LRTNFTTRQLTELEKEFH-----FNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             CCCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCcCcCHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            478999999999888887     5999999999999999999999999999999999999653

>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=99.71  E-value=1.9e-18  Score=104.05  Aligned_cols=57  Identities=19%  Similarity=0.303  Sum_probs=52.3

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+|+++++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        19 r~Rt~ft~~Ql~~Le~~f~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           19 RLRTTITPEQLEILYQKYL-----LDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             TCCSSCCTTTHHHHHHHHH-----HCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            3578899999999888877     49999999999999999999999999999999999984

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

Probab=99.71  E-value=4.4e-18  Score=104.30  Aligned_cols=57  Identities=40%  Similarity=0.660  Sum_probs=52.3

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        30 r~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           30 RQRTSYTRYQTLELEKEFH-----FNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             -CCCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCcCHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            3578999999999888887     59999999999999999999999999999999999974

>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=99.71  E-value=5.4e-18  Score=103.63  Aligned_cols=68  Identities=22%  Similarity=0.320  Sum_probs=53.9

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHHh
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMV   73 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~~   73 (120)
                      ..++.|+..|++++..-|..  ...++||+..++++||..+||++.+|++||||||+|+|+.........
T Consensus         3 r~R~~ft~~q~~~Le~~f~~--h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~~~~   70 (87)
T 1b72_B            3 RKRRNFNKQATEILNEYFYS--HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEA   70 (87)
T ss_dssp             CCCCCCCHHHHHHHHHHHHT--TTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHH--hccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccccccc
Confidence            35788999998885544410  014999999999999999999999999999999999999755544433

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

Probab=99.71  E-value=1.4e-18  Score=102.21  Aligned_cols=57  Identities=33%  Similarity=0.524  Sum_probs=52.3

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+..|+++++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2djn_A            9 KPRTIYSSFQLAALQRRFQ-----KTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS   65 (70)
T ss_dssp             CSSCSSCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSS
T ss_pred             CCCCCCCHHHHHHHHHHHc-----CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhccc
Confidence            3578999999999888876     59999999999999999999999999999999999873

>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=5e-18  Score=96.99  Aligned_cols=55  Identities=27%  Similarity=0.329  Sum_probs=49.6

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhc---ccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYV---DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~---~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      +++.|+.+|++++...+.     .   ++||+..++++||..+||++.+|++||+|||+|+|+
T Consensus         1 rr~~ft~~q~~~Le~~f~-----~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk   58 (60)
T 1k61_A            1 RGHRFTKENVRILESWFA-----KNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHH-----HTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CcCcCCHHHHHHHHHHHH-----HcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHccccc
Confidence            367899999999766665     4   899999999999999999999999999999999986

>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=99.71  E-value=2.4e-18  Score=100.16  Aligned_cols=56  Identities=27%  Similarity=0.308  Sum_probs=51.5

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+.+|++++...|.     .++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         6 ~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            6 VRTVLNEKQLHTLRTCYA-----ANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCCCCSHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            578999999999887776     49999999999999999999999999999999999873

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

Probab=99.71  E-value=5.2e-18  Score=98.99  Aligned_cols=56  Identities=34%  Similarity=0.446  Sum_probs=51.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+.+|++++...|.     .++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         4 ~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (67)
T 2k40_A            4 PRTAFTQNQIEVLENVFR-----VNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS   59 (67)
T ss_dssp             CSCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHh
Confidence            578999999999888776     59999999999999999999999999999999999984

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

Probab=99.71  E-value=2.4e-18  Score=104.56  Aligned_cols=56  Identities=38%  Similarity=0.498  Sum_probs=52.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..|+.+++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        25 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   80 (84)
T 2kt0_A           25 TRTVFSSTQLCVLNDRFQ-----RQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW   80 (84)
T ss_dssp             CSSCCCHHHHHHHHHHHH-----HSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSC
T ss_pred             CCCCCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence            578999999999888887     49999999999999999999999999999999999874

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

Probab=99.71  E-value=4.9e-18  Score=105.50  Aligned_cols=60  Identities=20%  Similarity=0.333  Sum_probs=54.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhc---------------chhhhhhccccchhHHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN---------------LTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~---------------l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ..|+.|+..||.++++.|.     .++||+..++++||..++               |++.+|++||||||+|+|+....
T Consensus         9 r~R~~ft~~ql~~Le~~F~-----~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            9 GSRFTWRKECLAVMESYFN-----ENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             CCSCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCcCCHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            3578999999999888887     499999999999999999               99999999999999999996543

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

Probab=99.70  E-value=5.9e-18  Score=95.91  Aligned_cols=55  Identities=35%  Similarity=0.535  Sum_probs=50.4

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      ..++.|+..|+.++...|.     .++||+..++++||..+||++.+|++||||||+|+|
T Consensus         4 r~Rt~~t~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            4 KPRVLFSQAQVYELERRFK-----QQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             CCCCCcCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            3578999999999888876     599999999999999999999999999999999975

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

Probab=99.70  E-value=3.1e-18  Score=102.30  Aligned_cols=56  Identities=16%  Similarity=0.267  Sum_probs=51.8

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+.+||++++..|.     .++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus        11 ~R~~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~   66 (76)
T 2dn0_A           11 YKNKKSHEQLSALKGSFC-----RNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL   66 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSC
T ss_pred             CCccCCHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHh
Confidence            478899999999888876     49999999999999999999999999999999999984

>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=99.70  E-value=2.4e-18  Score=103.82  Aligned_cols=55  Identities=9%  Similarity=0.062  Sum_probs=50.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhc----ccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYV----DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~----~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .++.|+.+|+++++..|.     .    ++||+..+|++||..+||++.+|+|||||||+|+++
T Consensus        20 ~Rt~ft~~Ql~~Le~~f~-----~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           20 HRTKFTAEQKERMLALAE-----RIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CSCCCCHHHHHHHHHHHH-----HHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCccCCHHHHHHHHHHHH-----hccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            578999999999888765     4    899999999999999999999999999999999764

>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=99.70  E-value=6.5e-18  Score=96.80  Aligned_cols=54  Identities=20%  Similarity=0.293  Sum_probs=45.6

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      .++.|+.+|+.++...|.     .++||+..++.+||..+||++.+|++||||||+++|
T Consensus         8 ~Rt~ft~~q~~~Le~~f~-----~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            8 GKSSISPQARAFLEEVFR-----RKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----CCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCHHHHHHHHHHHH-----hCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            578899999999777766     499999999999999999999999999999999975

>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=99.70  E-value=2e-18  Score=104.15  Aligned_cols=60  Identities=8%  Similarity=0.047  Sum_probs=51.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..+|.||.+|+..++ .|..+..=.++||+..+|++||..++|++.+|+|||||||+|+++
T Consensus        19 R~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           19 RFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            357899999999998 777321111899999999999999999999999999999999764

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

Probab=99.69  E-value=1.6e-18  Score=102.58  Aligned_cols=56  Identities=25%  Similarity=0.227  Sum_probs=49.3

Q ss_pred             hhccCCCHHHHHHHHhhh-HhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNR-RTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~-r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..+..++.+|+++++..| .     .++||+..+|++||..+||++.+|+|||||||+|+|+
T Consensus        10 k~r~r~~~~ql~~LE~~F~~-----~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~   66 (72)
T 2cqx_A           10 KDSPVNKVEPNDTLEKVFVS-----VTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP   66 (72)
T ss_dssp             CCCCCSCSCSTTHHHHHHHH-----TCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCHHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCC
Confidence            345567778888887777 5     5999999999999999999999999999999999986

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

Probab=99.69  E-value=7.3e-18  Score=100.13  Aligned_cols=56  Identities=21%  Similarity=0.276  Sum_probs=52.3

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus         9 ~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   64 (74)
T 2ly9_A            9 IRAKKTKEQLAELKVSYL-----KNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNS   64 (74)
T ss_dssp             TTCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTT
T ss_pred             CCcCCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhh
Confidence            578999999999888887     49999999999999999999999999999999999984

>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=99.69  E-value=1.5e-17  Score=102.22  Aligned_cols=54  Identities=19%  Similarity=0.219  Sum_probs=50.0

Q ss_pred             cCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           7 LNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         7 ~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      -.+|.+||++++..|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        18 k~~t~~Ql~~Le~~F~-----~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~   71 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFL-----KSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSM   71 (89)
T ss_dssp             CCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTS
T ss_pred             ccCCHHHHHHHHHHHc-----cCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHH
Confidence            3589999999988887     49999999999999999999999999999999999884

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

Probab=99.69  E-value=5.9e-18  Score=99.30  Aligned_cols=52  Identities=42%  Similarity=0.614  Sum_probs=47.2

Q ss_pred             CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ++..|+.+++..|.     .++||+...|.+||..+||++++|+|||||||+|+|+.
T Consensus        11 ~t~~ql~~LE~~F~-----~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~   62 (69)
T 2l9r_A           11 MSHTQVIELERKFS-----HQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK   62 (69)
T ss_dssp             CCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCS
T ss_pred             CCHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhh
Confidence            57788888877776     49999999999999999999999999999999999874

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

Probab=99.68  E-value=1.5e-17  Score=98.87  Aligned_cols=56  Identities=32%  Similarity=0.552  Sum_probs=51.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        12 ~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   67 (75)
T 2m0c_A           12 NRTTFTSYQLEELEKVFQ-----KTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR   67 (75)
T ss_dssp             CSCSSCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHH
Confidence            578899999999888876     49999999999999999999999999999999999984

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

Probab=99.67  E-value=1.2e-17  Score=96.36  Aligned_cols=49  Identities=22%  Similarity=0.224  Sum_probs=41.5

Q ss_pred             HHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877          12 VQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus        12 ~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .++.+++..|..    .++||+..+|.+||..++|+++||+|||||||+|+|+
T Consensus        10 ~~~~~LE~~F~~----~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A           10 QPNAILEKVFTA----ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             CHHHHHHHHHHT----TCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             hHHHHHHHHHHH----cCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            455565555521    4899999999999999999999999999999999886

>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=99.66  E-value=6e-17  Score=95.94  Aligned_cols=62  Identities=24%  Similarity=0.380  Sum_probs=50.7

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      ..++.|+..|+.++..-+..  ...++||+..++++||..+||++.+|++||||+|+|+|+...
T Consensus         3 r~R~~ft~~q~~~Le~~f~~--~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   64 (73)
T 1puf_B            3 RKRRNFNKQATEILNEYFYS--HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCHHHHHHHHHHHHH--TTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCcCCHHHHHHHHHHHHH--hccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccc
Confidence            35788999998885544410  014999999999999999999999999999999999998543

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

Probab=99.66  E-value=3.3e-17  Score=101.90  Aligned_cols=57  Identities=23%  Similarity=0.321  Sum_probs=52.8

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        27 r~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   83 (96)
T 3nar_A           27 GKICKKTPEQLHMLKSAFV-----RTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG   83 (96)
T ss_dssp             CCSSSSCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTT
T ss_pred             CCCccCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhh
Confidence            4678999999999888877     49999999999999999999999999999999999985

>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=99.66  E-value=2e-17  Score=100.38  Aligned_cols=57  Identities=30%  Similarity=0.476  Sum_probs=49.0

Q ss_pred             hhccCCCHHHHHH---HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~---~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..++.|+.+++.+   ||....     .++||+..+|++||..+||++.+|+|||||+|+|+++.
T Consensus         9 k~R~~~s~~q~~~L~~~f~~~~-----~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A            9 KRKGNLPAESVKILRDWMYKHR-----FKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             CCCSSCCHHHHHHHHHHHHHTT-----TTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             CCCCcCCHHHHHHHHHHHHHhc-----cCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            4577899988877   555433     37999999999999999999999999999999999884

>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=99.66  E-value=6.9e-17  Score=95.66  Aligned_cols=59  Identities=19%  Similarity=0.202  Sum_probs=48.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..|++++..-|..  ...++||+..++++||..+||++.+|++||||+|+|+++.
T Consensus        10 ~R~~~~~~q~~~Le~~f~~--~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A           10 KRGVLPKHATNVMRSWLFQ--HIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             SSCCCCHHHHHHHHHHHHH--TTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCcCCHHHHHHHHHHHHH--hCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            5678999988775444320  0028999999999999999999999999999999999984

>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=99.66  E-value=1.2e-16  Score=99.93  Aligned_cols=60  Identities=22%  Similarity=0.235  Sum_probs=54.4

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhh---------------------cchhhhhhccccchhHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLL---------------------NLTEVQIKTWFQNRRTKW   62 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~---------------------~l~~~~vqvWFqNrRak~   62 (120)
                      ..|+.|+..|++++++.|.     .++||+..+|++||..+                     .|++.+|+|||||||+++
T Consensus         8 r~Rt~ft~~ql~~Le~~F~-----~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            8 RNRFKWGPASQQILYQAYD-----RQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             CCCCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHc-----CCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            4678999999999999988     59999999999999999                     799999999999999999


Q ss_pred             HHHHHH
Q psy4877          63 KKQLAS   68 (120)
Q Consensus        63 rr~~~~   68 (120)
                      ++....
T Consensus        83 kr~~~~   88 (102)
T 2da6_A           83 AFRQKL   88 (102)
T ss_dssp             HHHHHH
T ss_pred             HHhhHh
Confidence            986443

>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=5.2e-17  Score=94.00  Aligned_cols=53  Identities=11%  Similarity=0.098  Sum_probs=47.7

Q ss_pred             cCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           7 LNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         7 ~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ...+++|+.+++..|.     .++||+..+|++||..+||++++|+|||||||+|.++
T Consensus         8 ~~p~~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYA-----LNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCccHHHHHHHHHHHh-----cCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            4567899999888876     5999999999999999999999999999999998654

>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=99.65  E-value=3.5e-17  Score=99.27  Aligned_cols=59  Identities=24%  Similarity=0.275  Sum_probs=49.4

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+..|++++..-|..  ...++||+..++++||..+||++.+|++||||||+|+|+.
T Consensus         5 rr~rft~~q~~~Le~~f~~--h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~   63 (83)
T 1le8_B            5 RGHRFTKENVRILESWFAK--NIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI   63 (83)
T ss_dssp             CCCCCCHHHHHHHHHHHHH--TSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCHHHHHHHHHHHHh--hCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccc
Confidence            4567999998886555540  0128999999999999999999999999999999999985

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

Probab=99.64  E-value=1.6e-17  Score=96.01  Aligned_cols=59  Identities=22%  Similarity=0.334  Sum_probs=48.0

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..++.|+..|++++..-+..  ...++||+..++++||..+||++.+|++||+|+|+|+|+
T Consensus         5 r~R~~ft~~q~~~Le~~f~~--~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            5 IEGRHMNKQATEILNEYFYS--HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCSSTTTHHHHHHHHHHH--TTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCcCCHHHHHHHHHHHHH--cccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            35778999888775444410  014999999999999999999999999999999999875

>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=99.63  E-value=1.5e-16  Score=97.26  Aligned_cols=54  Identities=28%  Similarity=0.334  Sum_probs=48.7

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhc---ccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYV---DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~---~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      .++.|+..|++++...|.     .   ++||+..++++||..+||++.+|++||||||+|+|
T Consensus        30 ~r~~ft~~q~~~Le~~f~-----~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           30 RGHRFTKENVRILESWFA-----KNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             TTCCCCHHHHHHHHHHHH-----HTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCcCCHHHHHHHHHHHH-----HhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            578899999988666554     4   89999999999999999999999999999999986

>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=99.61  E-value=2.1e-16  Score=106.54  Aligned_cols=56  Identities=20%  Similarity=0.236  Sum_probs=51.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..|+.|+..|+.+++..|.     .++||+..+|++||..+||++.+|+|||||||+|+|+
T Consensus       103 r~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  158 (160)
T 1e3o_C          103 KKRTSIETNIRVALEKSFM-----ENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR  158 (160)
T ss_dssp             -CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             cCccccCHHHHHHHHHHHh-----hcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhc
Confidence            3678999999999888877     4999999999999999999999999999999999987

>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=99.61  E-value=1.8e-16  Score=105.42  Aligned_cols=55  Identities=20%  Similarity=0.287  Sum_probs=51.6

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.|+..|+.+++..|.     .++||+..+|++||..+||++.+|+|||||||+|+|+
T Consensus        90 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  144 (146)
T 1au7_A           90 RRTTISIAAKDALERHFG-----EHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR  144 (146)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCcCccHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhc
Confidence            578999999999888887     4999999999999999999999999999999999987

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

Probab=99.61  E-value=2.1e-16  Score=107.02  Aligned_cols=57  Identities=21%  Similarity=0.158  Sum_probs=49.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..|+.|+..|+.++...|.     .++||+..+|++||..+||++.+|+|||||||+|+|+.
T Consensus       101 r~Rt~ft~~Ql~~LE~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  157 (164)
T 2xsd_C          101 KKRTSIEVGVKGALESHFL-----KCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRM  157 (164)
T ss_dssp             -----CCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBS
T ss_pred             CCceeccHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhc
Confidence            3578999999999888877     49999999999999999999999999999999999985

>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=3.1e-16  Score=91.47  Aligned_cols=53  Identities=23%  Similarity=0.430  Sum_probs=44.2

Q ss_pred             CCCHHHHHH---HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           8 NLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         8 ~~~~~~~q~---~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .|+.+++++   ||....     .++||+..++++||..+||++.+|++||+|+|+|+++.
T Consensus         4 ~f~~~~~~~L~~~f~~h~-----~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~   59 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHL-----THPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP   59 (67)
T ss_dssp             --CHHHHHHHHHHHHHTT-----TSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSC
T ss_pred             cCCHHHHHHHHHHHHHhc-----cCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHH
Confidence            467766665   776433     39999999999999999999999999999999999974

>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=99.59  E-value=4.8e-16  Score=89.79  Aligned_cols=53  Identities=21%  Similarity=0.187  Sum_probs=47.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK   61 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak   61 (120)
                      .||.|+.+|+..+...+..    .++||+...|++||..+||++++|+|||||+|-.
T Consensus        10 ~RT~~s~eQL~~Lqs~f~~----~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A           10 SRTKISLEALGILQSFIHD----VGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCSHHHHHHHHHHHH----HCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHHh----cCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            4788999999987776651    3899999999999999999999999999999975

>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=99.59  E-value=4.3e-16  Score=104.10  Aligned_cols=55  Identities=22%  Similarity=0.309  Sum_probs=50.7

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+||
T Consensus        96 ~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           96 RRTSFTPQAIEALNAYFE-----KNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCcccCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            578899999999777776     4999999999999999999999999999999999986

>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=99.57  E-value=8.9e-16  Score=103.02  Aligned_cols=56  Identities=20%  Similarity=0.210  Sum_probs=51.6

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .|+.|+..|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        99 ~Rt~ft~~Q~~~Le~~F~-----~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           99 KRTSIENRVRWSLETMFL-----KSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCCCCCHHHHHHHHTTTT-----TCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             CCcccCHHHHHHHHHHHc-----cCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            578999999999888876     59999999999999999999999999999999999973

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

Probab=99.57  E-value=6.1e-16  Score=96.61  Aligned_cols=57  Identities=26%  Similarity=0.338  Sum_probs=51.0

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhh------------------hc---chhhhhhccccchhHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKL------------------LN---LTEVQIKTWFQNRRTKW   62 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~------------------~~---l~~~~vqvWFqNrRak~   62 (120)
                      ..|+.|+..|+.+++..|.     .++||+...|++||..                  +|   |++.+|+|||||||+++
T Consensus        11 r~Rt~ft~~Ql~~LE~~F~-----~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A           11 RNRFKWGPASQQILFQAYE-----RQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             --CCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCcCcCHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4578999999999998887     5999999999999999                  88   99999999999999998


Q ss_pred             HHH
Q psy4877          63 KKQ   65 (120)
Q Consensus        63 rr~   65 (120)
                      ++.
T Consensus        86 k~k   88 (99)
T 1lfb_A           86 AFR   88 (99)
T ss_dssp             SCC
T ss_pred             HHh
Confidence            764

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

Probab=99.53  E-value=1.4e-15  Score=102.87  Aligned_cols=57  Identities=23%  Similarity=0.250  Sum_probs=51.7

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..|+.|+..|++++...|.     .++||+...|++||..+||++.+|+|||||||+|+|+.
T Consensus        99 r~Rt~ft~~q~~~Le~~F~-----~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~  155 (164)
T 2d5v_A           99 KPRLVFTDVQRRTLHAIFK-----ENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155 (164)
T ss_dssp             -CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC
T ss_pred             CCCCcCCHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcccccc
Confidence            3578899999999888777     49999999999999999999999999999999998874

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

Probab=99.52  E-value=1e-14  Score=88.97  Aligned_cols=56  Identities=23%  Similarity=0.468  Sum_probs=46.3

Q ss_pred             CCCHHHHHH---HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           8 NLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         8 ~~~~~~~q~---~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      -|+++++++   ||....     .++||+..+|++||..+||++.||++||+|+|.|+++....
T Consensus        11 ~l~~~~~~iL~~W~~~h~-----~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~   69 (89)
T 2lk2_A           11 MLPKESVQILRDWLYEHR-----YNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLR   69 (89)
T ss_dssp             CCCHHHHHHHHHHHHHTS-----GGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhc-----cCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHH
Confidence            366666655   775433     39999999999999999999999999999999999885443

>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=99.41  E-value=1.2e-13  Score=80.19  Aligned_cols=46  Identities=13%  Similarity=0.257  Sum_probs=40.6

Q ss_pred             HHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877          11 EVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK   61 (120)
Q Consensus        11 ~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak   61 (120)
                      ++|+.++...|-     .|++|+..++..||..+||+.++|+|||||||++
T Consensus        14 k~ql~~Lk~yF~-----~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYA-----MNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            467777766666     3999999999999999999999999999999974

>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=99.39  E-value=6.9e-14  Score=96.77  Aligned_cols=56  Identities=27%  Similarity=0.322  Sum_probs=50.8

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhc---------------------chhhhhhccccchhHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN---------------------LTEVQIKTWFQNRRTKW   62 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~---------------------l~~~~vqvWFqNrRak~   62 (120)
                      ..|+.|+..|+.++++.|.     .++||+...|++||..++                     |++.+|++||||||++.
T Consensus       117 r~R~~ft~~ql~~Le~~F~-----~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          117 RNRFKWGPASQQILFQAYE-----RQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             CCCcccCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            3578899999999998887     499999999999999999                     99999999999999986


Q ss_pred             HH
Q psy4877          63 KK   64 (120)
Q Consensus        63 rr   64 (120)
                      +.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            53

>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=99.31  E-value=3.2e-13  Score=101.44  Aligned_cols=53  Identities=23%  Similarity=0.315  Sum_probs=47.4

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      +.-|+..+++.+.+.|+     .++||+..+|++||.++||+++||+|||||||+|+|
T Consensus       369 ~~~~~~~q~~~Le~~f~-----~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          369 AAAISPQARAFLEQVFR-----RKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HCSSCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhcchHHHHHHHHHh-----cCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            44678888888888876     599999999999999999999999999999999864

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

Probab=99.27  E-value=1.7e-12  Score=91.03  Aligned_cols=53  Identities=26%  Similarity=0.375  Sum_probs=48.2

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhc---------------------chhhhhhccccchhHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN---------------------LTEVQIKTWFQNRRTK   61 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~---------------------l~~~~vqvWFqNrRak   61 (120)
                      ..|+.|+..|++++++.|.     .++||+..+|++||..++                     |++.+|++||+|||+.
T Consensus       144 R~R~~ft~~ql~~Le~~F~-----~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          144 RNRFKWGPASQQILYQAYD-----RQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             CCCcCCCHHHHHHHHHHHH-----cCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            3578899999999888887     499999999999999988                     8999999999999986

>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=99.18  E-value=5.6e-12  Score=72.51  Aligned_cols=27  Identities=37%  Similarity=0.540  Sum_probs=25.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.||++||||||+|+|+.
T Consensus        33 ~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A           33 GLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             HHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            799999999999999999999999864

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

Probab=99.14  E-value=1.6e-11  Score=68.85  Aligned_cols=27  Identities=59%  Similarity=1.078  Sum_probs=25.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.||++||||||+|++++
T Consensus        29 ~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A           29 ALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            699999999999999999999999975

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

Probab=99.14  E-value=1.7e-11  Score=74.88  Aligned_cols=29  Identities=21%  Similarity=0.454  Sum_probs=26.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||..|||++.||+|||||||+||++..+
T Consensus        43 ~LA~~lgLte~qVkvWFqNRR~k~rk~~~   71 (89)
T 2ecb_A           43 RLRAQTKLTRREIDAWFTEKKKSKALKEE   71 (89)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHhCcChHHCeecccccchHHHHHHH
Confidence            79999999999999999999999998543

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

Probab=99.13  E-value=1.8e-11  Score=71.48  Aligned_cols=28  Identities=57%  Similarity=0.768  Sum_probs=26.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.+||++.||++||||||+|+++..
T Consensus        36 ~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A           36 HLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             HHHHHhCCChhheeecchhhhhhhhhhh
Confidence            6999999999999999999999999764

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

Probab=99.11  E-value=2.6e-11  Score=71.38  Aligned_cols=27  Identities=37%  Similarity=0.566  Sum_probs=25.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.||+|||||||+|+++.
T Consensus        41 ~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A           41 GLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHhCCChhhcchhhhhcccCCCCC
Confidence            799999999999999999999999864

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

Probab=99.09  E-value=3.4e-11  Score=69.35  Aligned_cols=26  Identities=27%  Similarity=0.591  Sum_probs=24.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||..|||++.||++||||||+||++
T Consensus        36 eLA~~tgLt~~qVkvWFqNRR~k~Kk   61 (66)
T 3nau_A           36 RLIEVTGLARSEIKKWFSDHRYRCQR   61 (66)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCcCHHHhhHhcccchhhhhc
Confidence            79999999999999999999999986

>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=99.07  E-value=5.2e-11  Score=70.64  Aligned_cols=27  Identities=26%  Similarity=0.454  Sum_probs=25.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.|||++.||++||||+|+|+++.
T Consensus        35 ~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A           35 KLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            799999999999999999999999874

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

Probab=99.07  E-value=4.4e-11  Score=67.85  Aligned_cols=29  Identities=52%  Similarity=0.984  Sum_probs=24.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||||+|+++..+
T Consensus        31 ~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A           31 ELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            69999999999999999999999998653

>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=99.06  E-value=1.5e-11  Score=63.03  Aligned_cols=21  Identities=62%  Similarity=1.110  Sum_probs=17.8

Q ss_pred             hhhhccccchhHHHHHHHHHH
Q psy4877          49 VQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus        49 ~~vqvWFqNrRak~rr~~~~~   69 (120)
                      +||+|||||||+|||+.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            489999999999999976553

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

Probab=99.05  E-value=6.2e-11  Score=67.87  Aligned_cols=27  Identities=67%  Similarity=1.068  Sum_probs=25.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||..+||++.||++||||||+|+++.
T Consensus        35 ~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A           35 ELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            699999999999999999999999975

>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=99.05  E-value=6.2e-11  Score=70.98  Aligned_cols=29  Identities=48%  Similarity=0.958  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.||++||||||+|+++...
T Consensus        49 ~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           49 DLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             HHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            69999999999999999999999998653

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

Probab=99.05  E-value=6.8e-11  Score=67.47  Aligned_cols=27  Identities=59%  Similarity=0.832  Sum_probs=25.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.+|++||||+|+|+++.
T Consensus        35 ~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A           35 ELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             HHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            699999999999999999999999874

>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=99.04  E-value=7.6e-11  Score=68.87  Aligned_cols=29  Identities=45%  Similarity=0.611  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.||++||||||+|+++...
T Consensus        39 ~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A           39 KISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             HHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            69999999999999999999999998653

>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=99.04  E-value=7.5e-11  Score=68.55  Aligned_cols=29  Identities=62%  Similarity=1.007  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||||+|+++...
T Consensus        34 ~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P           34 EIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            69999999999999999999999998654

>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=99.03  E-value=8.5e-11  Score=66.84  Aligned_cols=26  Identities=54%  Similarity=0.822  Sum_probs=24.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.+|++||||+|+|+++
T Consensus        35 ~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A           35 QLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCcCHHHHHHHhhhhcccccc
Confidence            69999999999999999999999986

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

Probab=99.03  E-value=9e-11  Score=70.82  Aligned_cols=29  Identities=59%  Similarity=0.803  Sum_probs=26.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.+|++||||||+|+++..+
T Consensus        54 ~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           54 ELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            69999999999999999999999998643

>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=99.03  E-value=8.5e-11  Score=69.01  Aligned_cols=29  Identities=28%  Similarity=0.603  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||||+|+++...
T Consensus        34 ~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A           34 LIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            69999999999999999999999998654

>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=99.02  E-value=1.1e-10  Score=67.87  Aligned_cols=30  Identities=40%  Similarity=0.883  Sum_probs=27.2

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      .+||+.+||++.+|++||||+|+|+++...
T Consensus        34 ~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P           34 EEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             THHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            379999999999999999999999998654

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

Probab=99.02  E-value=1.1e-10  Score=71.08  Aligned_cols=28  Identities=61%  Similarity=0.984  Sum_probs=26.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.+||++.+|++||||||+|+++..
T Consensus        60 ~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           60 EIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            6999999999999999999999999864

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

Probab=99.01  E-value=1.1e-10  Score=68.08  Aligned_cols=29  Identities=34%  Similarity=0.862  Sum_probs=26.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.||++||||+|+|+++...
T Consensus        39 ~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A           39 QLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             HHHHHHCCCHHHeehccccccccccccCC
Confidence            69999999999999999999999998653

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

Probab=99.01  E-value=1e-10  Score=68.89  Aligned_cols=29  Identities=28%  Similarity=0.603  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||||+|+++...
T Consensus        35 ~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A           35 LIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            69999999999999999999999998654

>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=99.01  E-value=1.1e-10  Score=68.03  Aligned_cols=29  Identities=28%  Similarity=0.392  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.+|++||||+|+|+++..+
T Consensus        39 ~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A           39 EMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            69999999999999999999999998754

>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=99.01  E-value=1.1e-10  Score=70.04  Aligned_cols=28  Identities=57%  Similarity=0.757  Sum_probs=26.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||||+|++++.
T Consensus        52 ~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           52 EMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            6999999999999999999999999864

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

Probab=99.01  E-value=1.3e-10  Score=65.37  Aligned_cols=26  Identities=62%  Similarity=0.870  Sum_probs=24.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.||++||||+|+|+++
T Consensus        32 ~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A           32 EFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            69999999999999999999999886

>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=99.01  E-value=1.2e-10  Score=67.89  Aligned_cols=29  Identities=45%  Similarity=0.619  Sum_probs=26.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.+|++||||+|+|+++...
T Consensus        39 ~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A           39 QLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             HHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            69999999999999999999999998643

>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=99.01  E-value=1.2e-10  Score=69.64  Aligned_cols=28  Identities=21%  Similarity=0.496  Sum_probs=26.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.|||++.||++||||||+|+++.+
T Consensus        49 ~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           49 HIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            6999999999999999999999999865

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

Probab=99.01  E-value=1.1e-10  Score=68.13  Aligned_cols=29  Identities=48%  Similarity=0.745  Sum_probs=26.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||+|+|+++...
T Consensus        39 ~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A           39 ELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             HHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             HHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            69999999999999999999999998643

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

Probab=99.00  E-value=1e-10  Score=70.04  Aligned_cols=29  Identities=41%  Similarity=0.922  Sum_probs=26.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.+|++||||||+|+++...
T Consensus        39 ~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (80)
T 2cue_A           39 RLAAKIDLPEARIQVWFSNRRAKWRREEK   67 (80)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHhhHHHHHHHHHHHHHhh
Confidence            69999999999999999999999998643

>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=99.00  E-value=1.3e-10  Score=71.04  Aligned_cols=29  Identities=24%  Similarity=0.499  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.+|++||||||+|+++...
T Consensus        45 ~La~~~~l~~~qV~vWFqNRR~k~r~~~~   73 (89)
T 2dmp_A           45 RLRVETKLSRREIDSWFSERRKLRDSMEQ   73 (89)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHTSCS
T ss_pred             HHHHHhCCCHHhccHhhHhHHHHHHHHhH
Confidence            69999999999999999999999998654

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

Probab=99.00  E-value=1.3e-10  Score=69.58  Aligned_cols=27  Identities=30%  Similarity=0.619  Sum_probs=25.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.|||++.||+|||||+|+|+++.
T Consensus        44 ~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A           44 AVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            699999999999999999999999874

>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=99.00  E-value=1.2e-10  Score=68.95  Aligned_cols=29  Identities=28%  Similarity=0.510  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.||++||||||+|+++...
T Consensus        39 ~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A           39 RLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             HHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            69999999999999999999999998654

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

Probab=99.00  E-value=1.1e-10  Score=67.21  Aligned_cols=27  Identities=22%  Similarity=0.398  Sum_probs=24.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.+|++||||||||.++.
T Consensus        35 ~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A           35 KIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             HHHHHhCcChhhcCcchhcccCCCCCC
Confidence            699999999999999999999987653

>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=98.99  E-value=1.1e-10  Score=69.45  Aligned_cols=28  Identities=61%  Similarity=0.983  Sum_probs=26.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.+||++.||++||||||+|+++..
T Consensus        45 ~LA~~l~l~~~qV~vWFqNRR~k~kk~~   72 (77)
T 1puf_A           45 EVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHhh
Confidence            6999999999999999999999998753

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

Probab=98.99  E-value=1.6e-10  Score=69.20  Aligned_cols=29  Identities=34%  Similarity=0.716  Sum_probs=26.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.+|++||||||+|+++...
T Consensus        39 ~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A           39 EVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             HHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            69999999999999999999999998644

>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=98.99  E-value=1.6e-10  Score=67.45  Aligned_cols=29  Identities=55%  Similarity=1.026  Sum_probs=26.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||||+|+++...
T Consensus        39 ~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A           39 RLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            69999999999999999999999997643

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

Probab=98.99  E-value=1.6e-10  Score=67.14  Aligned_cols=29  Identities=45%  Similarity=0.723  Sum_probs=26.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||..+||++.+|++||||||+|+++...
T Consensus        34 ~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A           34 HLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            69999999999999999999999998653

>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=98.98  E-value=1.5e-10  Score=66.79  Aligned_cols=29  Identities=34%  Similarity=0.531  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||+|+|+++.+.
T Consensus        35 ~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A           35 QLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             HHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            68999999999999999999999998754

>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=98.98  E-value=1e-10  Score=70.10  Aligned_cols=26  Identities=12%  Similarity=0.298  Sum_probs=24.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.|||++.||+|||||+|+|+++
T Consensus        53 ~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           53 RFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             HHHHHhCCCcccccCCccccCcCCCC
Confidence            79999999999999999999998875

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

Probab=98.97  E-value=1.9e-10  Score=65.16  Aligned_cols=27  Identities=59%  Similarity=0.775  Sum_probs=25.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.+|++||||+|+|++++
T Consensus        33 ~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A           33 ELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            699999999999999999999999874

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

Probab=98.97  E-value=1.8e-10  Score=68.30  Aligned_cols=29  Identities=24%  Similarity=0.623  Sum_probs=26.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.||++||||||+|+++...
T Consensus        40 ~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A           40 HLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             HHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            69999999999999999999999998643

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

Probab=98.97  E-value=2.1e-10  Score=67.63  Aligned_cols=30  Identities=40%  Similarity=0.939  Sum_probs=27.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKY   31 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~y   31 (120)
                      +||..+||++.+|++||||+|+|+++....
T Consensus        41 ~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A           41 QLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             HHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            699999999999999999999999987664

>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=98.97  E-value=2.3e-10  Score=68.03  Aligned_cols=27  Identities=48%  Similarity=0.733  Sum_probs=25.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||..+||++.||++||||||+|+++.
T Consensus        41 ~La~~l~l~~~qV~~WFqNRR~k~kr~   67 (77)
T 1nk2_P           41 HLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHhHHhhcchhhh
Confidence            699999999999999999999999874

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

Probab=98.96  E-value=1.7e-10  Score=67.89  Aligned_cols=28  Identities=50%  Similarity=0.659  Sum_probs=26.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.||++||||||+|+++..
T Consensus        39 ~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A           39 RISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             HHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            6999999999999999999999999864

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

Probab=98.96  E-value=1.7e-10  Score=66.98  Aligned_cols=28  Identities=43%  Similarity=0.720  Sum_probs=26.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||||+|+++..
T Consensus        34 ~La~~l~l~~~qV~~WFqNRR~k~kk~~   61 (68)
T 1zq3_P           34 DLSAKLALGTAQVKIWFKNRRRRHKIQS   61 (68)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCcCHHHhhHhhHHHHHHHHHHh
Confidence            6999999999999999999999998753

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

Probab=98.96  E-value=2.5e-10  Score=70.27  Aligned_cols=29  Identities=52%  Similarity=0.963  Sum_probs=27.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||..+||++.||+|||||||+|+++...
T Consensus        49 ~LA~~l~L~~~qV~vWFqNRR~k~kr~~~   77 (93)
T 3a01_A           49 ALARGLKMTDAQVKTWFQNRRTKWRRQTA   77 (93)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhCCChhhcccccHhhhhhhhhhhH
Confidence            69999999999999999999999998655

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

Probab=98.96  E-value=2.4e-10  Score=67.32  Aligned_cols=29  Identities=31%  Similarity=0.538  Sum_probs=26.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||..+||++.||++||||||+|+++...
T Consensus        38 ~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A           38 RLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             HHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            69999999999999999999999998654

>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=98.96  E-value=1.1e-10  Score=69.92  Aligned_cols=26  Identities=12%  Similarity=0.284  Sum_probs=24.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||..|||++.||+|||||||+|+++
T Consensus        53 ~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           53 QFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             HHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             HHHHHhCcCcCcccccccccccCCCC
Confidence            79999999999999999999998874

>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=98.96  E-value=2.4e-10  Score=64.71  Aligned_cols=27  Identities=44%  Similarity=0.661  Sum_probs=25.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.||++||||+|+|+++.
T Consensus        33 ~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A           33 NLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            699999999999999999999999864

>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=98.95  E-value=1.9e-10  Score=68.99  Aligned_cols=28  Identities=46%  Similarity=0.796  Sum_probs=26.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.+||++.||++||||||+|++++.
T Consensus        50 ~LA~~l~l~~~qV~~WFqNrR~k~rk~~   77 (81)
T 1fjl_A           50 ELAQRTNLTEARIQVWFQNRRARLRKQH   77 (81)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHHHhhhhhhhc
Confidence            6999999999999999999999999764

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

Probab=98.94  E-value=3.1e-10  Score=65.66  Aligned_cols=29  Identities=45%  Similarity=0.728  Sum_probs=26.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.+|++||||+|+|+++...
T Consensus        33 ~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A           33 DLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             HHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            68999999999999999999999998643

>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=98.92  E-value=4e-10  Score=67.32  Aligned_cols=27  Identities=33%  Similarity=0.639  Sum_probs=25.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.|||++.+|++||||||+|++++
T Consensus        39 ~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (80)
T 2dmq_A           39 QLAQKTGLTKRVLQVWFQNARAKFRRN   65 (80)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHhhHccHHHHHHHHHH
Confidence            699999999999999999999999985

>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=98.92  E-value=3.4e-10  Score=70.08  Aligned_cols=29  Identities=48%  Similarity=0.790  Sum_probs=26.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.|||++.||++||||||+|+++...
T Consensus        66 ~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           66 EIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            69999999999999999999999997643

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

Probab=98.91  E-value=4.5e-10  Score=69.45  Aligned_cols=28  Identities=32%  Similarity=0.646  Sum_probs=26.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..|||++.||++||||||+|+++.+
T Consensus        57 ~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           57 KLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            6999999999999999999999999864

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

Probab=98.91  E-value=3.1e-10  Score=65.05  Aligned_cols=26  Identities=38%  Similarity=0.721  Sum_probs=24.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.||++||||+|+|++|
T Consensus        38 ~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A           38 ELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            69999999999999999999999876

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

Probab=98.91  E-value=4.5e-10  Score=62.98  Aligned_cols=25  Identities=56%  Similarity=0.891  Sum_probs=23.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWK   26 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~   26 (120)
                      +||..+||++.||++||||+|+|++
T Consensus        34 ~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A           34 QLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhCcCHHHHHHhhHHhhccCC
Confidence            6999999999999999999999864

>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=98.90  E-value=5.2e-10  Score=67.39  Aligned_cols=29  Identities=38%  Similarity=0.549  Sum_probs=26.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||..+||++.||++||||+|+|+++...
T Consensus        37 ~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B           37 NLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHCCCHHHcccccHHHHcccccccc
Confidence            69999999999999999999999998654

>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=98.88  E-value=6.5e-10  Score=65.31  Aligned_cols=27  Identities=30%  Similarity=0.517  Sum_probs=25.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.+||++.||++||||+|+|+++.
T Consensus        42 ~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A           42 QIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            699999999999999999999999864

>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=98.88  E-value=5.8e-10  Score=63.28  Aligned_cols=25  Identities=36%  Similarity=0.721  Sum_probs=22.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWK   26 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~   26 (120)
                      +||+.+||++.||++||||+|+|++
T Consensus        37 ~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A           37 EVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHCcCHHHHHHHHHHHHhccC
Confidence            6999999999999999999999874

>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=98.85  E-value=9e-10  Score=64.69  Aligned_cols=28  Identities=36%  Similarity=0.598  Sum_probs=25.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.+||++.||++||||+|+|+++..
T Consensus        36 ~La~~~~L~~~qV~~WFqNrR~r~kk~~   63 (73)
T 1puf_B           36 ELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHCcCHHHHHHHHHHHHhhccccc
Confidence            6999999999999999999999998754

>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=98.84  E-value=1.2e-09  Score=66.25  Aligned_cols=29  Identities=34%  Similarity=0.565  Sum_probs=26.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.||++||||+|+|+++...
T Consensus        36 ~La~~~~l~~~qV~~WFqNrR~r~kk~~~   64 (87)
T 1b72_B           36 ELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (87)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHCGG
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHhhhccc
Confidence            69999999999999999999999998643

>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=98.80  E-value=1.8e-09  Score=65.06  Aligned_cols=26  Identities=38%  Similarity=0.517  Sum_probs=24.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||..|||++.||++||||+|+|+++
T Consensus        42 ~LA~~~gLs~~qV~~WFqNrR~r~k~   67 (83)
T 2dmn_A           42 MLSEKTNLSLLQISNWFINARRRILP   67 (83)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHCcCHHHhhHHhhhhHhhhcH
Confidence            69999999999999999999999876

>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=98.78  E-value=2.1e-09  Score=62.22  Aligned_cols=27  Identities=30%  Similarity=0.480  Sum_probs=25.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||..+||++.||++||||+|+|+++.
T Consensus        33 ~La~~~~l~~~qV~~WFqNrR~r~kk~   59 (67)
T 3k2a_A           33 QLAQDTGLTILQVNNWFINARRRIVQP   59 (67)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHhCcCHHHhhhhhHHHHHHHhHH
Confidence            699999999999999999999998864

>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=98.63  E-value=1.2e-08  Score=58.88  Aligned_cols=22  Identities=41%  Similarity=0.561  Sum_probs=20.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRT   23 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~   23 (120)
                      +||+.|||++++|||||||+|-
T Consensus        40 ~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A           40 TLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHhhcccee
Confidence            6999999999999999999983

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

Probab=98.63  E-value=8.4e-09  Score=63.52  Aligned_cols=28  Identities=32%  Similarity=0.614  Sum_probs=25.5

Q ss_pred             cchhccC---------------CCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLN---------------LTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~---------------~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||+.+|               |++.+|++||||||+|+++..
T Consensus        39 ~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A           39 EIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             HHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            6889999               999999999999999998754

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

Probab=98.62  E-value=1.4e-08  Score=61.72  Aligned_cols=26  Identities=31%  Similarity=0.484  Sum_probs=24.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.|||++.||++||+|+|+|+++
T Consensus        40 ~LA~~tgLt~~QV~~WF~NrR~R~kk   65 (89)
T 2lk2_A           40 LLSQQTHLSTLQVCNWFINARRRLLP   65 (89)
T ss_dssp             HHHHHSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHhhh
Confidence            79999999999999999999988875

>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=98.50  E-value=3.5e-09  Score=54.13  Aligned_cols=18  Identities=67%  Similarity=1.038  Sum_probs=15.9

Q ss_pred             HHHHHHhhhHhhhhhccc
Q psy4877          13 QIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus        13 ~~q~~fq~~r~k~~~~~~   30 (120)
                      ||+||||||||||+|.+.
T Consensus         2 QVkIWFQNRRaK~Kk~~~   19 (37)
T 2nzz_A            2 QIKIWFQNRRMKWKKRVF   19 (37)
T ss_dssp             CTTTTTTCSHHHHTSSHH
T ss_pred             CceeccHHHHHHHHHHhH
Confidence            789999999999998644

>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=98.47  E-value=5.9e-08  Score=56.21  Aligned_cols=22  Identities=27%  Similarity=0.661  Sum_probs=20.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRT   23 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~   23 (120)
                      +||+.|||+++.|+|||||+|+
T Consensus        37 ~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           37 KISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHhhccc
Confidence            6899999999999999999996

>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=98.45  E-value=7.3e-08  Score=59.98  Aligned_cols=21  Identities=38%  Similarity=0.718  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHHhhhHhhhhhc
Q psy4877           8 NLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         8 ~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +++|.+|++||||||+|+++.
T Consensus        65 ~lte~~V~~WFqNRR~k~kr~   85 (102)
T 2da6_A           65 LVTEVRVYNWFANRRKEEAFR   85 (102)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHH
T ss_pred             cccccceeeeecchHHHHHHh
Confidence            799999999999999988864

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

Probab=98.44  E-value=6.1e-08  Score=60.17  Aligned_cols=23  Identities=39%  Similarity=0.768  Sum_probs=20.7

Q ss_pred             cC---CCHHHHHHHHhhhHhhhhhcc
Q psy4877           7 LN---LTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         7 ~~---~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +|   +++.+|++||||||+|.++..
T Consensus        64 lg~~~lse~qV~vWFqNRR~k~k~k~   89 (99)
T 1lfb_A           64 LGSNLVTEVRVYNWFANRRKEEAFRH   89 (99)
T ss_dssp             TGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             cCccccCcceeeeccHHHHHHHHHhc
Confidence            88   999999999999999887654

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=95.07  E-value=0.02  Score=32.87  Aligned_cols=45  Identities=11%  Similarity=0.214  Sum_probs=26.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTW   54 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvW   54 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++...+--|
T Consensus        30 ~lA~~~gvs~~~is~~e~g~--------~~~~~~~~~~ia~~l~v~~~~l~~~   74 (80)
T 3kz3_A           30 SVADKMGMGQSAVAALFNGI--------NALNAYNAALLAKILKVSVEEFSPS   74 (80)
T ss_dssp             HHHHHTTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTSCGGGTCHH
T ss_pred             HHHHHhCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHhCCCHHHHhHH
Confidence            46666666666666666652        3455556666666666665444333

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=94.75  E-value=0.037  Score=30.99  Aligned_cols=40  Identities=18%  Similarity=0.313  Sum_probs=33.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|.-|+.+.        ..|+...-..||..+|++..
T Consensus        26 ~lA~~~gis~~~is~~e~g~--------~~~~~~~l~~ia~~l~v~~~   65 (73)
T 3omt_A           26 WLTETLDKNKTTVSKWCTND--------VQPSLETLFDIAEALNVDVR   65 (73)
T ss_dssp             HHHHHTTCCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTSCGG
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCHH
Confidence            68899999999999998883        35888888889998888764

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=94.54  E-value=0.042  Score=30.56  Aligned_cols=39  Identities=15%  Similarity=0.205  Sum_probs=23.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..+|++.
T Consensus        31 ~lA~~~gis~~~i~~~e~g--------~~~~~~~~l~~l~~~l~~~~   69 (74)
T 1y7y_A           31 TLAFLSGLDRSYVGGVERG--------QRNVSLVNILKLATALDIEP   69 (74)
T ss_dssp             HHHHHHTCCHHHHHHHHTT--------CSCCBHHHHHHHHHHTTSCG
T ss_pred             HHHHHHCcCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCcCH
Confidence            4566666666666666655        23455555566666666554

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=94.49  E-value=0.041  Score=30.02  Aligned_cols=39  Identities=23%  Similarity=0.396  Sum_probs=25.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..+|++.
T Consensus        23 ~lA~~~gis~~~i~~~e~g--------~~~~~~~~l~~i~~~l~~~~   61 (68)
T 2r1j_L           23 ALGKMVGVSNVAISQWERS--------ETEPNGENLLALSKALQCSP   61 (68)
T ss_dssp             HHHHHHTSCHHHHHHHHTT--------SSCCBHHHHHHHHHHTTSCH
T ss_pred             HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCH
Confidence            4677777777777777766        23456666666777776655

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=94.41  E-value=0.045  Score=30.66  Aligned_cols=39  Identities=23%  Similarity=0.389  Sum_probs=28.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+......||..+|++.
T Consensus        28 ~lA~~~gis~~~i~~~e~g~--------~~~~~~~l~~ia~~l~~~~   66 (76)
T 3bs3_A           28 WLAEQMGKSENTISRWCSNK--------SQPSLDMLVKVAELLNVDP   66 (76)
T ss_dssp             HHHHHHTCCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTSCG
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCH
Confidence            57777888888887777763        3466777777777777765

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=94.36  E-value=0.044  Score=29.69  Aligned_cols=40  Identities=23%  Similarity=0.242  Sum_probs=29.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.        ..|+...-..|+..+|++..
T Consensus        19 ~lA~~~gis~~~i~~~e~g~--------~~~~~~~l~~i~~~l~~~~~   58 (66)
T 2xi8_A           19 ELAALLEVSRQTINGIEKNK--------YNPSLQLALKIAYYLNTPLE   58 (66)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------CCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCHH
Confidence            57888888888888888773        35677777778888877664

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=94.32  E-value=0.037  Score=31.41  Aligned_cols=39  Identities=10%  Similarity=0.072  Sum_probs=22.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+......||..+|++.
T Consensus        20 ~lA~~~gis~~~i~~~e~g~--------~~p~~~~l~~ia~~l~v~~   58 (77)
T 2k9q_A           20 SVAEEMGISRQQLCNIEQSE--------TAPVVVKYIAFLRSKGVDL   58 (77)
T ss_dssp             HHHHHHTSCHHHHHHHHTCC--------SCCHHHHHHHHHHHTTCCH
T ss_pred             HHHHHhCCCHHHHHHHHcCC--------CCCCHHHHHHHHHHhCcCH
Confidence            45666666666666666552        2355555556666666554

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=94.27  E-value=0.048  Score=30.60  Aligned_cols=39  Identities=18%  Similarity=0.249  Sum_probs=25.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++.
T Consensus        28 ~lA~~~gis~~~i~~~e~g~--------~~~~~~~l~~la~~l~~~~   66 (77)
T 2b5a_A           28 ELADLAGLHRTYISEVERGD--------RNISLINIHKICAALDIPA   66 (77)
T ss_dssp             HHHHHHTCCHHHHHHHHTTC--------SCCBHHHHHHHHHHTTCCH
T ss_pred             HHHHHHCCCHHHHHHHHCCC--------CCCCHHHHHHHHHHhCcCH
Confidence            46777777777777777662        3466666666777776665

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=94.24  E-value=0.045  Score=31.35  Aligned_cols=40  Identities=15%  Similarity=0.135  Sum_probs=30.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++..
T Consensus        32 elA~~~gis~~~is~~e~g~--------~~~~~~~l~~l~~~l~~~~~   71 (83)
T 3f6w_A           32 ELAARLGRPQSFVSKTENAE--------RRLDVIEFMDFCRGIGTDPY   71 (83)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHCcCHHHHHHHHCCC--------CCCCHHHHHHHHHHcCCCHH
Confidence            57888888888888888773        35777777888888887764

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=94.11  E-value=0.051  Score=30.35  Aligned_cols=39  Identities=23%  Similarity=0.376  Sum_probs=23.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++.
T Consensus        23 ~lA~~~gis~~~i~~~e~g~--------~~~~~~~l~~ia~~l~~~~   61 (76)
T 1adr_A           23 ALGKMVGVSNVAISQWERSE--------TEPNGENLLALSKALQCSP   61 (76)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHTTSCH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCH
Confidence            45666666666666666652        2455555566666666554

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=93.92  E-value=0.061  Score=30.74  Aligned_cols=40  Identities=23%  Similarity=0.241  Sum_probs=32.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..++++..
T Consensus        29 ~lA~~~gis~~~i~~~e~g--------~~~~~~~~l~~ia~~l~v~~~   68 (82)
T 3s8q_A           29 DLAYKSNLDRTYISGIERN--------SRNLTIKSLELIMKGLEVSDV   68 (82)
T ss_dssp             HHHHHHTCCHHHHHHHHTT--------CCCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHhCcCHHHHHHHHCC--------CCCCCHHHHHHHHHHHCcCHH
Confidence            5788888888888888887        346788888888888888764

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=93.80  E-value=0.049  Score=31.20  Aligned_cols=41  Identities=15%  Similarity=0.142  Sum_probs=33.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.       ...|+......||..++++..
T Consensus        28 elA~~~gis~~~is~~E~G~-------~~~p~~~~l~~ia~~l~v~~~   68 (78)
T 3qq6_A           28 ELAEKAGVAKSYLSSIERNL-------QTNPSIQFLEKVSAVLDVSVH   68 (78)
T ss_dssp             HHHHHHTCCHHHHHHHHTTS-------CCCCBHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC-------CCCCCHHHHHHHHHHHCcCHH
Confidence            68899999999999888872       246888888889999888764

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=93.76  E-value=0.086  Score=29.06  Aligned_cols=39  Identities=10%  Similarity=0.210  Sum_probs=28.3

Q ss_pred             cchhccC--CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLN--LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~--~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|  ++...|..|+...        ..|+...-..||..+|++.
T Consensus        26 ~lA~~~g~~is~~~i~~~e~g~--------~~~~~~~l~~la~~l~v~~   66 (71)
T 2ewt_A           26 GVEEKSQGRWKAVVVGSYERGD--------RAVTVQRLAELADFYGVPV   66 (71)
T ss_dssp             HHHHHTTTSSCHHHHHHHHHTC--------SCCCHHHHHHHHHHHTSCG
T ss_pred             HHHHHHCCcCCHHHHHHHHCCC--------CCCCHHHHHHHHHHHCcCH
Confidence            5777788  7887787777773        3567777777777777765

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=93.74  E-value=0.06  Score=31.79  Aligned_cols=24  Identities=17%  Similarity=0.475  Sum_probs=15.2

Q ss_pred             HHHHHhhhhcchhhhhhccccchh
Q psy4877          36 KRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        36 ~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ...+||..+|++...|..|..+++
T Consensus        24 sq~~lA~~~gis~~~is~~e~G~~   47 (94)
T 2kpj_A           24 TQLEIAKSIGVSPQTFNTWCKGIA   47 (94)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCC
Confidence            345666677777766666666543

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=93.63  E-value=0.07  Score=32.16  Aligned_cols=40  Identities=23%  Similarity=0.235  Sum_probs=31.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.        ..|+......||..+|++..
T Consensus        46 elA~~~gis~~~is~iE~G~--------~~ps~~~l~~ia~~l~v~~~   85 (99)
T 3g5g_A           46 DLAYKSNLDRTYISGIERNS--------RNLTIKSLELIMKGLEVSDV   85 (99)
T ss_dssp             HHHHHHTCCHHHHHHHHTTC--------SCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHCcCHHHHHHHHCCC--------CCCCHHHHHHHHHHHCcCHH
Confidence            57888888888888888873        46788888888888888764

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=93.44  E-value=0.074  Score=29.86  Aligned_cols=40  Identities=15%  Similarity=0.321  Sum_probs=23.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.       ...|+...-..||..+|++.
T Consensus        25 ~lA~~~gis~~~i~~~e~g~-------~~~~~~~~l~~ia~~l~~~~   64 (78)
T 3b7h_A           25 RVATLAGLNQSTVNAMFEGR-------SKRPTITTIRKVCGTLGISV   64 (78)
T ss_dssp             HHHHHHTCCHHHHHHHHCTT-------CCCCCHHHHHHHHHHHTCCH
T ss_pred             HHHHHHCcCHHHHHHHHcCC-------CCCCCHHHHHHHHHHcCCCH
Confidence            46666666666666666652       11455666666666666655

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=93.42  E-value=0.083  Score=30.45  Aligned_cols=23  Identities=4%  Similarity=-0.031  Sum_probs=15.7

Q ss_pred             HHHHhhhhcchhhhhhccccchh
Q psy4877          37 RMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        37 r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ..+||..+|++...|..|-.+++
T Consensus        30 q~~lA~~~gis~~~is~~E~g~~   52 (86)
T 2ofy_A           30 MVTVAFDAGISVETLRKIETGRI   52 (86)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             HHHHHHHhCCCHHHHHHHHcCCC
Confidence            34677777777777777776654

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=93.07  E-value=0.094  Score=30.55  Aligned_cols=39  Identities=13%  Similarity=0.253  Sum_probs=25.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++.
T Consensus        35 ~lA~~~gis~~~is~~e~g~--------~~~~~~~l~~ia~~l~v~~   73 (92)
T 1lmb_3           35 SVADKMGMGQSGVGALFNGI--------NALNAYNAALLAKILKVSV   73 (92)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTSCG
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCCCH
Confidence            46777777777777777662        3466666666777777665

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=92.93  E-value=0.11  Score=30.14  Aligned_cols=40  Identities=13%  Similarity=0.067  Sum_probs=31.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.        ..|+...-..|+..+|++..
T Consensus        32 elA~~~gis~~~is~~E~G~--------~~p~~~~l~~ia~~l~v~~~   71 (86)
T 3eus_A           32 DLAERLDKPQSFVAKVETRE--------RRLDVIEFAKWMAACEGLDV   71 (86)
T ss_dssp             HHHHHTTCCHHHHHHHHTTS--------SCCBHHHHHHHHHHTTCGGG
T ss_pred             HHHHHhCcCHHHHHHHHCCC--------CCCCHHHHHHHHHHcCCCcH
Confidence            68888888888888888873        46778888888888887653

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=92.69  E-value=0.13  Score=29.19  Aligned_cols=39  Identities=13%  Similarity=0.303  Sum_probs=29.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhc--chhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN--LTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~--l~~~   49 (120)
                      +||+++|++...|..|+.+.        ..| ...-..|+..+|  ++..
T Consensus        16 ~lA~~lgvs~~~is~~e~g~--------~~p-~~~l~~ia~~l~~~v~~~   56 (79)
T 3bd1_A           16 ALAASLGVRQSAISNWRARG--------RVP-AERCIDIERVTNGAVICR   56 (79)
T ss_dssp             HHHHHHTCCHHHHHHHHHHT--------CCC-GGGHHHHHHHTTTSSCHH
T ss_pred             HHHHHHCCCHHHHHHHHHCC--------CCC-HHHHHHHHHHHCCCCcHH
Confidence            57888888888888888773        355 666777888888  7664

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=92.69  E-value=0.1  Score=30.05  Aligned_cols=21  Identities=24%  Similarity=0.423  Sum_probs=10.9

Q ss_pred             HHHHhhhhcchhhhhhccccc
Q psy4877          37 RMELSKLLNLTEVQIKTWFQN   57 (120)
Q Consensus        37 r~~La~~~~l~~~~vqvWFqN   57 (120)
                      ..+||..+|++...|..|..+
T Consensus        28 q~~lA~~~gis~~~i~~~e~g   48 (88)
T 2wiu_B           28 QSELAKKIGIKQATISNFENN   48 (88)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHHHHhCCCHHHHHHHHcC
Confidence            344555555555555555544

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=92.62  E-value=0.097  Score=32.10  Aligned_cols=41  Identities=17%  Similarity=0.221  Sum_probs=32.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|+.++        ..|+...-..||..+|++...
T Consensus        39 elA~~~gis~~~is~~E~G~--------~~p~~~~l~~ia~~l~v~~~~   79 (114)
T 3vk0_A           39 ELARQCGLDRTYVSAVERKR--------WNIALSNIEKMAAALGVAAYQ   79 (114)
T ss_dssp             HHHHHHTCCHHHHHHHTTTC--------CCCCHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHhCCCHHH
Confidence            68888888888888888873        357888888888888887743

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=92.60  E-value=0.12  Score=31.47  Aligned_cols=42  Identities=14%  Similarity=0.335  Sum_probs=35.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++...+
T Consensus        27 ~lA~~~gis~~~i~~~e~g~--------~~p~~~~l~~la~~l~v~~~~l   68 (114)
T 3op9_A           27 QIAELLNVQTRTVAYYMSGE--------TKPDIEKLIRLATYFHLSIDEL   68 (114)
T ss_dssp             HHHHHHTSCHHHHHHHHHTS--------SCCCHHHHHHHHHHHTCCHHHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHhCCCHHHH
Confidence            68999999999999999984        4588888899999999887544

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=92.60  E-value=0.15  Score=30.21  Aligned_cols=41  Identities=15%  Similarity=0.213  Sum_probs=35.6

Q ss_pred             cchhccCCCHHH----HHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQ----IKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~----~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...    |.-|+.+        ...|+...-..||..+|++..-
T Consensus        19 ~lA~~~gis~~~~~~~is~~E~g--------~~~p~~~~l~~la~~l~v~~~~   63 (98)
T 3lfp_A           19 KLGVLAGIDEASASARMNQYEKG--------KHAPDFEMANRLAKVLKIPVSY   63 (98)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHT--------SSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHhCCCcchhhhHHHHHHCC--------CCCCCHHHHHHHHHHHCcCHHH
Confidence            689999999999    9999988        3478899999999999998743

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=92.09  E-value=0.14  Score=29.84  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=13.3

Q ss_pred             HHHHhhhhcchhhhhhccccchh
Q psy4877          37 RMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        37 r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ..+||..+|++...|..|..+++
T Consensus        29 q~~lA~~~gis~~~is~~e~g~~   51 (91)
T 1x57_A           29 QKDLATKINEKPQVIADYESGRA   51 (91)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHTCS
T ss_pred             HHHHHHHHCcCHHHHHHHHcCCC
Confidence            44566666666666666655543

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=92.04  E-value=0.15  Score=29.86  Aligned_cols=44  Identities=11%  Similarity=0.337  Sum_probs=36.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhcccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQ   56 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFq   56 (120)
                      +||+++|++...|..|+.+        ...|+......|+..+|++.   ..||-
T Consensus        26 ~lA~~~gis~~~is~~e~g--------~~~~~~~~~~~i~~~l~v~~---~~~l~   69 (94)
T 2ict_A           26 EFARAMEIAPSTASRLLTG--------KAALTPEMAIKLSVVIGSSP---QMWLN   69 (94)
T ss_dssp             HHHHHHTCCHHHHHHHHHT--------SSCCCHHHHHHHHHHTCSCH---HHHHH
T ss_pred             HHHHHhCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHHCcCH---HHHHH
Confidence            6899999999999999988        34678888888999999876   34774

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=91.86  E-value=0.14  Score=31.76  Aligned_cols=42  Identities=12%  Similarity=0.182  Sum_probs=35.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++...+
T Consensus        30 ~lA~~~gis~~~is~~E~g~--------~~p~~~~l~~ia~~l~v~~~~l   71 (126)
T 3ivp_A           30 QVGAMIEIDPRYLTNIENKG--------QHPSLQVLYDLVSLLNVSVDEF   71 (126)
T ss_dssp             HHHHHHTCCHHHHHHHHHSC--------CCCCHHHHHHHHHHHTCCSHHH
T ss_pred             HHHHHhCcCHHHHHHHHCCC--------CCCCHHHHHHHHHHHCcCHHHH
Confidence            68999999999999999883        4688888889999999887544

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=91.75  E-value=0.18  Score=30.84  Aligned_cols=39  Identities=15%  Similarity=0.109  Sum_probs=31.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++.
T Consensus        46 ~lA~~~gis~~~is~~E~g~--------~~~~~~~l~~la~~l~v~~   84 (117)
T 3f52_A           46 ELAEASRVSPGYLSELERGR--------KEVSSELLASVCHALGASV   84 (117)
T ss_dssp             HHHHHTTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTCCH
T ss_pred             HHHHHHCcCHHHHHHHHCCC--------CCCCHHHHHHHHHHhCCCH
Confidence            68888899888888888873        3678888888888888876

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=91.73  E-value=0.15  Score=31.25  Aligned_cols=41  Identities=15%  Similarity=0.151  Sum_probs=35.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++...
T Consensus        41 elA~~~gis~~~is~~E~G~--------~~ps~~~l~~ia~~l~v~~~~   81 (111)
T 3mlf_A           41 ELGDLFKVSSRTIQNMEKDS--------TNIKDSLLSKYMSAFNVKYDD   81 (111)
T ss_dssp             HHHHHHTSCHHHHHHHHHCC--------TTCCHHHHHHHHHHHTCCGGG
T ss_pred             HHHHHHCcCHHHHHHHHCCC--------CCCCHHHHHHHHHHhCcCHHH
Confidence            68999999999999999984        468888899999999988754

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=91.72  E-value=0.16  Score=27.58  Aligned_cols=38  Identities=18%  Similarity=0.144  Sum_probs=26.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.+        .|+.. -..||..++++.
T Consensus        19 ~lA~~~gis~~~i~~~e~g~~--------~~~~~-l~~la~~l~~~~   56 (69)
T 1r69_A           19 ELAQKVGTTQQSIEQLENGKT--------KRPRF-LPELASALGVSV   56 (69)
T ss_dssp             HHHHHHTSCHHHHHHHHTTSC--------SSCTT-HHHHHHHTTCCH
T ss_pred             HHHHHHCcCHHHHHHHHcCCC--------CCchH-HHHHHHHHCcCH
Confidence            577788888888888877732        24444 666777777765

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=91.04  E-value=0.37  Score=29.27  Aligned_cols=39  Identities=15%  Similarity=0.345  Sum_probs=34.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.++        ..|+...-..||..+|++.
T Consensus        32 eLA~~lGis~~~is~ie~G~--------~~~s~~~~~kla~~lgvs~   70 (104)
T 3trb_A           32 QLAKHLAIPTNRVTAILNGA--------RSITADTALRLAKFFGTTP   70 (104)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTCCH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCH
Confidence            68999999999999999884        3688888999999999985

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=90.93  E-value=0.2  Score=28.78  Aligned_cols=23  Identities=13%  Similarity=0.375  Sum_probs=13.2

Q ss_pred             HHHHhhhhcchhhhhhccccchh
Q psy4877          37 RMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        37 r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ..+||..+|++...|..|..+++
T Consensus        34 q~elA~~~gis~~~is~~e~g~~   56 (83)
T 2a6c_A           34 QFKAAELLGVTQPRVSDLMRGKI   56 (83)
T ss_dssp             HHHHHHHHTSCHHHHHHHHTTCG
T ss_pred             HHHHHHHHCcCHHHHHHHHcCCC
Confidence            45556666666666666655544

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=90.86  E-value=0.14  Score=28.77  Aligned_cols=19  Identities=11%  Similarity=0.076  Sum_probs=10.4

Q ss_pred             cchhccCCCHHHHHHHHhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQN   20 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~   20 (120)
                      |||+++|++...|.-|+..
T Consensus        29 elA~~~gvs~~tis~~E~G   47 (73)
T 3fmy_A           29 EASEIFGGGVNAFSRYEKG   47 (73)
T ss_dssp             HHHHHHCSCTTHHHHHHTT
T ss_pred             HHHHHhCcCHHHHHHHHcC
Confidence            4555555555555555555

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=90.80  E-value=0.23  Score=31.37  Aligned_cols=44  Identities=14%  Similarity=0.114  Sum_probs=34.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccch----hHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSV----SKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~----~~r~~La~~~~l~~~~v   51 (120)
                      |||+++|++...|..|+.+.+      +..|+.    ..-..+|..+|++...+
T Consensus        21 elA~~~gis~~~is~iE~g~~------~~~~~~~~~~~~l~~ia~~L~v~~~~l   68 (130)
T 3fym_A           21 ELEQRTGIKREMLVHIENNEF------DQLPNKNYSEGFIRKYASVVNIEPNQL   68 (130)
T ss_dssp             HHHHHHCCCHHHHHHHHTTCG------GGSSSGGGHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHCcCHHHHHHHHCCCC------CCCchhhhHHHHHHHHHHHhCCCHHHH
Confidence            689999999999999999965      344433    44677899999988654

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=90.62  E-value=0.2  Score=30.41  Aligned_cols=40  Identities=23%  Similarity=0.375  Sum_probs=34.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.        ..|+...-..||..+|++..
T Consensus        29 ~lA~~~gis~~~is~~e~g~--------~~~~~~~l~~la~~l~~~~~   68 (113)
T 2eby_A           29 ELAELLHVHRNSVSALINNN--------RKLTTEMAFRLAKVFDTTVD   68 (113)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCHH
Confidence            68999999999999999883        46888888899999998875

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=90.52  E-value=0.21  Score=30.88  Aligned_cols=45  Identities=16%  Similarity=0.114  Sum_probs=34.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccc----hhHHHHHhhhhcchhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLS----VSKRMELSKLLNLTEVQIK   52 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~----~~~r~~La~~~~l~~~~vq   52 (120)
                      +||+++|++...|..|+.+.+      +..|+    ......||..+|++...+-
T Consensus        25 eLA~~~gis~~~is~iE~G~~------~~~p~~~~~~~~l~~iA~~Lgv~~~~L~   73 (112)
T 2wus_R           25 DASLFTNINPSKLKRIEEGDL------KGLDAEVYIKSYIKRYSEFLELSPDEML   73 (112)
T ss_dssp             HHHHHSSCCHHHHHHHHHTCC------TTSSCHHHHHHHHHHHHHHSSCCHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHCCCC------CCCcchhHHHHHHHHHHHHhCcCHHHHH
Confidence            689999999999999999864      34453    3455678999999886553

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

Probab=90.27  E-value=0.22  Score=28.47  Aligned_cols=28  Identities=25%  Similarity=0.422  Sum_probs=24.7

Q ss_pred             ccccchhHHHHHhhhhcchhhhhhcccc
Q psy4877          29 DKYLSVSKRMELSKLLNLTEVQIKTWFQ   56 (120)
Q Consensus        29 ~~yp~~~~r~~La~~~~l~~~~vqvWFq   56 (120)
                      .+.+....-..|+.+..|+..+|+-||-
T Consensus        28 hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           28 HQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             TCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             hcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            5677788889999999999999999994

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=90.16  E-value=0.21  Score=30.38  Aligned_cols=24  Identities=17%  Similarity=0.249  Sum_probs=17.6

Q ss_pred             HHHHHhhhhcchhhhhhccccchh
Q psy4877          36 KRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        36 ~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ...+||..+|++...|..|-.+++
T Consensus        51 sq~elA~~~gis~~~is~~E~G~~   74 (107)
T 2jvl_A           51 TQAELGKEIGETAATVASYERGTA   74 (107)
T ss_dssp             CHHHHHHHHTCCHHHHHHHTTTCS
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCC
Confidence            456678888888888887777655

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=90.03  E-value=0.27  Score=26.78  Aligned_cols=38  Identities=16%  Similarity=0.056  Sum_probs=22.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.+        .|... -..|+..++++.
T Consensus        21 ~lA~~~gis~~~i~~~e~g~~--------~~~~~-l~~i~~~l~~~~   58 (71)
T 1zug_A           21 ELATKAGVKQQSIQLIEAGVT--------KRPRF-LFEIAMALNCDP   58 (71)
T ss_dssp             HHHHHHTSCHHHHHHHHTTCC--------SSCST-HHHHHHHTTSCH
T ss_pred             HHHHHhCCCHHHHHHHHcCCC--------CChHH-HHHHHHHHCCCH
Confidence            466777777777777776632        13222 555666666655

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=89.88  E-value=0.31  Score=29.06  Aligned_cols=39  Identities=15%  Similarity=0.317  Sum_probs=33.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+.        ..|+......|+..+|++.
T Consensus        36 ~lA~~~gis~~~is~~e~g~--------~~~~~~~l~~l~~~l~v~~   74 (104)
T 3cec_A           36 NFAEILGVSNQTIQEVINGQ--------RSITVDIAIRLGKALGNGP   74 (104)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS--------SCCCHHHHHHHHHHHTSCH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------cCCCHHHHHHHHHHHCcCH
Confidence            68999999999999999883        4678888889999999886

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=89.66  E-value=0.26  Score=29.29  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=23.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+.+.        ..|+.. -..|+..++++...+
T Consensus        48 elA~~lgvs~~~is~~E~G~--------~~p~~~-~~~l~~~l~~~~~~l   88 (99)
T 2ppx_A           48 EFSARYHIPLGTLRDWEQGR--------SEPDQP-ARAYLKIIAVDPEGT   88 (99)
T ss_dssp             HHHHHHTCCHHHHHHHHTTS--------SCCCHH-HHHHHHHHHHCHHHH
T ss_pred             HHHHHhCcCHHHHHHHHcCC--------CCCCHH-HHHHHHHHCcCHHHH
Confidence            46666666666666666653        234433 345666666655433

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=89.52  E-value=0.39  Score=30.74  Aligned_cols=41  Identities=15%  Similarity=0.206  Sum_probs=33.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|+.+.        ..|+......||..+|++...
T Consensus        86 elA~~lGis~s~is~~E~G~--------~~ps~~~l~~la~~lgv~~~~  126 (141)
T 3kxa_A           86 ELATAAGLPQPYLSRIENSK--------QSLQDKTVQKLANALGVSPLE  126 (141)
T ss_dssp             HHHHHTTCCHHHHHHHHHTC--------SCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCCCHHH
Confidence            58888899998888888883        357888888888888887743

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=88.63  E-value=0.2  Score=28.69  Aligned_cols=19  Identities=11%  Similarity=0.202  Sum_probs=8.7

Q ss_pred             HHHhhhhcchhhhhhcccc
Q psy4877          38 MELSKLLNLTEVQIKTWFQ   56 (120)
Q Consensus        38 ~~La~~~~l~~~~vqvWFq   56 (120)
                      .+||..+|++...|..|..
T Consensus        26 ~~LA~~~Gvs~stls~~~~   44 (74)
T 1neq_A           26 SALSRQFGYAPTTLANALE   44 (74)
T ss_dssp             HHHHHHHSSCHHHHHHTTT
T ss_pred             HHHHHHHCcCHHHHHHHHc
Confidence            3344444444444444443

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=88.52  E-value=0.51  Score=26.59  Aligned_cols=19  Identities=26%  Similarity=0.277  Sum_probs=12.1

Q ss_pred             cchhccCCCHHHHHHHHhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQN   20 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~   20 (120)
                      +||+++|++...|..|+.+
T Consensus        28 ~lA~~~gis~~~i~~~e~g   46 (84)
T 2ef8_A           28 ELAIFLGLSQSDISKIESF   46 (84)
T ss_dssp             HHHHHHTCCHHHHHHHHTT
T ss_pred             HHHHHhCCCHHHHHHHHcC
Confidence            4666666666666666665

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=88.49  E-value=0.25  Score=29.08  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=14.6

Q ss_pred             HHHHhhhhcchhhhhhccccchh
Q psy4877          37 RMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        37 r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ..+||..+|++...|..|..+++
T Consensus        20 q~~lA~~~gis~~~is~~e~g~~   42 (99)
T 2l49_A           20 RQQLADLTGVPYGTLSYYESGRS   42 (99)
T ss_dssp             HHHHHHHHCCCHHHHHHHTTTSS
T ss_pred             HHHHHHHHCcCHHHHHHHHcCCC
Confidence            45566666666666666666544

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=88.46  E-value=0.35  Score=28.93  Aligned_cols=41  Identities=15%  Similarity=0.142  Sum_probs=31.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+.       ...|+...-..||..+|++..
T Consensus        19 ~lA~~~gis~~~i~~~e~g~-------~~~p~~~~l~~ia~~l~v~~~   59 (111)
T 1b0n_A           19 ELAEKAGVAKSYLSSIERNL-------QTNPSIQFLEKVSAVLDVSVH   59 (111)
T ss_dssp             HHHHHHTCCHHHHHHHHTTC-------CSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHCcCHHHHHHHHcCC-------CCCCCHHHHHHHHHHHCcCHH
Confidence            68888899988888888872       235777778888888888764

>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15

Probab=88.45  E-value=0.38  Score=31.89  Aligned_cols=40  Identities=5%  Similarity=0.071  Sum_probs=32.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..++++..
T Consensus        29 ~lA~~~gis~~~is~~e~g--------~~~p~~~~l~~ia~~l~v~~~   68 (192)
T 1y9q_A           29 ATAQLTGVSKAMLGQIERG--------ESSPTIATLWKIASGLEASFS   68 (192)
T ss_dssp             HHHHHHSSCHHHHHHHHTT--------CSCCCHHHHHHHHHHHTCCSG
T ss_pred             HHHHHHCcCHHHHHHHHcC--------CCCCCHHHHHHHHHHHCcCHH
Confidence            6888899999888888887        346788888888988888763

>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A

Probab=87.00  E-value=0.58  Score=31.03  Aligned_cols=39  Identities=18%  Similarity=0.324  Sum_probs=27.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc-ccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK-YLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~-yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|..|+.+        .. .|+...-..||..++++.
T Consensus        28 ~la~~~gis~~~ls~~e~g--------~~~~p~~~~l~~ia~~l~~~~   67 (198)
T 2bnm_A           28 ALASLLGETPETVAAWENG--------EGGELTLTQLGRIAHVLGTSI   67 (198)
T ss_dssp             HHHHHHTCCHHHHHHHHTT--------TCTTCBHHHHHHHHHHTTSCT
T ss_pred             HHHHHHCcCHHHHHHHHcC--------CCCCCCHHHHHHHHHHhCCCH
Confidence            5777777777777777776        23 566777777777777665

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=84.47  E-value=0.91  Score=29.85  Aligned_cols=19  Identities=5%  Similarity=0.351  Sum_probs=9.8

Q ss_pred             cchhccCCCHHHHHHHHhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQN   20 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~   20 (120)
                      |||+++|++...|..|+..
T Consensus        25 elA~~~Gis~~~i~~~e~g   43 (189)
T 2fjr_A           25 QLANHFDIASSSLSNRYTR   43 (189)
T ss_dssp             HHHHHTTCCHHHHHHHHHS
T ss_pred             HHHHHhCcCHHHHHHHHhC
Confidence            3555555555555555543

>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, PR structure initiative; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13

Probab=83.93  E-value=0.86  Score=28.33  Aligned_cols=25  Identities=4%  Similarity=0.068  Sum_probs=18.4

Q ss_pred             hHHHHHhhhhcchhhhhhccccchh
Q psy4877          35 SKRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus        35 ~~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      ....+||..+|++...|.-|..+++
T Consensus        54 lTQ~eLA~~lGis~~~Is~iE~G~~   78 (120)
T 2o38_A           54 LSQAAAAARLGINQPKVSALRNYKL   78 (120)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            3456788888888888888877654

>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI, protei structure initiative, midwest center for structural genomic; HET: SO4; 1.65A {Escherichia coli} SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A 2iu7_A 2iv1_A 2iuo_A 2ivg_A

Probab=83.76  E-value=1.2  Score=29.29  Aligned_cols=43  Identities=19%  Similarity=0.171  Sum_probs=34.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK   52 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq   52 (120)
                      +||+.+|+++.=+-..|..        ++-++...-+.|++.++|+...+.
T Consensus        31 ~IAe~iG~S~v~vtaa~lG--------Q~~ls~e~A~kLa~~LgL~~e~~~   73 (156)
T 1dw9_A           31 EIADGTGLAEAFVTAALLG--------QQALPADAARLVGAKLDLDEDSIL   73 (156)
T ss_dssp             HHHTTSSSCHHHHHHHHTT--------SSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHhCcCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCcCHHHHH
Confidence            5788888888887777777        667888888889999999886544

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

Probab=82.41  E-value=1.9  Score=25.09  Aligned_cols=48  Identities=10%  Similarity=0.109  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .|++.+-+++.-.          |-....-.++|..+|+++..|+.+...-+.+.++.
T Consensus        37 ~L~~~~r~vl~l~----------~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~   84 (92)
T 3hug_A           37 QLSAEHRAVIQRS----------YYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLT   84 (92)
T ss_dssp             TSCHHHHHHHHHH----------HTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHH----------HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4566555554332          33456678999999999999999887666666654

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

Probab=81.54  E-value=0.86  Score=25.95  Aligned_cols=21  Identities=33%  Similarity=0.627  Sum_probs=18.2

Q ss_pred             cchhccCCCHHHHHHHHhhhH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRR   22 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r   22 (120)
                      .|..++.++-.||+.||-.+.
T Consensus        38 ~L~~kskms~qqvkdwFa~k~   58 (70)
T 2ys9_A           38 QLSQASRLSTQQVLDWFDSRL   58 (70)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHS
T ss_pred             HHHHHhCCCHHHHHHHHHhcc
Confidence            478899999999999997753

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=81.26  E-value=0.88  Score=30.99  Aligned_cols=44  Identities=14%  Similarity=0.228  Sum_probs=30.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQN   57 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqN   57 (120)
                      +||+++|++...|..|+..        ...|+......||..++++.    .||-.
T Consensus        35 ~lA~~~gis~~~i~~~~~g--------~~~p~~~~l~~ia~~l~v~~----~~l~~   78 (236)
T 3bdn_A           35 SVADKMGMGQSGVGALFNG--------INALNAYNAALLAKILKVSV----EEFSP   78 (236)
T ss_dssp             HHHHHHTSCHHHHHHHTTT--------TSCCCHHHHHHTTTTTTSCG----GGTCH
T ss_pred             HHHHHHCcCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCcCH----HHhhc
Confidence            5777888888778777766        23566677777777777765    45543

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=81.16  E-value=0.92  Score=26.67  Aligned_cols=35  Identities=20%  Similarity=0.204  Sum_probs=27.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNL   46 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l   46 (120)
                      +||+++|++..-|-....+        .-+|+..  ..+|+.+|+
T Consensus        37 eLAK~iGIsqsTLSaIenG--------~~~PsL~--~kIAk~fg~   71 (83)
T 2l1p_A           37 SLAKECPLSQSMISSIVNS--------TYYANVS--AAKCQEFGR   71 (83)
T ss_dssp             HHHHHSSSCHHHHHHHHTC--------SSCCCCC--SHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHcC--------CCCCCch--HHHHHHHHH
Confidence            6899999999999988888        3457666  677777763

---

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	120
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	2e-13
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-08
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-12
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	7e-08
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-12
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	3e-08
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	2e-12
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	2e-08
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-11
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	4e-07
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	6e-11
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	2e-07
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-10
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	6e-07
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-10
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-06
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-10
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-07
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-10
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	8e-07
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	3e-10
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	9e-07
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	9e-10
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	9e-07
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	9e-10
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	4e-06
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-09
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	6e-06
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-09
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-06
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-09
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-06
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	5e-09
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	5e-09
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-05
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	6e-09
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-05
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	6e-09
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	6e-06
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-08
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	5e-06
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	1e-08
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	4e-06
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-08
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-05
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-08
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	5e-06
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-08
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-06
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-08
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	5e-05
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	2e-08
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	7e-05
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	3e-08
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-06
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-07
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-04
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	3e-07
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	4e-04
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-06
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	5e-05
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	5e-06

>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 = 57.9 bits (140), Expect = 2e-13
 Identities = 21/37 (56%), Positives = 30/37 (81%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          ++YL+  +R+E++  L+LTE QIK WFQNRR KWKK+
Sbjct: 19 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 55

>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 = 44.8 bits (106), Expect = 3e-08
 Identities = 17/26 (65%), Positives = 21/26 (80%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +E++  L+LTE QIK WFQNRR KWK
Sbjct: 28 IEIAHALSLTERQIKIWFQNRRMKWK 53

>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 = 56.4 bits (136), Expect = 2e-12
 Identities = 22/43 (51%), Positives = 30/43 (69%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71
          + YL+  +R E+++LLNLTE Q+K WFQNRR K KK    + K
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAK 77

>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 = 44.4 bits (105), Expect = 7e-08
 Identities = 17/25 (68%), Positives = 21/25 (84%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          E+++LLNLTE Q+K WFQNRR K K
Sbjct: 45 EVARLLNLTERQVKIWFQNRRMKMK 69

>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 = 55.5 bits (134), Expect = 2e-12
 Identities = 11/35 (31%), Positives = 17/35 (48%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          K+    +   LSK L+     I+ WF+ RR + K 
Sbjct: 17 KHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 44.7 bits (106), Expect = 3e-08
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           LSK L+     I+ WF+ RR + K
Sbjct: 26 GLSKQLDWDVRSIQRWFRQRRNQEK 50

>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 = 55.6 bits (134), Expect = 2e-12
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
            Y  V  R  L+  ++L E +I+ WF NRR KW+++
Sbjct: 23 THYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 59

>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 = 45.6 bits (108), Expect = 2e-08
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           L+  ++L E +I+ WF NRR KW+
Sbjct: 33 RLAAKIDLPEARIQVWFSNRRAKWR 57

>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 = 52.5 bits (126), Expect = 3e-11
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
            KYLS  +R  L+K+L L+E Q+KTWFQNRR KW++
Sbjct: 21 TQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 41.7 bits (98), Expect = 4e-07
 Identities = 16/25 (64%), Positives = 21/25 (84%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           L+K+L L+E Q+KTWFQNRR KW+
Sbjct: 32 RLAKMLQLSERQVKTWFQNRRAKWR 56

>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 = 6e-11
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
          KY    +   LSK L+ +  +I+ WF++RR + K
Sbjct: 25 KYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 42.4 bits (100), Expect = 2e-07
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           LSK L+ +  +I+ WF++RR + K
Sbjct: 34 GLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 50.9 bits (122), Expect = 1e-10
 Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 15 KTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++WF            YL       L K  +L+ +QIK W  NRR K K 
Sbjct: 14 ESWFAKNIEN-----PYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 41.3 bits (97), Expect = 6e-07
 Identities = 12/25 (48%), Positives = 15/25 (60%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           L K  +L+ +QIK W  NRR K K
Sbjct: 33 NLMKNTSLSRIQIKNWVSNRRRKEK 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 = 50.3 bits (120), Expect = 2e-10
 Identities = 20/37 (54%), Positives = 25/37 (67%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          + Y+S  +R EL+  LNL E  IK WFQNRR K K+Q
Sbjct: 21 ENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 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 = 40.3 bits (94), Expect = 2e-06
 Identities = 16/26 (61%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           EL+  LNL E  IK WFQNRR K K
Sbjct: 30 CELAAQLNLPESTIKVWFQNRRMKDK 55

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.3 bits (120), Expect = 2e-10
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          K+++  KR ++S   +L+E QI  WFQNRR K KK
Sbjct: 24 KFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 42.6 bits (100), Expect = 2e-07
 Identities = 13/26 (50%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           ++S   +L+E QI  WFQNRR K K
Sbjct: 32 RKISAATSLSERQITIWFQNRRVKEK 57

>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 = 50.8 bits (121), Expect = 3e-10
 Identities = 22/51 (43%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 16 TWFQNRRTKWKY-VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          T  Q    + ++  +KYLS ++R+E++  L L E Q+K WFQNRR K KK+
Sbjct: 35 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 85

>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 = 41.9 bits (98), Expect = 8e-07
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
          +E++  L L E Q+K WFQNRR K K
Sbjct: 58 VEIAATLELNETQVKIWFQNRRMKQK 83

>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 = 50.3 bits (120), Expect = 3e-10
 Identities = 13/38 (34%), Positives = 22/38 (57%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66
          + Y S   + EL+K   +T  Q+  WF N+R ++KK +
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI 63

>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 = 41.1 bits (96), Expect = 9e-07
 Identities = 10/25 (40%), Positives = 16/25 (64%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          EL+K   +T  Q+  WF N+R ++K
Sbjct: 36 ELAKKCGITVSQVSNWFGNKRIRYK 60

>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 = 48.7 bits (116), Expect = 9e-10
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +       + +L ++  L+   I+ WFQN+R K KK+
Sbjct: 25 NPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 = 41.0 bits (96), Expect = 9e-07
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           +L ++  L+   I+ WFQN+R K K
Sbjct: 34 EQLVEMTGLSPRVIRVWFQNKRCKDK 59

>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 = 49.2 bits (117), Expect = 9e-10
 Identities = 10/39 (25%), Positives = 20/39 (51%)

Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           V+K+   +    ++    LTE Q + WF+ R  +W++ 
Sbjct: 22 KVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 39.6 bits (92), Expect = 4e-06
 Identities = 8/25 (32%), Positives = 14/25 (56%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           ++    LTE Q + WF+ R  +W+
Sbjct: 34 LIAAEAGLTEEQTQKWFKQRLAEWR 58

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (114), Expect = 2e-09
 Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 5/50 (10%)

Query: 15 KTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
          ++W             Y +  ++ +++   NLT +Q+  WF N R +  +
Sbjct: 18 RSWLFQHIGH-----PYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 38.9 bits (91), Expect = 6e-06
 Identities = 8/23 (34%), Positives = 14/23 (60%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTK 24
          +++   NLT +Q+  WF N R +
Sbjct: 37 QIAAQTNLTLLQVNNWFINARRR 59

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 48.0 bits (114), Expect = 2e-09
 Identities = 11/35 (31%), Positives = 20/35 (57%)

Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
            S  + M +++ LNL +  ++ WF NRR + K+ 
Sbjct: 23 KPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV 57

>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 = 39.5 bits (92), Expect = 3e-06
 Identities = 9/25 (36%), Positives = 16/25 (64%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           +++ LNL +  ++ WF NRR + K
Sbjct: 31 RMAEELNLEKEVVRVWFCNRRQREK 55

>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 = 47.6 bits (113), Expect = 2e-09
 Identities = 17/37 (45%), Positives = 25/37 (67%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           +Y  +  R EL++  NLTE +I+ WFQNRR + +KQ
Sbjct: 24 TQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

>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 = 39.9 bits (93), Expect = 3e-06
 Identities = 13/25 (52%), Positives = 19/25 (76%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          EL++  NLTE +I+ WFQNRR + +
Sbjct: 34 ELAQRTNLTEARIQVWFQNRRARLR 58

>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 = 46.9 bits (111), Expect = 5e-09
 Identities = 16/37 (43%), Positives = 27/37 (72%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          ++Y  +S R E++   NLTE +++ WF+NRR KW+K+
Sbjct: 23 NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>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 = 37.6 bits (87), Expect = 2e-05
 Identities = 12/26 (46%), Positives = 19/26 (73%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           E++   NLTE +++ WF+NRR KW+
Sbjct: 32 EEIAVWTNLTEARVRVWFKNRRAKWR 57

>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 = 47.0 bits (111), Expect = 5e-09
 Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 16 TWFQNRRTKWKY--VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +       +     V  Y        LS  L+L +  I  +FQN+R   K  
Sbjct: 15 SLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>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 = 37.4 bits (86), Expect = 2e-05
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           LS  L+L +  I  +FQN+R   K
Sbjct: 40 TLSAQLDLPKHTIIKFFQNQRYHVK 64

>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 = 46.5 bits (110), Expect = 6e-09
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 24 KWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          K    ++  +      +++ LN+ +  I+ WF NRR K K+ 
Sbjct: 15 KSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 56

>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 = 36.8 bits (85), Expect = 3e-05
 Identities = 10/25 (40%), Positives = 16/25 (64%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           +++ LN+ +  I+ WF NRR K K
Sbjct: 30 LIAEQLNMEKEVIRVWFSNRRQKEK 54

>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 = 46.9 bits (111), Expect = 6e-09
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           +YL+  +  +LS  L L   Q+K WF+NRR + K Q
Sbjct: 23 GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 59

>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 = 39.1 bits (91), Expect = 6e-06
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           +LS  L L   Q+K WF+NRR + K
Sbjct: 32 ADLSAKLALGTAQVKIWFKNRRRRHK 57

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 46.1 bits (109), Expect = 1e-08
 Identities = 18/37 (48%), Positives = 25/37 (67%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
           KYLS  +R  L+ +++LT  Q+K WFQN R K K+Q
Sbjct: 24 QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

>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 = 39.1 bits (91), Expect = 5e-06
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+ +++LT  Q+K WFQN R K K
Sbjct: 33 EHLASMIHLTPTQVKIWFQNHRYKMK 58

>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 = 45.7 bits (108), Expect = 1e-08
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
           +YLS+++R E S  L+LTE Q+K WFQNRR K K+
Sbjct: 22 KQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.1 bits (91), Expect = 4e-06
 Identities = 14/20 (70%), Positives = 16/20 (80%)

Query: 7  LNLTEVQIKTWFQNRRTKWK 26
          L+LTE Q+K WFQNRR K K
Sbjct: 37 LSLTETQVKIWFQNRRAKAK 56

>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 = 45.2 bits (107), Expect = 1e-08
 Identities = 8/31 (25%), Positives = 15/31 (48%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRR 59
          +K  S   ++ +S+ L L    +  +F N R
Sbjct: 20 NKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 37.9 bits (88), Expect = 1e-05
 Identities = 6/22 (27%), Positives = 11/22 (50%)

Query: 1  MELSKLLNLTEVQIKTWFQNRR 22
          + +S+ L L    +  +F N R
Sbjct: 29 ITISQQLGLELSTVSNFFMNAR 50

>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 = 1e-08
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 15/52 (28%)

Query: 29 DKYLSVSKRMELSKLLN---------------LTEVQIKTWFQNRRTKWKKQ 65
          ++Y   +KR E++   N               +T +++  WF NRR + K++
Sbjct: 22 NQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR 73

>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 = 39.7 bits (92), Expect = 5e-06
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           +LS L  +T +++  WF NRR + K
Sbjct: 46 KKLSDLERVTSLKVYNWFANRRKEIK 71

>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 = 45.8 bits (108), Expect = 2e-08
 Identities = 3/39 (7%), Positives = 9/39 (23%)

Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          +  +        +      +    +K W  N +      
Sbjct: 41 WRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS 79

>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 = 40.0 bits (93), Expect = 4e-06
 Identities = 3/25 (12%), Positives = 7/25 (28%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          +      +    +K W  N +    
Sbjct: 53 QFCAETGVRRQVLKIWMHNNKNSGP 77

>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 = 45.3 bits (107), Expect = 2e-08
 Identities = 10/35 (28%), Positives = 22/35 (62%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
           + L+  ++ E++K   +T +Q++ WF N+R + K
Sbjct: 19 KQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 36.4 bits (84), Expect = 5e-05
 Identities = 9/25 (36%), Positives = 17/25 (68%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
          E++K   +T +Q++ WF N+R + K
Sbjct: 29 EVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 45.4 bits (107), Expect = 2e-08
 Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 5/58 (8%)

Query: 8  NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
          ++      +                S+ +   ++  L L +  ++ WF NRR K K+ 
Sbjct: 14 SIENRVRWSL-----ETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66

>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 = 36.1 bits (83), Expect = 7e-05
 Identities = 9/25 (36%), Positives = 14/25 (56%)

Query: 2  ELSKLLNLTEVQIKTWFQNRRTKWK 26
           ++  L L +  ++ WF NRR K K
Sbjct: 40 HIANQLGLEKDVVRVWFCNRRQKGK 64

>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 = 44.5 bits (105), Expect = 3e-08
 Identities = 17/33 (51%), Positives = 22/33 (66%)

Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61
          ++YL+  +R +LS  L L E QIK WFQN R K
Sbjct: 21 NRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 39.8 bits (93), Expect = 2e-06
 Identities = 14/22 (63%), Positives = 14/22 (63%)

Query: 3  LSKLLNLTEVQIKTWFQNRRTK 24
          LS  L L E QIK WFQN R K
Sbjct: 32 LSSELGLNEAQIKIWFQNARAK 53

>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 = 43.1 bits (101), Expect = 2e-07
 Identities = 17/38 (44%), Positives = 23/38 (60%)

Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
            +YLS  +R  L+ L+ LT  Q+K WFQN R K K+ 
Sbjct: 30 QQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67

>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 = 35.0 bits (80), Expect = 2e-04
 Identities = 13/26 (50%), Positives = 16/26 (61%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L+ L+ LT  Q+K WFQN R K K
Sbjct: 40 EHLASLIRLTPTQVKIWFQNHRYKTK 65

>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 = 42.4 bits (99), Expect = 3e-07
 Identities = 7/42 (16%), Positives = 13/42 (30%)

Query: 24 KWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
                  L+  +   L     LT  +I  WF  ++     +
Sbjct: 21 ASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK 62

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 4e-04
 Identities = 6/26 (23%), Positives = 9/26 (34%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
            L     LT  +I  WF  ++    
Sbjct: 35 NRLRAQTKLTRREIDAWFTEKKKSKA 60

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 40.5 bits (94), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 21/58 (36%)

Query: 29 DKYLSVSKRMELSKLLN---------------------LTEVQIKTWFQNRRTKWKKQ 65
           K  S  +R  L +  N                     +TEV++  WF NRR +   +
Sbjct: 19 QKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR 76

>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 = 37.1 bits (85), Expect = 5e-05
 Identities = 8/26 (30%), Positives = 13/26 (50%)

Query: 1  MELSKLLNLTEVQIKTWFQNRRTKWK 26
           +      +TEV++  WF NRR +  
Sbjct: 49 AQGLGSNLVTEVRVYNWFANRRKEEA 74

>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 = 39.3 bits (91), Expect = 5e-06
 Identities = 9/57 (15%), Positives = 19/57 (33%)

Query: 24 KWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTG 80
           +    ++       +L ++  L   +I  WF + R   K       +  A    +G
Sbjct: 20 SFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDNASGPSSG 76

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	120
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.83
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.82
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.8
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.8
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.8
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.8
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.79
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.79
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.79
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.78
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.77
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.77
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.76
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.76
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.74
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.72
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.72
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.71
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.71
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.7
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.7
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.67
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.66
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.66
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.65
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.63
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.57
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.57
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.57
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.55
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.52
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.25
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.2
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.17
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.16
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.11
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.11
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.08
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.04
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.01
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.0
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	98.99
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	98.98
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	98.97
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	98.97
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	98.94
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	98.91
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	98.9
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	98.9
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	98.87
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	98.84
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	98.83
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	98.8
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	98.8
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	98.77
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	98.71
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	98.69
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	98.64
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	98.62
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	98.59
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	98.57
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	98.36
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	98.24
d1y7ya1	69	Restriction-modification controller protein C.AhdI	95.7
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	95.65
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	95.11
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	94.59
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	94.4
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	94.34
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	94.03
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	93.93
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	93.84
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	93.64
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	93.2
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	91.29
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	90.98
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	89.89
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	87.88
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	81.48

>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=1.6e-21  Score=108.59  Aligned_cols=55  Identities=42%  Similarity=0.672  Sum_probs=52.0

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      |+.||++|++++...|.     .++||+...+++||..+||++.+|+|||||||+|+|++
T Consensus         1 Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFH-----FNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            57899999999999987     59999999999999999999999999999999999984

>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=99.82  E-value=4e-21  Score=107.57  Aligned_cols=55  Identities=38%  Similarity=0.488  Sum_probs=52.5

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.||.+|++++...|.     .++||+...+++||..+||++.+|+|||||+|+|+|+
T Consensus         2 ~Rt~fT~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           2 YRTAFTRDQLGRLEKEFY-----KENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            478999999999999998     4999999999999999999999999999999999997

>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=99.80  E-value=1.2e-20  Score=105.64  Aligned_cols=55  Identities=40%  Similarity=0.680  Sum_probs=52.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.||..|+.++.+.|.     .++||+..++++||..+||++.+|+|||||||+++||
T Consensus         3 ~R~~ft~~Q~~~Le~~F~-----~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           3 GQVRFSNDQTIELEKKFE-----TQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            578999999999999988     5999999999999999999999999999999999986

>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=99.80  E-value=3.5e-21  Score=108.05  Aligned_cols=55  Identities=35%  Similarity=0.520  Sum_probs=51.6

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.||.+|++++...|.     .++||+..++++||..+||++.+|+|||||||+|+||
T Consensus         4 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           4 KRIPYSKGQLRELEREYA-----ANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             SCCCSCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCHHHHHHHHHHHh-----hcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            578999999999999988     4999999999999999999999999999999999874

>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=99.80  E-value=1.3e-20  Score=105.84  Aligned_cols=55  Identities=42%  Similarity=0.600  Sum_probs=52.3

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.|+.+|++++...|.     +++||+..++++||..+||++.+|+|||||+|+|+|+
T Consensus         3 ~Rt~ft~~Ql~~Le~~F~-----~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           3 PRTPFTTAQLLALERKFR-----QKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            578999999999999988     5999999999999999999999999999999999987

>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=99.80  E-value=2.2e-20  Score=107.67  Aligned_cols=58  Identities=33%  Similarity=0.439  Sum_probs=54.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      .|+.||..|+.++.+.|.     .++||+..++.+||..+||++.+|+|||||||+|+|++..
T Consensus         4 ~Rt~ft~~Ql~~Le~~F~-----~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           4 TRTTFTSSQIAELEQHFL-----QGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             CSCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            578999999999999998     5999999999999999999999999999999999998654

>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=3.6e-20  Score=108.03  Aligned_cols=57  Identities=25%  Similarity=0.364  Sum_probs=52.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.||.+||+++...|..    .++||+...+++||..+||++++|+|||||||+|+|+.
T Consensus         4 ~r~~fT~~Ql~~Le~~F~~----~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           4 GAATMTEDQVEILEYNFNK----VNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCCCCHHHHHHHHHHHHS----SCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHH----ccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            4789999999999888851    37899999999999999999999999999999999984

>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=99.79  E-value=2e-20  Score=103.22  Aligned_cols=52  Identities=35%  Similarity=0.521  Sum_probs=49.1

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK   61 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak   61 (120)
                      .|+.|+..|++++...|.     .++||+..+|++||..+||++.+|+|||||||+|
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~-----~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           2 PRTAFSSEQLARLKREFN-----ENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCccCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            478999999999999987     5999999999999999999999999999999986

>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=99.79  E-value=6.4e-20  Score=108.32  Aligned_cols=60  Identities=40%  Similarity=0.503  Sum_probs=55.5

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS   68 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~   68 (120)
                      ..|+.|+.+||.++...|.     .++||+...+++||..+||++.+|+|||||||+|+|+....
T Consensus        15 r~Rt~ft~~Ql~~Le~~F~-----~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          15 KKRCPYTKHQTLELEKEFL-----FNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            3578999999999999998     49999999999999999999999999999999999997554

>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=99.78  E-value=1e-19  Score=104.29  Aligned_cols=59  Identities=31%  Similarity=0.472  Sum_probs=54.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA   67 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~   67 (120)
                      ..|+.|+++|++++...|.     +++||+..++++||..+||++.+|++||||+|+|+|++..
T Consensus         4 r~Rt~ft~~Q~~~Le~~F~-----~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           4 RSRTTFSASQLDELERAFE-----RTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            3578999999999888887     5999999999999999999999999999999999998543

>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=99.77  E-value=1.8e-19  Score=104.09  Aligned_cols=60  Identities=28%  Similarity=0.520  Sum_probs=55.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK   69 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~   69 (120)
                      .|+.||++||.++...|.     .++||+...+++||..+||++.+|+|||||+|+|+|+.....
T Consensus         4 ~Rt~ft~~Ql~~Le~~F~-----~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           4 NRTSFTQEQIEALEKEFE-----RTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             CCCCSCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            578999999999999988     599999999999999999999999999999999999865543

>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=99.77  E-value=9e-20  Score=110.23  Aligned_cols=57  Identities=40%  Similarity=0.575  Sum_probs=53.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~   66 (120)
                      .|+.|+++|+.++...|.     .++||+..++++||..+||++.+|+|||||+|+|+|+..
T Consensus        30 ~Rt~ft~~Ql~~Le~~F~-----~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          30 LRTNFTTRQLTELEKEFH-----FNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             CCCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCCCHHHHHHHHHHHH-----hCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            578899999999888887     599999999999999999999999999999999999864

>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=99.76  E-value=1.7e-19  Score=101.91  Aligned_cols=57  Identities=32%  Similarity=0.615  Sum_probs=53.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      ..|+.|+++|+.++...|.     .++||+..++++||..+||++.+|++||+|+|+|+|++
T Consensus         3 r~Rt~ft~~Q~~~Le~~F~-----~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           3 RQRTHFTSQQLQQLEATFQ-----RNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             CSCCCCCHHHHHHHHHHHT-----TCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            4588999999999888887     59999999999999999999999999999999999985

>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=99.76  E-value=2.8e-19  Score=103.21  Aligned_cols=59  Identities=32%  Similarity=0.526  Sum_probs=54.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .-..|+.||+.|+.++...|.     .++||+...+++||..+||++.+|+|||||+|+|+|+.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~-----~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFK-----QQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHH-----HSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            345788999999999998887     59999999999999999999999999999999999984

>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=99.74  E-value=3e-19  Score=98.39  Aligned_cols=53  Identities=23%  Similarity=0.311  Sum_probs=49.2

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      |+.|+.+|+.++...|.     .++||+..++.+||..+||++.+|++||||+|+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~-----~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFR-----RKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            57899999999888887     499999999999999999999999999999999864

>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=99.72  E-value=2.5e-18  Score=102.64  Aligned_cols=58  Identities=21%  Similarity=0.356  Sum_probs=52.8

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhc---------------chhhhhhccccchhHHHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN---------------LTEVQIKTWFQNRRTKWKKQL   66 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~---------------l~~~~vqvWFqNrRak~rr~~   66 (120)
                      ..|+.|++.|++++...|.     +|+||+..+|++||..+|               |++.+|+|||||||+|+|+..
T Consensus         2 r~R~~ft~~Ql~~LE~~F~-----~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~   74 (82)
T d2cufa1           2 GSRFTWRKECLAVMESYFN-----ENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   74 (82)
T ss_dssp             CCSCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhh
Confidence            3688999999999888887     599999999999999876               999999999999999999954

>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=99.72  E-value=9.5e-19  Score=98.07  Aligned_cols=55  Identities=20%  Similarity=0.287  Sum_probs=51.4

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      +|+.|+.+|+.++...|.     .++||+..++.+||..+||++.+|+|||||+|+++|+
T Consensus         2 ~Rt~~s~~q~~~Le~~F~-----~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           2 RRTTISIAAKDALERHFG-----EHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCHHHHHHHHHHHH-----HccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            588999999999888887     4999999999999999999999999999999999876

>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=99.71  E-value=1.7e-18  Score=96.68  Aligned_cols=55  Identities=20%  Similarity=0.239  Sum_probs=51.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      +||.|+.+|..++...|.     .++||+..++++||..+||++.+|++||||+|+++|+
T Consensus         1 kRT~~~~~q~~~Le~~F~-----~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFM-----ENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHH-----hcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            478999999999888887     4999999999999999999999999999999999986

>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=99.71  E-value=3.4e-19  Score=105.24  Aligned_cols=55  Identities=36%  Similarity=0.534  Sum_probs=51.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.||.+|+.++...|.     .++||+..++++||..+||++.+|+|||||||+|+|+
T Consensus        12 ~Rt~ft~~Q~~~Le~~F~-----~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   66 (77)
T d1vnda_          12 RRVLFTKAQTYELERRFR-----QQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR   66 (77)
T ss_dssp             SCCCCCTTHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSS
T ss_pred             CCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHH
Confidence            478899999999999988     4999999999999999999999999999999999886

>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=99.70  E-value=8.1e-19  Score=100.98  Aligned_cols=56  Identities=20%  Similarity=0.170  Sum_probs=52.2

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..|+.|++.|+.++...|.     +++||+..++++||..+||++.+|++||||+|+++|+
T Consensus        10 r~Rt~~t~~q~~~Le~~F~-----~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_          10 RKRTSIENRVRWSLETMFL-----KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             SCCSSCCHHHHHHHHHHHS-----SCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             CCCCCCCHHHHHHHHHHHH-----HccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            4688999999999888887     6999999999999999999999999999999999876

>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=99.70  E-value=1.9e-18  Score=99.17  Aligned_cols=55  Identities=27%  Similarity=0.304  Sum_probs=51.5

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.|+++|++++...|.     +|+||+..++++||..+||++.+|++||||+|++.|+
T Consensus         6 ~Rt~~t~~Q~~~Le~~F~-----~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk   60 (66)
T d1bw5a_           6 VRTVLNEKQLHTLRTCYA-----ANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK   60 (66)
T ss_dssp             CCCCCSHHHHHHHHHHHH-----HCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSS
T ss_pred             CCcCcCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHH
Confidence            578999999999888887     5999999999999999999999999999999999876

>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=99.67  E-value=4.9e-18  Score=100.05  Aligned_cols=55  Identities=16%  Similarity=0.148  Sum_probs=50.9

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .+..+|++|++++...|.     .++||+..++++||..+||++.+|++||+|+|+++|+
T Consensus         6 ~~~r~T~eQ~~~Le~~F~-----~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~   60 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFL-----QCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH   60 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHH-----HcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHh
Confidence            456789999999888887     4999999999999999999999999999999999987

>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=99.66  E-value=1.1e-17  Score=90.97  Aligned_cols=49  Identities=27%  Similarity=0.300  Sum_probs=46.3

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchh
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRR   59 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrR   59 (120)
                      |+-||++|++++...|.     .++||+..++++||..+||++.+|++||||+|
T Consensus         2 Rt~ft~~Q~~~Le~~F~-----~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           2 RLVFTDVQRRTLHAIFK-----ENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CSCCCHHHHHHHHHHTT-----SSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            67899999999888887     59999999999999999999999999999998

>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=99.66  E-value=8.3e-18  Score=97.83  Aligned_cols=57  Identities=21%  Similarity=0.180  Sum_probs=50.1

Q ss_pred             hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ..++.|+++|+.++...|..    .++||+..++++||..+||++.+|++||||+|+++|+
T Consensus         9 r~R~~~t~~Q~~~Le~~F~~----~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           9 RSRTKISLEALGILQSFIHD----VGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCSHHHHHHHHHHHH----HCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCccCCHHHHHHHHHHHHH----hcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            35789999999996666631    3899999999999999999999999999999999876

>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=99.65  E-value=3.8e-17  Score=96.13  Aligned_cols=55  Identities=18%  Similarity=0.212  Sum_probs=49.4

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      ++-.+|.+||.++...|.     .++||+..++++||..+||++.+|++||||||++.++
T Consensus         7 k~k~~T~~Q~~~Le~~F~-----~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~   61 (76)
T d2ecba1           7 KFKEKTAEQLRVLQASFL-----NSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL   61 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHH-----HCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCHHHHHHHHHHHH-----HCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHH
Confidence            344679999999888887     4999999999999999999999999999999998766

>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=99.63  E-value=7.8e-17  Score=94.09  Aligned_cols=56  Identities=29%  Similarity=0.491  Sum_probs=48.7

Q ss_pred             hccCCCHHHHHH---HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877           5 KLLNLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ   65 (120)
Q Consensus         5 ~~~~~~~~~~q~---~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~   65 (120)
                      .++.|+.+|+++   ||....     .++||+..++++||..+||++.+|++||+|+|+|.++.
T Consensus         4 ~R~~~t~~q~~~Le~~f~~~~-----~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_           4 KRRNFNKQATEILNEYFYSHL-----SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTT-----TSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHHHhc-----CCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            578899999777   665433     38899999999999999999999999999999998873

>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=99.63  E-value=1.6e-17  Score=90.93  Aligned_cols=49  Identities=22%  Similarity=0.224  Sum_probs=40.1

Q ss_pred             HHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877          12 VQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus        12 ~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.++...|..    .++||+..++++||..+||++++|+|||||||+++|+
T Consensus         3 ~q~~iLE~~F~~----~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           3 QPNAILEKVFTA----ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             CHHHHHHHHHHT----TCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             hHHHHHHHHHHH----cCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            345555555431    3689999999999999999999999999999999764

>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=99.57  E-value=6.3e-16  Score=86.90  Aligned_cols=52  Identities=33%  Similarity=0.571  Sum_probs=44.1

Q ss_pred             CCCHHHHHH---HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877           8 NLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         8 ~~~~~~~q~---~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr   64 (120)
                      .|+.+++++   ||..-.     .++||+..++++||..+||++.+|++||+|+|++.|.
T Consensus         4 Rft~~q~~~L~~~f~~~~-----~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNI-----ENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTT-----TSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcC-----CCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            478888877   555432     3689999999999999999999999999999998764

>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=99.57  E-value=1.5e-16  Score=89.20  Aligned_cols=35  Identities=34%  Similarity=0.538  Sum_probs=33.6

Q ss_pred             ccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877          29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus        29 ~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      ++||+..++++||..+||++++|++||||||+++|
T Consensus        24 ~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1          24 TKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            68999999999999999999999999999999975

>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=99.57  E-value=2.7e-16  Score=92.68  Aligned_cols=54  Identities=28%  Similarity=0.331  Sum_probs=49.1

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhc---------------------chhhhhhccccchhHHHHH
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLN---------------------LTEVQIKTWFQNRRTKWKK   64 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~---------------------l~~~~vqvWFqNrRak~rr   64 (120)
                      |+.|+..|++++...|.     .++||+...|++||.+++                     |++.+|++||+|||++.|+
T Consensus         1 R~~~tp~Ql~~Le~~F~-----~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr   75 (78)
T d1lfba_           1 RFKWGPASQQILFQAYE-----RQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF   75 (78)
T ss_dssp             CCCCCHHHHHHHHHHHT-----TCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSC
T ss_pred             CccCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHH
Confidence            56799999999888887     599999999999999995                     8889999999999999875

>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=99.55  E-value=5.2e-16  Score=91.98  Aligned_cols=58  Identities=9%  Similarity=0.053  Sum_probs=48.2

Q ss_pred             hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      .|+.||..|++.+...|. +....++||+..++++||..+||++.+|+|||||+|++.+
T Consensus        20 ~Rt~ft~~Q~~~L~~~fe-~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k   77 (80)
T d1wh7a_          20 FRTKFTAEQKEKMLAFAE-RLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             CCCCCCHHHHHHHHHHHH-HHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             ccccCCHHHHHHHHHHHH-HhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCC
Confidence            578999999999754332 2222489999999999999999999999999999998754

>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=99.52  E-value=4.7e-15  Score=83.75  Aligned_cols=54  Identities=22%  Similarity=0.367  Sum_probs=46.1

Q ss_pred             hccCCCHHHHHH---HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877           5 KLLNLTEVQIKT---WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK   63 (120)
Q Consensus         5 ~~~~~~~~~~q~---~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r   63 (120)
                      .+..|+.+++++   ||....     .+.||+..++.+||..+||+..+|++||+|+|+|..
T Consensus         5 kR~~~~~~~~~iL~~wf~~~~-----~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           5 KRGVLPKHATNVMRSWLFQHI-----GHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             SSCCCCHHHHHHHHHHHHHTT-----TSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHhc-----cCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            466789887777   776544     389999999999999999999999999999998753

>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=99.25  E-value=1.1e-12  Score=72.23  Aligned_cols=28  Identities=61%  Similarity=1.005  Sum_probs=26.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||||+|++|++
T Consensus        29 ~LA~~l~l~~~~V~iWFQNrRak~kk~~   56 (56)
T d9anta_          29 EIAHALSLTERQIKIWFQNRRMKWKKEN   56 (56)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHhCCChhHeeeccccchhhhhhcC
Confidence            7999999999999999999999999864

>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=99.20  E-value=2.7e-12  Score=71.21  Aligned_cols=26  Identities=50%  Similarity=0.700  Sum_probs=24.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.||+|||||+|+|++|
T Consensus        33 ~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1          33 KISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHcCCCHHHeeecccchhhhccC
Confidence            79999999999999999999999875

>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=99.17  E-value=4.1e-12  Score=73.32  Aligned_cols=32  Identities=28%  Similarity=0.546  Sum_probs=28.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLS   33 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~   33 (120)
                      +||..+||++.+|++||||||+|+++....|.
T Consensus        34 ~LA~~lgL~~~~VqvWFqNrRak~rk~~~~p~   65 (72)
T d1uhsa_          34 LIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPS   65 (72)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHhccCCcc
Confidence            69999999999999999999999998765443

>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=99.16  E-value=5e-12  Score=69.89  Aligned_cols=27  Identities=59%  Similarity=0.775  Sum_probs=25.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+++||++.+|++||||+|+|.+|+
T Consensus        31 ~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_          31 ELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            799999999999999999999998864

>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=99.11  E-value=1.3e-11  Score=68.34  Aligned_cols=26  Identities=62%  Similarity=0.870  Sum_probs=24.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.+|++||||+|+|.+|
T Consensus        32 ~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_          32 EFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCChhheeecCcchHhHhcc
Confidence            79999999999999999999999876

>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=99.11  E-value=1.4e-11  Score=68.06  Aligned_cols=26  Identities=62%  Similarity=1.163  Sum_probs=24.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.||++||||+|+|++|
T Consensus        32 ~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1          32 RLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            79999999999999999999999875

>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=99.08  E-value=1.6e-11  Score=66.84  Aligned_cols=23  Identities=61%  Similarity=0.908  Sum_probs=22.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTK   24 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k   24 (120)
                      +||..|||++.+|++||||||||
T Consensus        31 ~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_          31 QLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             HHHHHhCCChHHhhhcccccCCC
Confidence            79999999999999999999986

>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=99.04  E-value=3.2e-11  Score=68.61  Aligned_cols=27  Identities=44%  Similarity=0.741  Sum_probs=25.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.|||++.+|++||||+|+|+++.
T Consensus        33 ~LA~~l~l~~~~V~iWFqNrR~k~kk~   59 (67)
T d1zq3p1          33 DLSAKLALGTAQVKIWFKNRRRRHKIQ   59 (67)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCccceeeccccHHHhHhhh
Confidence            799999999999999999999999874

>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=99.01  E-value=5.8e-11  Score=65.47  Aligned_cols=28  Identities=36%  Similarity=0.666  Sum_probs=26.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||.++||++.+|++||||+|+|+++.|
T Consensus        30 ~LA~~lgL~~~qV~~WFqNrR~k~kk~n   57 (57)
T d1e3oc1          30 LIAEQLNMEKEVIRVWFSNRRQKEKRIN   57 (57)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHccC
Confidence            6999999999999999999999998754

>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=99.00  E-value=4.8e-11  Score=69.62  Aligned_cols=28  Identities=61%  Similarity=0.983  Sum_probs=25.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||+|+|+++..
T Consensus        45 ~LA~~l~l~~~qV~iWFqNrR~k~kr~~   72 (77)
T d1pufa_          45 EVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHhhhhhhhhHHHHHHHH
Confidence            7999999999999999999999998753

>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=98.99  E-value=7.5e-11  Score=65.65  Aligned_cols=28  Identities=43%  Similarity=0.900  Sum_probs=25.8

Q ss_pred             CcchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           1 MELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      .+||.++||++.+|++||||+|+|.+++
T Consensus        32 ~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1          32 EEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             THHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            3799999999999999999999999875

>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=98.98  E-value=7.2e-11  Score=70.51  Aligned_cols=28  Identities=50%  Similarity=0.786  Sum_probs=26.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||+|+|+++..
T Consensus        59 ~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          59 EIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            7999999999999999999999998753

>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=98.97  E-value=7.4e-11  Score=66.70  Aligned_cols=29  Identities=45%  Similarity=0.770  Sum_probs=26.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||+.+||++.+|++||||+|+|+++++.
T Consensus        34 ~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_          34 ELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            69999999999999999999999987543

>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=98.97  E-value=8.2e-11  Score=63.66  Aligned_cols=26  Identities=38%  Similarity=0.574  Sum_probs=23.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+++||++.+|++||||||+|.|+
T Consensus        26 ~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1          26 GLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             HHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            69999999999999999999998763

>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=98.94  E-value=1.6e-10  Score=65.85  Aligned_cols=28  Identities=43%  Similarity=0.711  Sum_probs=26.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||+|+|+++..
T Consensus        34 ~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_          34 HLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhCCCccceeeecccHHHHHhhcc
Confidence            6999999999999999999999998753

>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=98.91  E-value=9.9e-11  Score=68.27  Aligned_cols=28  Identities=46%  Similarity=0.718  Sum_probs=25.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.||++||||+|+|.++..
T Consensus        41 ~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_          41 HLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             HHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             HHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            7999999999999999999999988743

>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=98.90  E-value=2.2e-10  Score=63.25  Aligned_cols=26  Identities=35%  Similarity=0.639  Sum_probs=24.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.+|++||||+|+|.++
T Consensus        31 ~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1          31 RMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            69999999999999999999999876

>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=98.90  E-value=2.3e-10  Score=62.13  Aligned_cols=25  Identities=36%  Similarity=0.721  Sum_probs=23.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWK   26 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~   26 (120)
                      +||+.+||++.||++||||+|+|.|
T Consensus        29 ~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_          29 EVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             HHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHCCCHHHHHHHHHhhhhccC
Confidence            6999999999999999999998754

>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=98.87  E-value=4.1e-10  Score=64.11  Aligned_cols=27  Identities=41%  Similarity=0.918  Sum_probs=25.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||..+||++.+|++||||+|+|+++.
T Consensus        33 ~LA~~l~L~~~~V~~WFqNrR~k~kr~   59 (68)
T d2cuea1          33 RLAAKIDLPEARIQVWFSNRRAKWRRE   59 (68)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCcChhheeecCcchhHHHHhh
Confidence            699999999999999999999999874

>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=98.84  E-value=5.9e-10  Score=61.71  Aligned_cols=25  Identities=40%  Similarity=0.666  Sum_probs=22.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWK   26 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~   26 (120)
                      +||+++||++.||++||||+|+|.|
T Consensus        34 ~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1          34 GLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHCcCHHHHHHHHHhhhcccC
Confidence            6999999999999999999998654

>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=98.83  E-value=4.2e-10  Score=63.86  Aligned_cols=27  Identities=33%  Similarity=0.569  Sum_probs=25.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||..+||++.+|++||||+|+|+++.
T Consensus        40 ~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_          40 HIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             HHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            699999999999999999999998864

>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=98.80  E-value=9.5e-10  Score=63.84  Aligned_cols=29  Identities=21%  Similarity=0.454  Sum_probs=25.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      +||..|||++.+|++||||+|+|.++...
T Consensus        36 ~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          36 RLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            69999999999999999999998776443

>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=98.80  E-value=8.1e-10  Score=63.32  Aligned_cols=27  Identities=37%  Similarity=0.433  Sum_probs=25.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.|||++.+|++||||+|+|.++.
T Consensus        40 ~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_          40 TLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             HHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            699999999999999999999988863

>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=98.77  E-value=1.1e-09  Score=61.92  Aligned_cols=28  Identities=36%  Similarity=0.575  Sum_probs=25.7

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD   29 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~   29 (120)
                      +||..+||++.+|++||||+|+|.++..
T Consensus        35 ~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_          35 QLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             HHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            6999999999999999999999988754

>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=98.71  E-value=2.7e-09  Score=61.88  Aligned_cols=27  Identities=26%  Similarity=0.454  Sum_probs=25.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||+.|||++.+|++||+|+|+|+|+.
T Consensus        35 ~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1          35 KLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             HHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            699999999999999999999998863

>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=98.69  E-value=3e-09  Score=61.21  Aligned_cols=27  Identities=37%  Similarity=0.667  Sum_probs=25.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +||.++||++.||++||+|+|+|.++.
T Consensus        36 ~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_          36 ELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            799999999999999999999988764

>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=98.64  E-value=5.1e-09  Score=57.99  Aligned_cols=26  Identities=46%  Similarity=0.647  Sum_probs=24.0

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKY   27 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~   27 (120)
                      +||+.+||++.||++||+|+|+|.++
T Consensus        33 ~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_          33 NLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHCcCHHHHhHHhHhhcccccc
Confidence            69999999999999999999987764

>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=98.62  E-value=3.6e-09  Score=62.18  Aligned_cols=25  Identities=32%  Similarity=0.593  Sum_probs=21.6

Q ss_pred             ccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877           6 LLNLTEVQIKTWFQNRRTKWKYVDK   30 (120)
Q Consensus         6 ~~~~~~~~~q~~fq~~r~k~~~~~~   30 (120)
                      .+++++.+|++||||||+|+++++.
T Consensus        51 ~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1          51 LERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             TTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            3469999999999999999998654

>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=98.59  E-value=4.3e-09  Score=61.56  Aligned_cols=25  Identities=12%  Similarity=0.320  Sum_probs=22.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWK   26 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~   26 (120)
                      +||++|||++.+|+|||||+|.+.+
T Consensus        53 ~la~~~gl~~~~i~vWFqN~R~~~k   77 (80)
T d1wh7a_          53 QFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             HHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             HHHHHHCCCHHHeeeecccCcCCCC
Confidence            6999999999999999999986554

>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=98.57  E-value=5.4e-09  Score=55.81  Aligned_cols=21  Identities=29%  Similarity=0.485  Sum_probs=20.0

Q ss_pred             cchhccCCCHHHHHHHHhhhH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRR   22 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r   22 (120)
                      +||.++||++.+|++||||+|
T Consensus        30 ~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1          30 TISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             HHHTTSCSSSHHHHHHHHHCC
T ss_pred             HHHHHHCcCHHHhhhcCCcCc
Confidence            799999999999999999986

>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=98.36  E-value=7.9e-08  Score=53.37  Aligned_cols=24  Identities=33%  Similarity=0.648  Sum_probs=22.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKW   25 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~   25 (120)
                      +||..+||+..||++||+|+|+|.
T Consensus        37 ~La~~~~l~~~qI~~WF~N~R~R~   60 (62)
T d1x2na1          37 QIAAQTNLTLLQVNNWFINARRRI   60 (62)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHhHHHHHHHHHHh
Confidence            699999999999999999999764

>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=98.24  E-value=3e-07  Score=53.17  Aligned_cols=27  Identities=30%  Similarity=0.423  Sum_probs=21.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYV   28 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~   28 (120)
                      +|+...++++.+|++||+|||+|-++.
T Consensus        50 ~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_          50 QGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             TTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             ccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            344555799999999999999987754

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=95.70  E-value=0.0056  Score=33.31  Aligned_cols=41  Identities=15%  Similarity=0.193  Sum_probs=35.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..++++...
T Consensus        27 ~lA~~~gis~~~i~~~E~g--------~~~p~~~~l~~ia~~l~v~~~~   67 (69)
T d1y7ya1          27 TLAFLSGLDRSYVGGVERG--------QRNVSLVNILKLATALDIEPRE   67 (69)
T ss_dssp             HHHHHHTCCHHHHHHHHTT--------CSCCBHHHHHHHHHHTTSCGGG
T ss_pred             HHHhHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCcCHHH
Confidence            6899999999999999988        4579999999999999988754

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=95.65  E-value=0.0053  Score=33.15  Aligned_cols=42  Identities=24%  Similarity=0.252  Sum_probs=37.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      |||+++|++...|..|+.+        ...|+...-..||..+|++...+
T Consensus        19 elA~~~gis~~~is~~e~g--------~~~p~~~~l~~ia~~l~v~~~~l   60 (66)
T d1utxa_          19 ELAALLEVSRQTINGIEKN--------KYNPSLQLALKIAYYLNTPLEDI   60 (66)
T ss_dssp             HHHHHHTSCHHHHHHHHTT--------SCCCCHHHHHHHHHHTTSCHHHH
T ss_pred             HHHHhcccCHHHHHHHHcC--------CCCCCHHHHHHHHHHHCCCHHHH
Confidence            6899999999999999999        45799999999999999987654

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=95.11  E-value=0.011  Score=32.01  Aligned_cols=43  Identities=14%  Similarity=0.157  Sum_probs=35.6

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+.+.       ...|+...-..||..++++...+
T Consensus        19 ~la~~~gis~~~i~~~E~g~-------~~~ps~~~l~~ia~~l~v~~~~l   61 (68)
T d1b0na2          19 ELAEKAGVAKSYLSSIERNL-------QTNPSIQFLEKVSAVLDVSVHTL   61 (68)
T ss_dssp             HHHHHHTCCHHHHHHHHTTC-------CSCCCHHHHHHHHHHHTCCHHHH
T ss_pred             HHHHHHCCCHHHHHHHHcCC-------CCCCCHHHHHHHHHHHCCcHHHH
Confidence            68999999999999999873       23588899999999999887543

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=94.59  E-value=0.018  Score=32.59  Aligned_cols=42  Identities=7%  Similarity=0.014  Sum_probs=34.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      |||+++|++..-|..|+.++       ...|+...-..||..+|++...
T Consensus        30 eLA~~~Gvs~~~ls~iE~G~-------~~~ps~~tl~kia~~L~v~~~~   71 (82)
T d2ofya1          30 TVAFDAGISVETLRKIETGR-------IATPAFFTIAAVARVLDLSLDD   71 (82)
T ss_dssp             HHHHHHTCCHHHHHHHHTTC-------CSSCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHcCCHHHHHHHHcCC-------cCCCCHHHHHHHHHHHCCCHHH
Confidence            68888999999898888873       3578888888899888887754

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.40  E-value=0.018  Score=32.08  Aligned_cols=39  Identities=10%  Similarity=0.076  Sum_probs=33.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      +||+++|++...|.-|+.+        ...|+......||..+|++-
T Consensus        24 ~lA~~~gis~~~is~~E~G--------~~~p~~~~l~~la~~l~v~l   62 (78)
T d1x57a1          24 DLATKINEKPQVIADYESG--------RAIPNNQVLGKIERAIGLKL   62 (78)
T ss_dssp             HHHHHHTSCHHHHHHHHHT--------CSCCCHHHHHHHHHHHTBCC
T ss_pred             HHHHcCCCCHHHHHHHHcc--------CCCCCHHHHHHHHHHhCCcc
Confidence            6899999999999999999        45788999999999998764

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=94.34  E-value=0.021  Score=31.42  Aligned_cols=41  Identities=20%  Similarity=0.269  Sum_probs=34.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ   50 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~   50 (120)
                      +||+++|++...|..|+..        ...|+...-..||..+|++...
T Consensus        28 ~lA~~~gis~~~i~~~e~g--------~~~p~~~~l~~ia~~l~v~~~~   68 (77)
T d2b5aa1          28 ELADLAGLHRTYISEVERG--------DRNISLINIHKICAALDIPAST   68 (77)
T ss_dssp             HHHHHHTCCHHHHHHHHTT--------CSCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence            6888899999999888887        4578888888999999888653

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=94.03  E-value=0.027  Score=30.01  Aligned_cols=40  Identities=23%  Similarity=0.362  Sum_probs=34.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..++++..
T Consensus        21 ~lA~~~gvs~~~i~~~e~g--------~~~p~~~~l~~ia~~l~v~~~   60 (66)
T d2r1jl1          21 ALGKMVGVSNVAISQWERS--------ETEPNGENLLALSKALQCSPD   60 (66)
T ss_dssp             HHHHHHTSCHHHHHHHHTT--------SSCCBHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCHH
Confidence            6899999999999999988        347888999999999988864

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=93.93  E-value=0.025  Score=31.26  Aligned_cols=40  Identities=5%  Similarity=0.071  Sum_probs=32.2

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..++++..
T Consensus        26 ~lA~~~gis~~~i~~~E~g--------~~~p~~~~l~~ia~~l~v~~~   65 (79)
T d1y9qa1          26 ATAQLTGVSKAMLGQIERG--------ESSPTIATLWKIASGLEASFS   65 (79)
T ss_dssp             HHHHHHSSCHHHHHHHHTT--------CSCCCHHHHHHHHHHHTCCSG
T ss_pred             HHHHHHCcchhHHHHHHcC--------CCCCCHHHHHHHHHHHCCCHH
Confidence            6788888888888888887        347888888888888888763

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=93.84  E-value=0.028  Score=31.91  Aligned_cols=40  Identities=10%  Similarity=0.228  Sum_probs=35.9

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      +||+++|++...|..|..++        ..|+...-..||..+|++..
T Consensus        19 ~LA~~lGvs~~~is~ie~g~--------~~~s~~~~~kla~~lgvs~~   58 (87)
T d2icta1          19 EFARAMEIAPSTASRLLTGK--------AALTPEMAIKLSVVIGSSPQ   58 (87)
T ss_dssp             HHHHHHTCCHHHHHHHHHTS--------SCCCHHHHHHHHHHTCSCHH
T ss_pred             HHHHHHhhcHHHHHHHHHhc--------cCCCHHHHHHHHHHHCcCHH
Confidence            69999999999999999994        47888999999999999864

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=93.64  E-value=0.026  Score=30.56  Aligned_cols=40  Identities=13%  Similarity=0.297  Sum_probs=31.4

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      |||+.+|++...|..|+.++       ...|+...-..+|..+|++.
T Consensus        24 elA~~~gv~~~~is~ie~g~-------~~~~s~~~L~~ia~~Lg~~i   63 (69)
T d2a6ca1          24 KAAELLGVTQPRVSDLMRGK-------IDLFSLESLIDMITSIGLKV   63 (69)
T ss_dssp             HHHHHHTSCHHHHHHHHTTC-------GGGCCHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHcCHhHHHHHHccc-------ccchhHHHHHHHHHHhCCCc
Confidence            67888888888888888874       34677888888888888765

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=93.20  E-value=0.042  Score=31.12  Aligned_cols=42  Identities=12%  Similarity=0.230  Sum_probs=35.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI   51 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v   51 (120)
                      +||+++|++...|..|+.+        ...|+...-..||..++++...+
T Consensus        30 ~lA~~lgis~~~is~~E~g--------~~~~s~~~l~~ia~~l~v~~~~~   71 (87)
T d1lmb3_          30 SVADKMGMGQSGVGALFNG--------INALNAYNAALLAKILKVSVEEF   71 (87)
T ss_dssp             HHHHHHTSCHHHHHHHHTT--------SSCCCHHHHHHHHHHHTSCGGGT
T ss_pred             HHHHHhCccHHHHHHHHhc--------cCCCcHHHHHHHHHHHCCCHHHH
Confidence            6889999999999999888        45789999999999999988544

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=91.29  E-value=0.11  Score=27.33  Aligned_cols=32  Identities=22%  Similarity=0.276  Sum_probs=23.8

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELS   41 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La   41 (120)
                      |||+.+|++...|..|+.++        ..|+......|+
T Consensus        17 elA~~lGvs~~tvs~~E~G~--------~~P~~~~~~ll~   48 (62)
T d2ppxa1          17 EFSARYHIPLGTLRDWEQGR--------SEPDQPARAYLK   48 (62)
T ss_dssp             HHHHHHTCCHHHHHHHHTTS--------SCCCHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHCCC--------CCCCHHHHHHHH
Confidence            68888899998898899884        366666555443

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=90.98  E-value=0.088  Score=27.57  Aligned_cols=39  Identities=18%  Similarity=0.111  Sum_probs=29.5

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      |||+++|++...|..|+.++         .|+...-..||..++++..
T Consensus        19 elA~~~gvs~~~is~~E~g~---------~~~~~~l~~ia~~l~v~~~   57 (63)
T d1r69a_          19 ELAQKVGTTQQSIEQLENGK---------TKRPRFLPELASALGVSVD   57 (63)
T ss_dssp             HHHHHHTSCHHHHHHHHTTS---------CSSCTTHHHHHHHTTCCHH
T ss_pred             HHHHHhCcCHHHHHHHHCCC---------CcCHHHHHHHHHHHCcCHH
Confidence            68889999999998888762         2445556778888888774

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=89.89  E-value=0.14  Score=27.02  Aligned_cols=39  Identities=18%  Similarity=0.095  Sum_probs=28.3

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV   49 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~   49 (120)
                      |||+++|++...|..|+.+..        -|+ ..-..||..++++..
T Consensus        21 ~lA~~~gvs~~ti~~~E~g~~--------~~~-~~l~~ia~~l~v~~~   59 (65)
T d2croa_          21 ELATKAGVKQQSIQLIEAGVT--------KRP-RFLFEIAMALNCDPV   59 (65)
T ss_dssp             HHHHHHTSCHHHHHHHHTTCC--------SSC-TTHHHHHHHTTSCHH
T ss_pred             HHHHHHCcCHhHHHHHHCCCC--------CCH-HHHHHHHHHhCCCHH
Confidence            688888888888888887632        233 456778888888763

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=87.88  E-value=0.21  Score=28.09  Aligned_cols=40  Identities=15%  Similarity=0.154  Sum_probs=29.1

Q ss_pred             cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE   48 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~   48 (120)
                      |||+++|++...|..|+..+       .+.|+...-..++..+|++.
T Consensus        29 ~lA~~~gis~~~is~ie~G~-------~~~~~~~~L~~ia~~Lg~~i   68 (89)
T d2o38a1          29 AAAARLGINQPKVSALRNYK-------LEGFSVERLMTLLNALDQDV   68 (89)
T ss_dssp             HHHHHHTCCHHHHHHHHTTC-------CTTCCHHHHHHHHHHTTEEE
T ss_pred             HHHHHHHhhHhHHHHHHcCC-------CCCCcHHHHHHHHHHcCCCH
Confidence            57778888888887777763       35677777777777777664

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=81.48  E-value=0.23  Score=26.70  Aligned_cols=21  Identities=5%  Similarity=0.178  Sum_probs=18.2

Q ss_pred             cchhccCCCHHHHHHHHhhhH
Q psy4877           2 ELSKLLNLTEVQIKTWFQNRR   22 (120)
Q Consensus         2 ~la~~~~~~~~~~q~~fq~~r   22 (120)
                      |||+++|++..-|+-|+.+++
T Consensus        19 elA~~LGvs~~ti~~yE~G~r   39 (67)
T d2auwa1          19 TAAEALGISRRMVSYYRTAHK   39 (67)
T ss_dssp             HHHHHHTSCHHHHHHHHTTSS
T ss_pred             HHHHHhCCCHHHHHHHHcCCC
Confidence            689999999999999998864