Psyllid ID: psy10851

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------16
Protein Sequence
MPQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSEGESEWVSLDWRSSVQSPVGDKKKSSSVLKIGYELGFFIQEEEEEEEEEEEEEEEEEEEEEEEEV
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccEEEEEHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEccccccccccccccccccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MPQYWFQNFQTIRLLNLKVKLktsfnsccpghktTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKqqegdksldkedsephikqephsegesewvsldwrssvqspvgdkkksssVLKIGYELGFfiqeeeeeeeeeeeeeeeeeeeeeeeev
Flexible Loop (DISEMBL)
MPQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIqrkakqqegdksldkedsephikqephsegesewvsldwrssvqspvgdkkksssvlKIGYELGffiqeeeeeeeeeeeeeeeeeeeeeeeev
Low Complexity Region (SEG)
MPQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSEGESEWVSLDWRSSVQSPVGDKKKSSSVLKIGYELGFFIQeeeeeeeeeeeeeeeeeeeeeeeeV
Disordered region (IsUnstruct)
***YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQN***************************************************************VLKIGYELGFFI**************************
Disordered Region (DISOPRED)
******QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQ****************************************************************************************************
Disordered Region (DISEMBL)
MPQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQ******************************************SLDWRS*************SVLKIGYELGFFIQE************************
Disordered Region (DISPRO)
*PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK************************************RSSV**************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWxxxxxxxxxxxxxxxxxxxxxKSLDKEDSEPHIKQEPHSEGESEWVSLDWRSSVQSPVGDKKKSSSVLKIGYExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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	159	2.2.26 [Sep-21-2011]
Q60564	369	LIM homeobox transcriptio	N/A	N/A	0.213	0.092	0.794	2e-09
O88609	372	LIM homeobox transcriptio	yes	N/A	0.213	0.091	0.794	2e-09
O60663	379	LIM homeobox transcriptio	yes	N/A	0.213	0.089	0.794	2e-09
P53413	377	LIM/homeobox protein LMX-	yes	N/A	0.213	0.090	0.794	2e-09
Q8UVR3	400	LIM homeobox transcriptio	N/A	N/A	0.213	0.085	0.764	8e-09
Q8TE12	382	LIM homeobox transcriptio	no	N/A	0.194	0.081	0.838	1e-08
Q9JKU8	382	LIM homeobox transcriptio	no	N/A	0.194	0.081	0.838	1e-08
Q04650	382	LIM homeobox transcriptio	N/A	N/A	0.194	0.081	0.838	1e-08
Q25132	692	LIM/homeobox protein Lhx3	N/A	N/A	0.320	0.073	0.490	2e-06
P20271	351	Homeobox protein ceh-14 O	no	N/A	0.238	0.108	0.578	2e-06

>sp|Q60564|LMX1B_MESAU LIM homeobox transcription factor 1-beta (Fragment) OS=Mesocricetus auratus GN=LMX1B PE=2 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/34 (79%), Positives = 31/34 (91%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R+
Sbjct: 214 KVRETLAAETGLSVRVVQVWFQNQRAKMKKLARR 247

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels. Mediates physical interaction and transcriptional synergy with E47/PAN-1.
Mesocricetus auratus (taxid: 10036)

>sp|O88609|LMX1B_MOUSE LIM homeobox transcription factor 1-beta OS=Mus musculus GN=Lmx1b PE=2 SV=2

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/34 (79%), Positives = 31/34 (91%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R+
Sbjct: 224 KVRETLAAETGLSVRVVQVWFQNQRAKMKKLARR 257

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Mus musculus (taxid: 10090)

>sp|O60663|LMX1B_HUMAN LIM homeobox transcription factor 1-beta OS=Homo sapiens GN=LMX1B PE=1 SV=2

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/34 (79%), Positives = 31/34 (91%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R+
Sbjct: 224 KVRETLAAETGLSVRVVQVWFQNQRAKMKKLARR 257

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Homo sapiens (taxid: 9606)

>sp|P53413|LMX1B_CHICK LIM/homeobox protein LMX-1.2 OS=Gallus gallus GN=LMX1B PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/34 (79%), Positives = 31/34 (91%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R+
Sbjct: 223 KVRETLAAETGLSVRVVQVWFQNQRAKMKKLARR 256

Specifies dorsal cell fate during limb development.

Gallus gallus (taxid: 9031)

>sp|Q8UVR3|LMX1B_XENLA LIM homeobox transcription factor 1-beta.1 OS=Xenopus laevis GN=lmx1b.1 PE=2 SV=1

 Score = 59.7 bits (143), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 26/34 (76%), Positives = 31/34 (91%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
           +VRE LA +TGLSVRVVQVWFQNQRAK+KK+ R+
Sbjct: 246 KVRETLAAETGLSVRVVQVWFQNQRAKIKKLARR 279

Required for early specification of the kidney glomus, lying upstream of wt1 in the pathway controlling glomus differentiation. The balance in levels and expression patterns of binding partners such as lhx1/lim-1 influences differentiation into glomus or tubule derivatives. Involved in specification of serotonergic neurons.

Xenopus laevis (taxid: 8355)

>sp|Q8TE12|LMX1A_HUMAN LIM homeobox transcription factor 1-alpha OS=Homo sapiens GN=LMX1A PE=2 SV=1

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 29/31 (93%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+
Sbjct: 223 KVRETLAAETGLSVRVVQVWFQNQRAKMKKL 253

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Homo sapiens (taxid: 9606)

>sp|Q9JKU8|LMX1A_MOUSE LIM homeobox transcription factor 1-alpha OS=Mus musculus GN=Lmx1a PE=2 SV=1

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 29/31 (93%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+
Sbjct: 223 KVRETLAAETGLSVRVVQVWFQNQRAKMKKL 253

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Mus musculus (taxid: 10090)

>sp|Q04650|LMX1A_MESAU LIM homeobox transcription factor 1-alpha OS=Mesocricetus auratus GN=LMX1A PE=2 SV=1

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 29/31 (93%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
           +VRE LA +TGLSVRVVQVWFQNQRAKMKK+
Sbjct: 223 KVRETLAAETGLSVRVVQVWFQNQRAKMKKL 253

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Mesocricetus auratus (taxid: 10036)

>sp|Q25132|LHX3_HALRO LIM/homeobox protein Lhx3 OS=Halocynthia roretzi GN=LHX3 PE=2 SV=2

 Score = 51.6 bits (122), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/53 (49%), Positives = 36/53 (67%), Gaps = 2/53 (3%)

Query: 21  LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73
           LK+++N          VRE L+ +TGL +RVVQVWFQN+RAK K+I+R   +Q
Sbjct: 425 LKSAYNQ--SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRIKRDTGRQ 475

May be involved in the determination of cell lineage of endoderm and notochord cells before gastrulation, and in specification of a distinct group of cells in neural tissue after gastrulation.

Halocynthia roretzi (taxid: 7729)

>sp|P20271|HM14_CAEEL Homeobox protein ceh-14 OS=Caenorhabditis elegans GN=ceh-14 PE=2 SV=3

 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 31/38 (81%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73
            VRE LA +TGL +RVVQVWFQN+RAK K++++ A ++
Sbjct: 208 HVREQLASETGLDMRVVQVWFQNRRAKEKRLKKDAGRR 245

Confers thermosensory function to neurons. Required for correct AFD-mediated thermotaxis.

Caenorhabditis elegans (taxid: 6239)

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	159
307204532	402	LIM homeobox transcription factor 1 beta	0.427	0.169	0.619	3e-14
332025158	400	LIM homeobox transcription factor 1-beta	0.427	0.17	0.619	3e-14
307189897	402	LIM homeobox transcription factor 1 beta	0.427	0.169	0.619	3e-14
383861320	402	PREDICTED: LIM homeobox transcription fa	0.427	0.169	0.605	4e-14
328779726	402	PREDICTED: LIM homeobox transcription fa	0.427	0.169	0.605	4e-14
380030211	402	PREDICTED: LOW QUALITY PROTEIN: LIM home	0.427	0.169	0.605	4e-14
242007294	389	Homeobox protein ceh-14, putative [Pedic	0.421	0.172	0.647	5e-14
156543668	419	PREDICTED: LIM homeobox transcription fa	0.421	0.159	0.619	1e-13
195440764	636	GK10148 [Drosophila willistoni] gi|19416	0.578	0.144	0.509	1e-13
350402518	402	PREDICTED: LIM homeobox transcription fa	0.427	0.169	0.591	2e-13

>gi|307204532|gb|EFN83212.1| LIM homeobox transcription factor 1 beta [Harpegnathos saltator]

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 227 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 283

Query: 96  GESEWVSLDWR 106
                 +L+ R
Sbjct: 284 HSHYLNALNMR 294

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025158|gb|EGI65338.1| LIM homeobox transcription factor 1-beta [Acromyrmex echinatior]

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 225 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 281

Query: 96  GESEWVSLDWR 106
                 +L+ R
Sbjct: 282 HSHYLNALNMR 292

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189897|gb|EFN74141.1| LIM homeobox transcription factor 1 beta [Camponotus floridanus]

 Score = 83.2 bits (204), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 227 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 283

Query: 96  GESEWVSLDWR 106
                 +L+ R
Sbjct: 284 HSHYLNALNMR 294

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861320|ref|XP_003706134.1| PREDICTED: LIM homeobox transcription factor 1-beta-like [Megachile rotundata]

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 43/71 (60%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 226 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 282

Query: 96  GESEWVSLDWR 106
                 +++ R
Sbjct: 283 HSHYLNAMNMR 293

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328779726|ref|XP_001120677.2| PREDICTED: LIM homeobox transcription factor 1-beta-like [Apis mellifera]

 Score = 82.8 bits (203), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 43/71 (60%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 226 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 282

Query: 96  GESEWVSLDWR 106
                 +++ R
Sbjct: 283 HSHYLNAMNMR 293

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380030211|ref|XP_003698747.1| PREDICTED: LOW QUALITY PROTEIN: LIM homeobox transcription factor 1-beta-like [Apis florea]

 Score = 82.8 bits (203), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 43/71 (60%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 226 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 282

Query: 96  GESEWVSLDWR 106
                 +++ R
Sbjct: 283 HSHYLNAMNMR 293

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007294|ref|XP_002424476.1| Homeobox protein ceh-14, putative [Pediculus humanus corporis] gi|212507894|gb|EEB11738.1| Homeobox protein ceh-14, putative [Pediculus humanus corporis]

 Score = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 44/68 (64%), Positives = 53/68 (77%), Gaps = 1/68 (1%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAK+TGLSVRVVQVWFQNQRAK+KKIQRKAKQ++ DK LDK+  E  IK E    
Sbjct: 200 KVREALAKETGLSVRVVQVWFQNQRAKVKKIQRKAKQEQ-DKGLDKDKDEKSIKVESPDS 258

Query: 96  GESEWVSL 103
            +  ++ L
Sbjct: 259 DQVHYLGL 266

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156543668|ref|XP_001605174.1| PREDICTED: LIM homeobox transcription factor 1-beta-like [Nasonia vitripennis]

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 52/71 (73%), Gaps = 4/71 (5%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAKDTGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 236 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERKPESPHSD 292

Query: 96  GESEWVSLDWR 106
             S +++   R
Sbjct: 293 -HSHYMNAMMR 302

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195440764|ref|XP_002068210.1| GK10148 [Drosophila willistoni] gi|194164295|gb|EDW79196.1| GK10148 [Drosophila willistoni]

 Score = 80.9 bits (198), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/110 (50%), Positives = 61/110 (55%), Gaps = 18/110 (16%)

Query: 10  QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
           +TI     + + K SF+ S  P  K   VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR
Sbjct: 423 RTILTSQQRKQFKASFDQSPKPCRK---VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 479

Query: 69  KAKQQEG--------------DKSLDKEDSEPHIKQEPHSEGESEWVSLD 104
           KAKQ  G              D     E  E  IKQE  +E  S    LD
Sbjct: 480 KAKQNGGTTTNGRGNGNSNAADDKDTNEKEEKSIKQELGTESGSYLGGLD 529

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350402518|ref|XP_003486514.1| PREDICTED: LIM homeobox transcription factor 1-beta-like [Bombus impatiens]

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 42/71 (59%), Positives = 51/71 (71%), Gaps = 3/71 (4%)

Query: 36  QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSLDKEDSEPHIKQEPHSE 95
           +VREALAK+TGLSVRVVQVWFQNQRAKMKK+QRKAK + G    DKE  E    + PHS+
Sbjct: 226 KVREALAKETGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGS---DKEPKEERRTESPHSD 282

Query: 96  GESEWVSLDWR 106
                 +++ R
Sbjct: 283 HSHYLNAMNMR 293

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

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	159
FB|FBgn0036274	544	CG4328 [Drosophila melanogaste	0.402	0.117	0.575	7.7e-14
FB|FBgn0052105	640	CG32105 [Drosophila melanogast	0.402	0.1	0.651	1.7e-13
UNIPROTKB|F1S229	295	LMX1A "Uncharacterized protein	0.408	0.220	0.550	2.5e-11
UNIPROTKB|E1C2D6	386	E1C2D6 "Uncharacterized protei	0.503	0.207	0.465	2.5e-11
UNIPROTKB|I3L863	296	LMX1A "Uncharacterized protein	0.408	0.219	0.550	2.5e-11
UNIPROTKB|H9L043	280	H9L043 "Uncharacterized protei	0.471	0.267	0.481	4.4e-11
UNIPROTKB|F1MC25	382	LMX1A "Uncharacterized protein	0.408	0.170	0.550	5.2e-11
UNIPROTKB|F1PDJ1	382	LMX1A "Uncharacterized protein	0.408	0.170	0.550	5.2e-11
UNIPROTKB|Q8TE12	382	LMX1A "LIM homeobox transcript	0.408	0.170	0.550	5.2e-11
MGI|MGI:1888519	382	Lmx1a "LIM homeobox transcript	0.408	0.170	0.550	5.2e-11

FB|FBgn0036274 CG4328 [Drosophila melanogaster (taxid:7227)]

 Score = 188 (71.2 bits), Expect = 7.7e-14, P = 7.7e-14
 Identities = 42/73 (57%), Positives = 52/73 (71%)

Query:    36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKSL-DKEDSEPH------- 87
             +VRE LAKDTGLS+R+VQVWFQNQRAK+KKIQ+KAKQ+   K   D +DS+         
Sbjct:   369 KVRENLAKDTGLSLRIVQVWFQNQRAKVKKIQKKAKQEPPSKGASDSQDSQESLDSSLAT 428

Query:    88 -IKQEPHSEGESE 99
              IK E HS+ ES+
Sbjct:   429 KIKDEAHSDSESQ 441

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

GO:0005634 "nucleus" evidence=ISS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0048813 "dendrite morphogenesis" evidence=IMP

GO:0006911 "phagocytosis, engulfment" evidence=IMP

FB|FBgn0052105 CG32105 [Drosophila melanogaster (taxid:7227)]

 Score = 186 (70.5 bits), Expect = 1.7e-13, P = 1.7e-13
 Identities = 43/66 (65%), Positives = 48/66 (72%)

Query:    10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
             +TI     + + K SF+   P     +VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK
Sbjct:   428 RTILTSQQRKQFKASFDQS-P-KPCRKVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 485

Query:    70 AKQQEG 75
             AKQ  G
Sbjct:   486 AKQNGG 491

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1S229 LMX1A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 159 (61.0 bits), Expect = 2.5e-11, P = 2.5e-11
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   112 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 168

Query:    69 KAKQQEGDK 77
             + +QQ+ D+
Sbjct:   169 RQQQQQQDQ 177

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|E1C2D6 E1C2D6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 162 (62.1 bits), Expect = 2.5e-11, P = 2.5e-11
 Identities = 41/88 (46%), Positives = 55/88 (62%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   204 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 260

Query:    69 KAKQQEGDKSLDKEDSEPHIKQEPHSEG 96
             + +QQ+ D+    ++++     +P+S G
Sbjct:   261 RQQQQQQDQ----QNTQRLSSAQPNSSG 284

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0001558 "regulation of cell growth" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

UNIPROTKB|I3L863 LMX1A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 159 (61.0 bits), Expect = 2.5e-11, P = 2.5e-11
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   112 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 168

Query:    69 KAKQQEGDK 77
             + +QQ+ D+
Sbjct:   169 RQQQQQQDQ 177

GO:0005634 "nucleus" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001558 "regulation of cell growth" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|H9L043 H9L043 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 156 (60.0 bits), Expect = 4.4e-11, P = 4.4e-11
 Identities = 38/79 (48%), Positives = 48/79 (60%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGL+VRVVQVWFQNQRAKMKKI R
Sbjct:   107 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLTVRVVQVWFQNQRAKMKKIAR 163

Query:    69 KAKQQEGDKSLDKEDSEPH 87
             + +QQ+  +   +  +  H
Sbjct:   164 RQQQQQQQQQEQEHGASVH 182

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1MC25 LMX1A "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 159 (61.0 bits), Expect = 5.2e-11, P = 5.2e-11
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   199 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 255

Query:    69 KAKQQEGDK 77
             + +QQ+ D+
Sbjct:   256 RQQQQQQDQ 264

GO:0005634 "nucleus" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001558 "regulation of cell growth" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1PDJ1 LMX1A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 159 (61.0 bits), Expect = 5.2e-11, P = 5.2e-11
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   199 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 255

Query:    69 KAKQQEGDK 77
             + +QQ+ D+
Sbjct:   256 RQQQQQQDQ 264

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|Q8TE12 LMX1A "LIM homeobox transcription factor 1-alpha" [Homo sapiens (taxid:9606)]

 Score = 159 (61.0 bits), Expect = 5.2e-11, P = 5.2e-11
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   199 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 255

Query:    69 KAKQQEGDK 77
             + +QQ+ D+
Sbjct:   256 RQQQQQQDQ 264

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0001558 "regulation of cell growth" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1888519 Lmx1a "LIM homeobox transcription factor 1 alpha" [Mus musculus (taxid:10090)]

 Score = 159 (61.0 bits), Expect = 5.2e-11, P = 5.2e-11
 Identities = 38/69 (55%), Positives = 46/69 (66%)

Query:    10 QTIRLLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
             +TI     +   K SF  S  P  K   VRE LA +TGLSVRVVQVWFQNQRAKMKK+ R
Sbjct:   199 RTILTTQQRRAFKASFEVSSKPCRK---VRETLAAETGLSVRVVQVWFQNQRAKMKKLAR 255

Query:    69 KAKQQEGDK 77
             + +QQ+ D+
Sbjct:   256 RQQQQQQDQ 264

GO:0001558 "regulation of cell growth" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007411 "axon guidance" evidence=IMP

GO:0007417 "central nervous system development" evidence=IMP

GO:0007420 "brain development" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0021542 "dentate gyrus development" evidence=IMP

GO:0021549 "cerebellum development" evidence=IMP

GO:0021766 "hippocampus development" evidence=IMP

GO:0021953 "central nervous system neuron differentiation" evidence=IMP

GO:0030182 "neuron differentiation" evidence=IMP

GO:0030901 "midbrain development" evidence=IMP

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IMP

---

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	159
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-09
smart00389	57	smart00389, HOX, Homeodomain	3e-08
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	4e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-07
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-07
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-07
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	9e-07
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	2e-05
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	9e-05
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	9e-05
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	1e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	1e-04
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	1e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	1e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	2e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	2e-04
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	3e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	4e-04
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	4e-04
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	4e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	4e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	6e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	6e-04
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	7e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.001
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.001
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.001
pfam05920	40	pfam05920, Homeobox_KN, Homeobox KN domain	0.001
TIGR03779	410	TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative	0.001
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.002
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.003
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.003
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	0.003
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	0.003
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	0.004

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

 Score = 50.2 bits (121), Expect = 2e-09
 Identities = 18/32 (56%), Positives = 24/32 (75%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          + + RE LAK  GL+ R V+VWFQN+RAK K+
Sbjct: 26 SAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 47.2 bits (113), Expect = 3e-08
 Identities = 21/44 (47%), Positives = 27/44 (61%), Gaps = 2/44 (4%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64
          L+  F      + + + RE LAK  GLS R V+VWFQN+RAK K
Sbjct: 16 LEKEFQKNP--YPSREEREELAKKLGLSERQVKVWFQNRRAKWK 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 = 47.2 bits (113), Expect = 4e-08
 Identities = 17/34 (50%), Positives = 27/34 (79%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
          + + RE LAK+ GL+ R V++WFQN+RAK+K+ +
Sbjct: 26 SREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 50.8 bits (121), Expect = 5e-08
 Identities = 24/25 (96%), Positives = 25/25 (100%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           +EEEEEEEEEEEEEEEEEEEEEEEE
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEEE 889

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 50.4 bits (120), Expect = 6e-08
 Identities = 24/25 (96%), Positives = 25/25 (100%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           +EEEEEEEEEEEEEEEEEEEEEEEE
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEE 888

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 50.0 bits (119), Expect = 1e-07
 Identities = 23/25 (92%), Positives = 24/25 (96%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           +EEEEEEEEEEEEEEEEEEEEEEE 
Sbjct: 866 EEEEEEEEEEEEEEEEEEEEEEEEN 890

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 49.6 bits (118), Expect = 1e-07
 Identities = 23/25 (92%), Positives = 24/25 (96%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           +EEEEEEEEEEEEEEEEEEEEEE E
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENE 891

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 49.6 bits (118), Expect = 1e-07
 Identities = 23/25 (92%), Positives = 24/25 (96%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           +EEEEEEEEEEEEEEEEEEEEE EE
Sbjct: 868 EEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 46.9 bits (111), Expect = 9e-07
 Identities = 22/24 (91%), Positives = 23/24 (95%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEE 158
           + EEEEEEEEEEEEEEEEEEEEEE
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEE 885

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 21/25 (84%), Positives = 21/25 (84%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
            E EEEEEEEEE  EEEEEEEEEEE
Sbjct: 303 PEPEEEEEEEEEVPEEEEEEEEEEE 327

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
              E EEEEEEEEE  EEEEEEEEE
Sbjct: 301 SPPEPEEEEEEEEEVPEEEEEEEEE 325

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 41.2 bits (96), Expect = 9e-05
 Identities = 14/25 (56%), Positives = 25/25 (100%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEEV 159
           ++E+E+E++++EE++EEEEEEEEE+
Sbjct: 156 DDEDEDEDDDDEEDDEEEEEEEEEI 180

Length = 2849

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 20/24 (83%), Positives = 20/24 (83%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEE 158
            EEEEEEEEE  EEEEEEEEEEE 
Sbjct: 305 PEEEEEEEEEVPEEEEEEEEEEER 328

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 18/25 (72%), Positives = 18/25 (72%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
               E EEEEEEEEE  EEEEEEEE
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEE 324

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 15/28 (53%), Positives = 26/28 (92%)

Query: 131 FFIQEEEEEEEEEEEEEEEEEEEEEEEE 158
           F I +++E+E+E++++EE++EEEEEEEE
Sbjct: 151 FVIDDDDEDEDEDDDDEEDDEEEEEEEE 178

Length = 2849

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 18/26 (69%), Positives = 22/26 (84%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEEV 159
           ++EEEE+E+EEEEEEEEE EE E E 
Sbjct: 347 KDEEEEQEDEEEEEEEEEPEEPEPEE 372

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/29 (79%), Positives = 23/29 (79%), Gaps = 4/29 (13%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEE----EEV 159
           EEEEEEEEE  EEEEEEEEEEE    EEV
Sbjct: 306 EEEEEEEEEVPEEEEEEEEEEERTFEEEV 334

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 17/28 (60%), Positives = 23/28 (82%)

Query: 131 FFIQEEEEEEEEEEEEEEEEEEEEEEEE 158
           +   E+++EEEE+E+EEEEEEEEE EE 
Sbjct: 341 WVNPEQKDEEEEQEDEEEEEEEEEPEEP 368

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 18/24 (75%), Positives = 18/24 (75%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEE 157
           Q    EEEEEEEEEEEEEE  EEE
Sbjct: 297 QAAAAEEEEEEEEEEEEEEPSEEE 320

Length = 330

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 18/26 (69%), Positives = 22/26 (84%)

Query: 133 IQEEEEEEEEEEEEEEEEEEEEEEEE 158
            Q++EEEE+E+EEEEEEEEE EE E 
Sbjct: 345 EQKDEEEEQEDEEEEEEEEEPEEPEP 370

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
            +    EEEEEEEEEEEEEE  EEE
Sbjct: 296 AQAAAAEEEEEEEEEEEEEEPSEEE 320

Length = 330

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           Q +    EEEEEEEEEEEEEE  EE
Sbjct: 295 QAQAAAAEEEEEEEEEEEEEEPSEE 319

Length = 330

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
                EEEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 18/25 (72%), Positives = 21/25 (84%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           +EEE+E+EEEEEEEEE EE E EE 
Sbjct: 349 EEEEQEDEEEEEEEEEPEEPEPEEG 373

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 15/24 (62%), Positives = 18/24 (75%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEE 158
                EE++EEEEEEEE+EE EEE
Sbjct: 73  AAAAAEEKKEEEEEEEEKEESEEE 96

Length = 106

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 38.9 bits (90), Expect = 7e-04
 Identities = 14/24 (58%), Positives = 23/24 (95%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEE 157
            +E+E+E++++EE++EEEEEEEEE
Sbjct: 156 DDEDEDEDDDDEEDDEEEEEEEEE 179

Length = 2849

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 15/25 (60%), Positives = 18/25 (72%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
              EE++EEEEEEEE+EE EEE   
Sbjct: 75  AAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 15/23 (65%), Positives = 18/23 (78%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEE 156
               EE++EEEEEEEE+EE EEE
Sbjct: 74  AAAAEEKKEEEEEEEEKEESEEE 96

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 14/24 (58%), Positives = 17/24 (70%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEE 158
                 EE++EEEEEEEE+EE EE
Sbjct: 72  AAAAAAEEKKEEEEEEEEKEESEE 95

Length = 106

>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain

 Score = 34.8 bits (81), Expect = 0.001
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 36 QVREALAKDTGLSVRVVQVWFQNQR 60
          + +  LA+ TGLS + +  WF N R
Sbjct: 14 EEKSELARQTGLSRKQIDNWFINAR 38

This is a homeobox transcription factor KN domain conserved from fungi to human and plants. Length = 40

>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM protein

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 6/105 (5%)

Query: 57  QNQRAKMKKIQRKAK--QQEGDKSLDKEDSEPHIKQEPHSEGESEWVSLDWRSSVQSPVG 114
           Q Q+ K + +Q  A   ++   +S D   S+    +EP    E+       RSS  +   
Sbjct: 69  QKQKDKKRTLQDLADSFEKSDKESQDYSSSDSGFDEEPDEPAETAGSLRPIRSSAAAY-- 126

Query: 115 DKKKSSSVLKIGYELGFFIQEEEEEEEEEEEEEEEEEEEEEEEEV 159
             +  +  L   YE     +E+E   E EE E     E     E+
Sbjct: 127 --RDINRELGSFYEYPKTDEEKELLREVEELESRLATEPSPAPEL 169

Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage [Cellular processes, DNA transformation]. Length = 410

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 14/26 (53%), Positives = 23/26 (88%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEEV 159
            ++EE+EEEE++EE+++E+E EEEE 
Sbjct: 115 DDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 12/25 (48%), Positives = 23/25 (92%)

Query: 134 QEEEEEEEEEEEEEEEEEEEEEEEE 158
           + +++EE+EEEE++EE+++E+E EE
Sbjct: 113 ESDDDEEDEEEEDDEEDDDEDESEE 137

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 15/33 (45%), Positives = 24/33 (72%)

Query: 125 IGYELGFFIQEEEEEEEEEEEEEEEEEEEEEEE 157
           +  E      +EE+EEEE++EE+++E+E EEEE
Sbjct: 107 VASEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 18/25 (72%), Positives = 18/25 (72%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEEV 159
           EEEEEEEEEEEEE  E E   EE V
Sbjct: 403 EEEEEEEEEEEEEAAEAEAPMEEPV 427

Length = 470

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 14/36 (38%), Positives = 21/36 (58%)

Query: 38  REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73
           R  L+    +  + VQ+WFQN+RAK KK +    +Q
Sbjct: 81  RIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ 116

Length = 156

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 17/24 (70%), Positives = 17/24 (70%)

Query: 135 EEEEEEEEEEEEEEEEEEEEEEEE 158
            EEEEEEEEEEEEE  E E   EE
Sbjct: 402 AEEEEEEEEEEEEEAAEAEAPMEE 425

Length = 470

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	159
KOG0484|consensus	125		99.89
KOG2251|consensus	228		99.87
KOG0850|consensus	245		99.86
KOG0843|consensus	197		99.84
KOG0842|consensus	307		99.84
KOG0485|consensus	268		99.84
KOG0488|consensus	309		99.84
KOG0489|consensus	261		99.84
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.81
KOG0487|consensus	308		99.8
KOG0848|consensus	317		99.78
KOG0492|consensus	246		99.78
KOG0494|consensus	332		99.77
KOG0491|consensus	194		99.72
KOG0493|consensus	342		99.72
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.71
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.71
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.71
KOG4577|consensus	383		99.69
COG5576	156	Homeodomain-containing transcription factor [Trans	99.68
KOG0486|consensus	351		99.67
KOG3802|consensus	398		99.65
KOG0844|consensus	408		99.65
KOG0483|consensus	198		99.64
KOG0847|consensus	288		99.57
KOG0775|consensus	304		99.54
KOG0490|consensus	235		99.48
KOG0849|consensus	354		99.44
KOG0774|consensus	334		99.37
KOG1168|consensus	385		99.33
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	99.08
KOG2252|consensus	558		99.06
KOG0490|consensus	235		98.61
KOG1146|consensus	1406		98.35
KOG0773|consensus	342		97.76
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.64
KOG3623|consensus	1007		97.0
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	96.82
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	92.83
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	91.87
PF06524	314	NOA36: NOA36 protein; InterPro: IPR010531 This fam	91.76
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	91.51
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	91.44
KOG1832|consensus	1516		91.08
KOG1146|consensus	1406		90.79
PRK03975	141	tfx putative transcriptional regulator; Provisiona	90.31
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	88.17
PRK00118	104	putative DNA-binding protein; Validated	88.12
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	87.62
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.19
PRK06759	154	RNA polymerase factor sigma-70; Validated	86.92
PRK12526	206	RNA polymerase sigma factor; Provisional	86.69
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	86.33
KOG1832|consensus	1516		85.55
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	85.53
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	85.3
PRK11924	179	RNA polymerase sigma factor; Provisional	85.28
PRK04217	110	hypothetical protein; Provisional	85.11
PRK06930	170	positive control sigma-like factor; Validated	84.98
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	84.71
PF00424	91	REV: REV protein (anti-repression trans-activator	84.2
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	84.08
PRK12519	194	RNA polymerase sigma factor; Provisional	84.02
PRK12512	184	RNA polymerase sigma factor; Provisional	83.81
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	83.69
TIGR00927	1096	2A1904 K+-dependent Na+/Ca+ exchanger.	83.62
PRK12530	189	RNA polymerase sigma factor; Provisional	83.6
PRK12514	179	RNA polymerase sigma factor; Provisional	83.43
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	83.15
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	83.03
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	83.02
PRK05602	186	RNA polymerase sigma factor; Reviewed	83.01
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	82.95
KOG3755|consensus	769		82.84
PRK12515	189	RNA polymerase sigma factor; Provisional	82.66
PRK12543	179	RNA polymerase sigma factor; Provisional	82.62
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	82.51
PRK12532	195	RNA polymerase sigma factor; Provisional	82.26
PRK09047	161	RNA polymerase factor sigma-70; Validated	82.08
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	81.26
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	80.99
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	80.98
PRK09413	121	IS2 repressor TnpA; Reviewed	80.78
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	80.62
PRK12537	182	RNA polymerase sigma factor; Provisional	80.19
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	80.18
PRK12541	161	RNA polymerase sigma factor; Provisional	80.12

>KOG0484|consensus

Probab=99.89  E-value=3.3e-23  Score=138.60  Aligned_cols=70  Identities=29%  Similarity=0.307  Sum_probs=64.0

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhcC
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEG   75 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~~   75 (159)
                      ++-||-||+||..||..|+..|...  |||++-.|++||.++.|++..|||||||||+|.||+.+.......
T Consensus        15 rKQRRIRTTFTS~QLkELErvF~ET--HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~   84 (125)
T KOG0484|consen   15 RKQRRIRTTFTSAQLKELERVFAET--HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMA   84 (125)
T ss_pred             HHhhhhhhhhhHHHHHHHHHHHHhh--cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhh
Confidence            3457789999999999999999999  899999999999999999999999999999999999877665554

>KOG2251|consensus

Probab=99.87  E-value=9.6e-22  Score=147.83  Aligned_cols=66  Identities=27%  Similarity=0.276  Sum_probs=62.7

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA   70 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~   70 (159)
                      .++.||.||+|+..|+.+|+.+|.+. + ||+..+|++||.+|+|.+.+|+|||+|||+|||+++...
T Consensus        34 pRkqRRERTtFtr~QlevLe~LF~kT-q-YPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   34 PRKQRRERTTFTRKQLEVLEALFAKT-Q-YPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             chhcccccceecHHHHHHHHHHHHhh-c-CccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            46788999999999999999999999 7 999999999999999999999999999999999988765

>KOG0850|consensus

Probab=99.86  E-value=1.5e-21  Score=147.40  Aligned_cols=66  Identities=27%  Similarity=0.359  Sum_probs=62.6

Q ss_pred             CCcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          2 PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         2 ~~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      +.++.|++||.|+.-||..|++.|.++ + |.-..+|.+||..|||+.+||||||||||.|.||..+.
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkT-Q-YLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~  183 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQT-Q-YLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ  183 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhc-c-hhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence            356889999999999999999999999 8 99999999999999999999999999999999998874

>KOG0843|consensus

Probab=99.84  E-value=2.1e-21  Score=141.81  Aligned_cols=65  Identities=29%  Similarity=0.382  Sum_probs=61.2

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA   70 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~   70 (159)
                      ++-||.||.||..||..|+.+|..+  +|-...+|+.||+.|+|++.||+|||||||.|.||.+...
T Consensus       100 ~~~kr~RT~ft~~Ql~~LE~~F~~~--~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  100 MRPKRIRTAFTPEQLLKLEHAFEGN--QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             cCCCccccccCHHHHHHHHHHHhcC--CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            3789999999999999999999999  5999999999999999999999999999999999986654

>KOG0842|consensus

Probab=99.84  E-value=2.5e-21  Score=153.49  Aligned_cols=71  Identities=23%  Similarity=0.245  Sum_probs=64.1

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhcC
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEG   75 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~~   75 (159)
                      .+++||+|..||+.|+-.||+-|+++ + |.+..+|+.||..|+|+.+||||||||||.|+||+.+.......
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-R-YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~  220 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQ-R-YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL  220 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhh-h-ccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence            34678889999999999999999999 7 99999999999999999999999999999999998776554443

>KOG0485|consensus

Probab=99.84  E-value=8.9e-21  Score=142.19  Aligned_cols=68  Identities=22%  Similarity=0.264  Sum_probs=62.6

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHh
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ   72 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~   72 (159)
                      +.+.||.||+|+..|+-.|+..|... + |.+..+|..||+.|.|+++||||||||||.||||+......
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~k-r-YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e  168 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELK-R-YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE  168 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHH-h-hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence            45789999999999999999999999 7 99999999999999999999999999999999998654433

>KOG0488|consensus

Probab=99.84  E-value=3.2e-21  Score=154.60  Aligned_cols=68  Identities=24%  Similarity=0.235  Sum_probs=63.3

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ   73 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~   73 (159)
                      ++.||.||.||..||..||+.|.+. + |.+..+|..||..|||+..||++||||||+||||+.......
T Consensus       170 kK~RksRTaFT~~Ql~~LEkrF~~Q-K-YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~  237 (309)
T KOG0488|consen  170 KKRRKSRTAFSDHQLFELEKRFEKQ-K-YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGEL  237 (309)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHh-h-cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence            6788899999999999999999999 8 999999999999999999999999999999999997764433

>KOG0489|consensus

Probab=99.84  E-value=1.3e-21  Score=154.02  Aligned_cols=67  Identities=25%  Similarity=0.286  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ   73 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~   73 (159)
                      ..||.||.||..|+..||+.|..| + |.++..|.+||..|+|+++||||||||||+||||..+.....
T Consensus       158 ~~kR~RtayT~~QllELEkEFhfN-~-YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  158 KSKRRRTAFTRYQLLELEKEFHFN-K-YLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCcccchhhhhhhhhhhccc-c-ccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            479999999999999999999999 6 999999999999999999999999999999999976644433

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.81  E-value=6.2e-20  Score=112.58  Aligned_cols=57  Identities=37%  Similarity=0.464  Sum_probs=55.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ||+|+.||..|+.+|+.+|..+ + ||+..++..||..|||+..+|++||+|||++.||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~-~-~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQEN-P-YPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHS-S-SCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHh-c-cccccccccccccccccccccccCHHHhHHHhCc
Confidence            6899999999999999999999 7 9999999999999999999999999999999986

; 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 ....

>KOG0487|consensus

Probab=99.80  E-value=3.7e-20  Score=146.85  Aligned_cols=68  Identities=25%  Similarity=0.313  Sum_probs=62.6

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ   73 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~   73 (159)
                      +..||||.-+|+.|+..||+.|..| . |++...|.+|++.|+|+++||||||||||+|.||..+....+
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN-~-YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~  300 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFN-M-YITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK  300 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHH-H-HHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence            5678999999999999999999999 5 999999999999999999999999999999999988654443

>KOG0848|consensus

Probab=99.78  E-value=3.6e-19  Score=137.16  Aligned_cols=62  Identities=31%  Similarity=0.530  Sum_probs=58.1

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      |-|.++|..|+..||+.|..+ + |.++..+.+||..|||+++||||||||||+|.||..++..
T Consensus       201 KYRvVYTDhQRLELEKEfh~S-r-yITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTS-R-YITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             ceeEEecchhhhhhhhhhccc-c-ceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            458899999999999999999 7 9999999999999999999999999999999999977764

>KOG0492|consensus

Probab=99.78  E-value=4.5e-19  Score=132.19  Aligned_cols=66  Identities=23%  Similarity=0.311  Sum_probs=60.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhc
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE   74 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~   74 (159)
                      |++||-||.+||..|++.|+.. + |.++.+|.+++..|.|+++||||||||||+|.||.+......-
T Consensus       145 RkPRtPFTtqQLlaLErkfrek-q-YLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~  210 (246)
T KOG0492|consen  145 RKPRTPFTTQQLLALERKFREK-Q-YLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKL  210 (246)
T ss_pred             CCCCCCCCHHHHHHHHHHHhHh-h-hhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHh
Confidence            5689999999999999999999 7 9999999999999999999999999999999999876554443

>KOG0494|consensus

Probab=99.77  E-value=3.6e-19  Score=136.68  Aligned_cols=65  Identities=32%  Similarity=0.442  Sum_probs=59.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ   73 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~   73 (159)
                      |+-||.||..|+..|+..|+..  |||+..-|+.||.++.|.+.+|+|||||||+||||..+.....
T Consensus       142 Rh~RTiFT~~Qle~LEkaFkea--HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s  206 (332)
T KOG0494|consen  142 RHFRTIFTSYQLEELEKAFKEA--HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS  206 (332)
T ss_pred             ccccchhhHHHHHHHHHHHhhc--cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence            3349999999999999999999  8999999999999999999999999999999999987765443

>KOG0491|consensus

Probab=99.72  E-value=4.2e-18  Score=122.84  Aligned_cols=65  Identities=31%  Similarity=0.321  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      ++++.||+|+..|+..|++.|... + |.+..+|.+||-+|+|+++||+.||||||+|.||.+++..
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-r-YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQ-R-YLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhh-h-hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            356789999999999999999999 7 9999999999999999999999999999999999877654

>KOG0493|consensus

Probab=99.72  E-value=5.4e-18  Score=130.39  Aligned_cols=58  Identities=34%  Similarity=0.483  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ||+||.||.+||..|+..|..+ + |.+...|..||..|+|++.||+|||||+|+|.||.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~en-R-YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs  304 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQEN-R-YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS  304 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhh-h-hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence            6899999999999999999999 7 99999999999999999999999999999999985

>smart00389 HOX Homeodomain

Probab=99.71  E-value=1.7e-17  Score=101.09  Aligned_cols=56  Identities=39%  Similarity=0.509  Sum_probs=52.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      ++.|++|+..|+.+|+..|..+ + ||+..++..||..+||+..+|++||+|||++.|
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~-~-~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKN-P-YPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5788999999999999999999 6 999999999999999999999999999998864

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

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

Probab=99.71  E-value=3.1e-17  Score=100.78  Aligned_cols=58  Identities=36%  Similarity=0.544  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ++.|+.|+..|+.+|+.+|..+ + ||+..++..||..+||+..+|++||+|||++.++.
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~~-~-~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEKN-P-YPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            4688999999999999999999 7 99999999999999999999999999999998863

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.71  E-value=8.4e-18  Score=102.86  Aligned_cols=52  Identities=17%  Similarity=0.297  Sum_probs=50.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCC----CCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGH----KTTQVREALAKDTGLSVRVVQVWFQNQR   60 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~y----p~~~~r~~La~~l~l~~~~V~vWFqNRR   60 (159)
                      ||.||.||.+|+..|+.+|..+ + |    |+..+|.+||..|||+.++|+|||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~-~-y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKL-G-WKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHc-C-CCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            8999999999999999999999 5 9    9999999999999999999999999965

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

>KOG4577|consensus

Probab=99.69  E-value=9.8e-17  Score=125.03  Aligned_cols=62  Identities=40%  Similarity=0.644  Sum_probs=59.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      -||+||+||..||..|+..|+.. + .|.+..|++|+..+||.-++|||||||||||.||.++.
T Consensus       167 nKRPRTTItAKqLETLK~AYn~S-p-KPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  167 NKRPRTTITAKQLETLKQAYNTS-P-KPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             cCCCcceeeHHHHHHHHHHhcCC-C-chhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            58999999999999999999999 8 99999999999999999999999999999999997653

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.68  E-value=6.3e-17  Score=117.96  Aligned_cols=66  Identities=24%  Similarity=0.239  Sum_probs=61.4

Q ss_pred             CCcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          2 PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         2 ~~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ..+..+++|++.|..|+.+|+..|..+ + ||+...|..|+..|||+++-|+|||||||++.|+....
T Consensus        47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~-p-~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          47 GSSPPKSKRRRTTDEQLMVLEREFEIN-P-YPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             CCCcCcccceechHHHHHHHHHHhccC-C-CCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            346789999999999999999999999 7 99999999999999999999999999999999987554

>KOG0486|consensus

Probab=99.67  E-value=2.6e-17  Score=129.44  Aligned_cols=65  Identities=28%  Similarity=0.320  Sum_probs=61.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      +-||.||.||.+|+..|+.+|.++ + ||+...|++||..++|++..|+|||+|||+||||+.+...
T Consensus       111 KqrrQrthFtSqqlqele~tF~rN-r-ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRN-R-YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhc-c-CCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            457889999999999999999999 7 9999999999999999999999999999999999988766

>KOG3802|consensus

Probab=99.65  E-value=4e-17  Score=132.28  Aligned_cols=63  Identities=30%  Similarity=0.372  Sum_probs=59.4

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .++||+||.|+...+.+|+.+|.+| + .|+..++..||..|+|.+.+|+|||||||+|.||...
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~n-p-KPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKN-P-KPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            3678899999999999999999999 8 9999999999999999999999999999999998644

>KOG0844|consensus

Probab=99.65  E-value=3.5e-17  Score=128.40  Aligned_cols=64  Identities=23%  Similarity=0.300  Sum_probs=59.5

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      +.+-||-||.||.+|+..|++.|.+.  +|-++..|.+||..|||.+..|||||||||+|+||+..
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrE--NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRE--NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHh--ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            34578999999999999999999998  69999999999999999999999999999999999754

>KOG0483|consensus

Probab=99.64  E-value=1.2e-16  Score=120.25  Aligned_cols=60  Identities=33%  Similarity=0.369  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+++..+|+.+|+..|+..|...  +|..+..+..||+.|||.++||.|||||||||||..+
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~--~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESE--KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccccccHHHHHHhHHhhccc--cccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            45667789999999999999999  6999999999999999999999999999999999864

>KOG0847|consensus

Probab=99.57  E-value=3.7e-15  Score=112.29  Aligned_cols=67  Identities=21%  Similarity=0.251  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ   73 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~   73 (159)
                      ++|..|.+|+..|+..|+..|.+. + |+-...|.+||..+||++.||+|||||||.||||+.......
T Consensus       166 ~rk~srPTf~g~qi~~le~~feqt-k-ylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas  232 (288)
T KOG0847|consen  166 QRKQSRPTFTGHQIYQLERKFEQT-K-YLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS  232 (288)
T ss_pred             cccccCCCccchhhhhhhhhhhhh-h-cccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence            455678899999999999999999 7 999999999999999999999999999999999986544433

>KOG0775|consensus

Probab=99.54  E-value=4.8e-14  Score=109.31  Aligned_cols=59  Identities=25%  Similarity=0.380  Sum_probs=51.8

Q ss_pred             CCCCCCCCCHHH---------HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNL---------KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q---------~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      |--+||.+..++         ..+|+.+|.++ + ||++.++.+||+++||+..||-+||+|||+|+|..
T Consensus       167 fPlPrTIWDGEet~yCFKekSR~~LrewY~~~-~-YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~  234 (304)
T KOG0775|consen  167 FPLPRTIWDGEETVYCFKEKSRSLLREWYLQN-P-YPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA  234 (304)
T ss_pred             CCCCCccccCceeeeehhHhhHHHHHHHHhcC-C-CCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence            334677766555         68999999999 8 99999999999999999999999999999999944

>KOG0490|consensus

Probab=99.48  E-value=3.5e-14  Score=109.41  Aligned_cols=64  Identities=28%  Similarity=0.255  Sum_probs=60.4

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ....||.|++|+..|+..|+..|..+  |||+...|+.||..++|++..|+|||||||+|||++..
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~--h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKV--HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCC--CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            34678899999999999999999999  79999999999999999999999999999999999875

>KOG0849|consensus

Probab=99.44  E-value=3.5e-13  Score=110.35  Aligned_cols=65  Identities=37%  Similarity=0.408  Sum_probs=61.0

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      .++.+|.||+|+..|+..|++.|..+ + ||+...|+.||..++|++..|+|||+|||+|+||....
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt-~-yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRT-P-YPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCC-C-CCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            36788899999999999999999999 6 99999999999999999999999999999999998743

>KOG0774|consensus

Probab=99.37  E-value=1.6e-12  Score=100.41  Aligned_cols=63  Identities=27%  Similarity=0.315  Sum_probs=57.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      .||+|..|++.-..+|..+|...  || ||+...+++||+++|++..||.+||.|+|-+.||....
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nP-YPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k  252 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNP-YPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK  252 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCC-CCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence            47889999999999999999654  69 99999999999999999999999999999999997543

>KOG1168|consensus

Probab=99.33  E-value=4.5e-13  Score=104.76  Aligned_cols=65  Identities=31%  Similarity=0.362  Sum_probs=60.0

Q ss_pred             CCcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          2 PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         2 ~~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      |---.||+||.+-.-..+.|+.+|..+ | .|+.+.+..||.+|.|...+|+|||||.|+|-||...
T Consensus       305 ~~~ekKRKRTSIAAPEKRsLEayFavQ-P-RPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  305 PGGEKKRKRTSIAAPEKRSLEAYFAVQ-P-RPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             CccccccccccccCcccccHHHHhccC-C-CCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            344578999999999999999999999 8 9999999999999999999999999999999998654

>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=99.08  E-value=1.1e-10  Score=66.25  Aligned_cols=33  Identities=39%  Similarity=0.672  Sum_probs=28.5

Q ss_pred             CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851         29 CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK   62 (159)
Q Consensus        29 ~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k   62 (159)
                      || ||+..++..||..+||+..||.+||-|.|.|
T Consensus         8 nP-YPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    8 NP-YPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             SG-S--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CC-CCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            49 9999999999999999999999999999975

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

>KOG2252|consensus

Probab=99.06  E-value=4.5e-10  Score=94.68  Aligned_cols=56  Identities=16%  Similarity=0.224  Sum_probs=53.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM   63 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~   63 (159)
                      -||+|.+||..|+..|..+|+.+ + ||+..+.+.|+.+|||..+.|.+||.|.|.|.
T Consensus       420 ~KKPRlVfTd~QkrTL~aiFke~-~-RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  420 TKKPRLVFTDIQKRTLQAIFKEN-K-RPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             CCCceeeecHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            57899999999999999999999 8 99999999999999999999999999999876

>KOG0490|consensus

Probab=98.61  E-value=4.2e-08  Score=75.43  Aligned_cols=63  Identities=43%  Similarity=0.547  Sum_probs=58.9

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .+.++.|+.++..|+..|...|..+ . ||+...+..|+..+|++...|++||+|+|++.++...
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~-~-~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  151 KKPRRPRTTFTENQLEVLETVFRAT-P-KPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             cccCCCccccccchhHhhhhcccCC-C-CCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            4577889999999999999999999 5 9999999999999999999999999999999998755

>KOG1146|consensus

Probab=98.35  E-value=5.9e-07  Score=82.45  Aligned_cols=63  Identities=33%  Similarity=0.374  Sum_probs=59.3

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      +.||+.|+.++..||.+|..+|... . ||.....+-|...++|..++|++||||.|+|.||...
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q-~-~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQ-R-TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhc-c-CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            4578899999999999999999999 5 9999999999999999999999999999999999876

>KOG0773|consensus

Probab=97.76  E-value=1.5e-05  Score=65.14  Aligned_cols=62  Identities=26%  Similarity=0.171  Sum_probs=51.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .+|++..+......+|+.++..+  .| ||+...+..||..+||+..||.+||-|.|-|..+-..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~P-YPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~  302 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHP-YPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI  302 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCC-CCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence            34556689999999999885442  27 9999999999999999999999999999988776544

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

Probab=97.64  E-value=4.6e-05  Score=46.03  Aligned_cols=41  Identities=15%  Similarity=0.256  Sum_probs=31.1

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851         18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR   60 (159)
Q Consensus        18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR   60 (159)
                      +..|+.+|... + ++.......|..+.+|+..||+.||--|+
T Consensus        10 ~~pL~~Yy~~h-~-~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKH-K-QLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT------TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHc-C-CccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            46799999999 5 99999999999999999999999996553

>KOG3623|consensus

Probab=97.00  E-value=0.0012  Score=58.30  Aligned_cols=49  Identities=22%  Similarity=0.423  Sum_probs=45.3

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      +..|+.+|..| . .|+..+...||...||....|++||++++++-+...+
T Consensus       568 ~sllkayyaln-~-~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r  616 (1007)
T KOG3623|consen  568 TSLLKAYYALN-G-LPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER  616 (1007)
T ss_pred             HHHHHHHHHhc-C-CCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence            78999999999 5 9999999999999999999999999999998877554

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

Probab=96.82  E-value=0.005  Score=36.84  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=35.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR   60 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR   60 (159)
                      ||+|..+|-.+...+-..+... .      ....||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g-~------s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEG-E------SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCT-T-------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcC-C------CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            6899999999977777777655 2      578899999999999999999864

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

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

Probab=92.83  E-value=0.43  Score=27.57  Aligned_cols=47  Identities=15%  Similarity=0.145  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+++.+..+|...|-..       ..-.++|..+|++...|+.+...-..|.|+
T Consensus         4 ~L~~~er~vi~~~y~~~-------~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEG-------LTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             TS-HHHHHHHHHHHTST--------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCC-------CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            46788899999888544       246789999999999999998776666653

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

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

Probab=91.87  E-value=0.21  Score=31.29  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=28.5

Q ss_pred             CCCCCCCHHHHHHHHHHH-hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851          8 NFQTIRLLNLKVKLKTSF-NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ   57 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F-~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq   57 (159)
                      ++|.+||.++...+-..+ ...       .....||..+||+...|..|-.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g-------~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG-------ESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH-------CHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC-------CceEeeecccccccccccHHHH
Confidence            577899999976665555 333       3788999999999999999953

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

>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues

Probab=91.76  E-value=0.065  Score=42.22  Aligned_cols=6  Identities=17%  Similarity=0.578  Sum_probs=2.4

Q ss_pred             hhhhhh
Q psy10851         53 QVWFQN   58 (159)
Q Consensus        53 ~vWFqN   58 (159)
                      ++-|+.
T Consensus       189 K~cfCd  194 (314)
T PF06524_consen  189 KICFCD  194 (314)
T ss_pred             eeeehh
Confidence            344443

The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=91.51  E-value=0.69  Score=27.00  Aligned_cols=44  Identities=14%  Similarity=0.049  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK   62 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k   62 (159)
                      .+++.+..++...|-..       ....++|..+|++...|++|.+.-|.+
T Consensus        10 ~L~~~~r~i~~l~~~~g-------~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   10 QLPERQREIFLLRYFQG-------MSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             CS-HHHHHHHHHHHTS----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHC-------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            34556666666554433       467889999999999999999766654

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

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

Probab=91.44  E-value=0.46  Score=26.80  Aligned_cols=44  Identities=16%  Similarity=0.058  Sum_probs=33.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK   62 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k   62 (159)
                      .++..+..++...|...   +    ....+|..+|++...|..|....+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~---~----~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG---L----SYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            46777888887776433   2    46678999999999999998766554

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

>KOG1832|consensus

Probab=91.08  E-value=0.072  Score=48.72  Aligned_cols=10  Identities=30%  Similarity=0.202  Sum_probs=4.6

Q ss_pred             ccccccCCCC
Q psy10851        123 LKIGYELGFF  132 (159)
Q Consensus       123 ~~~~~~~~~~  132 (159)
                      ....|+.|--
T Consensus      1391 ~~r~yEIGR~ 1400 (1516)
T KOG1832|consen 1391 SARMYEIGRR 1400 (1516)
T ss_pred             hhhhhhhccc
Confidence            3444555543

>KOG1146|consensus

Probab=90.79  E-value=0.3  Score=46.32  Aligned_cols=63  Identities=19%  Similarity=0.213  Sum_probs=57.9

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+.-|+.|+.+-..++.+|-.+|-.+  +-|+...+..|......+.+++.+||+|-|.|.++..
T Consensus       702 ~~~~~~~~~~~~~~aa~~l~~a~~~~--~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~  764 (1406)
T KOG1146|consen  702 SPRDKLLRLTILPEAAMILGRAYMQD--NSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ  764 (1406)
T ss_pred             CcccccCcccccHHHHhhhhhcccCC--CCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence            45667888999999999999999999  6899999999999999999999999999999999865

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=90.31  E-value=1.3  Score=31.98  Aligned_cols=52  Identities=13%  Similarity=0.076  Sum_probs=41.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ...+++.|+.+|... ...   +    ...+||..+|++...|+.|-++.+.|.|+....
T Consensus         4 ~~~Lt~rqreVL~lr-~~G---l----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          4 ESFLTERQIEVLRLR-ERG---L----TQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             ccCCCHHHHHHHHHH-HcC---C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            457899999999874 333   1    356899999999999999999988888886543

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=88.17  E-value=1.5  Score=32.58  Aligned_cols=31  Identities=6%  Similarity=0.179  Sum_probs=26.9

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...+||..+|++...|+++...-|.+.|+..
T Consensus       160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l  190 (194)
T PRK09646        160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCL  190 (194)
T ss_pred             CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence            5778999999999999999988888887754

>PRK00118 putative DNA-binding protein; Validated

Probab=88.12  E-value=2.6  Score=28.77  Aligned_cols=50  Identities=6%  Similarity=0.002  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .++..|..++...|... .      ...+||..+|++...|..|....|.+.|+...
T Consensus        17 ~L~ekqRevl~L~y~eg-~------S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~   66 (104)
T PRK00118         17 LLTEKQRNYMELYYLDD-Y------SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE   66 (104)
T ss_pred             cCCHHHHHHHHHHHHcC-C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            45677777776665554 2      46779999999999999999988888887643

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=87.62  E-value=2  Score=30.89  Aligned_cols=49  Identities=12%  Similarity=0.045  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+++.+..+|...|-..       .....||..+|++...|+.|...-+.+.|+..
T Consensus       128 ~L~~~~r~vl~l~~~~~-------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  176 (182)
T PRK09652        128 SLPEELRTAITLREIEG-------LSYEEIAEIMGCPIGTVRSRIFRAREALRAKL  176 (182)
T ss_pred             hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            45566666666554333       24668899999999999999987777777654

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

Probab=87.19  E-value=1.1  Score=26.77  Aligned_cols=41  Identities=20%  Similarity=0.106  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHHHhhcCCC--CCCHHHHHHHHHHhCCCchhhhhh
Q psy10851         13 RLLNLKVKLKTSFNSCCPG--HKTTQVREALAKDTGLSVRVVQVW   55 (159)
Q Consensus        13 ~s~~Q~~~Le~~F~~~~~~--yp~~~~r~~La~~l~l~~~~V~vW   55 (159)
                      +|..|+.+|...|...  .  +|.......||..+|++...|..-
T Consensus         1 LT~~Q~e~L~~A~~~G--Yfd~PR~~tl~elA~~lgis~st~~~~   43 (53)
T PF04967_consen    1 LTDRQREILKAAYELG--YFDVPRRITLEELAEELGISKSTVSEH   43 (53)
T ss_pred             CCHHHHHHHHHHHHcC--CCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence            5789999999998765  1  366678889999999998766543

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=86.92  E-value=1.8  Score=30.58  Aligned_cols=46  Identities=15%  Similarity=0.089  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      +++.+..++...|-..       ....+||..+|++...|++|...-|.+.|+
T Consensus       107 L~~~~r~ii~l~~~~~-------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~  152 (154)
T PRK06759        107 LDEKEKYIIFERFFVG-------KTMGEIALETEMTYYQVRWIYRQALEKMRN  152 (154)
T ss_pred             CCHHHHHHHHHHHhcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence            4455555554444333       347889999999999999999877777665

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=86.69  E-value=2  Score=32.25  Aligned_cols=32  Identities=22%  Similarity=0.216  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ....+||..+|++...|+++...-|.+.|+..
T Consensus       170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  201 (206)
T PRK12526        170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM  201 (206)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            35778999999999999999988888877754

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=86.33  E-value=3  Score=29.95  Aligned_cols=33  Identities=15%  Similarity=0.206  Sum_probs=27.7

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ...+||..+|++...|++|.+--|.+.|+....
T Consensus       126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~  158 (165)
T PRK09644        126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE  158 (165)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            467899999999999999998888888776443

>KOG1832|consensus

Probab=85.55  E-value=0.26  Score=45.31  Aligned_cols=21  Identities=29%  Similarity=0.246  Sum_probs=8.6

Q ss_pred             CCccccccccCCCCCcchhhh
Q psy10851        119 SSSVLKIGYELGFFIQEEEEE  139 (159)
Q Consensus       119 ~s~~~~~~~~~~~~~~ee~ee  139 (159)
                      +.-..-+|-.-.-.++.++||
T Consensus      1391 ~~r~yEIGR~r~~~dd~Deee 1411 (1516)
T KOG1832|consen 1391 SARMYEIGRRRPTDDDSDEEE 1411 (1516)
T ss_pred             hhhhhhhcccCCCccccCccc
Confidence            344444444444344433333

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=85.53  E-value=3.1  Score=29.61  Aligned_cols=31  Identities=19%  Similarity=0.208  Sum_probs=26.6

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...+||..+|++...|++.+..-|.+.|+..
T Consensus       124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  154 (160)
T PRK09642        124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW  154 (160)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999988888877754

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

Probab=85.30  E-value=2.8  Score=24.88  Aligned_cols=46  Identities=13%  Similarity=0.050  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .||..++.+|.-+..-.        ...++|..+|++.+.|..+..+=+.|..-
T Consensus         3 ~LT~~E~~vl~~l~~G~--------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    3 SLTERELEVLRLLAQGM--------SNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             SS-HHHHHHHHHHHTTS---------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             ccCHHHHHHHHHHHhcC--------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            57888999887765433        47789999999999999998887777543

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

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=85.28  E-value=3.3  Score=29.64  Aligned_cols=32  Identities=16%  Similarity=0.239  Sum_probs=27.0

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ...+||..+|++...|+.|..--|.|.|+.-.
T Consensus       143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~  174 (179)
T PRK11924        143 SYREIAEILGVPVGTVKSRLRRARQLLRECLE  174 (179)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999888888776543

>PRK04217 hypothetical protein; Provisional

Probab=85.11  E-value=3.5  Score=28.37  Aligned_cols=51  Identities=16%  Similarity=0.041  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ..++..++.++...|...   +    ...+||+.+|++...|...+...+.+.|....
T Consensus        41 ~~Lt~eereai~l~~~eG---l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~   91 (110)
T PRK04217         41 IFMTYEEFEALRLVDYEG---L----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV   91 (110)
T ss_pred             ccCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            367888888887766544   2    57789999999999999999888887776543

>PRK06930 positive control sigma-like factor; Validated

Probab=84.98  E-value=3.7  Score=30.37  Aligned_cols=50  Identities=10%  Similarity=-0.034  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .+++.+..++...|...       ....+||..+|++...|+++...-+.|.++...
T Consensus       114 ~L~~rer~V~~L~~~eg-------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~  163 (170)
T PRK06930        114 VLTEREKEVYLMHRGYG-------LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN  163 (170)
T ss_pred             hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            45666666666654433       246789999999999999999988888887644

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=84.71  E-value=3.9  Score=29.16  Aligned_cols=48  Identities=19%  Similarity=0.165  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ++..+..+|...| ..       ....+||..+|++...|+++...-|.+.|+...
T Consensus       113 L~~~~r~il~l~~-~g-------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~  160 (166)
T PRK09639        113 MTERDRTVLLLRF-SG-------YSYKEIAEALGIKESSVGTTLARAKKKFRKIYE  160 (166)
T ss_pred             CCHHHHHHHHHHH-cC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            4444555555444 22       356789999999999999999888888877644

>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production

Probab=84.20  E-value=2.7  Score=27.97  Aligned_cols=39  Identities=21%  Similarity=0.315  Sum_probs=21.6

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHh
Q psy10851         18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ   72 (159)
Q Consensus        18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~   72 (159)
                      +.+.+-+|..| | ||...--.. |.             .|||.+||+.+.+...
T Consensus        14 vRiIk~Lyqsn-P-yP~~~GTr~-aR-------------RnRRRRWR~rq~QI~~   52 (91)
T PF00424_consen   14 VRIIKILYQSN-P-YPSPEGTRQ-AR-------------RNRRRRWRARQRQIRA   52 (91)
T ss_dssp             HHHHHHHHHTS---S--S-S-HH-HH-------------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccc-c-CCCCCCccc-cc-------------cchhhhHHHHHHHHHH
Confidence            34555668777 9 997441111 11             7999999998765443

It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=84.08  E-value=3  Score=28.56  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+++.+..++...|-..       .....||..+|++...|..|.+.-+.|.|+
T Consensus       110 ~L~~~~~~ii~~~~~~g-------~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~  156 (158)
T TIGR02937       110 KLPEREREVLVLRYLEG-------LSYKEIAEILGISVGTVKRRLKRARKKLRE  156 (158)
T ss_pred             hCCHHHHHHHhhHHhcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            45566666665443322       246689999999999999999877777665

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=84.02  E-value=2.4  Score=31.28  Aligned_cols=36  Identities=14%  Similarity=0.196  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      |.......+||..+|++...|++|+..-|.+.|+..
T Consensus       154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  189 (194)
T PRK12519        154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL  189 (194)
T ss_pred             hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            334446788999999999999999988888877753

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=83.81  E-value=3.4  Score=30.19  Aligned_cols=32  Identities=19%  Similarity=0.099  Sum_probs=27.5

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ...+||..+|++...|++++..-|.+.|+...
T Consensus       149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~  180 (184)
T PRK12512        149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR  180 (184)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence            56789999999999999999988888887543

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=83.69  E-value=3.6  Score=28.87  Aligned_cols=29  Identities=21%  Similarity=0.417  Sum_probs=24.1

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ...+||..+|++...|+++...-|.|.|+
T Consensus       131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~  159 (161)
T TIGR02985       131 SYKEIAEELGISVKTVEYHISKALKELRK  159 (161)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            46778999999999999998777777665

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger

Probab=83.62  E-value=0.45  Score=44.05  Aligned_cols=12  Identities=17%  Similarity=0.725  Sum_probs=6.4

Q ss_pred             hhhhhhhhhHHH
Q psy10851         50 RVVQVWFQNQRA   61 (159)
Q Consensus        50 ~~V~vWFqNRR~   61 (159)
                      ++|+.|+..+..
T Consensus       606 ~~i~~~~~~~~~  617 (1096)
T TIGR00927       606 KQIELWVKEQLS  617 (1096)
T ss_pred             HHHHHHHHHhhh
Confidence            556666654433

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=83.60  E-value=4.7  Score=29.78  Aligned_cols=33  Identities=12%  Similarity=0.228  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ....+||..+|++...|+++...-|.+.|+...
T Consensus       151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~  183 (189)
T PRK12530        151 LSSEQICQECDISTSNLHVLLYRARLQLQACLS  183 (189)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            357889999999999999999888877777543

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=83.43  E-value=3.9  Score=29.71  Aligned_cols=30  Identities=13%  Similarity=0.407  Sum_probs=26.2

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...+||..+|++...|+++.+.-|.+.|+.
T Consensus       147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  176 (179)
T PRK12514        147 SYKELAERHDVPLNTMRTWLRRSLLKLREC  176 (179)
T ss_pred             CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence            477899999999999999998888887765

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=83.15  E-value=4  Score=29.67  Aligned_cols=30  Identities=30%  Similarity=0.278  Sum_probs=26.0

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...+||..+|++...|++....-|.+.|+.
T Consensus       152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  181 (183)
T TIGR02999       152 TVEEIAELLGVSVRTVERDWRFARAWLADE  181 (183)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999998888877764

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=83.03  E-value=3.6  Score=29.12  Aligned_cols=30  Identities=23%  Similarity=0.283  Sum_probs=24.1

Q ss_pred             HHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         36 QVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ....+||..+|++...|+++...-|.+.|.
T Consensus       128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~  157 (159)
T TIGR02989       128 VSLTALAEQLGRTVNAVYKALSRLRVRLRD  157 (159)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence            357789999999999999998766666554

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=83.02  E-value=3.1  Score=30.37  Aligned_cols=35  Identities=14%  Similarity=0.018  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         33 KTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        33 p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .......+||..+|++...|+++...-|.+.|+..
T Consensus       152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l  186 (190)
T TIGR02939       152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL  186 (190)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            33345788999999999999999987777777654

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=83.01  E-value=4  Score=29.89  Aligned_cols=32  Identities=13%  Similarity=0.104  Sum_probs=26.9

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ...+||..+|++...|+++...-|.+.|+...
T Consensus       146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~  177 (186)
T PRK05602        146 SNIEAAAVMDISVDALESLLARGRRALRAQLA  177 (186)
T ss_pred             CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999888888777544

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=82.95  E-value=1.8  Score=24.48  Aligned_cols=41  Identities=12%  Similarity=0.008  Sum_probs=21.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ   57 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq   57 (159)
                      .+.+|..+...+..++... .      -...||..+|.+...|..|.+
T Consensus         2 ~~~Lt~~eR~~I~~l~~~G-~------s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen    2 YKHLTPEERNQIEALLEQG-M------SIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             ----------HHHHHHCS----------HHHHHHHTT--HHHHHHHHH
T ss_pred             ccchhhhHHHHHHHHHHcC-C------CHHHHHHHHCcCcHHHHHHHh
Confidence            3568888888888887655 2      466799999999999988864

>KOG3755|consensus

Probab=82.84  E-value=0.53  Score=41.31  Aligned_cols=45  Identities=13%  Similarity=0.158  Sum_probs=30.8

Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHhC-------CCchhhhhhhhhHHHHHHHHHH
Q psy10851         22 KTSFNSCCPGHKTTQVREALAKDTG-------LSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        22 e~~F~~~~~~yp~~~~r~~La~~l~-------l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      +.+|.++ . .++.....+.-..+.       ...+.|+.||+|||.++++.+.
T Consensus       708 ~~w~~k~-~-s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~  759 (769)
T KOG3755|consen  708 HHWKLKT-R-SGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM  759 (769)
T ss_pred             hhheecc-c-CchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence            4456666 3 677666655544443       3456799999999999998644

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=82.66  E-value=5  Score=29.48  Aligned_cols=32  Identities=16%  Similarity=0.249  Sum_probs=27.4

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ...+||..+|++...|++-+..-|.+.|+...
T Consensus       149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  180 (189)
T PRK12515        149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK  180 (189)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999888888887644

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=82.62  E-value=6  Score=28.81  Aligned_cols=34  Identities=12%  Similarity=0.202  Sum_probs=29.4

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA   70 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~   70 (159)
                      ...+||..+|++...|++....-|++.|+.-...
T Consensus       135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  168 (179)
T PRK12543        135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE  168 (179)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            5778999999999999999999999998875543

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=82.51  E-value=3.4  Score=30.11  Aligned_cols=33  Identities=15%  Similarity=0.180  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         35 TQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        35 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .....+||..+|++...|+++++.-|.+.|+..
T Consensus       152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l  184 (187)
T TIGR02948       152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQL  184 (187)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            345778999999999999999988888777643

This sigma factor is restricted to certain lineages of the order Bacillales.

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=82.26  E-value=6  Score=29.22  Aligned_cols=34  Identities=9%  Similarity=0.204  Sum_probs=28.7

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA   70 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~   70 (159)
                      ...+||..+|++...|++....-|.+.|+.....
T Consensus       154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~  187 (195)
T PRK12532        154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK  187 (195)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999988888888875433

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=82.08  E-value=5.8  Score=28.07  Aligned_cols=31  Identities=16%  Similarity=0.042  Sum_probs=25.6

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...+||..+|++...|++....-|.+.|+..
T Consensus       124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l  154 (161)
T PRK09047        124 DVAETAAAMGCSEGSVKTHCSRATHALAKAL  154 (161)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999887777777654

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=81.26  E-value=3.5  Score=33.62  Aligned_cols=54  Identities=15%  Similarity=0.110  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .++..|..+|...|-..   |-......+||..+|++...|+.+...-+.|.|+...
T Consensus       262 ~L~~~~R~vl~lrygL~---~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~  315 (325)
T PRK05657        262 ELNDKQREVLARRFGLL---GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ  315 (325)
T ss_pred             cCCHHHHHHHHHHhccC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            56777777777766433   3444567899999999999999999888888887643

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

Probab=80.99  E-value=5  Score=19.94  Aligned_cols=39  Identities=8%  Similarity=0.045  Sum_probs=27.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWF   56 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWF   56 (159)
                      ..++..+...+...|...   +    ....+|..+|++...|..|.
T Consensus         4 ~~~~~~~~~~i~~~~~~~---~----s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           4 PKLTPEQIEEARRLLAAG---E----SVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CcCCHHHHHHHHHHHHcC---C----CHHHHHHHHCCCHHHHHHhC
Confidence            346677766666666533   3    45678899999999888874

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

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=80.98  E-value=6.6  Score=28.42  Aligned_cols=50  Identities=16%  Similarity=0.147  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .+++.+..+|...|-..       ....+||..+|++...|+++.+--|.+.|+...
T Consensus       100 ~L~~~~r~v~~l~~~~g-------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  149 (170)
T TIGR02959       100 ELPDEYREAIRLTELEG-------LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE  149 (170)
T ss_pred             hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555544333       246789999999999999999877777777544

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=80.78  E-value=4  Score=28.24  Aligned_cols=43  Identities=16%  Similarity=0.291  Sum_probs=30.3

Q ss_pred             CCCCCCCHHHHH-HHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851          8 NFQTIRLLNLKV-KLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ   57 (159)
Q Consensus         8 r~Rt~~s~~Q~~-~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq   57 (159)
                      ++|.+||.+... ++...+...       .....||..+|++..+|..|.+
T Consensus         8 ~~rr~ys~EfK~~aV~~~~~~g-------~sv~evA~e~gIs~~tl~~W~r   51 (121)
T PRK09413          8 EKRRRRTTQEKIAIVQQSFEPG-------MTVSLVARQHGVAASQLFLWRK   51 (121)
T ss_pred             CCCCCCCHHHHHHHHHHHHcCC-------CCHHHHHHHHCcCHHHHHHHHH
Confidence            456778888854 444444322       2467789999999999999953

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=80.62  E-value=5.3  Score=29.30  Aligned_cols=31  Identities=19%  Similarity=0.157  Sum_probs=25.7

Q ss_pred             HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ....+||..+|++...|+++...-|.+.|+.
T Consensus       156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  186 (189)
T PRK09648        156 LSAEETAEAVGSTPGAVRVAQHRALARLRAE  186 (189)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3578899999999999999997777777664

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=80.19  E-value=5.7  Score=29.03  Aligned_cols=30  Identities=13%  Similarity=0.402  Sum_probs=25.5

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...+||..+|++...|++|...-|.+.|+.
T Consensus       151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  180 (182)
T PRK12537        151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC  180 (182)
T ss_pred             CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence            467899999999999999998777777654

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=80.18  E-value=4.3  Score=29.96  Aligned_cols=38  Identities=13%  Similarity=0.143  Sum_probs=31.1

Q ss_pred             CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851         32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus        32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      |.......+||..+|++...|+++...-|.+.|+....
T Consensus       144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34444678899999999999999999888888887554

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=80.12  E-value=4.5  Score=28.82  Aligned_cols=30  Identities=30%  Similarity=0.390  Sum_probs=25.0

Q ss_pred             HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...+||..+|++...|+++...-|.+.|+.
T Consensus       130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541        130 SYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            467889999999999999988777776653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	159
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.89
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.89
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.88
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.88
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.88
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.88
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.88
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.88
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.88
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.88
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.88
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.88
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.88
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.88
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.88
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.88
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.87
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.87
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.87
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.87
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.87
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.87
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.87
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.87
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.87
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.87
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.86
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.86
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.86
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.86
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.86
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.86
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.86
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.86
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.86
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.86
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.86
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.86
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.85
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.85
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.85
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.85
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.85
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.85
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.85
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.85
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.85
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.85
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.85
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.84
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.84
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.83
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.83
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.83
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.83
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.83
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.83
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.83
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.82
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.82
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.82
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.81
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.81
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.81
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.81
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.79
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.79
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.79
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.78
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.78
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.77
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.76
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.68
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.68
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.67
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.61
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.52
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	99.1
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.68
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.77
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	92.11
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	91.79
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	91.38
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	90.94
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	90.02
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	89.58
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	89.02
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	88.66
3c57_A	95	Two component transcriptional regulatory protein;	88.22
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	88.19
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	87.72
3lph_A	72	Protein REV; helix-loop-helix, RNA-binding arginin	86.26
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	86.1
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	85.82
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	85.82
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	85.61
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	85.21
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	85.2
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	84.27
2x7l_M	115	HIV REV; nuclear export, immune system, post-trans	84.16
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	84.15
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	84.0
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	82.85
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	81.73

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

Probab=99.89  E-value=5e-23  Score=134.01  Aligned_cols=70  Identities=26%  Similarity=0.261  Sum_probs=63.8

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhcC
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEG   75 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~~   75 (159)
                      ...||.|++||..|+.+|+.+|..+ + ||+..++..||..|||++.+|+|||||||+|+|+..........
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~~~~   74 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERT-H-YPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRRQ   74 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhcc-C-CCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhccCC
Confidence            3568899999999999999999999 6 99999999999999999999999999999999998776655443

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

Probab=99.89  E-value=4.6e-23  Score=126.23  Aligned_cols=57  Identities=25%  Similarity=0.339  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ||+|++||..|+.+|+..|..+ + ||+..++..||..+||++.+|+|||||||+|+||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQK-Q-YLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            6899999999999999999999 6 9999999999999999999999999999999997

>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=99.88  E-value=3.2e-23  Score=128.27  Aligned_cols=59  Identities=31%  Similarity=0.423  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ..||+|++||..|+.+|+..|..+ + ||+..++..||..+||+..+|+|||||||+|+||
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFNEN-R-YLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcc-C-CCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            358899999999999999999999 6 9999999999999999999999999999999997

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

Probab=99.88  E-value=5.2e-23  Score=128.11  Aligned_cols=59  Identities=27%  Similarity=0.280  Sum_probs=55.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .||.|++||..|+.+|+..|..+ + ||+..++..||..|||++.+|+|||||||+|+||.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFN-K-YISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            57899999999999999999999 6 99999999999999999999999999999999985

>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=99.88  E-value=7.6e-23  Score=133.09  Aligned_cols=63  Identities=30%  Similarity=0.347  Sum_probs=59.5

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ...||.||+||..|+.+|+.+|..+ + ||+..++..||..|||++.+|+|||||||+|+||...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAIN-H-NPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL   67 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHH
Confidence            4578999999999999999999999 6 9999999999999999999999999999999999754

>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=99.88  E-value=1.4e-22  Score=131.00  Aligned_cols=64  Identities=25%  Similarity=0.279  Sum_probs=59.7

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      .+.||.|++||..|+.+|+..|..+ + ||+..++..||..|||++.+|+|||||||+|+|+....
T Consensus         7 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQTYELERRFRQQ-R-YLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhhc-C-CCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            4568899999999999999999999 6 99999999999999999999999999999999997553

>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=99.88  E-value=1.8e-22  Score=130.45  Aligned_cols=65  Identities=28%  Similarity=0.312  Sum_probs=60.7

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ....||+|++||..|+.+|+..|..+ + ||+..++..||..|||++.+|+|||||||+|+|+....
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFN-M-YLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhcc-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            35578899999999999999999999 6 99999999999999999999999999999999998654

>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=99.88  E-value=5.5e-23  Score=133.82  Aligned_cols=62  Identities=29%  Similarity=0.257  Sum_probs=58.7

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ..+.||.||+||..|+.+|+.+|..+ + ||+..+|..||..|||++.+|+|||||||+|+||.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQ-K-YLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            45678899999999999999999999 6 99999999999999999999999999999999984

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

Probab=99.88  E-value=3.4e-23  Score=134.78  Aligned_cols=62  Identities=27%  Similarity=0.234  Sum_probs=58.8

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...||+|++||..|+.+|+.+|..+ + ||+..++..||..|||++.+|+|||||||+|+|+..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~   66 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKT-R-YPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQ   66 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcc-C-CCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHH
Confidence            4678999999999999999999999 7 999999999999999999999999999999999853

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

Probab=99.88  E-value=1e-22  Score=125.53  Aligned_cols=59  Identities=25%  Similarity=0.336  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .||.|++||..|+.+|+..|..+ + ||+..++..||..+||+..+|++||||||+|+|++
T Consensus         1 ~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            1 VRRYRTAFTRDQLGRLEKEFYKE-N-YVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            37899999999999999999999 6 99999999999999999999999999999999984

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

Probab=99.88  E-value=1.4e-22  Score=128.62  Aligned_cols=61  Identities=28%  Similarity=0.322  Sum_probs=58.1

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...||+|++||..|+.+|+.+|..+ + ||+..++..||..|||++.+|+|||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQET-K-YPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS   65 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcc-C-CCCHHHHHHHHHHHCCCHHHeehcccccccccccc
Confidence            4568899999999999999999999 7 99999999999999999999999999999999985

>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=99.88  E-value=5.1e-23  Score=129.27  Aligned_cols=61  Identities=34%  Similarity=0.476  Sum_probs=58.1

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ++.||+||+||..|+.+|+.+|..+ + ||+..++..||..+||+..+|+|||||||+|+|+.
T Consensus         1 ~k~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A            1 MKTTRVRTVLNEKQLHTLRTCYAAN-P-RPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCCSCCCCCCSHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            4678999999999999999999999 7 99999999999999999999999999999999874

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

Probab=99.88  E-value=1.4e-22  Score=128.00  Aligned_cols=62  Identities=19%  Similarity=0.218  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      .||.||+||..|+.+|+..|..+ + ||+..++..||..|||+..+|+|||||||+|+|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQG-R-YLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            47899999999999999999999 6 99999999999999999999999999999999997653

>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=99.88  E-value=1.7e-22  Score=131.77  Aligned_cols=63  Identities=29%  Similarity=0.357  Sum_probs=59.1

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .+.||.|++||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+|+...
T Consensus        16 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           16 RKQRRSRTTFSASQLDELERAFERT-Q-YPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             -CCCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            4578899999999999999999999 6 9999999999999999999999999999999999764

>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=99.88  E-value=9.4e-23  Score=128.81  Aligned_cols=60  Identities=25%  Similarity=0.311  Sum_probs=57.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .||.|++||..|+..|+..|..+ + ||+..++..||..+||++++|+|||||||+|+|+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFN-R-YLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHC-S-SCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccC-C-CCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            47899999999999999999999 6 999999999999999999999999999999999964

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

Probab=99.88  E-value=3.2e-23  Score=128.64  Aligned_cols=59  Identities=31%  Similarity=0.335  Sum_probs=52.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .||+||+||..|+.+|+..|..+ + ||+..++..||..+||++.+|+|||||||+|+|+.
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQ-K-YLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            57899999999999999999999 6 99999999999999999999999999999999974

>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=99.87  E-value=6.7e-23  Score=130.18  Aligned_cols=61  Identities=25%  Similarity=0.272  Sum_probs=58.1

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...||+|++||..|+.+|+..|..+ + ||+..++..||..|||++.+|+|||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAAN-K-FITKDKRRKISAATSLSERQITIWFQNRRVKEKKS   65 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhccc
Confidence            4578999999999999999999999 7 99999999999999999999999999999999984

>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=99.87  E-value=9.9e-23  Score=132.49  Aligned_cols=62  Identities=29%  Similarity=0.356  Sum_probs=58.8

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      +.+.||.||+||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+||.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLD-S-NPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHC-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            45678899999999999999999999 7 99999999999999999999999999999999984

>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=99.87  E-value=2.2e-22  Score=127.76  Aligned_cols=62  Identities=29%  Similarity=0.289  Sum_probs=58.4

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...||+|++||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+|+..
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQ-K-YLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcC-C-CcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            3468899999999999999999999 7 999999999999999999999999999999999863

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

Probab=99.87  E-value=2.3e-22  Score=126.99  Aligned_cols=60  Identities=27%  Similarity=0.318  Sum_probs=57.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .||.|++||..|+.+|+..|..+ + ||+..++..||..|||++.+|+|||||||+|+|+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~   61 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQ-K-YLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHS-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCccCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhh
Confidence            57899999999999999999999 6 999999999999999999999999999999999864

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

Probab=99.87  E-value=1.2e-22  Score=135.76  Aligned_cols=66  Identities=21%  Similarity=0.240  Sum_probs=60.5

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      ...||+||+||..|+..|+..|..+ + ||+..+|..||..|||++++|+|||||||+|+|+......
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           15 PKRKKPRTSFTRIQVAELEKRFHKQ-K-YLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHcC-C-CcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            4578899999999999999999999 6 9999999999999999999999999999999999765433

>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=99.87  E-value=1.2e-22  Score=128.87  Aligned_cols=62  Identities=18%  Similarity=0.195  Sum_probs=58.6

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ....||+|++||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+|+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDIN-N-SPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS   65 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHC-S-SCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhh
Confidence            34678999999999999999999999 6 99999999999999999999999999999999984

>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=99.87  E-value=1.4e-22  Score=128.64  Aligned_cols=61  Identities=26%  Similarity=0.213  Sum_probs=58.1

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...||+|++||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+||.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDAN-A-YPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS   65 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcC-C-CcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhc
Confidence            4578899999999999999999999 6 99999999999999999999999999999999974

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

Probab=99.87  E-value=2.1e-22  Score=128.86  Aligned_cols=61  Identities=26%  Similarity=0.303  Sum_probs=58.0

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...||+|++||..|+.+|+..|..+ + ||+..++..||..+||++.+|+|||||||+|+|+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATN-K-FITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHT-S-CCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhC-C-CcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            3568899999999999999999999 7 99999999999999999999999999999999984

>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=99.87  E-value=3.6e-22  Score=127.99  Aligned_cols=60  Identities=23%  Similarity=0.267  Sum_probs=56.1

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ..|++||..|+.+|+..|..+ + ||+..+|.+||..|||+++||+|||||||+|+|+....
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~-~-YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~   64 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQC-Q-WARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHH
Confidence            467889999999999999999 7 99999999999999999999999999999999986544

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

Probab=99.87  E-value=1.8e-22  Score=132.49  Aligned_cols=62  Identities=27%  Similarity=0.254  Sum_probs=58.5

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ....||.||+||..|+.+|+.+|..+ + ||+..+|..||..|||++.+|+|||||||+|+||.
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   80 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQRQ-K-YLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW   80 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHHS-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence            34678899999999999999999999 6 99999999999999999999999999999999985

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

Probab=99.86  E-value=1.4e-22  Score=128.67  Aligned_cols=61  Identities=30%  Similarity=0.330  Sum_probs=57.9

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...||+|++||..|+.+|+.+|..+ + ||+..++..||..|||++.+|+|||||||+|+||.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKT-Q-YLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS   65 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCC-C-CCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhccc
Confidence            4578999999999999999999999 6 99999999999999999999999999999999874

>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=99.86  E-value=5.5e-22  Score=126.59  Aligned_cols=59  Identities=19%  Similarity=0.258  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNS-CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~-~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .++|++||..|+.+|+..|.. + + ||+..++..||..|||++++|+|||||||+|+|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVN-K-HPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccC-C-CCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            578999999999999999996 8 7 999999999999999999999999999999999965

>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=99.86  E-value=1.5e-22  Score=127.86  Aligned_cols=62  Identities=27%  Similarity=0.303  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ..||.|++||..|+.+|+..|..+ + ||+..++..||..|||++.+|+|||||||+|+|+...
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRN-R-YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTC-S-SCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcc-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            358899999999999999999999 6 9999999999999999999999999999999998654

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

Probab=99.86  E-value=5.8e-22  Score=126.80  Aligned_cols=59  Identities=19%  Similarity=0.252  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNS-CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~-~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      +++|++||..|+.+|+..|.. + + ||+..++..||..+||++++|+|||||||+|+|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~-~-yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVN-K-HPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTT-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            578999999999999999995 8 6 999999999999999999999999999999999965

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

Probab=99.86  E-value=3.5e-22  Score=125.75  Aligned_cols=59  Identities=29%  Similarity=0.338  Sum_probs=56.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .||+|++||..|+.+|+..|..+ + ||+..++..||..+||+..+|+|||||||+|+|+.
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVN-C-YPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS   59 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCS
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHh
Confidence            37899999999999999999999 7 99999999999999999999999999999999985

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

Probab=99.86  E-value=3.5e-22  Score=122.12  Aligned_cols=57  Identities=25%  Similarity=0.296  Sum_probs=54.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      .||.|++||..|+.+|+..|..+ + ||+..++..||..+||+..+|+|||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQ-R-YLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            47899999999999999999999 6 999999999999999999999999999999975

>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=99.86  E-value=9e-23  Score=132.79  Aligned_cols=60  Identities=15%  Similarity=0.235  Sum_probs=56.6

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhh----cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNS----CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~----~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ...||+||+||..|+..|+.+|..    + + ||+..+|..||..|||++++|+|||||||+|+|+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~-~-yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRI-Q-RQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCC-C-TTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcC-C-CcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            357889999999999999999999    8 6 9999999999999999999999999999999874

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

Probab=99.86  E-value=3.2e-22  Score=123.33  Aligned_cols=57  Identities=32%  Similarity=0.378  Sum_probs=50.4

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .|++||..|+.+|+..|..+ + ||+..++..||..+||++++|++||||||+|+|+..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRT-H-YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcC-C-CcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            58999999999999999999 6 999999999999999999999999999999999865

>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=99.86  E-value=5e-22  Score=129.58  Aligned_cols=60  Identities=25%  Similarity=0.347  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ..||.||+||..|+.+|+..|..+ + ||+..+|..||..|||++++|+|||||||+|+||.
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEFHTN-H-YLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCcccCHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            467899999999999999999999 6 99999999999999999999999999999999985

>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=99.86  E-value=4.2e-22  Score=123.15  Aligned_cols=58  Identities=22%  Similarity=0.292  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      +.||.|++||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+|
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f~~~-~-yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVFRRK-Q-SLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             --------CCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhC-C-CcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            467899999999999999999999 7 999999999999999999999999999999986

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

Probab=99.86  E-value=7.7e-22  Score=120.00  Aligned_cols=54  Identities=28%  Similarity=0.332  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      |.||..|+..|+..|..+ + ||+..+|..||..+||++++|+|||||||+|+||+
T Consensus         2 T~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQ-K-YLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhc-C-CcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            689999999999999999 6 99999999999999999999999999999999985

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

Probab=99.86  E-value=4e-22  Score=131.81  Aligned_cols=56  Identities=18%  Similarity=0.216  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ..+||..|+.+|+..|..+ + ||+..+|.+||..|||+++||+|||||||+|||+..
T Consensus        15 ~k~~t~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           15 FKEKTAEQLRVLQASFLNS-S-VLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             hccCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            3489999999999999999 6 999999999999999999999999999999999854

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

Probab=99.85  E-value=7.9e-22  Score=130.52  Aligned_cols=60  Identities=27%  Similarity=0.310  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ..||.||+||..|+.+|+..|..+ + ||+..+|..||..|||++++|+|||||||+|+||.
T Consensus        27 ~~rr~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           27 ETKRQRTSYTRYQTLELEKEFHFN-R-YLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcc-C-CCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            468899999999999999999999 6 99999999999999999999999999999999984

>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=99.85  E-value=4.6e-22  Score=131.31  Aligned_cols=63  Identities=29%  Similarity=0.342  Sum_probs=57.7

Q ss_pred             CCCCCCCCHHHHHHHHHHH---hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSF---NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F---~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      ||+|++|+..|+.+|+.+|   ..+ + ||+..++..||..|||+..||+|||||||+|+|+......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~-~-yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   67 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSN-P-YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTS-C-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccC-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccccc
Confidence            7899999999999999999   778 7 9999999999999999999999999999999999754433

>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=99.85  E-value=1.1e-21  Score=132.09  Aligned_cols=62  Identities=26%  Similarity=0.284  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ..||+||+||..|+.+|+..|..+ + ||+..+|..||..|||++++|+|||||||+|+|+...
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   94 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEFHFN-K-YLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   94 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCcCHHHHHHHHHHHhcc-C-CCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhc
Confidence            457889999999999999999999 6 9999999999999999999999999999999999753

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

Probab=99.85  E-value=1.2e-21  Score=125.71  Aligned_cols=62  Identities=32%  Similarity=0.295  Sum_probs=58.3

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+.||.|++||..|+.+|+..|..+ + ||+..++..||..|||+..+|+|||||||+|+||..
T Consensus         7 ~~~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   68 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQLEELEKVFQKT-H-YPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE   68 (75)
T ss_dssp             SCCCSCSCSSCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHH
Confidence            4568889999999999999999999 6 999999999999999999999999999999999853

>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=99.85  E-value=1.9e-21  Score=124.37  Aligned_cols=60  Identities=28%  Similarity=0.346  Sum_probs=56.7

Q ss_pred             CCCCCCCCHHHHHHHHHHH---hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSF---NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F---~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ||+|++||..|+.+|+.+|   ..+ + ||+..++..||..+||+..+|+|||||||+|+|+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~-~-yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   64 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSN-P-YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTS-C-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccC-C-CcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccc
Confidence            7899999999999999999   788 7 9999999999999999999999999999999998543

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

Probab=99.85  E-value=1.4e-21  Score=125.30  Aligned_cols=59  Identities=19%  Similarity=0.218  Sum_probs=56.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      -++.|+.||..|+.+|+..|..+ + ||+..++..||..+||+..+|+|||||||+|+||.
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   64 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKN-Q-FPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNS   64 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhh
Confidence            57899999999999999999999 6 99999999999999999999999999999999985

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

Probab=99.85  E-value=1e-21  Score=127.77  Aligned_cols=63  Identities=17%  Similarity=0.155  Sum_probs=57.9

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcC---CCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCC---PGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~---~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ....||.||+||..|+.+|+.+|..++   + ||+..+|..||..|||++.+|+|||||||+|+|+.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~-yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLG-SVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCS-HHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCC-CcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            346788999999999999999997652   7 99999999999999999999999999999999983

>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=99.85  E-value=2.3e-22  Score=130.80  Aligned_cols=59  Identities=19%  Similarity=0.298  Sum_probs=55.4

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhh-----cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNS-----CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~-----~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ...||.||+||..|+..|+ .|..     + + ||+..+|..||..|||++++|+|||||||+|+|+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~-~-yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           15 GTTKRFRTKFTAEQKEKML-AFAERLGWRI-Q-KHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHH-HHHHHHTSCC-C-SSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCccCCHHHHHHHH-HHHHHcCcCC-C-CCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            4578899999999999999 7999     8 6 9999999999999999999999999999999875

>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=99.85  E-value=3.7e-21  Score=123.03  Aligned_cols=61  Identities=18%  Similarity=0.220  Sum_probs=57.6

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNS---CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~---~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ...||+|++|+..|+.+|+.+|..   + + ||+..++..||..+||+..||+|||||||+|+|+.
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~-~-yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGH-P-YPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTS-C-CCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCC-C-CCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            457889999999999999999987   7 8 99999999999999999999999999999999985

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

Probab=99.85  E-value=2.4e-21  Score=129.97  Aligned_cols=64  Identities=17%  Similarity=0.172  Sum_probs=60.1

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC---------------CCchhhhhhhhhHHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG---------------LSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~---------------l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .+.||.|++|+..|+.+|+.+|..+ + ||+..+|..||..||               |+..+|+|||||||+|+|+...
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~-~-yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNEN-Q-YPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            4678899999999999999999999 7 999999999999999               9999999999999999999765


Q ss_pred             H
Q psy10851         69 K   69 (159)
Q Consensus        69 ~   69 (159)
                      .
T Consensus        83 ~   83 (95)
T 2cuf_A           83 I   83 (95)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.85  E-value=2.5e-21  Score=124.47  Aligned_cols=61  Identities=20%  Similarity=0.251  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...++|++||..|+.+|+..|..+ + ||+..+|..||..|||+.++|+|||||||+|+|+..
T Consensus         6 ~~~~kr~~~t~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            6 SGPTKYKERAPEQLRALESSFAQN-P-LPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             CSSCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHhcc-C-CCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            345678899999999999999999 6 999999999999999999999999999999999853

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

Probab=99.84  E-value=1.3e-21  Score=131.46  Aligned_cols=65  Identities=20%  Similarity=0.198  Sum_probs=57.0

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ....+|+|++||..|+.+|+..|..+ + ||+..++..||..|||+.++|+|||||||+|+||....
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk   86 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRT-Q-WPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLK   86 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhccc
Confidence            34567899999999999999999999 6 99999999999999999999999999999999997543

>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=99.84  E-value=3.7e-21  Score=118.47  Aligned_cols=56  Identities=29%  Similarity=0.233  Sum_probs=53.4

Q ss_pred             CCCCCCHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNS---CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~---~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      +|++||..|+.+|+.+|..   + + ||+..++..||..+||+..+|++||||||+|+|+.
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~-~-yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIEN-P-YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTS-C-CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCC-C-CcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            4789999999999999999   8 7 99999999999999999999999999999999973

>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=99.83  E-value=7.4e-21  Score=124.53  Aligned_cols=63  Identities=14%  Similarity=0.085  Sum_probs=57.9

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ...||+|++|+..|+.+|+.+|..+  |+ ||+..+|..||..|||+..||+|||||||+|+|+..
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~p-YPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKA-YPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTC-CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCC-CCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            4578899999999999999999873  38 999999999999999999999999999999999853

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

Probab=99.83  E-value=2.4e-21  Score=124.86  Aligned_cols=58  Identities=28%  Similarity=0.377  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .+.|++||..|+.+|+..|..+ + ||+..++..||..|||+.++|+|||||||+|+||.
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~   66 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRN-Q-FPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL   66 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHS-S-SCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSC
T ss_pred             CCCCccCCHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHh
Confidence            3569999999999999999999 6 99999999999999999999999999999999984

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

Probab=99.83  E-value=1.4e-21  Score=121.95  Aligned_cols=59  Identities=29%  Similarity=0.311  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH---hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSF---NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F---~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ..+|+|++|+..|+.+|+.+|   ..+ + ||+..++..||..+||+..||+|||||||+|+||
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~-~-yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSN-P-YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTS-C-CCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccC-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            357899999999999999999   778 7 9999999999999999999999999999999886

>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=99.83  E-value=2.5e-20  Score=125.50  Aligned_cols=67  Identities=18%  Similarity=0.098  Sum_probs=61.3

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHh---------------------CCCchhhhhhhhhHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDT---------------------GLSVRVVQVWFQNQRAK   62 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l---------------------~l~~~~V~vWFqNRR~k   62 (159)
                      ...||.|++|++.|+.+|+..|..+ + ||+..+|..||..|                     +|++.+|+|||||||+|
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~-~-yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQ-K-NPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCC-C-CCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            4578899999999999999999999 7 99999999999999                     79999999999999999


Q ss_pred             HHHHHHHHHh
Q psy10851         63 MKKIQRKAKQ   72 (159)
Q Consensus        63 ~rk~~~~~~~   72 (159)
                      +|+.......
T Consensus        82 ~kr~~~~~~~   91 (102)
T 2da6_A           82 EAFRQKLAMD   91 (102)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHhhHhhhc
Confidence            9998665443

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

Probab=99.83  E-value=9.8e-21  Score=117.55  Aligned_cols=54  Identities=20%  Similarity=0.264  Sum_probs=50.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .-|..|+..|+..|..+ + ||+..+|.+||..|||+.++|++||||||+|+|+..
T Consensus        10 ~~~~~Ql~~LE~~F~~~-~-YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           10 KKTKEQIAHLKASFLQS-Q-FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             -CCHHHHHHHHHHHHGG-G-SCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            45799999999999999 7 999999999999999999999999999999999864

>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=99.83  E-value=6.2e-21  Score=126.46  Aligned_cols=57  Identities=21%  Similarity=0.242  Sum_probs=53.0

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ++..||..|+.+|+..|..+ + ||+..+|..||..|||+.++|+|||||||+|+|+..
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~-~-yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKS-S-FPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             ccccCCHHHHHHHHHHHccC-C-CCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            45569999999999999999 6 999999999999999999999999999999999753

>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=99.83  E-value=1e-20  Score=124.84  Aligned_cols=58  Identities=26%  Similarity=0.153  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNS---CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~---~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      ..+|+|++|+..|+.+|+.+|..   + + ||+..++..||..+||+..||+|||||||+|+|
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~-~-yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIEN-P-YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSS-C-CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCC-C-CcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            45678999999999999999999   8 7 999999999999999999999999999999987

>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=99.82  E-value=1.7e-20  Score=116.35  Aligned_cols=59  Identities=19%  Similarity=0.090  Sum_probs=54.9

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNS-CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~-~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      +..||.||.|+.+|+.+|+.+|.. + + ||+...|..||..|||++++|+|||||||.-.+
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~-~-yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVG-L-YPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            457899999999999999999999 8 5 999999999999999999999999999997543

>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=99.82  E-value=1.6e-20  Score=122.93  Aligned_cols=59  Identities=27%  Similarity=0.204  Sum_probs=54.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNS---CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~---~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      +++|++|+..|+.+|+.+|..   + + ||+..++..||..+||+..||+|||||||+|+|+..
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~-~-yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIEN-P-YLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSS-C-CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCC-C-CcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            356777999999999999999   8 7 999999999999999999999999999999999853

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

Probab=99.82  E-value=6.4e-21  Score=121.62  Aligned_cols=59  Identities=20%  Similarity=0.250  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH-hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSF-NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F-~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      -..+.|++++..|+.+|+..| ..+ + ||+..+|..||..|||++++|+|||||||+|+|+
T Consensus         7 ~g~k~r~r~~~~ql~~LE~~F~~~~-~-yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~   66 (72)
T 2cqx_A            7 GGIKDSPVNKVEPNDTLEKVFVSVT-K-YPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP   66 (72)
T ss_dssp             CCCCCCCCSCSCSTTHHHHHHHHTC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHhCCChhhcchhhhhcccCCCC
Confidence            356778889999999999999 888 6 9999999999999999999999999999999996

>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=99.81  E-value=1.8e-20  Score=136.84  Aligned_cols=61  Identities=28%  Similarity=0.393  Sum_probs=54.5

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .+.||+||+||..|+.+|+.+|..+ + ||+..+|..||..+||++++|+|||||||+|+||.
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMEN-Q-KPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhc-C-CCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            3678899999999999999999999 7 99999999999999999999999999999999974

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

Probab=99.81  E-value=1.4e-20  Score=137.87  Aligned_cols=62  Identities=29%  Similarity=0.418  Sum_probs=51.3

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+.||+||+||..|+.+|+.+|..+ + ||+..+|..||..+||++++|+|||||||+|+||..
T Consensus        97 ~~~rr~Rt~ft~~Ql~~LE~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           97 GRKRKKRTSIEVGVKGALESHFLKC-P-KPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             ---------CCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             ccCCCCceeccHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            5678899999999999999999999 7 999999999999999999999999999999999854

>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=99.81  E-value=2.3e-20  Score=134.32  Aligned_cols=61  Identities=25%  Similarity=0.346  Sum_probs=55.2

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .+.||+||+||..|+.+|+..|..+ + ||+..+|..||..+||++++|+|||||||+|+||.
T Consensus        85 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           85 ERKRKRRTTISIAAKDALERHFGEH-S-KPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCcCccHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            4567889999999999999999999 7 99999999999999999999999999999999974

>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=99.81  E-value=3.7e-20  Score=133.95  Aligned_cols=60  Identities=27%  Similarity=0.303  Sum_probs=57.2

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+.||+|++|+..|+.+|+.+|..+ + ||+..+|..||..+||+.++|+|||||||+|+||
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKN-P-LPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            4578899999999999999999999 7 9999999999999999999999999999999986

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

Probab=99.79  E-value=6.3e-20  Score=115.90  Aligned_cols=55  Identities=27%  Similarity=0.384  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      -...|..|+..|+..|..+ + ||+...|..||..|||++++|+|||||||+|+||.
T Consensus         8 ~~~~t~~ql~~LE~~F~~~-~-yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~   62 (69)
T 2l9r_A            8 HSHMSHTQVIELERKFSHQ-K-YLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK   62 (69)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCS
T ss_pred             CCcCCHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhCCChhheeecchhhhhhhhhh
Confidence            3578999999999999999 7 99999999999999999999999999999999984

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

Probab=99.79  E-value=2.5e-20  Score=125.67  Aligned_cols=63  Identities=16%  Similarity=0.123  Sum_probs=53.1

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH------------------hC---CCchhhhhhhhhHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKD------------------TG---LSVRVVQVWFQNQRA   61 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~------------------l~---l~~~~V~vWFqNRR~   61 (159)
                      ..+.||.|++|+..|+.+|+..|..+ + ||+...|.+||..                  ||   |++.+|+|||||||+
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~-~-yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~   83 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQ-K-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK   83 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHH
Confidence            45678899999999999999999999 6 9999999999999                  88   999999999999999


Q ss_pred             HHHHHH
Q psy10851         62 KMKKIQ   67 (159)
Q Consensus        62 k~rk~~   67 (159)
                      +.|+..
T Consensus        84 k~k~k~   89 (99)
T 1lfb_A           84 EEAFRH   89 (99)
T ss_dssp             TTSCCC
T ss_pred             HHHHhc
Confidence            887654

>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=99.79  E-value=8.1e-20  Score=132.66  Aligned_cols=61  Identities=30%  Similarity=0.349  Sum_probs=57.4

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .+.||+|++|+..|+..|+..|..+ + ||+..+|..||..+||+.++|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~-~-yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKS-P-KPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTC-S-CCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccC-C-CCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            3578899999999999999999999 6 99999999999999999999999999999999984

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

Probab=99.78  E-value=1.4e-19  Score=112.86  Aligned_cols=55  Identities=22%  Similarity=0.280  Sum_probs=50.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+..++..|+..|+..|..+ + ||+..+|..||..|||++++|+|||||||+|.++
T Consensus         6 ~~~~p~~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            6 SGQPPLKNLLSLLKAYYALN-A-QPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             SCCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCCccHHHHHHHHHHHhcC-C-CcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            35567899999999999999 6 9999999999999999999999999999998765

>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=99.78  E-value=1.1e-19  Score=112.86  Aligned_cols=50  Identities=26%  Similarity=0.404  Sum_probs=45.8

Q ss_pred             CHHHHHHHHHHHh-hcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         14 LLNLKVKLKTSFN-SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        14 s~~Q~~~Le~~F~-~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ...|+..|+..|. .+ + ||+..+|..||..|||+++||+|||||||+|+|+
T Consensus         8 ~~~~~~~LE~~F~~~~-~-yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A            8 TAQPNAILEKVFTAIT-K-HPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             SSCHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             CchHHHHHHHHHHHcC-C-CcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            3568999999994 57 6 9999999999999999999999999999999986

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

Probab=99.77  E-value=2.2e-19  Score=131.40  Aligned_cols=61  Identities=13%  Similarity=0.152  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ..||+|++||..|+.+|+..|..+ + ||+..+|..||..|||+.++|+|||||||+|+|+..
T Consensus        96 ~~rr~Rt~ft~~q~~~Le~~F~~~-~-yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~  156 (164)
T 2d5v_A           96 TPKKPRLVFTDVQRRTLHAIFKEN-K-RPSKELQITISQQLGLELSTVSNFFMNARRRSLDKW  156 (164)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccC
Confidence            468899999999999999999999 7 999999999999999999999999999999998753

>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=99.76  E-value=1.1e-18  Score=109.73  Aligned_cols=55  Identities=24%  Similarity=0.344  Sum_probs=49.9

Q ss_pred             CCCCHHHHHHHHHHHh---hcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFN---SCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~---~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+|+..|+.+|+.+|.   .+ + ||+..++..||..+||+..||++||||||+|+|+..
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~-p-yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   60 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTH-P-YPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM   60 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTS-C-CCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CcCCHHHHHHHHHHHHHhccC-C-CCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHH
Confidence            4799999999999999   88 8 999999999999999999999999999999999854

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

Probab=99.68  E-value=2e-16  Score=103.97  Aligned_cols=59  Identities=19%  Similarity=0.160  Sum_probs=54.0

Q ss_pred             CCCCCHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNS---CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA   70 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~---~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~   70 (159)
                      -..|+..++.+|+.+|..   + | ||+..+|..||..+||+.+||++||+|+|.|+++.....
T Consensus         9 ~~~l~~~~~~iL~~W~~~h~~n-p-YPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A            9 SHMLPKESVQILRDWLYEHRYN-A-YPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHTSGG-G-SCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHhccC-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            357899999999999987   6 8 999999999999999999999999999999999876543

>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=99.68  E-value=1e-17  Score=125.41  Aligned_cols=60  Identities=15%  Similarity=0.106  Sum_probs=53.5

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC---------------------CCchhhhhhhhhHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG---------------------LSVRVVQVWFQNQRAK   62 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~---------------------l~~~~V~vWFqNRR~k   62 (159)
                      ++.||.|++|+..|+.+|+..|..+ + ||+...|..||..||                     |++.+|+|||||||+|
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~-~-yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQ-K-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHH-C-CCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4678899999999999999999999 6 999999999999999                     9999999999999998


Q ss_pred             HHH
Q psy10851         63 MKK   65 (159)
Q Consensus        63 ~rk   65 (159)
                      .|.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            764

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=8.1e-17  Score=100.49  Aligned_cols=46  Identities=15%  Similarity=0.255  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851         15 LNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK   62 (159)
Q Consensus        15 ~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k   62 (159)
                      +.|+.+|+.+|..+ + +|+..++..||..+||+.++|+|||||||++
T Consensus        14 k~ql~~Lk~yF~~n-~-~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMN-M-EPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            57899999999999 5 9999999999999999999999999999973

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

Probab=99.61  E-value=3.9e-16  Score=118.19  Aligned_cols=58  Identities=17%  Similarity=0.210  Sum_probs=52.6

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC---------------------CCchhhhhhhhhHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG---------------------LSVRVVQVWFQNQRA   61 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~---------------------l~~~~V~vWFqNRR~   61 (159)
                      .++.||.|++|++.|+.+|+.+|..+ + ||+..+|..||..||                     |++.+|+|||||||+
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~-~-YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQ-K-NPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcC-C-CCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            35678899999999999999999999 7 999999999999998                     899999999999997


Q ss_pred             H
Q psy10851         62 K   62 (159)
Q Consensus        62 k   62 (159)
                      +
T Consensus       217 ~  217 (221)
T 2h8r_A          217 E  217 (221)
T ss_dssp             T
T ss_pred             h
Confidence            5

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.52  E-value=2e-15  Score=123.26  Aligned_cols=56  Identities=23%  Similarity=0.342  Sum_probs=52.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      ++.|+.|+..|+..|+..|..+ + ||+..+|.+||..|||+++||+|||||||+|+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~-~-yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRK-Q-SLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcC-C-CcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            4567899999999999999999 6 999999999999999999999999999999875

>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=99.10  E-value=1.3e-11  Score=67.80  Aligned_cols=22  Identities=41%  Similarity=0.693  Sum_probs=19.1

Q ss_pred             hhhhhhhhhHHHHHHHHHHHHH
Q psy10851         50 RVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus        50 ~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      +||+|||||||+||||......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            5899999999999999877643

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

Probab=96.68  E-value=0.0019  Score=39.83  Aligned_cols=44  Identities=16%  Similarity=0.120  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ   57 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq   57 (159)
                      ..++.-..+|+.+|... + .+.......|+.+..|+..||+-||-
T Consensus        12 ~~~p~~~e~L~~Yy~~h-k-~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           12 PPPPPDIQPLERYWAAH-Q-QLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             CCCCCCCHHHHHHHHHT-C-CCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCCCCcchHHHHHHHHh-c-ccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            44555578999999999 6 99999999999999999999999994

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

Probab=93.77  E-value=0.2  Score=31.77  Aligned_cols=50  Identities=10%  Similarity=0.124  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      .++..+..+|...|-..   +    ...+||..+|++...|+.+...-|.|.|+...
T Consensus        37 ~L~~~~r~vl~l~~~~g---~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~   86 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRG---W----STAQIATDLGIAEGTVKSRLHYAVRALRLTLQ   86 (92)
T ss_dssp             TSCHHHHHHHHHHHTSC---C----CHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            46777888887765444   2    46789999999999999999888888887644

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

Probab=92.11  E-value=0.27  Score=28.60  Aligned_cols=47  Identities=19%  Similarity=0.289  Sum_probs=33.1

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhh
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQN   58 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqN   58 (159)
                      +|.+||.+....+..++...   .........+|..+|++...|..|...
T Consensus         2 ~r~~ys~efK~~~~~~~~~g---~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            2 SRRIFTPHFKLQVLESYRND---NDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCCHHHHHHHHHHHHHC---TTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCCcCCHHHHHHHHHHHHcC---CCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            35679999876665444433   432223678999999999999999754

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=91.79  E-value=0.58  Score=31.31  Aligned_cols=50  Identities=12%  Similarity=0.151  Sum_probs=38.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK   62 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k   62 (159)
                      ++|+.||.++...+-..+..+ + ....   ..||..+|++...|..|..+++..
T Consensus         3 ~~r~~~t~e~K~~iv~~~~~~-g-~~~~---~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            3 PKRRQLTFREKSRIIQEVEEN-P-DLRK---GEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHC-T-TSCH---HHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             CcceeCCHHHHHHHHHHHHHC-C-CCcH---HHHHHHhCCCHHHHHHHHhchhhh
Confidence            468899999987777777555 4 5543   368999999999999998776654

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

Probab=91.38  E-value=0.53  Score=29.58  Aligned_cols=44  Identities=11%  Similarity=0.165  Sum_probs=32.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ   57 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq   57 (159)
                      |+.+.+|+.++....-..+. . . .    ....||..+|++...|..|..
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~-~-g-~----s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIH-D-G-E----SKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHH-H-T-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH-C-C-C----CHHHHHHHHCcCHHHHHHHHH
Confidence            45677899988655555564 4 2 3    256889999999999999974

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

Probab=90.94  E-value=0.4  Score=28.23  Aligned_cols=49  Identities=10%  Similarity=-0.077  Sum_probs=37.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ..+++.+..+|...|...   +    ...+||..+|++...|+.+...-+.+.|+.
T Consensus        14 ~~L~~~~r~il~l~~~~g---~----s~~eIA~~lgis~~tv~~~~~ra~~~l~~~   62 (70)
T 2o8x_A           14 ADLTTDQREALLLTQLLG---L----SYADAAAVCGCPVGTIRSRVARARDALLAD   62 (70)
T ss_dssp             TSSCHHHHHHHHHHHTSC---C----CHHHHHHHHTSCHHHHHHHHHHHHHHHHC-
T ss_pred             HhCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            357888888888776444   2    357899999999999999998777777654

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=90.02  E-value=0.95  Score=30.07  Aligned_cols=50  Identities=8%  Similarity=0.031  Sum_probs=40.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ..+++.+..+|...|...   +    ...+||..+|++...|+.|...-|.+.|+..
T Consensus        21 ~~L~~~~r~vl~l~y~~g---~----s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   70 (113)
T 1s7o_A           21 ALLTDKQMNYIELYYADD---Y----SLAEIADEFGVSRQAVYDNIKRTEKILETYE   70 (113)
T ss_dssp             GGSCHHHHHHHHHHHHTC---C----CHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            357888888888876555   2    3678999999999999999998888887753

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=89.58  E-value=0.86  Score=31.47  Aligned_cols=51  Identities=12%  Similarity=-0.033  Sum_probs=37.9

Q ss_pred             CCCCCCCCHHHHHHHHHHH-hhcCCCCCCHHHHHHHHH-Hh--CCCchhhhhhhhhH
Q psy10851          7 QNFQTIRLLNLKVKLKTSF-NSCCPGHKTTQVREALAK-DT--GLSVRVVQVWFQNQ   59 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F-~~~~~~yp~~~~r~~La~-~l--~l~~~~V~vWFqNR   59 (159)
                      +++|+++|-+|...|-.++ ..+ + -.+..+....|. .+  +++...|..|..|+
T Consensus         6 ~~~R~~lT~~qK~~i~~~~~~~~-~-~~~q~~la~wa~~~f~~~is~stis~ilk~k   60 (144)
T 1iuf_A            6 KIKRRAITEHEKRALRHYFFQLQ-N-RSGQQDLIEWFREKFGKDISQPSVSQILSSK   60 (144)
T ss_dssp             CCSSSCCCSHHHHHHHHHHHSSS-S-CCCHHHHHHHHHHHHSSCCSSSSTTHHHHHH
T ss_pred             CCcCccCCHHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHHCCCCcHHHHHHHHhhH
Confidence            6789999999999999998 556 5 566554444332 56  78888999998653

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=89.02  E-value=1  Score=30.63  Aligned_cols=50  Identities=12%  Similarity=-0.063  Sum_probs=37.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      .+++.+..+|. .|-..   +    ...+||..+|++...|+.+...-|.+.|+....
T Consensus       109 ~L~~~~r~v~~-~~~~g---~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  158 (164)
T 3mzy_A          109 NFSKFEKEVLT-YLIRG---Y----SYREIATILSKNLKSIDNTIQRIRKKSEEWIKE  158 (164)
T ss_dssp             HSCHHHHHHHH-HHTTT---C----CHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-HHHcC---C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            46777777887 44333   2    467899999999999999998888887776443

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

Probab=88.66  E-value=1  Score=24.04  Aligned_cols=40  Identities=8%  Similarity=0.038  Sum_probs=28.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhh
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQN   58 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqN   58 (159)
                      .++..+...+...+...   +    ....||..+|++...|..|...
T Consensus         5 ~l~~~~~~~i~~~~~~g---~----s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN---V----SLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT---C----CHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHhh
Confidence            56777765555555433   3    2668899999999999999853

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

Probab=88.22  E-value=1.2  Score=28.45  Aligned_cols=47  Identities=13%  Similarity=-0.012  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ..++..+..+|..++. .   +    ...+||..+|++...|+.+..+-+.|.+.
T Consensus        26 ~~Lt~~e~~vl~l~~~-g---~----s~~eIA~~l~is~~tV~~~l~r~~~kL~~   72 (95)
T 3c57_A           26 SGLTDQERTLLGLLSE-G---L----TNKQIADRMFLAEKTVKNYVSRLLAKLGM   72 (95)
T ss_dssp             -CCCHHHHHHHHHHHT-T---C----CHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             hcCCHHHHHHHHHHHc-C---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            4689999999988632 2   2    24789999999999999998776666554

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=88.19  E-value=1.4  Score=29.20  Aligned_cols=49  Identities=8%  Similarity=-0.029  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+++.+..+|...|...   +    ...+||..+|++...|+.+...-|.+.|+..
T Consensus        25 ~L~~~~r~vl~l~~~~g---~----s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   73 (113)
T 1xsv_A           25 LLTNKQRNYLELFYLED---Y----SLSEIADTFNVSRQAVYDNIRRTGDLVEDYE   73 (113)
T ss_dssp             GSCHHHHHHHHHHHTSC---C----CHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            47788888888766544   2    3678999999999999999998888888754

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=87.72  E-value=1.3  Score=26.52  Aligned_cols=51  Identities=12%  Similarity=-0.010  Sum_probs=37.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      ..+++.+..+|...|-.. . . ....-.+||..+|++...|+.+...-+.|.|
T Consensus         9 ~~L~~~er~il~l~~~l~-~-~-~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            9 SKLSEREAMVLKMRKGLI-D-G-REHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TTSCHHHHHHHHHHHTTT-T-S-SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHhcc-c-C-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            457889999998887511 0 0 1123568999999999999999887777776

>3lph_A Protein REV; helix-loop-helix, RNA-binding arginine rich motif, protein oligomerization, AIDS, HOST cytoplasm, HOST nucleus; 2.50A {Human immunodeficiency virus type 1}

Probab=86.26  E-value=1.7  Score=26.54  Aligned_cols=38  Identities=21%  Similarity=0.287  Sum_probs=24.6

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851         18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK   71 (159)
Q Consensus        18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~   71 (159)
                      +.+++-+|..| | ||+..=- .-|.             .|||.+||..+.+..
T Consensus        18 vRiIkiLyQSN-P-~P~p~GT-rqaR-------------RNRRRRWR~RQrQI~   55 (72)
T 3lph_A           18 VRLIKFLYQSN-P-PPNPEGT-RQAR-------------RNRRRRWRERQRQIH   55 (72)
T ss_dssp             HHHHHHHHHTC-C-CCCCCSC-HHHH-------------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccC-C-CCCCCCc-hHHH-------------HHHHHHHHHHHHHHH
Confidence            34556668877 9 9985411 1121             699999999876543

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

Probab=86.10  E-value=3  Score=26.92  Aligned_cols=47  Identities=11%  Similarity=-0.002  Sum_probs=36.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      ...+|..++.+|.-++ ..   +    ...+||..+|++...|+.+..+-+.|..
T Consensus        32 ~~~Lt~re~~Vl~l~~-~G---~----s~~EIA~~L~iS~~TV~~~l~ri~~KLg   78 (99)
T 1p4w_A           32 DKRLSPKESEVLRLFA-EG---F----LVTEIAKKLNRSIKTISSQKKSAMMKLG   78 (99)
T ss_dssp             SSSCCHHHHHHHHHHH-HT---C----CHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHHH-cC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            5679999999997755 23   2    2478999999999999999876665543

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=85.82  E-value=1  Score=28.16  Aligned_cols=51  Identities=6%  Similarity=0.006  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+++.+..+|...|-.. . - ......+||..+|++...|+.+...-+.|.|+
T Consensus        18 ~L~~~er~vl~l~~~l~-~-~-~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~   68 (87)
T 1tty_A           18 TLSPREAMVLRMRYGLL-D-G-KPKTLEEVGQYFNVTRERIRQIEVKALRKLRH   68 (87)
T ss_dssp             TSCHHHHHHHHHHHTTT-T-S-SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBT
T ss_pred             hCCHHHHHHHHHHHccC-C-C-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            57788888888877410 0 0 11246788999999999999998777777665

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

Probab=85.82  E-value=0.5  Score=25.76  Aligned_cols=43  Identities=16%  Similarity=0.176  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRA   61 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~   61 (159)
                      .++..+...+..++...   .    ....||..+|++...|..|+.....
T Consensus         5 ~~~~~~~~~i~~l~~~g---~----s~~~ia~~lgvs~~Tv~r~l~~~~~   47 (52)
T 1jko_C            5 AINKHEQEQISRLLEKG---H----PRQQLAIIFGIGVSTLYRYFPASSI   47 (52)
T ss_dssp             SSCTTHHHHHHHHHHTT---C----CHHHHHHTTSCCHHHHHHHSCTTC-
T ss_pred             CCCHHHHHHHHHHHHcC---C----CHHHHHHHHCCCHHHHHHHHHHccc
Confidence            45666665555555432   2    3568899999999999999875443

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

Probab=85.61  E-value=1.4  Score=27.28  Aligned_cols=51  Identities=16%  Similarity=-0.004  Sum_probs=38.6

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ..-..++..+..+|..++  . . +    ...+||..+|++...|+.+..+-+.|.+..
T Consensus        17 ~~~~~Lt~~e~~vl~l~~--~-g-~----s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   67 (82)
T 1je8_A           17 RDVNQLTPRERDILKLIA--Q-G-L----PNKMIARRLDITESTVKVHVKHMLKKMKLK   67 (82)
T ss_dssp             CCGGGSCHHHHHHHHHHT--T-T-C----CHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             HHHccCCHHHHHHHHHHH--c-C-C----CHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            334578999999998843  3 1 2    367899999999999999988777776543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=85.21  E-value=1.8  Score=25.55  Aligned_cols=49  Identities=10%  Similarity=0.038  Sum_probs=37.4

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .-..+++.+..+|..+  .. . +    ...+||..+|++...|+.++.+-+.|.+.
T Consensus         8 ~~~~L~~~e~~il~~~--~~-g-~----s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A            8 SKPLLTKREREVFELL--VQ-D-K----TTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             CCCCCCHHHHHHHHHH--TT-T-C----CHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHH--Hc-C-C----CHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            3457899999999874  23 2 4    35679999999999999998876666544

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=85.20  E-value=0.99  Score=26.65  Aligned_cols=51  Identities=12%  Similarity=0.016  Sum_probs=36.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+++.+..+|...|-.. . + ....-.+||..+|++...|+.+...-+.|.|+
T Consensus         5 ~L~~~er~il~l~~~l~-~-~-~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~   55 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGID-M-N-TDYTLEEVGKQFDVTRERIRQIEAKALRKLRH   55 (68)
T ss_dssp             CCCHHHHHHHHHHTTTT-S-S-SCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGS
T ss_pred             cCCHHHHHHHHHHHccC-C-C-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            47888899998877321 0 1 11245789999999999999998776666654

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=84.27  E-value=1.9  Score=31.24  Aligned_cols=49  Identities=14%  Similarity=0.022  Sum_probs=37.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .+++.+..+|...|-..       ....+||..+|++...|+.+...-|.|.|+..
T Consensus       187 ~L~~~~r~vl~l~~~~g-------~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l  235 (239)
T 1rp3_A          187 KLPEREKLVIQLIFYEE-------LPAKEVAKILETSVSRVSQLKAKALERLREML  235 (239)
T ss_dssp             TSCHHHHHHHHHHHTSC-------CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHhcC-------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            45667777777666443       24678999999999999999988888888753

>2x7l_M HIV REV; nuclear export, immune system, post-transcriptional regulation; 3.17A {Human immunodeficiency virus type 3}

Probab=84.16  E-value=1.3  Score=29.62  Aligned_cols=39  Identities=21%  Similarity=0.290  Sum_probs=24.8

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHh
Q psy10851         18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ   72 (159)
Q Consensus        18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~   72 (159)
                      +.+++-+|..| | ||...=-. -|.             .|||.+||..+.+...
T Consensus        15 vRiIkiLyQSN-P-yP~peGTR-qaR-------------RNRRRRWR~RQrQI~~   53 (115)
T 2x7l_M           15 VRLIKFLYQSN-P-PPNPEGTR-QAR-------------RNRRRRWRERQRQIHS   53 (115)
T ss_dssp             HHHHHHHHHSS-C-CCCCCCCT-TTH-------------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccC-C-CCCCCCch-hhh-------------HhHHHHHHHHHHHHHH
Confidence            34555668777 9 99754110 011             7999999998766443

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=84.15  E-value=2  Score=30.13  Aligned_cols=47  Identities=13%  Similarity=0.028  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ++..+..+|.-.|-..       ....+||..+|++...|+.+...-|.|.|+.
T Consensus       141 L~~~~r~vl~l~~~~g-------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~  187 (194)
T 1or7_A          141 LPEDLRMAITLRELDG-------LSYEEIAAIMDCPVGTVRSRIFRAREAIDNK  187 (194)
T ss_dssp             SCHHHHHHHHHHHTTC-------CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhHHHHHcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4455555555544333       2357899999999999999998888887765

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=84.00  E-value=1  Score=28.27  Aligned_cols=48  Identities=10%  Similarity=0.050  Sum_probs=36.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      -..++..+..+|.-++ ..   +.    ..+||..+|++...|+.+..+-+.|.+.
T Consensus        27 l~~Lt~~e~~vl~l~~-~g---~s----~~eIA~~l~is~~tV~~~l~r~~~kL~~   74 (91)
T 2rnj_A           27 YEMLTEREMEILLLIA-KG---YS----NQEIASASHITIKTVKTHVSNILSKLEV   74 (91)
T ss_dssp             GGGCCSHHHHHHHHHH-TT---CC----TTHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HhcCCHHHHHHHHHHH-cC---CC----HHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3468899999998753 22   32    3578999999999999998877776654

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=82.85  E-value=1.4  Score=26.47  Aligned_cols=46  Identities=26%  Similarity=0.169  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+++.+..+|.-+|  . . +    ...+||..+|++...|+.+..+-+.|.+.
T Consensus        16 ~L~~~e~~vl~l~~--~-g-~----s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A           16 TLSERERQVLSAVV--A-G-L----PNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             HHCHHHHHHHHHHT--T-T-C----CHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             hCCHHHHHHHHHHH--c-C-C----CHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            46778888887742  3 2 3    24689999999999999999877777664

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=81.73  E-value=4  Score=25.72  Aligned_cols=46  Identities=15%  Similarity=0.073  Sum_probs=35.0

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM   63 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~   63 (159)
                      ...+|..++.+|.-++ ..   +    ...+||..+|++.+.|+...++-+.|.
T Consensus        27 ~~~Lt~rE~~Vl~l~~-~G---~----s~~eIA~~L~iS~~TV~~~~~~i~~Kl   72 (90)
T 3ulq_B           27 QDVLTPRECLILQEVE-KG---F----TNQEIADALHLSKRSIEYSLTSIFNKL   72 (90)
T ss_dssp             --CCCHHHHHHHHHHH-TT---C----CHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             ccCCCHHHHHHHHHHH-cC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4579999999998776 22   3    367899999999999998877665554

---

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	159
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-08
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-08
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	7e-08
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	7e-08
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	7e-08
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-07
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-07
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	6e-07
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	8e-07
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	1e-06
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	1e-06
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-06
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-06
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	4e-06
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	5e-06
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-05
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	2e-05
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-05
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	2e-05
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-05
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-05
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	4e-05
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	4e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	6e-05
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	6e-05
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	8e-05
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-04
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-04
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-04
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	5e-04

>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 = 46.3 bits (110), Expect = 2e-08
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          L+  F +    H   +  E L+K     VR +Q WF+ +R + K 
Sbjct: 8  LEKVFTAITK-HPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 45.9 bits (109), Expect = 3e-08
 Identities = 14/37 (37%), Positives = 21/37 (56%)

Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE 74
          RE LA    L    +QVWF N+RAK ++ ++   Q+ 
Sbjct: 31 RERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRR 67

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.8 bits (106), Expect = 7e-08
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
           T+  E L K+T LS   ++ W  N+R K K I
Sbjct: 27 DTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59

>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 = 44.7 bits (106), Expect = 7e-08
 Identities = 9/32 (28%), Positives = 17/32 (53%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          T   ++ +A  T L++  V  WF N R ++ +
Sbjct: 31 TEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 45.4 bits (107), Expect = 7e-08
 Identities = 7/48 (14%), Positives = 15/48 (31%), Gaps = 2/48 (4%)

Query: 20 KLKTSF--NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          K+                   E    +TG+  +V+++W  N +     
Sbjct: 31 KMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS 78

>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 = 44.2 bits (104), Expect = 2e-07
 Identities = 14/36 (38%), Positives = 22/36 (61%)

Query: 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73
          +E LAK  G++V  V  WF N+R + KK   K +++
Sbjct: 34 KEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69

>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 = 43.3 bits (102), Expect = 3e-07
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ 72
          T   R  +A+   L+ R V++WFQN+R KMKKI +   +
Sbjct: 39 TRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAK 77

>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 = 42.5 bits (100), Expect = 6e-07
 Identities = 18/38 (47%), Positives = 24/38 (63%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71
             ++E L + TGLS RV++VWFQN+R K KK     K
Sbjct: 29 DALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMMK 66

>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 = 42.7 bits (100), Expect = 8e-07
 Identities = 13/36 (36%), Positives = 21/36 (58%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69
          +   R  +A    L+   V++WFQN+R K KK +R+
Sbjct: 53 SRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 88

>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 = 41.7 bits (98), Expect = 1e-06
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64
          L+  F S    +   +  + L+K    SVR +Q WF+++R + K
Sbjct: 16 LEKVFVSVTK-YPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 41.4 bits (97), Expect = 1e-06
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          L+  F +    + +   R+ LAK   LS R V+ WFQN+RAK ++
Sbjct: 15 LEKKFETQK--YLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 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 = 40.7 bits (95), Expect = 2e-06
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 2/47 (4%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
          L+  F        ++Q    +A++  L   VV+VWF N+R + K+++
Sbjct: 14 LERHFGEHS--KPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 58

>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 = 40.5 bits (95), Expect = 3e-06
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          T + R  +A    L+ R +++WFQN+R K KK
Sbjct: 23 TRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>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 = 39.9 bits (93), Expect = 4e-06
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
          L+  F      + +   R   +    L+   V++WFQN+RAK K++
Sbjct: 15 LERKFRQKQ--YLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58

>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 = 40.4 bits (94), Expect = 5e-06
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ 72
          L+ +FN     H        +A + GL+    Q WF+ + A+ ++ +    +
Sbjct: 16 LEYNFNKVNK-HPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSE 66

>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 = 38.7 bits (90), Expect = 1e-05
 Identities = 14/32 (43%), Positives = 19/32 (59%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          T   R  ++  T LS R + +WFQN+R K KK
Sbjct: 27 TKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 39.3 bits (91), Expect = 2e-05
 Identities = 9/44 (20%), Positives = 18/44 (40%)

Query: 31 GHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE 74
               +  + L+    ++   V  WF N+R ++K+    A   E
Sbjct: 38 NAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAAILE 81

>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 = 38.3 bits (89), Expect = 2e-05
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62
          LK  FN     + T + R+ L+ + GL+   +++WFQN RAK
Sbjct: 14 LKREFNENR--YLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 38.8 bits (90), Expect = 2e-05
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE 74
          +   RE LA    L+   V++WFQN R KMK+  +    Q+
Sbjct: 28 SAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAAQQ 68

>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 = 38.8 bits (90), Expect = 2e-05
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 2/53 (3%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73
          L+  F      + T      L+    L    V++WF+N+R + K    + K Q
Sbjct: 16 LEQHFLQGR--YLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKDQ 66

>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 = 38.0 bits (88), Expect = 2e-05
 Identities = 11/33 (33%), Positives = 20/33 (60%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66
          T++    +A+   +   V++VWF N+R K K+I
Sbjct: 24 TSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 56

>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 = 37.6 bits (87), Expect = 4e-05
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 39 EALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68
          E LA+ T L+   +QVWFQN+RA+++K   
Sbjct: 33 EELAQRTNLTEARIQVWFQNRRARLRKQHT 62

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.2 bits (86), Expect = 4e-05
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 2/45 (4%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          L+  F      + +   R  LA    L    ++VWFQN+R K K+
Sbjct: 14 LEKEFYKEN--YVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 6e-05
 Identities = 8/30 (26%), Positives = 13/30 (43%)

Query: 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          +    L+    L    +  +FQNQR  +K 
Sbjct: 36 EAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

>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 = 36.8 bits (85), Expect = 6e-05
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64
           ++ +E +AK  G++   V+VWF N+R + K
Sbjct: 23 NSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (84), Expect = 8e-05
 Identities = 12/27 (44%), Positives = 19/27 (70%)

Query: 41 LAKDTGLSVRVVQVWFQNQRAKMKKIQ 67
          +A  T L+   V+VWF+N+RAK +K +
Sbjct: 34 IAVWTNLTEARVRVWFKNRRAKWRKRE 60

>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 = 36.5 bits (84), Expect = 1e-04
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65
          + Q    +A   GL   VV+VWF N+R K K+
Sbjct: 34 SLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65

>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 = 36.2 bits (83), Expect = 2e-04
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73
          +   RE LA    L+   V++WFQN R K K+ Q +   +
Sbjct: 35 SAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYE 74

>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 = 35.2 bits (81), Expect = 2e-04
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 2/40 (5%)

Query: 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60
          L   F        + +++  +++  GL +  V  +F N R
Sbjct: 13 LHAIFKENK--RPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 35.1 bits (80), Expect = 5e-04
 Identities = 9/47 (19%), Positives = 17/47 (36%)

Query: 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEGDKS 78
            T +    L   T L+ R +  WF  ++      + K +  E +  
Sbjct: 28 VLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNAG 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	159
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.92
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.92
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.91
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.91
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.91
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.91
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.91
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.9
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.9
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.9
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.9
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.9
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.89
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.89
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.88
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.88
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.87
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.87
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.87
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.87
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.86
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.86
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.84
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.82
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.82
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.82
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.81
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.81
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.79
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.79
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.78
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.77
d1hlva1	66	DNA-binding domain of centromere binding protein B	94.41
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	92.99
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	92.49
d1iufa1	78	Ars-binding protein 1, ABP1 {Fission yeast (Schizo	92.04
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	91.48
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	81.52

>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=99.92  E-value=5.8e-26  Score=137.39  Aligned_cols=58  Identities=26%  Similarity=0.326  Sum_probs=55.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .||+||+||..|+.+|+.+|..+ + ||+..+|..||..|||++++|+|||||||+|+||
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAAN-K-FITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhc-C-CCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            47899999999999999999999 6 9999999999999999999999999999999885

>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=99.92  E-value=3.1e-25  Score=134.45  Aligned_cols=57  Identities=25%  Similarity=0.339  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ||+|++||+.|+.+|+.+|..+ + ||+..++..||..|||++++|+|||||||+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~-~-yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQK-Q-YLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            6899999999999999999999 6 9999999999999999999999999999999997

>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=99.91  E-value=5.9e-25  Score=136.80  Aligned_cols=60  Identities=20%  Similarity=0.238  Sum_probs=57.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ||+||+||..|+.+|+.+|..+ + ||+..++..||..|||+.++|+|||||||+|+|+...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQG-R-YLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            6789999999999999999999 6 9999999999999999999999999999999998654

>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=99.91  E-value=5.8e-25  Score=132.71  Aligned_cols=57  Identities=32%  Similarity=0.391  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      |+.|++||+.|+.+|+.+|..+ + ||+..++..||..|||++++|+|||||||+|+||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n-~-yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQ-K-YLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            6899999999999999999999 6 9999999999999999999999999999999986

>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=99.91  E-value=1.1e-24  Score=138.88  Aligned_cols=65  Identities=28%  Similarity=0.312  Sum_probs=60.5

Q ss_pred             CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851          3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK   69 (159)
Q Consensus         3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~   69 (159)
                      ....||+||+||..|+.+|+.+|..+ + ||+..+|..||..|||++++|+|||||||+|+|+....
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~-~-yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFN-M-YLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            44568899999999999999999999 7 99999999999999999999999999999999997654

>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=99.91  E-value=8.4e-25  Score=132.00  Aligned_cols=57  Identities=26%  Similarity=0.339  Sum_probs=55.0

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      |.||+||+.|+.+|+..|..+ + ||+..++..||..+||++.+|+|||||||+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~-~-yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKE-N-YVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            689999999999999999999 6 99999999999999999999999999999999973

>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=99.91  E-value=8.3e-25  Score=131.13  Aligned_cols=55  Identities=27%  Similarity=0.375  Sum_probs=53.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ||+||..|+.+|+.+|..+ + ||+..+|..||..|||++++|+|||||||+|+||.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFN-R-YLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            8999999999999999999 7 99999999999999999999999999999999984

>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=99.90  E-value=2.8e-24  Score=134.10  Aligned_cols=63  Identities=27%  Similarity=0.294  Sum_probs=59.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA   70 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~   70 (159)
                      .||+||+||..|+.+|+.+|..+ + ||+..+|..||..|||++.+|+|||||+|+|+|+.....
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n-~-yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERT-H-YPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            47899999999999999999999 6 999999999999999999999999999999999976543

>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=99.90  E-value=2.9e-24  Score=132.92  Aligned_cols=62  Identities=29%  Similarity=0.373  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      +.||.||+||..|+.+|+.+|..+ + ||+..++..||..|||+..+|+|||||||+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n-~-yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERT-Q-YPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHc-C-CCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            357899999999999999999999 7 9999999999999999999999999999999998754

>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=99.90  E-value=2.5e-24  Score=135.44  Aligned_cols=61  Identities=18%  Similarity=0.221  Sum_probs=56.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      .++.|++||..|+.+|+..|..+|+ ||+...|..||..+||++++|+|||||||+|+||..
T Consensus         1 g~~~r~~fT~~Ql~~Le~~F~~~n~-yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           1 GSEGAATMTEDQVEILEYNFNKVNK-HPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHSSCS-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHccc-cCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            3689999999999999999987437 999999999999999999999999999999999864

>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=99.90  E-value=1.6e-24  Score=128.92  Aligned_cols=53  Identities=32%  Similarity=0.449  Sum_probs=51.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK   62 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k   62 (159)
                      |+||+||+.|+.+|+..|..+ + ||+..+|..||..|||++++|+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~-~-yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNEN-R-YLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            689999999999999999999 7 9999999999999999999999999999986

>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=99.90  E-value=6.1e-24  Score=132.48  Aligned_cols=59  Identities=27%  Similarity=0.325  Sum_probs=56.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .||+||+||+.|+.+|+.+|..+ + ||+..+|..||..|||+..+|+|||||||+|+|+.
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~-~-yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQ-K-YLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHS-S-SCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            47899999999999999999999 6 99999999999999999999999999999999985

>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=99.89  E-value=2e-24  Score=131.70  Aligned_cols=58  Identities=29%  Similarity=0.346  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ||+||+||+.|+.+|+.+|..+ + ||+..++..||..+||++.+|++||||||+|+|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~-~-yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRN-R-YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTC-S-SCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHc-C-CCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            6889999999999999999999 7 99999999999999999999999999999999985

>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=99.89  E-value=1.3e-23  Score=137.09  Aligned_cols=61  Identities=25%  Similarity=0.263  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ   67 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~   67 (159)
                      ..||.|++||..|+.+|+.+|..+ + ||+..+|..||..|||+.++|+|||||||+|+||..
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n-~-yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFN-K-YLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhC-C-CCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            347889999999999999999999 6 999999999999999999999999999999999864

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.88  E-value=3.8e-24  Score=136.51  Aligned_cols=61  Identities=25%  Similarity=0.270  Sum_probs=57.3

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .+.||.||+||..|+.+|+.+|..+ + ||+..++..||..|||+.++|+|||||||+|.|+.
T Consensus         7 ~k~rr~Rt~ft~~Q~~~Le~~F~~~-~-yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   67 (77)
T d1vnda_           7 NKKRKRRVLFTKAQTYELERRFRQQ-R-YLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             SSSCSSCCCCCTTHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHH
Confidence            4567899999999999999999999 6 99999999999999999999999999999998863

>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=99.88  E-value=3.1e-23  Score=128.54  Aligned_cols=60  Identities=35%  Similarity=0.485  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      +.||.||+||..|+.+|+.+|..+ + ||+..++..||..+||+..+|++||||||+|.|+.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n-~-~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAAN-P-RPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            568999999999999999999999 7 99999999999999999999999999999998874

>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=99.87  E-value=3.9e-23  Score=125.00  Aligned_cols=57  Identities=26%  Similarity=0.405  Sum_probs=54.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      |+||+|+..|+.+|+.+|..+ + ||+..++..||..|||++.+|+|||||||+|+|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~-~-~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEH-S-KPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHc-c-CCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            689999999999999999999 7 99999999999999999999999999999999863

>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=99.87  E-value=6.7e-23  Score=132.30  Aligned_cols=60  Identities=18%  Similarity=0.252  Sum_probs=56.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC---------------CCchhhhhhhhhHHHHHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG---------------LSVRVVQVWFQNQRAKMKKIQR   68 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~---------------l~~~~V~vWFqNRR~k~rk~~~   68 (159)
                      ||+|++||+.|+.+|+.+|..+ + ||+..+|..||..+|               |++.+|+|||||||+|+|+...
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n-~-yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNEN-Q-YPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            6899999999999999999999 6 999999999999885               9999999999999999999654

>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=99.87  E-value=1.8e-23  Score=129.94  Aligned_cols=59  Identities=32%  Similarity=0.430  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ..||+||+|+..|+.+|+.+|..+ + ||+..++..||..+||+.++|+|||||+|+|+||
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n-~-~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKC-P-KPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSC-S-CCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHc-c-CCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            357899999999999999999999 7 9999999999999999999999999999999886

>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=99.87  E-value=6.7e-23  Score=121.77  Aligned_cols=53  Identities=25%  Similarity=0.388  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      ||+||++|+.+|+..|..+ + ||+..++..||..+||+.++|++||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~-~-~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRK-Q-SLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            7999999999999999999 7 999999999999999999999999999999865

>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=99.86  E-value=1.5e-22  Score=121.92  Aligned_cols=55  Identities=29%  Similarity=0.438  Sum_probs=53.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      +||+|+..|+.+|+.+|..+ + ||+..++..||..+||++.+|++||||||+|+||
T Consensus         1 kRT~~~~~q~~~Le~~F~~~-~-~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMEN-Q-KPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            59999999999999999999 8 9999999999999999999999999999999987

>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=99.86  E-value=1.2e-22  Score=127.78  Aligned_cols=59  Identities=19%  Similarity=0.104  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          5 WFQNFQTIRLLNLKVKLKTSFNS-CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         5 ~~kr~Rt~~s~~Q~~~Le~~F~~-~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ..||+|++||..|+.+|+.+|.. + + ||+..++..||..|||+.++|+|||||||+|.|+
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~-~-~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVG-L-YPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHC-S-CCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            46889999999999999999975 6 7 9999999999999999999999999999999886

>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=99.84  E-value=3.7e-21  Score=121.44  Aligned_cols=59  Identities=29%  Similarity=0.364  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNS---CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~---~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .||+|++|+++|+.+|+.+|..   + | ||+..++..||..+||+.+||++||||+|+|.|+.
T Consensus         1 ~rk~R~~~t~~q~~~Le~~f~~~~~~-p-YPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_           1 ARRKRRNFNKQATEILNEYFYSHLSN-P-YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTS-C-CCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhcCC-C-CCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            3789999999999999999985   5 8 99999999999999999999999999999999874

>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=99.82  E-value=1.6e-21  Score=114.51  Aligned_cols=50  Identities=16%  Similarity=0.256  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR   60 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR   60 (159)
                      +||+||..|+.+|+..|..+ + ||+..++..||..|||+.++|+|||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n-~-~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKEN-K-RPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSS-C-SSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            59999999999999999999 6 99999999999999999999999999997

>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=99.82  E-value=6.4e-21  Score=121.24  Aligned_cols=57  Identities=21%  Similarity=0.260  Sum_probs=53.9

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      ..+++||.+|+.+|+.+|..| + ||+..++..||..|||+.++|++||||||+|+|+.
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n-~-~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQC-Q-WARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHc-C-CCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            456789999999999999999 7 99999999999999999999999999999999984

>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=99.82  E-value=1.3e-20  Score=119.75  Aligned_cols=56  Identities=18%  Similarity=0.186  Sum_probs=51.3

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      +|.++|.+|+.+|+.+|..+ + ||+..++..||..|||+.++|++||||||+|.|+.
T Consensus         7 k~k~~T~~Q~~~Le~~F~~~-~-~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~   62 (76)
T d2ecba1           7 KFKEKTAEQLRVLQASFLNS-S-VLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   62 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHC-S-SCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHH
Confidence            44456999999999999999 6 99999999999999999999999999999987753

>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=99.81  E-value=3e-21  Score=123.85  Aligned_cols=60  Identities=17%  Similarity=0.228  Sum_probs=54.9

Q ss_pred             cCCCCCCCCCCHHHHHHHHHHHhh----cCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851          4 YWFQNFQTIRLLNLKVKLKTSFNS----CCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus         4 ~~~kr~Rt~~s~~Q~~~Le~~F~~----~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      ...||.||+||..|+..|+.+|..    + + ||+..++..||..|||+..+|+|||||+|+++|+
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~-~-~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRI-Q-KHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCC-C-SSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccc-c-CcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            456889999999999999999987    6 6 9999999999999999999999999999987653

>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=99.81  E-value=5.9e-21  Score=112.69  Aligned_cols=51  Identities=25%  Similarity=0.408  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         14 LLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        14 s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      |.+|..+|+.+|..+|+ ||+..++..||..|||+.++|+|||||||+|.|+
T Consensus         1 T~~q~~iLE~~F~~~~~-~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITK-HPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCS-SCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCC-CcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            56799999999987437 9999999999999999999999999999999875

>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=99.79  E-value=8.2e-20  Score=110.93  Aligned_cols=54  Identities=28%  Similarity=0.231  Sum_probs=49.8

Q ss_pred             CCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851         11 TIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK   65 (159)
Q Consensus        11 t~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk   65 (159)
                      .+|+.+|+.+|+.+|..+  || ||+..++..||..+||+.+||++||||+|+|.|+
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~p-yPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENP-YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSC-CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCC-CcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            359999999999999765  47 9999999999999999999999999999999875

>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=99.79  E-value=2.4e-20  Score=112.80  Aligned_cols=57  Identities=23%  Similarity=0.317  Sum_probs=52.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      -|.+++++.++..+|+.+|..+++ ||+..++..||..|||+.++|++||||||+++|
T Consensus         2 ~k~~~~~k~~~~~iLE~~F~~~~~-yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           2 IKDSPVNKVEPNDTLEKVFVSVTK-YPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCS-SCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCccccHHHHHHHHHcCC-CcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            367889999999999999986437 999999999999999999999999999999986

>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=99.78  E-value=3.4e-19  Score=108.76  Aligned_cols=58  Identities=19%  Similarity=0.256  Sum_probs=53.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851          6 FQNFQTIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK   64 (159)
Q Consensus         6 ~kr~Rt~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r   64 (159)
                      .||+|+.|+++++.+|+.+|..+  || ||+..++..||..+||+..||++||+|+|+|..
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nP-yPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHP-YPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSC-CCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCC-CcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            47789999999999999999862  48 999999999999999999999999999998864

>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=99.77  E-value=5.9e-20  Score=116.91  Aligned_cols=55  Identities=16%  Similarity=0.174  Sum_probs=51.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC---------------------CCchhhhhhhhhHHHHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG---------------------LSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~---------------------l~~~~V~vWFqNRR~k~rk~   66 (159)
                      |++||+.|+.+|+.+|..+ + ||+..+|+.||..||                     |++.+|++||||||+|.|+.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n-~-yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQ-K-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTC-S-SCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             CccCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999999 7 999999999999995                     89999999999999998764

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.41  E-value=0.088  Score=30.60  Aligned_cols=47  Identities=11%  Similarity=0.183  Sum_probs=37.3

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851          9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR   60 (159)
Q Consensus         9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR   60 (159)
                      +|..+|-.+...+-..|... + ..+   ...||..+|+....|..|.+|+.
T Consensus         4 kRk~LT~~eK~~ii~~~e~g-~-k~s---q~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEEN-P-DLR---KGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHC-T-TSC---HHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             ccccCCHHHHHHHHHHHHcC-C-cch---HHHHHHHhCCChhHHHHHHHHHH
Confidence            45678988877777778777 5 333   55789999999999999998864

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=92.99  E-value=0.087  Score=28.47  Aligned_cols=41  Identities=17%  Similarity=0.190  Sum_probs=34.9

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ   57 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq   57 (159)
                      +..+|.+|+......+...   .    .+..||..+|++...|-.||-
T Consensus         3 ~~~lt~~q~~~a~~l~~~G---~----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKG---H----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTT---C----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CCcCCHHHHHHHHHHHHCC---C----CHHHHHHHHCcCHHHHHhhCC
Confidence            4579999999999999755   3    388899999999999999983

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.49  E-value=0.16  Score=29.14  Aligned_cols=48  Identities=15%  Similarity=0.028  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      .+++.+..++...|-.. -      ...+||..+|++...|++....-|.+.|+.
T Consensus        21 ~L~~~~r~v~~l~~~~~-~------s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEE-L------PAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             TSCHHHHHHHHHHHTSC-C------CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHh-C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            46777888887777555 2      578899999999999999988888777764

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=91.48  E-value=0.24  Score=28.21  Aligned_cols=47  Identities=13%  Similarity=0.023  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851         13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI   66 (159)
Q Consensus        13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~   66 (159)
                      +++.+..++.-.|-.. .      ...+||..+|++...|+++.+.-|.+.|+.
T Consensus        19 Lp~~~r~v~~l~~~~~-~------s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          19 LPEDLRMAITLRELDG-L------SYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             SCHHHHHHHHHHHTTC-C------CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhC-C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4566667776666554 2      367899999999999999998888877764

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=81.52  E-value=2  Score=24.03  Aligned_cols=46  Identities=11%  Similarity=0.089  Sum_probs=34.0

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851         10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM   63 (159)
Q Consensus        10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~   63 (159)
                      |..+|+.+..+|.-+- ..   +    .-.+||..+|++.+.|+.-.++=+.|.
T Consensus         2 ~p~LT~rE~~vl~l~~-~G---~----s~~eIA~~L~is~~TV~~~~~~i~~Kl   47 (67)
T d1fsea_           2 KPLLTKREREVFELLV-QD---K----TTKEIASELFISEKTVRNHISNAMQKL   47 (67)
T ss_dssp             CCCCCHHHHHHHHHHT-TT---C----CHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH-cc---C----CHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            4579999999996542 22   2    356789999999999988876655543