Psyllid ID: psy1904

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160---
Protein Sequence
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSGR
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHccccccccccEEEcccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHcccccccccccccHHHHHHccccccccccHHHHHHHHHcccccccccHHcHHHHHccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
HHHccccHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHcccccccccHHHHHHHHHHcccccccccccHHHHcHHHccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHEEEcHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
maaagvrpcvisrqlrvshGCVSKILNRYqetgsirpgviggskprvatpdVEKRIEEYkktnpnitswEVRDKLIkvsrlddsdtesepgivlkrkqrrsrttfTSAQLEELEKSFqrshypdiytrEALANKFGMTETRVQQFVLGTAGFLLsclpsvsgr
Flexible Loop (DISEMBL)
maaagvrpcvisrqlrvshgCVSKILNRyqetgsirpgviggskprvatpdVEKRIeeykktnpnitswevrdklikvsrlddsdtesepgivlkrkqrrsrttftsaqleeleksfqrshypdIYTREALANKFGMTETRVQQFVLGTAGfllsclpsvsgr
Low Complexity Region (SEG)
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSGR
Disordered region (IsUnstruct)
*****VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI*************************ITSWEVRDKLI********************************************HYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL******
Disordered Region (DISOPRED)
******R*CVISRQLRVSHGCVS**********************************************EVRDKLIKVSRLDD*****************************************IYTREALANKFGMTETRVQQFVLGTA*************
Disordered Region (DISEMBL)
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR*********PGIVLKR**********SAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSGR
Disordered Region (DISPRO)
****GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIV*********TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSGR
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	163	2.2.26 [Sep-21-2011]
P09083	449	Protein gooseberry-neuro	yes	N/A	0.877	0.318	0.6	4e-54
P09082	427	Protein gooseberry OS=Dro	no	N/A	0.877	0.334	0.565	8e-52
P47239	503	Paired box protein Pax-7	yes	N/A	0.877	0.284	0.542	1e-49
Q0IH87	483	Paired box protein Pax-3-	N/A	N/A	0.877	0.296	0.517	3e-49
P06601	613	Segmentation protein pair	no	N/A	0.877	0.233	0.5	1e-48
Q645N4	484	Paired box protein Pax-3-	N/A	N/A	0.877	0.295	0.514	1e-47
P24610	479	Paired box protein Pax-3	no	N/A	0.877	0.298	0.512	3e-45
P23760	479	Paired box protein Pax-3	no	N/A	0.877	0.298	0.512	4e-45
Q28DP6	461	Paired box protein Pax-3	yes	N/A	0.877	0.310	0.55	2e-44
P23759	520	Paired box protein Pax-7	no	N/A	0.539	0.169	0.741	3e-32

>sp|P09083|GSBN_DROME Protein gooseberry-neuro OS=Drosophila melanogaster GN=gsb-n PE=1 SV=2

 Score =  209 bits (533), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 108/180 (60%), Positives = 126/180 (70%), Gaps = 37/180 (20%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP+V +P++E RI+E +
Sbjct: 48  MAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPKVTSPEIETRIDELR 107

Query: 61  KTNPNITSWEVRDKLIK-----------VSRL--------------------------DD 83
           K NP+I SWE+R+KLIK           +SRL                          D 
Sbjct: 108 KENPSIFSWEIREKLIKEGFADPPSTSSISRLLRGSDRGSEDGRKDYTINGILGGRDSDI 167

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           SDTESEPGI LKRKQRRSRTTFT+ QLE LE++F R+ YPD+YTRE LA    +TE R+Q
Sbjct: 168 SDTESEPGIPLKRKQRRSRTTFTAEQLEALERAFSRTQYPDVYTREELAQTTALTEARIQ 227

Expressed in a segmentally repeating pattern to define the polarity of embryonic segments.
Drosophila melanogaster (taxid: 7227)

>sp|P09082|GSB_DROME Protein gooseberry OS=Drosophila melanogaster GN=gsb PE=2 SV=1

 Score =  202 bits (514), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 104/184 (56%), Positives = 124/184 (67%), Gaps = 41/184 (22%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNR+QETGSIRPGVIGGSKPRVATPD+E RIEE K
Sbjct: 47  MAAAGVRPCVISRQLRVSHGCVSKILNRFQETGSIRPGVIGGSKPRVATPDIESRIEELK 106

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL------------------------- 81
           ++ P I SWE+R KLI+              +SRL                         
Sbjct: 107 QSQPGIFSWEIRAKLIEAGVCDKQNAPSVSSISRLLRGSSGSGTSHSIDGILGGGAGSVG 166

Query: 82  --DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTE 139
             D+S+ ++EP + LKRKQRRSRTTF++ Q++ LE+ F R+ YPD+YTRE LA   G+TE
Sbjct: 167 SEDESEDDAEPSVQLKRKQRRSRTTFSNDQIDALERIFARTQYPDVYTREELAQSTGLTE 226

Query: 140 TRVQ 143
            RVQ
Sbjct: 227 ARVQ 230

Expressed in segmentally repeating pattern to define the polarity of embryonic segments.

Drosophila melanogaster (taxid: 7227)

>sp|P47239|PAX7_MOUSE Paired box protein Pax-7 OS=Mus musculus GN=Pax7 PE=2 SV=2

 Score =  195 bits (495), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 108/199 (54%), Positives = 126/199 (63%), Gaps = 56/199 (28%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVEK+IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query: 60  KKTNPNITSWEVRDKLIK--------------VSRL---------DDSDTE--------- 87
           K+ NP + SWE+RD+L+K              +SR+         DD + +         
Sbjct: 122 KRENPGMFSWEIRDRLLKDGHCDRSTVPSVSSISRVLRIKFGKKEDDEEGDKKEEDGEKK 181

Query: 88  -----------------------SEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPD 124
                                  SEP + LKRKQRRSRTTFT+ QLEELEK+F+R+HYPD
Sbjct: 182 AKHSIDGILGDKGNRLDEGSDVESEPDLPLKRKQRRSRTTFTAEQLEELEKAFERTHYPD 241

Query: 125 IYTREALANKFGMTETRVQ 143
           IYTRE LA +  +TE RVQ
Sbjct: 242 IYTREELAQRTKLTEARVQ 260

Probable transcription factor. May have a role in myogenesis.

Mus musculus (taxid: 10090)

>sp|Q0IH87|PAX3B_XENLA Paired box protein Pax-3-B OS=Xenopus laevis GN=pax3-b PE=2 SV=2

 Score =  194 bits (492), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 105/203 (51%), Positives = 125/203 (61%), Gaps = 60/203 (29%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+V TP+VEK+IEE+K
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKVTTPEVEKKIEEFK 121

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL--------DDSDTE----------- 87
           + NP + SWE+RDKL+K              +SR+        D+ D E           
Sbjct: 122 RDNPGMFSWEIRDKLLKDGVCDRNTVPSVSSISRILRSKFGKGDEEDMELDRKEQEESEK 181

Query: 88  ---------------------------SEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRS 120
                                      SEP + LKRKQRRSRTTFT+ QLEELE++F+R+
Sbjct: 182 RAKHSIDGILRERAPASPESEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERT 241

Query: 121 HYPDIYTREALANKFGMTETRVQ 143
           HYPDIYTRE LA +  +TE RVQ
Sbjct: 242 HYPDIYTREELAQRAKLTEARVQ 264

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus laevis (taxid: 8355)

>sp|P06601|PRD_DROME Segmentation protein paired OS=Drosophila melanogaster GN=prd PE=1 SV=1

 Score =  192 bits (487), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 102/204 (50%), Positives = 126/204 (61%), Gaps = 61/204 (29%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 55  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 114

Query: 61  KTNPNITSWEVRDKLIK--------------VSRLD-------DSDTESEPG-------- 91
           +++P + SWE+R+KLI+              +SRL        D+D  S  G        
Sbjct: 115 RSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGRDAPLDNDMSSASGSPAGDGTK 174

Query: 92  --------------------------------IVLKRKQRRSRTTFTSAQLEELEKSFQR 119
                                           I LKRKQRR RTTF+++QL+ELE++F+R
Sbjct: 175 ASSSCGSDVSGGHHNNGKPSDEDISDCESEPGIALKRKQRRCRTTFSASQLDELERAFER 234

Query: 120 SHYPDIYTREALANKFGMTETRVQ 143
           + YPDIYTRE LA +  +TE R+Q
Sbjct: 235 TQYPDIYTREELAQRTNLTEARIQ 258

Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.

Drosophila melanogaster (taxid: 7227)

>sp|Q645N4|PAX3A_XENLA Paired box protein Pax-3-A OS=Xenopus laevis GN=pax3-a PE=2 SV=1

 Score =  188 bits (478), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 105/204 (51%), Positives = 125/204 (61%), Gaps = 61/204 (29%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
           MA  GVRPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TP+VEK++EE+
Sbjct: 62  MAHHGVRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPEVEKKMEEF 121

Query: 60  KKTNPNITSWEVRDKLIK--------------VSRL--------DDSDTE---------- 87
           K+ NP + SWE+RDKL+K              +SR+        D+ D E          
Sbjct: 122 KRDNPGMFSWEIRDKLLKDGVCDRNTVPSVSSISRILRSKFGKGDEEDMELDRKEQEESE 181

Query: 88  ----------------------------SEPGIVLKRKQRRSRTTFTSAQLEELEKSFQR 119
                                       SEP + LKRKQRRSRTTFT+ QLEELE++F+R
Sbjct: 182 KRAKHSIDGILRERAPVSPESEEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFER 241

Query: 120 SHYPDIYTREALANKFGMTETRVQ 143
           +HYPDIYTRE LA +  +TE RVQ
Sbjct: 242 THYPDIYTREELAQRAKLTEARVQ 265

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus laevis (taxid: 8355)

>sp|P24610|PAX3_MOUSE Paired box protein Pax-3 OS=Mus musculus GN=Pax3 PE=1 SV=2

 Score =  180 bits (457), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 104/203 (51%), Positives = 125/203 (61%), Gaps = 60/203 (29%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TPDVEK+IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPDVEKKIEEY 121

Query: 60  KKTNPNITSWEVRDKLIK--------------VSRL----------DDSDTE-------- 87
           K+ NP + SWE+RDKL+K              +SR+          +++D E        
Sbjct: 122 KRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEESE 181

Query: 88  -----SEPGIVLKR----------------------KQRRSRTTFTSAQLEELEKSFQRS 120
                S  GI+ +R                      KQRRSRTTFT+ QLEELE++F+R+
Sbjct: 182 KKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERT 241

Query: 121 HYPDIYTREALANKFGMTETRVQ 143
           HYPDIYTRE LA +  +TE RVQ
Sbjct: 242 HYPDIYTREELAQRAKLTEARVQ 264

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Mus musculus (taxid: 10090)

>sp|P23760|PAX3_HUMAN Paired box protein Pax-3 OS=Homo sapiens GN=PAX3 PE=1 SV=2

 Score =  180 bits (456), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 104/203 (51%), Positives = 125/203 (61%), Gaps = 60/203 (29%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TPDVEK+IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPDVEKKIEEY 121

Query: 60  KKTNPNITSWEVRDKLIK--------------VSRL----------DDSDTE-------- 87
           K+ NP + SWE+RDKL+K              +SR+          +++D E        
Sbjct: 122 KRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEESE 181

Query: 88  -----SEPGIVLKR----------------------KQRRSRTTFTSAQLEELEKSFQRS 120
                S  GI+ +R                      KQRRSRTTFT+ QLEELE++F+R+
Sbjct: 182 KKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERT 241

Query: 121 HYPDIYTREALANKFGMTETRVQ 143
           HYPDIYTRE LA +  +TE RVQ
Sbjct: 242 HYPDIYTREELAQRAKLTEARVQ 264

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Homo sapiens (taxid: 9606)

>sp|Q28DP6|PAX3_XENTR Paired box protein Pax-3 OS=Xenopus tropicalis GN=pax3 PE=2 SV=2

 Score =  177 bits (449), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 99/180 (55%), Positives = 116/180 (64%), Gaps = 37/180 (20%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TP+VEK+IEE+
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPEVEKKIEEF 121

Query: 60  KKTNP-NITSWEVRDKLIKVSRLD-----------------------------------D 83
           K+ NP +  S  +R K  K    D                                    
Sbjct: 122 KRDNPVSSISRILRSKFGKGDEEDIELDRKEQEESEKRAKHSIDGILRERAPASPESEEG 181

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           SD +SEP + LKRKQRRSRTTFT+ QLEELE++F+R+HYPDIYTRE LA +  +TE RVQ
Sbjct: 182 SDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQ 241

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus tropicalis (taxid: 8364)

>sp|P23759|PAX7_HUMAN Paired box protein Pax-7 OS=Homo sapiens GN=PAX7 PE=2 SV=3

 Score =  137 bits (346), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 66/89 (74%), Positives = 73/89 (82%), Gaps = 1/89 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVEK+IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query: 60  KKTNPNITSWEVRDKLIKVSRLDDSDTES 88
           K+ NP + SWE+RD+L+K    D S   S
Sbjct: 122 KRENPGMFSWEIRDRLLKDGHCDRSTVPS 150

Probable transcription factor. May have a role in myogenesis.

Homo sapiens (taxid: 9606)

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	163
328713660	440	PREDICTED: protein gooseberry-like [Acyr	0.877	0.325	0.651	3e-58
350397864	522	PREDICTED: LOW QUALITY PROTEIN: protein	0.993	0.310	0.613	1e-56
242007394	439	Paired box protein Pax-7, putative [Pedi	0.877	0.325	0.647	2e-56
383854529	483	PREDICTED: paired box protein Pax-3-B-li	0.877	0.296	0.651	2e-56
340724544	502	PREDICTED: LOW QUALITY PROTEIN: segmenta	0.993	0.322	0.607	3e-56
307197090	481	Segmentation protein paired [Harpegnatho	0.877	0.297	0.64	4e-56
328778294	441	PREDICTED: protein gooseberry-neuro-like	0.877	0.324	0.631	5e-56
307212050	438	Protein gooseberry-neuro [Harpegnathos s	0.877	0.326	0.623	5e-56
380027561	442	PREDICTED: protein gooseberry-neuro-like	0.877	0.323	0.627	6e-56
383852872	398	PREDICTED: protein gooseberry-neuro-like	0.877	0.359	0.623	6e-56

>gi|328713660|ref|XP_001942974.2| PREDICTED: protein gooseberry-like [Acyrthosiphon pisum]

 Score =  229 bits (584), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 118/181 (65%), Positives = 129/181 (71%), Gaps = 38/181 (20%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE+RIEEYK
Sbjct: 47  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 106

Query: 61  KTNPNITSWEVRDKLIK---------------VSRL-----------------------D 82
           K NP + SWE+RDKL+K               +SRL                       D
Sbjct: 107 KANPAMFSWEIRDKLVKQDGICDKNSAPSISSISRLLRGGRRDELKNHSIDGILGPSSAD 166

Query: 83  DSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           DSDTESEPG  LKRKQRRSRTTFT  QLE+LE++F +S YPD+YTRE LA K  +TE RV
Sbjct: 167 DSDTESEPGFHLKRKQRRSRTTFTGEQLEDLERAFHKSQYPDVYTREELAQKTKLTEARV 226

Query: 143 Q 143
           Q
Sbjct: 227 Q 227

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350397864|ref|XP_003485014.1| PREDICTED: LOW QUALITY PROTEIN: protein gooseberry-like [Bombus impatiens]

 Score =  223 bits (569), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 119/194 (61%), Positives = 134/194 (69%), Gaps = 32/194 (16%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 85  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVESRIEEYK 144

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL------------------DDSDTES 88
           + NP I SWE+RD+LIK              +SRL                    SD ES
Sbjct: 145 RDNPGIFSWEIRDRLIKEGICDRTSAPSVSAISRLLRGRDPEDETKLGDRKTSSGSDCES 204

Query: 89  EPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLG 148
           EPGI LKRKQRRSRTTFT+ QL+ELE++F+R+ YPDIYTRE LA +  +TE R+Q +   
Sbjct: 205 EPGIPLKRKQRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKLTEARIQVWFSN 264

Query: 149 TAGFLLSCLPSVSG 162
               L   L S SG
Sbjct: 265 RRARLRKQLSSTSG 278

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007394|ref|XP_002424525.1| Paired box protein Pax-7, putative [Pediculus humanus corporis] gi|212507958|gb|EEB11787.1| Paired box protein Pax-7, putative [Pediculus humanus corporis]

 Score =  223 bits (568), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 130/176 (73%), Gaps = 33/176 (18%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MA AG+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VEKRIE+YK
Sbjct: 51  MAGAGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEKRIEDYK 110

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL-------------------DDSDTE 87
           + NP I SWE+RD+LIK              +SRL                   D+SD E
Sbjct: 111 RENPGIFSWEIRDRLIKEGICDRSSVPSVSAISRLLRGRDGEDDRKINDGCKNSDNSDCE 170

Query: 88  SEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           SEPGI LKRKQRRSRTTFT+ QL+ELEK+F+R+ YPDIYTRE LA +  +TE R+Q
Sbjct: 171 SEPGIPLKRKQRRSRTTFTALQLDELEKAFERTQYPDIYTREELAQRTKLTEARIQ 226

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383854529|ref|XP_003702773.1| PREDICTED: paired box protein Pax-3-B-like [Megachile rotundata]

 Score =  223 bits (568), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/175 (65%), Positives = 128/175 (73%), Gaps = 32/175 (18%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 40  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEEYK 99

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL------------------DDSDTES 88
           + NP I SWE+RD+LIK              +SRL                    SD ES
Sbjct: 100 RDNPGIFSWEIRDRLIKEGICDRTSAPSVSAISRLLRGRDPEDEAKLGDGKTSSGSDCES 159

Query: 89  EPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           EPGI LKRKQRRSRTTFT+ QL+ELE++F+R+ YPDIYTRE LA +  +TE R+Q
Sbjct: 160 EPGIPLKRKQRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 214

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340724544|ref|XP_003400641.1| PREDICTED: LOW QUALITY PROTEIN: segmentation protein paired-like [Bombus terrestris]

 Score =  223 bits (567), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 119/196 (60%), Positives = 134/196 (68%), Gaps = 34/196 (17%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 60  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVESRIEEYK 119

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL--------------------DDSDT 86
           + NP I SWE+RD+LIK              +SRL                      SD 
Sbjct: 120 RDNPGIFSWEIRDRLIKEGICDRTSAPSVSAISRLLRGRDPEDETKLGDRDGKTSSGSDC 179

Query: 87  ESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFV 146
           ESEPGI LKRKQRRSRTTFT+ QL+ELE++F+R+ YPDIYTRE LA +  +TE R+Q + 
Sbjct: 180 ESEPGIPLKRKQRRSRTTFTAHQLDELERAFERTQYPDIYTREELAQRTKLTEARIQVWF 239

Query: 147 LGTAGFLLSCLPSVSG 162
                 L   L S SG
Sbjct: 240 SNRRARLRKQLSSTSG 255

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197090|gb|EFN78458.1| Segmentation protein paired [Harpegnathos saltator]

 Score =  222 bits (566), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 112/175 (64%), Positives = 131/175 (74%), Gaps = 32/175 (18%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE +IEEYK
Sbjct: 1   MAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEAKIEEYK 60

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL-------DD-----------SDTES 88
           + NP++ SWE+RD+L+K              +SRL       DD           SD +S
Sbjct: 61  RENPSVFSWEIRDRLVKEGICEKANAPSVSAISRLIRGRDNEDDARIGEVKTSSGSDCDS 120

Query: 89  EPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           EPGI LKRKQRRSRTTFT+ QL+ELEK+F+R+ YPDIYTRE LA +  +TE R+Q
Sbjct: 121 EPGITLKRKQRRSRTTFTAHQLDELEKAFERTQYPDIYTREELAQRTKLTEARIQ 175

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328778294|ref|XP_394848.4| PREDICTED: protein gooseberry-neuro-like [Apis mellifera]

 Score =  222 bits (565), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 113/179 (63%), Positives = 128/179 (71%), Gaps = 36/179 (20%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP++E RIEE K
Sbjct: 46  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEIEARIEEMK 105

Query: 61  KTNPNITSWEVRDKLIK-----------VSRL-------------------------DDS 84
           + NP I SWE+R+KL+K           +SRL                         D+S
Sbjct: 106 RDNPGIFSWEIREKLVKEGFTDPPSVSSISRLLRGGRPGDDGKKDYTIDGILGGRCGDES 165

Query: 85  DTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           DTESEPGI LKRKQRRSRTTFT  QLE+LE +FQR+ YPD+Y RE LA + G+TE R+Q
Sbjct: 166 DTESEPGIPLKRKQRRSRTTFTGEQLEQLETAFQRAQYPDVYAREELAQRTGLTEARIQ 224

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307212050|gb|EFN87933.1| Protein gooseberry-neuro [Harpegnathos saltator]

 Score =  222 bits (565), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 116/186 (62%), Positives = 127/186 (68%), Gaps = 43/186 (23%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAG+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIE+ K
Sbjct: 25  MAAAGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEDLK 84

Query: 61  KTNPNITSWEVRDKLIK---------------VSRL------------------------ 81
           + NP I SWE+RDKLIK               +SRL                        
Sbjct: 85  RQNPGIFSWEIRDKLIKQDGVCDKASAPSVSSISRLLRGPANQTRPDDPRRNHSIDGILA 144

Query: 82  ----DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGM 137
               DDSDTESEPGI LKRKQRRSRTTFT  QLE+LE +F R+ YPD+YTRE LA K  +
Sbjct: 145 GSSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTKL 204

Query: 138 TETRVQ 143
           TE RVQ
Sbjct: 205 TEARVQ 210

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027561|ref|XP_003697490.1| PREDICTED: protein gooseberry-neuro-like [Apis florea]

 Score =  221 bits (564), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 113/180 (62%), Positives = 128/180 (71%), Gaps = 37/180 (20%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP++E RIEE K
Sbjct: 46  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEIEARIEEMK 105

Query: 61  KTNPNITSWEVRDKLIK-----------VSRL--------------------------DD 83
           + NP I SWE+R+KL+K           +SRL                          D+
Sbjct: 106 RDNPGIFSWEIREKLVKEGFTDPPSVSSISRLLRGGRPGDDGKKDYTIDGILGGGRCGDE 165

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           SDTESEPGI LKRKQRRSRTTFT  QLE+LE +FQR+ YPD+Y RE LA + G+TE R+Q
Sbjct: 166 SDTESEPGIPLKRKQRRSRTTFTGEQLEQLETAFQRAQYPDVYAREELAQRTGLTEARIQ 225

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383852872|ref|XP_003701949.1| PREDICTED: protein gooseberry-neuro-like, partial [Megachile rotundata]

 Score =  221 bits (564), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 116/186 (62%), Positives = 127/186 (68%), Gaps = 43/186 (23%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIE+ K
Sbjct: 41  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEDMK 100

Query: 61  KTNPNITSWEVRDKLIK--------------VSRL------------------------- 81
           + NP I SWE+R+KLIK              +SRL                         
Sbjct: 101 RQNPGIFSWEIREKLIKDGICDKASAPSVSSISRLLRGPTNQTRPGEDPRRNHSIDGILG 160

Query: 82  ----DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGM 137
               DDSDTESEPGI LKRKQRRSRTTFT  QLE+LE +F R+ YPD+YTRE LA K  +
Sbjct: 161 GSSGDDSDTESEPGIALKRKQRRSRTTFTGEQLEQLEAAFHRTQYPDVYTREELAQKTNL 220

Query: 138 TETRVQ 143
           TE RVQ
Sbjct: 221 TEARVQ 226

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	163
FB|FBgn0001147	449	gsb-n "gooseberry-neuro" [Dros	0.539	0.195	0.738	5.4e-53
ZFIN|ZDB-GENE-990415-201	507	pax7a "paired box gene 7a" [Da	0.472	0.151	0.833	6.1e-53
FB|FBgn0003145	613	prd "paired" [Drosophila melan	0.564	0.150	0.717	8e-53
UNIPROTKB|Q28DP6	461	pax3 "Paired box protein Pax-3	0.521	0.184	0.659	1.9e-44
UNIPROTKB|F1NUP3	491	F1NUP3 "Uncharacterized protei	0.533	0.177	0.528	4.5e-39
UNIPROTKB|F1NF66	422	PAX6 "Paired box protein Pax-6	0.466	0.180	0.644	4.3e-38
ZFIN|ZDB-GENE-001031-1	437	pax6b "paired box gene 6b" [Da	0.466	0.173	0.644	1.1e-37
UNIPROTKB|F1NXF7	186	PAX6 "Paired box protein Pax-6	0.877	0.768	0.548	1.5e-37
UNIPROTKB|E1C2N6	484	E1C2N6 "Uncharacterized protei	0.380	0.128	0.677	4e-37
WB|WBGene00006870	455	vab-3 [Caenorhabditis elegans	0.466	0.167	0.644	2.4e-36

FB|FBgn0001147 gsb-n "gooseberry-neuro" [Drosophila melanogaster (taxid:7227)]

 Score = 344 (126.2 bits), Expect = 5.4e-53, Sum P(2) = 5.4e-53
 Identities = 65/88 (73%), Positives = 75/88 (85%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
             MAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP+V +P++E RI+E +
Sbjct:    48 MAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPKVTSPEIETRIDELR 107

Query:    61 KTNPNITSWEVRDKLIKVSRLDDSDTES 88
             K NP+I SWE+R+KLIK    D   T S
Sbjct:   108 KENPSIFSWEIREKLIKEGFADPPSTSS 135

GO:0003677 "DNA binding" evidence=NAS

GO:0007367 "segment polarity determination" evidence=IEP;NAS

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

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

GO:0005667 "transcription factor complex" evidence=ISS

GO:0005634 "nucleus" evidence=NAS

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

ZFIN|ZDB-GENE-990415-201 pax7a "paired box gene 7a" [Danio rerio (taxid:7955)]

 Score = 336 (123.3 bits), Expect = 6.1e-53, Sum P(2) = 6.1e-53
 Identities = 65/78 (83%), Positives = 70/78 (89%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVEKRIEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKRIEEY 121

Query:    60 KKTNPNITSWEVRDKLIK 77
             K+ NP + SWE+RDKL+K
Sbjct:   122 KRENPGMFSWEIRDKLLK 139

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0048066 "developmental pigmentation" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

FB|FBgn0003145 prd "paired" [Drosophila melanogaster (taxid:7227)]

 Score = 350 (128.3 bits), Expect = 8.0e-53, Sum P(2) = 8.0e-53
 Identities = 66/92 (71%), Positives = 77/92 (83%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
             MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct:    55 MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 114

Query:    61 KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
             +++P + SWE+R+KLI+    D S   S   I
Sbjct:   115 RSSPGMFSWEIREKLIREGVCDRSTAPSVSAI 146

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

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

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

GO:0005667 "transcription factor complex" evidence=ISS

GO:0007366 "periodic partitioning by pair rule gene" evidence=NAS;TAS

GO:0003677 "DNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

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

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

UNIPROTKB|Q28DP6 pax3 "Paired box protein Pax-3" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 272 (100.8 bits), Expect = 1.9e-44, Sum P(2) = 1.9e-44
 Identities = 58/88 (65%), Positives = 68/88 (77%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TP+VEK+IEE+
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPEVEKKIEEF 121

Query:    60 KKTNPNITSWEVRDKLIKVSRLDDSDTE 87
             K+ NP ++S   R    K  + D+ D E
Sbjct:   122 KRDNP-VSSIS-RILRSKFGKGDEEDIE 147

GO:0005634 "nucleus" evidence=ISS

GO:0008543 "fibroblast growth factor receptor signaling pathway" evidence=ISS

GO:0014029 "neural crest formation" evidence=ISS

GO:0014034 "neural crest cell fate commitment" evidence=ISS

GO:0016055 "Wnt receptor signaling pathway" evidence=ISS

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

GO:0048785 "hatching gland development" evidence=ISS

UNIPROTKB|F1NUP3 F1NUP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 234 (87.4 bits), Expect = 4.5e-39, Sum P(2) = 4.5e-39
 Identities = 47/89 (52%), Positives = 60/89 (67%)

Query:    55 RIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELE 114
             +  +  K NP    W  + K       + SD +SEP + LKRKQRRSRTTFT+ QLEELE
Sbjct:   185 KTRQSSKRNPQ--GWSSKTKASAAQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELE 242

Query:   115 KSFQRSHYPDIYTREALANKFGMTETRVQ 143
             ++F+R+HYPDIYTRE LA +  +TE RVQ
Sbjct:   243 RAFERTHYPDIYTREELAQRAKLTEARVQ 271

GO:0005634 "nucleus" evidence=IEA

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

GO:0001755 "neural crest cell migration" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0007507 "heart development" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

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

GO:0048066 "developmental pigmentation" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0060594 "mammary gland specification" evidence=IEA

UNIPROTKB|F1NF66 PAX6 "Paired box protein Pax-6" [Gallus gallus (taxid:9031)]

 Score = 261 (96.9 bits), Expect = 4.3e-38, Sum P(2) = 4.3e-38
 Identities = 49/76 (64%), Positives = 62/76 (81%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
             +A +G RPC ISR L+VS+GCVSKIL RY ETGSIRP  IGGSKPRVATP+V  +I +YK
Sbjct:    32 LAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVSKIAQYK 91

Query:    61 KTNPNITSWEVRDKLI 76
             +  P+I +WE+RD+L+
Sbjct:    92 RECPSIFAWEIRDRLL 107

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-001031-1 pax6b "paired box gene 6b" [Danio rerio (taxid:7955)]

 Score = 259 (96.2 bits), Expect = 1.1e-37, Sum P(2) = 1.1e-37
 Identities = 49/76 (64%), Positives = 62/76 (81%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
             +A +G RPC ISR L+VS+GCVSKIL RY ETGSIRP  IGGSKPRVATP+V  +I +YK
Sbjct:    51 LAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVGKIAQYK 110

Query:    61 KTNPNITSWEVRDKLI 76
             +  P+I +WE+RD+L+
Sbjct:   111 RECPSIFAWEIRDRLL 126

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0002088 "lens development in camera-type eye" evidence=IMP

GO:0030902 "hindbrain development" evidence=IMP

GO:0009952 "anterior/posterior pattern specification" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

GO:0002089 "lens morphogenesis in camera-type eye" evidence=IMP

GO:0003310 "pancreatic A cell differentiation" evidence=IMP

GO:0003309 "type B pancreatic cell differentiation" evidence=IMP

GO:0003311 "pancreatic D cell differentiation" evidence=IMP

GO:0090104 "pancreatic epsilon cell differentiation" evidence=IMP

GO:0001071 "nucleic acid binding transcription factor activity" evidence=IDA

GO:2001141 "regulation of RNA biosynthetic process" evidence=IDA

UNIPROTKB|F1NXF7 PAX6 "Paired box protein Pax-6" [Gallus gallus (taxid:9031)]

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 79/144 (54%), Positives = 104/144 (72%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
             +A +G RPC ISR L+VS+GCVSKIL RY ETGSIRP  IGGSKPRVATP+V  +I +YK
Sbjct:    28 LAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVSKIAQYK 87

Query:    61 KTNPNITSWEVRDKLIKVSRLDDSDTESEPGIV-LKRKQRRSRTTFTSAQLEELEKSFQR 119
             +  P+I +WE+RD+L+      + +  S   I  LKRK +R+RT+FT  Q+E LEK F+R
Sbjct:    88 RECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRLKRKLQRNRTSFTQEQIEALEKEFER 147

Query:   120 SHYPDIYTREALANKFGMTETRVQ 143
             +HYPD++ RE LA K  + E R+Q
Sbjct:   148 THYPDVFARERLAAKIDLPEARIQ 171

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E1C2N6 E1C2N6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 221 (82.9 bits), Expect = 4.0e-37, Sum P(2) = 4.0e-37
 Identities = 42/62 (67%), Positives = 52/62 (83%)

Query:    82 DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
             + SD +SEP + LKRKQRRSRTTFT+ QLEELE++F+R+HYPDIYTRE LA +  +TE R
Sbjct:   203 EGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEAR 262

Query:   142 VQ 143
             VQ
Sbjct:   263 VQ 264

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

WB|WBGene00006870 vab-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 258 (95.9 bits), Expect = 2.4e-36, Sum P(2) = 2.4e-36
 Identities = 49/76 (64%), Positives = 62/76 (81%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
             +A  G RPC ISR L+VS+GCVSKIL RY E+G+IRP  IGGSKPRVAT DV ++IE+YK
Sbjct:    33 LAHKGCRPCDISRLLQVSNGCVSKILCRYYESGTIRPRAIGGSKPRVATSDVVEKIEDYK 92

Query:    61 KTNPNITSWEVRDKLI 76
             +  P+I +WE+RDKL+
Sbjct:    93 RDQPSIFAWEIRDKLL 108

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

GO:0005634 "nucleus" evidence=IEA;IDA

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0040039 "inductive cell migration" evidence=IMP

GO:0009952 "anterior/posterior pattern specification" evidence=IMP

GO:0045138 "tail tip morphogenesis" evidence=IMP

GO:0045165 "cell fate commitment" evidence=IMP

GO:0030155 "regulation of cell adhesion" evidence=IMP

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

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P09083	GSBN_DROME	No assigned EC number	0.6	0.8773	0.3184	yes	N/A
Q28DP6	PAX3_XENTR	No assigned EC number	0.55	0.8773	0.3101	yes	N/A
P47239	PAX7_MOUSE	No assigned EC number	0.5427	0.8773	0.2842	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	163
pfam00292	125	pfam00292, PAX, 'Paired box' domain	1e-47
cd00131	128	cd00131, PAX, Paired Box domain	2e-45
smart00351	125	smart00351, PAX, Paired Box domain	1e-42
pfam00046	57	pfam00046, Homeobox, Homeobox domain	3e-16
smart00389	57	smart00389, HOX, Homeodomain	7e-14
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-13
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	2e-05

>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain

 Score =  150 bits (380), Expect = 1e-47
 Identities = 61/92 (66%), Positives = 73/92 (79%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A +GVRPC ISRQLRVSHGCVSKIL RYQETGSIRPGVIGGSKP+VATP+V K+I EYK
Sbjct: 29  LAHSGVRPCDISRQLRVSHGCVSKILGRYQETGSIRPGVIGGSKPKVATPEVVKKIAEYK 88

Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
           + NP I +WE+RD+L+     D+ +  S   I
Sbjct: 89  RENPGIFAWEIRDRLLAEGVCDNDNVPSVSSI 120

Length = 125

>gnl|CDD|238076 cd00131, PAX, Paired Box domain

 Score =  144 bits (366), Expect = 2e-45
 Identities = 60/92 (65%), Positives = 73/92 (79%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A +G+RPC ISRQLRVSHGCVSKILNRY ETGSIRPG IGGSKPRVATP+V K+IE YK
Sbjct: 29  LAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYK 88

Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
           + NP + +WE+RD+L++    D S+  S   I
Sbjct: 89  QENPGMFAWEIRDRLLQEGVCDKSNVPSVSSI 120

Length = 128

>gnl|CDD|128645 smart00351, PAX, Paired Box domain

 Score =  137 bits (348), Expect = 1e-42
 Identities = 54/77 (70%), Positives = 63/77 (81%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A  GVRPC ISRQL VSHGCVSKIL RY ETGSIRPG IGGSKP+VATP V K+I +YK
Sbjct: 29  LAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88

Query: 61  KTNPNITSWEVRDKLIK 77
           + NP I +WE+RD+L+ 
Sbjct: 89  QENPGIFAWEIRDRLLS 105

Length = 125

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

 Score = 67.9 bits (167), Expect = 3e-16
 Identities = 26/45 (57%), Positives = 32/45 (71%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RR RTTFT  QLEELEK F+++ YP    RE LA K G+TE +V+
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 62.3 bits (152), Expect = 7e-14
 Identities = 25/46 (54%), Positives = 33/46 (71%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           +RR RT+FT  QLEELEK FQ++ YP    RE LA K G++E +V+
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46

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 = 61.9 bits (151), Expect = 1e-13
 Identities = 24/45 (53%), Positives = 31/45 (68%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RR RT FT  QLEELEK F+++ YP    RE LA + G+TE +V+
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45

Length = 59

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 27/72 (37%)

Query: 72  RDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREAL 131
             K  +     DS+ + E         +  R   T  QL  LE+ F+ + YP   TR  L
Sbjct: 25  TTKNKREVEAADSEMKLERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKL 84

Query: 132 ANKFGMTETRVQ 143
           +    M    VQ
Sbjct: 85  SLLLNMPPKSVQ 96

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	163
KOG0849|consensus	354		99.96
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	99.93
KOG3517|consensus	334		99.91
KOG0484|consensus	125		99.87
KOG0488|consensus	309		99.87
KOG0489|consensus	261		99.86
KOG0842|consensus	307		99.85
KOG0850|consensus	245		99.85
KOG0485|consensus	268		99.83
KOG0493|consensus	342		99.83
KOG0843|consensus	197		99.83
KOG0487|consensus	308		99.83
KOG0494|consensus	332		99.81
KOG0492|consensus	246		99.81
KOG3862|consensus	327		99.8
KOG2251|consensus	228		99.79
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.73
KOG0844|consensus	408		99.72
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.71
KOG0848|consensus	317		99.71
KOG0491|consensus	194		99.69
cd00131	128	PAX Paired Box domain	99.65
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.63
KOG0486|consensus	351		99.63
smart00351	125	PAX Paired Box domain.	99.62
KOG3802|consensus	398		99.6
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.6
KOG0483|consensus	198		99.58
COG5576	156	Homeodomain-containing transcription factor [Trans	99.54
KOG0847|consensus	288		99.52
KOG4577|consensus	383		99.48
KOG0490|consensus	235		99.47
KOG1168|consensus	385		99.21
KOG2252|consensus	558		99.21
COG3415	138	Transposase and inactivated derivatives [DNA repli	99.02
KOG0775|consensus	304		98.9
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	98.84
KOG0774|consensus	334		98.7
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.64
PF13551	112	HTH_29: Winged helix-turn helix	98.64
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	98.34
KOG0490|consensus	235		98.29
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	98.15
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	97.93
PF13518	52	HTH_28: Helix-turn-helix domain	97.86
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.84
KOG1146|consensus	1406		97.57
PF13565	77	HTH_32: Homeodomain-like domain	97.42
PRK09413	121	IS2 repressor TnpA; Reviewed	97.39
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	97.31
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	97.31
PHA02591	83	hypothetical protein; Provisional	97.03
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	96.86
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.84
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	96.78
KOG0773|consensus	342		96.77
PRK15418	318	transcriptional regulator LsrR; Provisional	96.73
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.69
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.64
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.61
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	96.48
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.43
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	96.38
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	96.32
COG2522	119	Predicted transcriptional regulator [General funct	96.29
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	96.21
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	96.12
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	96.11
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	96.09
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	96.07
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	96.04
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	95.92
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	95.9
PHA00542	82	putative Cro-like protein	95.89
PHA01976	67	helix-turn-helix protein	95.87
PRK10072	96	putative transcriptional regulator; Provisional	95.83
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	95.82
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	95.81
PF12728	51	HTH_17: Helix-turn-helix domain	95.81
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	95.78
COG2944	104	Predicted transcriptional regulator [Transcription	95.77
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.74
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	95.72
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	95.71
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.7
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	95.69
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	95.62
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.59
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.49
PRK04217	110	hypothetical protein; Provisional	95.44
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	95.42
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.38
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	95.36
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.35
PF10668	60	Phage_terminase: Phage terminase small subunit; In	95.33
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	95.29
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	95.26
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	95.26
TIGR02607	78	antidote_HigA addiction module antidote protein, H	95.21
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	95.07
PRK00118	104	putative DNA-binding protein; Validated	95.07
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	95.03
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	95.01
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.0
PHA02535	581	P terminase ATPase subunit; Provisional	95.0
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	94.97
TIGR01764	49	excise DNA binding domain, excisionase family. An	94.96
PRK11050	152	manganese transport regulator MntR; Provisional	94.9
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.88
PHA00738	108	putative HTH transcription regulator	94.87
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	94.83
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	94.82
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.81
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	94.81
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	94.77
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	94.76
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	94.74
PF13730	55	HTH_36: Helix-turn-helix domain	94.69
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	94.64
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	94.64
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	94.58
TIGR02844	80	spore_III_D sporulation transcriptional regulator	94.54
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	94.53
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	94.5
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	94.5
KOG3623|consensus	1007		94.49
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	94.42
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	94.41
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	94.4
PRK09726	88	antitoxin HipB; Provisional	94.32
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	94.3
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	94.28
PRK03975	141	tfx putative transcriptional regulator; Provisiona	94.26
PHA00675	78	hypothetical protein	94.2
COG2963	116	Transposase and inactivated derivatives [DNA repli	94.2
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	94.14
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.13
PRK11169	164	leucine-responsive transcriptional regulator; Prov	94.11
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	94.09
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	94.05
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	93.97
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	93.91
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	93.9
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	93.9
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	93.81
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	93.79
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	93.76
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	93.68
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	93.66
PF14493	91	HTH_40: Helix-turn-helix domain	93.66
PRK09706	135	transcriptional repressor DicA; Reviewed	93.65
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.61
PRK09492	315	treR trehalose repressor; Provisional	93.53
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	93.49
PRK13890	120	conjugal transfer protein TrbA; Provisional	93.47
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	93.45
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	93.43
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	93.39
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	93.38
PRK01381	99	Trp operon repressor; Provisional	93.3
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	93.27
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	93.27
PRK11014	141	transcriptional repressor NsrR; Provisional	93.26
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	93.21
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	93.21
PRK03573	144	transcriptional regulator SlyA; Provisional	93.2
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	93.15
PRK06424	144	transcription factor; Provisional	93.13
PF14502	48	HTH_41: Helix-turn-helix domain	93.11
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	93.1
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	92.98
PRK09526	342	lacI lac repressor; Reviewed	92.98
PF02376	87	CUT: CUT domain; InterPro: IPR003350 A class, also	92.97
COG3620	187	Predicted transcriptional regulator with C-termina	92.89
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	92.86
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	92.79
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	92.68
PRK14987	331	gluconate operon transcriptional regulator; Provis	92.65
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	92.61
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	92.59
COG1476	68	Predicted transcriptional regulators [Transcriptio	92.53
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	92.52
PRK08359	176	transcription factor; Validated	92.46
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	92.14
PF13309	64	HTH_22: HTH domain	92.03
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	92.03
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	91.98
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	91.98
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	91.93
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	91.9
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	91.86
PRK10423	327	transcriptional repressor RbsR; Provisional	91.75
PRK14165	217	winged helix-turn-helix domain-containing protein/	91.74
TIGR00270	154	conserved hypothetical protein TIGR00270.	91.72
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	91.62
TIGR00180	187	parB_part ParB-like partition proteins. This model	91.52
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	91.37
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	91.34
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	91.21
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	91.19
PRK10870	176	transcriptional repressor MprA; Provisional	91.13
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	91.12
PRK03902	142	manganese transport transcriptional regulator; Pro	90.93
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	90.93
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	90.87
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	90.78
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	90.76
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	90.69
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	90.68
COG1522	154	Lrp Transcriptional regulators [Transcription]	90.66
COG1342	99	Predicted DNA-binding proteins [General function p	90.63
PRK01905	77	DNA-binding protein Fis; Provisional	90.33
PRK00215	205	LexA repressor; Validated	90.27
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	90.24
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	90.19
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	90.19
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	90.16
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	90.08
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	90.0
PRK15431	78	ferrous iron transport protein FeoC; Provisional	89.99
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	89.92
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	89.92
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	89.9
PF08765	108	Mor: Mor transcription activator family; InterPro:	89.82
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	89.79
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	89.79
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	89.76
COG3093	104	VapI Plasmid maintenance system antidote protein [	89.68
PRK13182	175	racA polar chromosome segregation protein; Reviewe	89.64
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	89.61
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	89.6
PRK15320	251	transcriptional activator SprB; Provisional	89.46
PRK11569	274	transcriptional repressor IclR; Provisional	89.46
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	89.39
COG1959	150	Predicted transcriptional regulator [Transcription	89.35
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	89.34
PRK00430	95	fis global DNA-binding transcriptional dual regula	89.28
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	89.19
COG3355	126	Predicted transcriptional regulator [Transcription	89.16
PRK13509	251	transcriptional repressor UlaR; Provisional	89.13
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	89.05
COG5606	91	Uncharacterized conserved small protein [Function	89.03
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	88.99
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	88.97
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	88.97
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	88.87
PRK12511	182	RNA polymerase sigma factor; Provisional	88.82
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	88.72
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	88.62
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	88.62
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	88.59
PRK12516	187	RNA polymerase sigma factor; Provisional	88.57
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	88.48
PRK13777	185	transcriptional regulator Hpr; Provisional	88.38
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	88.32
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	88.26
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	88.19
PRK12533	216	RNA polymerase sigma factor; Provisional	88.17
PRK06474	178	hypothetical protein; Provisional	88.16
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	88.13
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	88.1
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	88.04
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	87.96
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	87.78
COG1414	246	IclR Transcriptional regulator [Transcription]	87.68
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	87.62
PRK15043	243	transcriptional regulator MirA; Provisional	87.62
COG1609	333	PurR Transcriptional regulators [Transcription]	87.53
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	87.47
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	87.22
PRK04140	317	hypothetical protein; Provisional	87.2
COG2524	294	Predicted transcriptional regulator, contains C-te	87.04
COG2452	193	Predicted site-specific integrase-resolvase [DNA r	86.88
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	86.83
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	86.66
PRK12540	182	RNA polymerase sigma factor; Provisional	86.64
COG3677	129	Transposase and inactivated derivatives [DNA repli	86.52
PRK09391	230	fixK transcriptional regulator FixK; Provisional	86.5
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	86.44
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	86.2
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	86.2
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	85.98
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	85.96
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	85.93
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	85.86
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	85.84
PRK08241	339	RNA polymerase factor sigma-70; Validated	85.69
PF04645	181	DUF603: Protein of unknown function, DUF603; Inter	85.59
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	85.54
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	85.44
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	85.35
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	85.31
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	85.25
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	85.16
COG3888	321	Predicted transcriptional regulator [Transcription	85.07
PRK12423	202	LexA repressor; Provisional	85.04
PRK09334	86	30S ribosomal protein S25e; Provisional	85.03
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	84.96
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	84.84
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	84.79
PHA02943	165	hypothetical protein; Provisional	84.71
COG1356	143	tfx Transcriptional regulator [DNA replication, re	84.66
PRK11922	231	RNA polymerase sigma factor; Provisional	84.64
COG5484	279	Uncharacterized conserved protein [Function unknow	84.53
COG1846	126	MarR Transcriptional regulators [Transcription]	84.41
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	84.28
TIGR03338	212	phnR_burk phosphonate utilization associated trans	84.26
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	84.21
PRK11013	309	DNA-binding transcriptional regulator LysR; Provis	84.13
TIGR02054	120	MerD mercuric resistence transcriptional repressor	83.96
PF09048	59	Cro: Cro; InterPro: IPR000655 Bacteriophage lambda	83.95
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	83.89
PRK09954	362	putative kinase; Provisional	83.89
PRK12546	188	RNA polymerase sigma factor; Provisional	83.78
PRK09906	296	DNA-binding transcriptional regulator HcaR; Provis	83.54
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	83.53
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	83.47
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	83.47
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	83.44
COG1813	165	Predicted transcription factor, homolog of eukaryo	83.44
PRK12682	309	transcriptional regulator CysB-like protein; Revie	83.35
PRK15201	198	fimbriae regulatory protein FimW; Provisional	83.32
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	83.22
PRK06704	228	RNA polymerase factor sigma-70; Validated	83.22
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	83.21
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	83.14
TIGR03339	279	phn_lysR aminoethylphosphonate catabolism associat	83.09
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	83.02
PF06322	64	Phage_NinH: Phage NinH protein; InterPro: IPR01045	82.97
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	82.96
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	82.93
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	82.84
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	82.76
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	82.74
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	82.4
PRK11233	305	nitrogen assimilation transcriptional regulator; P	82.27
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	81.96
COG3655	73	Predicted transcriptional regulator [Transcription	81.78
PRK11151	305	DNA-binding transcriptional regulator OxyR; Provis	81.6
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	81.56
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	81.32
PRK13832	520	plasmid partitioning protein; Provisional	81.27
PF12964	96	DUF3853: Protein of unknown function (DUF3853); In	81.14
COG2345	218	Predicted transcriptional regulator [Transcription	80.87
PRK09791	302	putative DNA-binding transcriptional regulator; Pr	80.86
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	80.78
PRK12684	313	transcriptional regulator CysB-like protein; Revie	80.69
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	80.52
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	80.39
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	80.31
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	80.25
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	80.21
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	80.12
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	80.1
PRK10840	216	transcriptional regulator RcsB; Provisional	80.03
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	80.02

>KOG0849|consensus

Probab=99.96  E-value=1.1e-29  Score=199.78  Aligned_cols=158  Identities=56%  Similarity=0.911  Sum_probs=139.5

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC-cCChHHHHHHHHHHHhCCCCCchhhhhhhhhhc
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEYKKTNPNITSWEVRDKLIKVS   79 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~-~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~   79 (163)
                      ||..|++||+|++.|.||++||++||++|.++|++.|+.+||.+|+ +.++.++..|.+++.++|++++|++++.+..+.
T Consensus        27 ~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~~~  106 (354)
T KOG0849|consen   27 MAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLHEG  106 (354)
T ss_pred             ccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccCcc
Confidence            6789999999999999999999999999999999999999999999 889999999999999999999999999999873


Q ss_pred             cCC----------------------C-----------------------------CCCCCCCccccccccccccCcCCHH
Q psy1904          80 RLD----------------------D-----------------------------SDTESEPGIVLKRKQRRSRTTFTSA  108 (163)
Q Consensus        80 ~~~----------------------~-----------------------------~~~~~~~~~~~~~~~rr~Rt~~t~~  108 (163)
                      .++                      .                             .+.+..+.....++.+|.||+|+..
T Consensus       107 ~~~~~t~Ps~ssi~r~~r~~~~~~d~~~~~~~~~~~~~~~~~~~~gs~~~~s~~~~~~~~~p~~~~~~~~rr~rtsft~~  186 (354)
T KOG0849|consen  107 LCTQATLPSVSSINRVLRNGALGKDQGLPSQQVTKEKSPSISGALGSQAGASLLSADDEEPPGYALQRGGRRNRTSFSPS  186 (354)
T ss_pred             cccCCCCCChhhhhHHhhccccccccccccccccccccCCcccccCCccccccccCCccccccccccccccccccccccc
Confidence            331                      1                             0001112223346678889999999


Q ss_pred             HHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904         109 QLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus       109 q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      |+..|+..|+.++||++..|+.||.++++++..|.|||+|+|++++|+..
T Consensus       187 Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  187 QLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             hHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            99999999999999999999999999999999999999999999999874

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]

Probab=99.93  E-value=6e-27  Score=156.96  Aligned_cols=90  Identities=67%  Similarity=1.094  Sum_probs=67.0

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      ||++|++|||||++|.||++||+|||++|+|||++.||.+||++|++.++.+++.|.+++.++|.+++||+++.|..+.-
T Consensus        29 la~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~~gv  108 (125)
T PF00292_consen   29 LAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIADGV  108 (125)
T ss_dssp             HHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTS
T ss_pred             HhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHHcCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCCCCCCCCC
Q psy1904          81 LDDSDTESEP   90 (163)
Q Consensus        81 ~~~~~~~~~~   90 (163)
                      ++.++.++.+
T Consensus       109 c~~~~~Psvs  118 (125)
T PF00292_consen  109 CDRSNVPSVS  118 (125)
T ss_dssp             S-TTTS--HH
T ss_pred             CCCCCCCCHH
Confidence            8877665543

Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.

>KOG3517|consensus

Probab=99.91  E-value=3.1e-25  Score=162.17  Aligned_cols=91  Identities=58%  Similarity=0.955  Sum_probs=85.1

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      ||+-|++||||+|+|.||++||||||.||.|||++-||.+||++|++.++.+++.|.++++.+|++++||++|+|..+.-
T Consensus        32 LarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgi  111 (334)
T KOG3517|consen   32 LARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGI  111 (334)
T ss_pred             HHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhhccc
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCCCCCCCCCc
Q psy1904          81 LDDSDTESEPG   91 (163)
Q Consensus        81 ~~~~~~~~~~~   91 (163)
                      ||..+.++.++
T Consensus       112 CDk~NvPSVSS  122 (334)
T KOG3517|consen  112 CDKYNVPSVSS  122 (334)
T ss_pred             ccccCCcchHH
Confidence            87666555443

>KOG0484|consensus

Probab=99.87  E-value=1.1e-23  Score=134.49  Aligned_cols=65  Identities=54%  Similarity=0.716  Sum_probs=61.3

Q ss_pred             ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ..++|+||.||.||..||.+||+.|.+.+||++.+|++||..++|++..|+|||||||+|.++|.
T Consensus        12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE   76 (125)
T KOG0484|consen   12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE   76 (125)
T ss_pred             hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence            34678899999999999999999999999999999999999999999999999999999998864

>KOG0488|consensus

Probab=99.87  E-value=3.7e-23  Score=159.74  Aligned_cols=66  Identities=30%  Similarity=0.446  Sum_probs=62.7

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      ++|.|+.||+||..|+..||+.|++.+|++..+|.+||..|||+..|||+||||||+||||+...+
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g  234 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG  234 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence            477888999999999999999999999999999999999999999999999999999999988763

>KOG0489|consensus

Probab=99.86  E-value=3.8e-23  Score=157.04  Aligned_cols=62  Identities=29%  Similarity=0.326  Sum_probs=58.8

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      +.||.||.||..|+.+||+.|+.|+|+++..|.+||..|.|+|+|||||||||||||||.-.
T Consensus       158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k  219 (261)
T KOG0489|consen  158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK  219 (261)
T ss_pred             CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence            46899999999999999999999999999999999999999999999999999999997543

>KOG0842|consensus

Probab=99.85  E-value=2.9e-22  Score=152.72  Aligned_cols=63  Identities=32%  Similarity=0.409  Sum_probs=59.6

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+++||.|..||..|+.+||+.|.+++|++.++|++||..|.||++||||||||||.|.||+-
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~  212 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ  212 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence            556778899999999999999999999999999999999999999999999999999999864

>KOG0850|consensus

Probab=99.85  E-value=1.7e-22  Score=146.28  Aligned_cols=69  Identities=29%  Similarity=0.443  Sum_probs=64.1

Q ss_pred             cccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCCC
Q psy1904          94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSG  162 (163)
Q Consensus        94 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~~  162 (163)
                      +.+|.|+.||.|+..||..|.+.|++++|+-.++|.+||..|||+.+||||||||||.|.||.+..+++
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            346778899999999999999999999999999999999999999999999999999999998886553

>KOG0485|consensus

Probab=99.83  E-value=5.2e-22  Score=142.50  Aligned_cols=65  Identities=25%  Similarity=0.347  Sum_probs=60.8

Q ss_pred             cccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        94 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      ...++|+.||+|+..|+..||..|+...|++..+|.-||.+|.|+|+||||||||||.||||+..
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a  164 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA  164 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence            34467789999999999999999999999999999999999999999999999999999999764

>KOG0493|consensus

Probab=99.83  E-value=7.8e-22  Score=145.13  Aligned_cols=97  Identities=19%  Similarity=0.355  Sum_probs=72.9

Q ss_pred             hCCCCC-chhhhhhhhhhccCCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcc
Q psy1904          62 TNPNIT-SWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTET  140 (163)
Q Consensus        62 ~~p~~~-~~e~~~~l~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~  140 (163)
                      +.|.|+ +|.+|.++.+......-.-..-......+--+|+||.||.+||..|+..|+.|.|++...|.+||.+|+|.|.
T Consensus       209 ~~p~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEs  288 (342)
T KOG0493|consen  209 AQPSMWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNES  288 (342)
T ss_pred             cCccccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHH
Confidence            345565 7999998876433221110000000011224688999999999999999999999999999999999999999


Q ss_pred             cccccccccccccccCCC
Q psy1904         141 RVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus       141 ~v~~WFqnrR~k~kr~~~  158 (163)
                      ||||||||+|+|.||.--
T Consensus       289 QIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  289 QIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             HhhHHhhhhhhhhhhccC
Confidence            999999999999998543

>KOG0843|consensus

Probab=99.83  E-value=1.4e-21  Score=136.64  Aligned_cols=60  Identities=28%  Similarity=0.385  Sum_probs=57.8

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +.+|.||+||.+||..||..|+.++|....+|+.||..|+|++.||||||||||.|.||.
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~  160 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRM  160 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHH
Confidence            678999999999999999999999999999999999999999999999999999999873

>KOG0487|consensus

Probab=99.83  E-value=2.1e-21  Score=148.00  Aligned_cols=66  Identities=24%  Similarity=0.236  Sum_probs=61.8

Q ss_pred             cccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          92 IVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        92 ~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ....+..|++|..+|+.|+.+||+.|..|.|++...|.+|+..|+|+++||||||||||+|.||..
T Consensus       229 ~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~  294 (308)
T KOG0487|consen  229 ASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN  294 (308)
T ss_pred             cccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence            344567889999999999999999999999999999999999999999999999999999999875

>KOG0494|consensus

Probab=99.81  E-value=7.9e-21  Score=139.72  Aligned_cols=68  Identities=44%  Similarity=0.658  Sum_probs=63.2

Q ss_pred             cccccc-cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCCCC
Q psy1904          96 RKQRRS-RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSGR  163 (163)
Q Consensus        96 ~~~rr~-Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~~~  163 (163)
                      +++||. ||.||..|+++||+.|++.+||+...|+.||..+.|.|.+|+|||||||+||+|-...|||+
T Consensus       138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s  206 (332)
T KOG0494|consen  138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS  206 (332)
T ss_pred             ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence            334454 99999999999999999999999999999999999999999999999999999999999874

>KOG0492|consensus

Probab=99.81  E-value=7.8e-21  Score=135.59  Aligned_cols=64  Identities=27%  Similarity=0.403  Sum_probs=59.6

Q ss_pred             ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .+++.+|++||.||.+||..||+.|.+.+|+++.+|.+++..|.||++||||||||||+|.||.
T Consensus       139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl  202 (246)
T KOG0492|consen  139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL  202 (246)
T ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence            3445678899999999999999999999999999999999999999999999999999999873

>KOG3862|consensus

Probab=99.80  E-value=3.2e-20  Score=137.27  Aligned_cols=85  Identities=66%  Similarity=1.109  Sum_probs=80.6

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      ||+.|++|||||++|.|||||||+||.+|.|||+++||.+||++|.+.++-+++.|..+++++|.|++||+++.+..+.-
T Consensus        37 La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~i  116 (327)
T KOG3862|consen   37 LAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPI  116 (327)
T ss_pred             HHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999866


Q ss_pred             CCCCC
Q psy1904          81 LDDSD   85 (163)
Q Consensus        81 ~~~~~   85 (163)
                      ++.+.
T Consensus       117 c~~d~  121 (327)
T KOG3862|consen  117 CDNDT  121 (327)
T ss_pred             cCCCC
Confidence            65444

>KOG2251|consensus

Probab=99.79  E-value=3.3e-20  Score=133.82  Aligned_cols=64  Identities=44%  Similarity=0.589  Sum_probs=60.9

Q ss_pred             ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ..+++.||.||.|+..|+++||..|.+.+||++..|++||.+|+|.+.+|+|||.|||+|++++
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q   95 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ   95 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence            4467899999999999999999999999999999999999999999999999999999999864

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.73  E-value=6.4e-19  Score=104.25  Aligned_cols=57  Identities=37%  Similarity=0.536  Sum_probs=54.7

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      |+.|+.||.+|+..|+..|..++||+..++..||..+||+..+|++||+|+|.++|+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            478899999999999999999999999999999999999999999999999999875

; 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 ....

>KOG0844|consensus

Probab=99.72  E-value=1.1e-18  Score=131.28  Aligned_cols=64  Identities=28%  Similarity=0.306  Sum_probs=60.3

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      ..-||.||.||.+|+..||+.|-+..|.+++.|.+||..|+|+|..|||||||||+|.|||.-.
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            4578999999999999999999999999999999999999999999999999999999998543

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.71  E-value=9.5e-18  Score=98.23  Aligned_cols=52  Identities=17%  Similarity=0.291  Sum_probs=50.4

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCC----CCHHHHHHHHHHhCCCcccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHY----PDIYTREALANKFGMTETRVQQFVLGTA  150 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~----p~~~~r~~la~~l~l~~~~v~~WFqnrR  150 (163)
                      +|.||.||.+|+..|+..|+.+.|    |+..++.+||..+||++.+|+|||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            688999999999999999999999    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.

>KOG0848|consensus

Probab=99.71  E-value=1.5e-18  Score=128.23  Aligned_cols=61  Identities=28%  Similarity=0.383  Sum_probs=56.7

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +.+-+.|.+||..|..+||+.|..++|.++..+.+||.-|+|+|+||||||||||+|++|.
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~  257 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD  257 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence            3444679999999999999999999999999999999999999999999999999999764

>KOG0491|consensus

Probab=99.69  E-value=1.1e-18  Score=120.52  Aligned_cols=62  Identities=31%  Similarity=0.452  Sum_probs=58.7

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      +.++.||+|+..|+..|++.|+...|++..++.+||..|+|++.|||.||||||+|.||++.
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r  160 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR  160 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999999999999999999999998765

>cd00131 PAX Paired Box domain

Probab=99.65  E-value=4.1e-16  Score=106.70  Aligned_cols=77  Identities=73%  Similarity=1.236  Sum_probs=70.6

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKV   78 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~   78 (163)
                      +.+|+++++||++|+||.+||++|+++|+++|++.|++.||.+|+..++..+..+..+.+++|+.+++|+++.|.++
T Consensus        30 ~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~  106 (128)
T cd00131          30 AQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQE  106 (128)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHc
Confidence            46899999999999999999999999999999999999988888888888888888889999999999999998754

>smart00389 HOX Homeodomain

Probab=99.63  E-value=1.7e-16  Score=93.42  Aligned_cols=55  Identities=44%  Similarity=0.643  Sum_probs=52.2

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      +.|+.|+..|+..|+..|..++||+..++..||..+||+..+|++||+|+|++.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5678899999999999999999999999999999999999999999999999864

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

>KOG0486|consensus

Probab=99.63  E-value=1.3e-16  Score=120.56  Aligned_cols=62  Identities=45%  Similarity=0.580  Sum_probs=59.0

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .|+||.||.||.+|+.+||..|++|.||+...|++||.-++|+|..|+|||.|||+||+|..
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE  171 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE  171 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence            37889999999999999999999999999999999999999999999999999999998754

>smart00351 PAX Paired Box domain

Probab=99.62  E-value=2.1e-15  Score=102.83  Aligned_cols=77  Identities=70%  Similarity=1.177  Sum_probs=71.3

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKV   78 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~   78 (163)
                      ..+|.+..+||++||||.+||++|+++|+++|++.|.+.||.+|...++.....|..+.+++|+++++++++.|.+.
T Consensus        30 ~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~  106 (125)
T smart00351       30 AQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSE  106 (125)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHc
Confidence            35899999999999999999999999999999999999998888888888888888899999999999999999854

>KOG3802|consensus

Probab=99.60  E-value=8.4e-16  Score=119.89  Aligned_cols=62  Identities=18%  Similarity=0.231  Sum_probs=59.6

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      ++|++||.|.......||.+|.+|+.|+..+..+||.+|+|....|+|||+|||.|.||--+
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            67889999999999999999999999999999999999999999999999999999999766

>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=99.60  E-value=5.1e-16  Score=92.18  Aligned_cols=57  Identities=42%  Similarity=0.630  Sum_probs=53.9

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|.+.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            467899999999999999999999999999999999999999999999999998764

>KOG0483|consensus

Probab=99.58  E-value=9.9e-16  Score=110.95  Aligned_cols=55  Identities=22%  Similarity=0.302  Sum_probs=52.0

Q ss_pred             ccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904         101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus       101 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ++-.|+.+|+..||..|+.+.|+....+..||..|||.++||.|||||||||||.
T Consensus        53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~  107 (198)
T KOG0483|consen   53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKT  107 (198)
T ss_pred             ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccc
Confidence            3457899999999999999999999999999999999999999999999999985

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.54  E-value=3.5e-15  Score=104.68  Aligned_cols=59  Identities=25%  Similarity=0.264  Sum_probs=54.1

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .+++|+.-|.+|+.+|++.|+.++||+..+|..|+..++|++..|+|||||+|++.|+.
T Consensus        51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~  109 (156)
T COG5576          51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK  109 (156)
T ss_pred             CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence            34556667999999999999999999999999999999999999999999999998753

>KOG0847|consensus

Probab=99.52  E-value=2.6e-15  Score=108.36  Aligned_cols=62  Identities=27%  Similarity=0.390  Sum_probs=57.0

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+++..|.+|+-.|+..||..|+..+|+-..++.+||..+|+++.||+|||||||.||+|..
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh  226 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH  226 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence            34556788999999999999999999999999999999999999999999999999998743

>KOG4577|consensus

Probab=99.48  E-value=1.6e-14  Score=108.14  Aligned_cols=61  Identities=28%  Similarity=0.334  Sum_probs=57.7

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ..+|+||++|..||+-|+.+|...+.|.+..|+.|+..+||..+.|+|||||||+|.||.-
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK  226 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK  226 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence            3579999999999999999999999999999999999999999999999999999998743

>KOG0490|consensus

Probab=99.47  E-value=2e-14  Score=107.62  Aligned_cols=63  Identities=33%  Similarity=0.356  Sum_probs=59.8

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ..++++.||.|+..|+.+|++.|+..+||+...++.||..+++++..|+|||||+|+||+++.
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            456789999999999999999999999999999999999999999999999999999998765

>KOG1168|consensus

Probab=99.21  E-value=4.7e-12  Score=95.12  Aligned_cols=64  Identities=19%  Similarity=0.211  Sum_probs=58.8

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      .++|+||.+-.-....||..|...+.|+......||.+|+|....|+|||+|.|.|.||.-.|.
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            3568899999999999999999999999999999999999999999999999999999865544

>KOG2252|consensus

Probab=99.21  E-value=2.4e-11  Score=98.48  Aligned_cols=132  Identities=17%  Similarity=0.275  Sum_probs=89.5

Q ss_pred             cCCCChhhhHH-HhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCc--hhhhhhhhhhc
Q psy1904           3 AAGVRPCVISR-QLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITS--WEVRDKLIKVS   79 (163)
Q Consensus         3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~--~e~~~~l~~~~   79 (163)
                      ..+|.++..|+ +|+.|+||+|.||...+....+.-|    .   .....+..++    + .|.+..  +.++..-.  .
T Consensus       341 ~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsG----R---etFrRM~~WL----~-eP~~~r~m~~L~~~a~--k  406 (558)
T KOG2252|consen  341 RYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSG----R---ETFRRMANWL----E-EPEFQRLMSALRKKAC--K  406 (558)
T ss_pred             hcCCcHHHHHHHHhhcccchHHHHhhCCCchhhhccc----c---HHHHHHHHHh----c-CHHHHHHHHHHHHHHh--h
Confidence            35789999998 8999999999999776555555543    1   1112222222    1 222111  11211111  1


Q ss_pred             cCCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccc
Q psy1904          80 RLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFL  153 (163)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~  153 (163)
                      +.+.     ++.....-..+++|.+||..|..-|...|+.+++|+..+.+.|+.+|+|....|.+||-|-|.+.
T Consensus       407 Rke~-----ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  407 RKEQ-----EPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             hccc-----CCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            1111     11111222456779999999999999999999999999999999999999999999999988773

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=99.02  E-value=9.6e-10  Score=75.61  Aligned_cols=76  Identities=21%  Similarity=0.176  Sum_probs=62.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      .|+|..+||++||||.+||++|+++++++|...|...++++|+..+....+.+.+..++.. ++.-+++..+..+..
T Consensus        20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~~e~g   95 (138)
T COG3415          20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELGLEFG   95 (138)
T ss_pred             cCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHhhhcC
Confidence            7999999999999999999999999999999988888889999888888887766665544 666666666554433

>KOG0775|consensus

Probab=98.90  E-value=1e-09  Score=82.07  Aligned_cols=55  Identities=20%  Similarity=0.246  Sum_probs=48.6

Q ss_pred             cccCcCCHHH---------HHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904         100 RSRTTFTSAQ---------LEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus       100 r~Rt~~t~~q---------~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      -+||.+..++         ...|...|..++||+..++.+||+.+||+..||-+||.|||.+.+
T Consensus       169 lPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR  232 (304)
T KOG0775|consen  169 LPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR  232 (304)
T ss_pred             CCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence            3566655544         568999999999999999999999999999999999999999986

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=98.84  E-value=5.3e-09  Score=70.73  Aligned_cols=66  Identities=23%  Similarity=0.375  Sum_probs=55.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKL   75 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l   75 (163)
                      ..|.+++++|++|+||.+||.+|++ ..++|++.|.+.|+.  ..    ..+.+.++.+++|+++..|+...+
T Consensus        16 ~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~--Ki----d~~~L~~~v~~~pd~tl~Ela~~l   81 (119)
T PF01710_consen   16 EKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRK--KI----DRDELKALVEENPDATLRELAERL   81 (119)
T ss_pred             HccchHHHHHHHhCcHHHHHHHHHH-hcccccccccccccc--cc----cHHHHHHHHHHCCCcCHHHHHHHc
Confidence            3688999999999999999999999 778999999886654  21    244577889999999999988765

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>KOG0774|consensus

Probab=98.70  E-value=1.3e-08  Score=75.70  Aligned_cols=60  Identities=23%  Similarity=0.323  Sum_probs=55.5

Q ss_pred             cccccCcCCHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          98 QRRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+|+|..|+..-.++|...|   -.|+||+...+++||.+++++..||-.||.|.|-++||.+
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence            46788899999999999998   4679999999999999999999999999999999999865

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

Probab=98.64  E-value=4.4e-09  Score=57.14  Aligned_cols=35  Identities=17%  Similarity=0.403  Sum_probs=29.2

Q ss_pred             cCCCCCCHHHHHHHHHHhCCCcccccccccccccc
Q psy1904         118 QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGF  152 (163)
Q Consensus       118 ~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k  152 (163)
                      ..++||+..++..||..+||+..||..||-|.|.+
T Consensus         6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            35799999999999999999999999999998864

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

>PF13551 HTH_29: Winged helix-turn helix

Probab=98.64  E-value=1.1e-07  Score=63.12  Aligned_cols=64  Identities=31%  Similarity=0.519  Sum_probs=51.4

Q ss_pred             CccCCCC-hhhhHHHhhcchhhHHHHHhhhhhcc--CCCCCCCCCCCCCc-CChHHHHHHHHHHHhCC
Q psy1904           1 MAAAGVR-PCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRV-ATPDVEKRIEEYKKTNP   64 (163)
Q Consensus         1 ~~~~g~~-~~~ia~~~~vs~~~vs~~l~~~~~tG--~~~Pg~~Gg~~p~~-~~~~~~~~i~~~~~~~p   64 (163)
                      |..+|.+ +.+||+.||||..||++|+++|.+.|  .+.+...++.+|.. .++.+.+.+.++..++|
T Consensus         7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p   74 (112)
T PF13551_consen    7 LLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENP   74 (112)
T ss_pred             HHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCC
Confidence            3468996 99999999999999999999999999  56662223344444 68888888888888887

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=98.34  E-value=1.3e-07  Score=53.89  Aligned_cols=31  Identities=32%  Similarity=0.485  Sum_probs=20.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG   33 (163)
                      .+|.+..+||+.||||.+||++|+++|++.|
T Consensus        15 ~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G   45 (50)
T PF13384_consen   15 REGWSIREIAKRLGVSRSTVYRWIKRYREEG   45 (50)
T ss_dssp             HHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence            3599999999999999999999999999887

>KOG0490|consensus

Probab=98.29  E-value=4.4e-07  Score=67.85  Aligned_cols=62  Identities=39%  Similarity=0.516  Sum_probs=57.7

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ..+.++.|+.|+..|+..+...|..+++|+...+..|+..+++++..|++||+|+|++.++.
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~  211 (235)
T KOG0490|consen  150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH  211 (235)
T ss_pred             ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence            34677889999999999999999999999999999999999999999999999999998763

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=98.15  E-value=8.5e-06  Score=51.30  Aligned_cols=57  Identities=28%  Similarity=0.339  Sum_probs=40.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC---CCCCCCcCChHHHHHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI---GGSKPRVATPDVEKRIEEY   59 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~---Gg~~p~~~~~~~~~~i~~~   59 (163)
                      ++|++..++|+.||||..|++||+.+|++.|.-..-.-   ....|.-..+..+..|..+
T Consensus        23 ~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~l   82 (85)
T PF13011_consen   23 EQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIEL   82 (85)
T ss_pred             HcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHH
Confidence            47899999999999999999999999999886543221   1123333345555555444

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=97.93  E-value=3e-06  Score=47.24  Aligned_cols=27  Identities=33%  Similarity=0.444  Sum_probs=21.5

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      |..+|++..+||+.||||.+||+++|.
T Consensus        17 l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   17 LYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            346899999999999999999999985

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PF13518 HTH_28: Helix-turn-helix domain

Probab=97.86  E-value=1e-05  Score=46.17  Aligned_cols=32  Identities=28%  Similarity=0.449  Sum_probs=29.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      .+|.+..+||+.||||.++|++|+++|.+.|.
T Consensus        10 ~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen   10 LEGESVREIAREFGISRSTVYRWIKRYREGGI   41 (52)
T ss_pred             HcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence            36889999999999999999999999999884

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

Probab=97.84  E-value=1.4e-05  Score=44.35  Aligned_cols=26  Identities=31%  Similarity=0.376  Sum_probs=19.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++|++..+||+.||+|++||++.|++
T Consensus        18 ~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen   18 EQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            58999999999999999999999976

>KOG1146|consensus

Probab=97.57  E-value=3.3e-05  Score=68.97  Aligned_cols=60  Identities=17%  Similarity=0.250  Sum_probs=56.2

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .+++.||.++..||..+...|....||...+.+.|-..+++..+.|.+||||-|.|.++.
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~  961 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA  961 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence            356789999999999999999999999999999999999999999999999999998874

>PF13565 HTH_32: Homeodomain-like domain

Probab=97.42  E-value=0.0006  Score=42.07  Aligned_cols=57  Identities=26%  Similarity=0.359  Sum_probs=44.0

Q ss_pred             hHHHHHhhhhhcc-----CCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhc
Q psy1904          21 CVSKILNRYQETG-----SIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVS   79 (163)
Q Consensus        21 ~vs~~l~~~~~tG-----~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~   79 (163)
                      ||++|+++|++.|     +..+++..|.. +. ++...+.|.++..++|.++..++...+...-
T Consensus         1 Tv~rw~~ry~~~G~~gL~~~~~~~~~Grp-~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~   62 (77)
T PF13565_consen    1 TVYRWLKRYREEGLEGLKDRKRRPRPGRP-RK-DPEQRERIIALIEEHPRWTPREIAEYLEEEF   62 (77)
T ss_pred             CHHHHHHHHHhhCchhhhcccccCCCCCC-CC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Confidence            7999999999999     65444444433 44 6777788889999999999988888877643

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=97.39  E-value=0.00054  Score=46.32  Aligned_cols=35  Identities=20%  Similarity=0.214  Sum_probs=30.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..|.+..+||+.||||.+++++|.++|++.|....
T Consensus        27 ~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~   61 (121)
T PRK09413         27 EPGMTVSLVARQHGVAASQLFLWRKQYQEGSLTAV   61 (121)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccccc
Confidence            46899999999999999999999999987665443

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=97.31  E-value=0.00015  Score=42.61  Aligned_cols=27  Identities=26%  Similarity=0.273  Sum_probs=25.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|+++.+||+.|||+.+||+.|.+++
T Consensus        11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   11 LQGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            479999999999999999999999887

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>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=97.31  E-value=9.5e-05  Score=42.62  Aligned_cols=28  Identities=32%  Similarity=0.345  Sum_probs=22.0

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+.|.+.++||+.|||+.+||+.|++.-
T Consensus        19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen   19 LEEGESKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             HHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence            3578999999999999999999999753

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.

>PHA02591 hypothetical protein; Provisional

Probab=97.03  E-value=0.00038  Score=42.70  Aligned_cols=27  Identities=30%  Similarity=0.254  Sum_probs=24.9

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      |+..|+++.+||+.|||++.+|+++|.
T Consensus        55 L~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         55 LARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            567899999999999999999999984

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=96.86  E-value=0.0011  Score=39.14  Aligned_cols=32  Identities=34%  Similarity=0.449  Sum_probs=27.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ..++..+||+.|+||++||+..++++.+.|=+
T Consensus        21 ~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV   52 (60)
T PF01325_consen   21 GPVRTKDIAERLGVSPPTVTEMLKRLAEKGLV   52 (60)
T ss_dssp             SSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCccHHHHHHHHCCChHHHHHHHHHHHHCCCE
Confidence            45899999999999999999999999887755

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.84  E-value=0.0014  Score=33.53  Aligned_cols=28  Identities=25%  Similarity=0.387  Sum_probs=23.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETG   33 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG   33 (163)
                      ++..|||..+|++.-||||+|+++++.|
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~g   30 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQG   30 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcC
Confidence            5678999999999999999999998876

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.78  E-value=0.0062  Score=33.94  Aligned_cols=19  Identities=37%  Similarity=0.396  Sum_probs=17.8

Q ss_pred             hhhhHHHhhcchhhHHHHH
Q psy1904           8 PCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|||+..|||.+|||+.|
T Consensus         2 i~dIA~~agvS~~TVSr~l   20 (46)
T PF00356_consen    2 IKDIAREAGVSKSTVSRVL   20 (46)
T ss_dssp             HHHHHHHHTSSHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHH
Confidence            4699999999999999999

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>KOG0773|consensus

Probab=96.77  E-value=0.0011  Score=52.70  Aligned_cols=60  Identities=17%  Similarity=0.268  Sum_probs=48.4

Q ss_pred             cccccCcCCHHHHHHHHHh-cc--CCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          98 QRRSRTTFTSAQLEELEKS-FQ--RSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~-F~--~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ..|.+..+......+|+.. |+  ..+||+..++..||.++||+..||.+||-|.|.+..+.+
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence            3445557888888888766 22  357999999999999999999999999999998876543

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=96.73  E-value=0.0012  Score=51.87  Aligned_cols=37  Identities=24%  Similarity=0.400  Sum_probs=33.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .+|+.+.|||++||||..+|+|+|+.-++.|-+.-..
T Consensus        27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I   63 (318)
T PRK15418         27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQI   63 (318)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEE
Confidence            3799999999999999999999999999999886554

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=96.69  E-value=0.0011  Score=37.07  Aligned_cols=33  Identities=21%  Similarity=0.343  Sum_probs=27.3

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      ++.-...||||+.|++|+++|++-|+..++.|=
T Consensus        12 ~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~gl   44 (47)
T PF01022_consen   12 SEGPLTVSELAEELGLSQSTVSHHLKKLREAGL   44 (47)
T ss_dssp             TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred             HhCCCchhhHHHhccccchHHHHHHHHHHHCcC
Confidence            343478999999999999999999999988774

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=96.64  E-value=0.0026  Score=35.57  Aligned_cols=31  Identities=19%  Similarity=0.384  Sum_probs=25.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      .+++..|||+.+|+|.++|++.++...+.|-
T Consensus        16 ~~~t~~ela~~~~is~~tv~~~l~~L~~~g~   46 (48)
T PF13412_consen   16 PRITQKELAEKLGISRSTVNRYLKKLEEKGL   46 (48)
T ss_dssp             TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence            4599999999999999999999999877663

...

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=96.61  E-value=0.0019  Score=36.87  Aligned_cols=32  Identities=22%  Similarity=0.363  Sum_probs=27.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      .+++..|||+.+|++.++|+++|..+.+.|=+
T Consensus        17 ~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v   48 (52)
T PF09339_consen   17 GPLTLSEIARALGLPKSTVHRLLQTLVEEGYV   48 (52)
T ss_dssp             SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCe
Confidence            45789999999999999999999999887754

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=96.48  E-value=0.015  Score=34.79  Aligned_cols=31  Identities=23%  Similarity=0.202  Sum_probs=24.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +++.|+|+.+|||.+++.+|.++.   |.+.|..
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~~---g~~~~~r   31 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRY---GLPAPQR   31 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCc
Confidence            367899999999999999997554   6555543

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

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

Probab=96.43  E-value=0.00076  Score=38.99  Aligned_cols=42  Identities=14%  Similarity=0.201  Sum_probs=30.8

Q ss_pred             HHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy1904         110 LEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAG  151 (163)
Q Consensus       110 ~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~  151 (163)
                      ...|+..|...+++.......|..+.+|+..||+.||-.+..
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            456999999999999999999999999999999999976543

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=96.38  E-value=0.0086  Score=32.93  Aligned_cols=30  Identities=13%  Similarity=0.169  Sum_probs=23.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++..|+|+.||||.+||.+|.+.    |.+.+..
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~   30 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIR   30 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCcee
Confidence            35789999999999999999854    6665443

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=96.32  E-value=0.0022  Score=40.13  Aligned_cols=25  Identities=24%  Similarity=0.396  Sum_probs=20.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ..|+++.|+|+.+||+++.||++++
T Consensus        29 ~~~ltQ~e~A~~lgisq~~vS~l~~   53 (80)
T PF13744_consen   29 ERGLTQAELAERLGISQPRVSRLEN   53 (80)
T ss_dssp             CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCChhHHHHHHc
Confidence            5799999999999999999999984

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=96.29  E-value=0.002  Score=43.23  Aligned_cols=29  Identities=21%  Similarity=0.351  Sum_probs=25.4

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      |..+|+++-+||..||||++-||++|+..
T Consensus        18 L~eeG~Sq~~iA~LLGltqaAVS~Yls~k   46 (119)
T COG2522          18 LIEEGLSQYRIAKLLGLTQAAVSQYLSGK   46 (119)
T ss_pred             HHHcCCcHHHHHHHhCCCHHHHHHHHccC
Confidence            34579999999999999999999999543

>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length

Probab=96.21  E-value=0.015  Score=38.78  Aligned_cols=53  Identities=17%  Similarity=0.210  Sum_probs=40.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC-CCcCChHHHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK-PRVATPDVEKRIEE   58 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~-p~~~~~~~~~~i~~   58 (163)
                      |.|.|+|..+|+|.=||.||.+..-=.....||+-||.. --..+..+.+.+..
T Consensus         1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~s   54 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIRS   54 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccccceeeeecHHHHHHHHh
Confidence            578999999999999999999888667777899877753 22444555555544

The function of this family is unknown.

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

Probab=96.12  E-value=0.0027  Score=37.53  Aligned_cols=26  Identities=31%  Similarity=0.488  Sum_probs=20.4

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      |++.|+++.++|+..|||.++|++|+
T Consensus         6 m~~~~it~~~La~~~gis~~tl~~~~   31 (63)
T PF13443_consen    6 MAERGITQKDLARKTGISRSTLSRIL   31 (63)
T ss_dssp             HHHTT--HHHHHHHHT--HHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            46789999999999999999999998

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=96.11  E-value=0.0067  Score=34.49  Aligned_cols=27  Identities=26%  Similarity=0.310  Sum_probs=24.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|++..+||+.|+||.++|++++.+.
T Consensus        16 ~~g~s~~eia~~l~is~~tv~~~~~~~   42 (58)
T smart00421       16 AEGLTNKEIAERLGISEKTVKTHLSNI   42 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            478999999999999999999999875

lux regulon (activates the bioluminescence operon

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

Probab=96.09  E-value=0.0048  Score=35.31  Aligned_cols=24  Identities=21%  Similarity=0.372  Sum_probs=20.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.|+|+.+|||.++|++|+
T Consensus         7 ~~gls~~~la~~~gis~~~i~~~~   30 (55)
T PF01381_consen    7 EKGLSQKELAEKLGISRSTISRIE   30 (55)
T ss_dssp             HTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCcchhHHHh
Confidence            479999999999999999999997

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

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

Probab=96.07  E-value=0.0045  Score=37.94  Aligned_cols=28  Identities=14%  Similarity=0.287  Sum_probs=25.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|.+..+||+.+||+.+++++|++.|.
T Consensus        21 ~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen   21 ESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HCCCceEeeecccccccccccHHHHHHh
Confidence            3678999999999999999999999997

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.

>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA

Probab=96.04  E-value=0.0039  Score=34.45  Aligned_cols=28  Identities=29%  Similarity=0.274  Sum_probs=25.2

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ||..|...+|+|+.|+||..||.+-|+.
T Consensus        17 ma~nG~GiRdtaRvL~I~~nTVlrtLK~   44 (46)
T PF12759_consen   17 MAFNGSGIRDTARVLKISINTVLRTLKN   44 (46)
T ss_pred             HHhcCCcchhhHhHhcchHHHHHHHHhc
Confidence            5778999999999999999999998864

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=95.92  E-value=0.0077  Score=36.94  Aligned_cols=28  Identities=21%  Similarity=0.220  Sum_probs=25.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      +|++..|||+.+|||.++|..++.....
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~   58 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKGETK   58 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence            7999999999999999999999976433

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

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=95.90  E-value=0.007  Score=38.59  Aligned_cols=24  Identities=17%  Similarity=0.171  Sum_probs=22.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|.+..+||+.||||.+||+++.
T Consensus        48 ~~G~S~~eIA~~LgISrsTIyRi~   71 (88)
T TIGR02531        48 KQGKTYSDIEAETGASTATISRVK   71 (88)
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHH
Confidence            478999999999999999999976

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PHA00542 putative Cro-like protein

Probab=95.89  E-value=0.0048  Score=38.79  Aligned_cols=24  Identities=25%  Similarity=0.259  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|+
T Consensus        29 ~~glTq~elA~~lgIs~~tIsr~e   52 (82)
T PHA00542         29 RAGWSQEQIADATDVSQPTICRIY   52 (82)
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHH
Confidence            468999999999999999999997

>PHA01976 helix-turn-helix protein

Probab=95.87  E-value=0.0094  Score=35.57  Aligned_cols=24  Identities=21%  Similarity=0.166  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|.
T Consensus        13 ~~glt~~~lA~~~gvs~~~v~~~e   36 (67)
T PHA01976         13 ARAWSAPELSRRAGVRHSLIYDFE   36 (67)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            478999999999999999999996

>PRK10072 putative transcriptional regulator; Provisional

Probab=95.83  E-value=0.0096  Score=38.59  Aligned_cols=24  Identities=25%  Similarity=0.212  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.++|+.+|||.++|++|.
T Consensus        44 ~~glTQ~elA~~lGvS~~TVs~WE   67 (96)
T PRK10072         44 GTGLKIDDFARVLGVSVAMVKEWE   67 (96)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            469999999999999999999997

>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=95.82  E-value=0.011  Score=33.31  Aligned_cols=26  Identities=31%  Similarity=0.437  Sum_probs=22.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+..|||+.||||.++|++++.+-
T Consensus        19 ~~~t~~eIa~~lg~s~~~V~~~~~~a   44 (50)
T PF04545_consen   19 EGLTLEEIAERLGISRSTVRRILKRA   44 (50)
T ss_dssp             ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence            68899999999999999999998664

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 ....

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=95.81  E-value=0.0081  Score=47.33  Aligned_cols=38  Identities=24%  Similarity=0.450  Sum_probs=34.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      .+|+.+.|||++||||..+|+++|+.-++.|-+.-...
T Consensus        24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~   61 (321)
T COG2390          24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN   61 (321)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence            47999999999999999999999999999998875543

>PF12728 HTH_17: Helix-turn-helix domain

Probab=95.81  E-value=0.012  Score=33.27  Aligned_cols=46  Identities=22%  Similarity=0.341  Sum_probs=30.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI   56 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i   56 (163)
                      +++.|+|+.||||.++|.+|++.    |.+.+-..|+. -.....++++.+
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~----g~i~~~~~g~~-~~~~~~~l~~~~   47 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ----GKIPPFKIGRK-WRIPKSDLDRWL   47 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCeEEeCCE-EEEeHHHHHHHH
Confidence            46789999999999999999844    66654433432 333334444443

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=95.78  E-value=0.012  Score=32.45  Aligned_cols=32  Identities=25%  Similarity=0.348  Sum_probs=28.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..|||+.+++|.++|++.|+.+.+.|-+..
T Consensus         9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~   40 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISR   40 (48)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            67889999999999999999999999887753

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=95.77  E-value=0.011  Score=38.61  Aligned_cols=30  Identities=37%  Similarity=0.466  Sum_probs=24.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      -|+++.+.|+.||||.+||++|     |.|-..|.
T Consensus        56 ~~lSQ~vFA~~L~vs~~Tv~~W-----EqGr~kPs   85 (104)
T COG2944          56 LGLSQPVFARYLGVSVSTVRKW-----EQGRKKPS   85 (104)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHH-----HcCCcCCC
Confidence            5799999999999999999999     45555443

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=95.74  E-value=0.0089  Score=34.26  Aligned_cols=26  Identities=15%  Similarity=0.293  Sum_probs=23.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|..-.++|.+||||++||++|...+
T Consensus        18 ~~~~~~~La~~FgIs~stvsri~~~~   43 (53)
T PF13613_consen   18 LNLTFQDLAYRFGISQSTVSRIFHEW   43 (53)
T ss_pred             cCCcHhHHhhheeecHHHHHHHHHHH
Confidence            46778899999999999999998766

>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=95.72  E-value=0.0088  Score=30.47  Aligned_cols=24  Identities=38%  Similarity=0.451  Sum_probs=21.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|.+..+||+.|+||.++|++|+
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHhC
Confidence            367899999999999999999985

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

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=95.71  E-value=0.0054  Score=39.43  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ..|+++.+||+.+|||.++|+|+-+
T Consensus        53 ~~~~tQrEIa~~lGiS~atIsR~sn   77 (94)
T TIGR01321        53 NGNMSQREIASKLGVSIATITRGSN   77 (94)
T ss_pred             hCCCCHHHHHHHhCCChhhhhHHHh
Confidence            3579999999999999999999853

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=95.70  E-value=0.0092  Score=34.94  Aligned_cols=31  Identities=23%  Similarity=0.483  Sum_probs=27.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +++.|||+.+++++++|++++++..+-|=+.
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~   52 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEKKGLVE   52 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            8999999999999999999999998887663

...

>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=95.69  E-value=0.014  Score=32.56  Aligned_cols=28  Identities=25%  Similarity=0.258  Sum_probs=25.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|+++.+||..+|+|.++|++++.+.+
T Consensus        24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~   51 (55)
T cd06171          24 GEGLSYEEIAEILGISRSTVRQRLHRAL   51 (55)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3789999999999999999999997764

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

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=95.62  E-value=0.0097  Score=34.08  Aligned_cols=24  Identities=13%  Similarity=0.147  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|.
T Consensus        13 ~~gltq~~lA~~~gvs~~~vs~~e   36 (58)
T TIGR03070        13 ALGLTQADLADLAGVGLRFIRDVE   36 (58)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            468999999999999999999997

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

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=95.59  E-value=0.014  Score=35.31  Aligned_cols=33  Identities=12%  Similarity=0.269  Sum_probs=30.5

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      |+++.|||+.|||+..+|.+.|..+.+.|-+.-
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~   54 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK   54 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            599999999999999999999999999988854

Helix-turn-helix-containing domain. Also known as Zab.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=95.49  E-value=0.012  Score=33.69  Aligned_cols=29  Identities=17%  Similarity=0.284  Sum_probs=26.2

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETG   33 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG   33 (163)
                      .++..+||+.|+||..||.+.++..++.|
T Consensus        15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   15 PITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            48999999999999999999999998888

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK04217 hypothetical protein; Provisional

Probab=95.44  E-value=0.016  Score=38.48  Aligned_cols=27  Identities=22%  Similarity=0.284  Sum_probs=24.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+|++..+||++||||.+||+++|.+.
T Consensus        56 ~eGlS~~EIAk~LGIS~sTV~r~L~RA   82 (110)
T PRK04217         56 YEGLTQEEAGKRMGVSRGTVWRALTSA   82 (110)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            378999999999999999999999654

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

Probab=95.42  E-value=0.016  Score=34.31  Aligned_cols=24  Identities=33%  Similarity=0.461  Sum_probs=20.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|++..++|+++|||.++|++|.
T Consensus        12 ~~gls~~~lA~~~g~s~s~v~~iE   35 (64)
T PF13560_consen   12 RAGLSQAQLADRLGVSQSTVSRIE   35 (64)
T ss_dssp             CHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999996

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=95.38  E-value=0.023  Score=33.67  Aligned_cols=34  Identities=24%  Similarity=0.274  Sum_probs=30.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..|||+.+|+|.++|+++|+.+.+.|-+..
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~   57 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR   57 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            3489999999999999999999999988887753

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=95.36  E-value=0.013  Score=35.48  Aligned_cols=20  Identities=30%  Similarity=0.305  Sum_probs=18.7

Q ss_pred             ChhhhHHHhhcchhhHHHHH
Q psy1904           7 RPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ...|||+.+|||.+|||++|
T Consensus         2 t~~~iA~~~gvS~~TVSr~l   21 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVL   21 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
Confidence            56799999999999999998

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.35  E-value=0.023  Score=31.73  Aligned_cols=34  Identities=24%  Similarity=0.270  Sum_probs=30.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..+||+.|+||.++|++.|+.+.+-|-+..
T Consensus        13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~   46 (53)
T smart00420       13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR   46 (53)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4689999999999999999999999988776653

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

Probab=95.33  E-value=0.011  Score=34.73  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=21.5

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++.--|||+.||||.+||++|-.+
T Consensus        22 ~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   22 KIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CccHHHHHHHHCCCHHHHHHHhhh
Confidence            388999999999999999999654

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

>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=95.29  E-value=0.016  Score=33.01  Aligned_cols=27  Identities=26%  Similarity=0.342  Sum_probs=20.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .|++..|||+.+|+|.++|..++.+-+
T Consensus        25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~   51 (54)
T PF08281_consen   25 QGMSYAEIAEILGISESTVKRRLRRAR   51 (54)
T ss_dssp             S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            789999999999999999999997754

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.

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

Probab=95.26  E-value=0.012  Score=33.16  Aligned_cols=17  Identities=41%  Similarity=0.462  Sum_probs=16.4

Q ss_pred             hhHHHhhcchhhHHHHH
Q psy1904          10 VISRQLRVSHGCVSKIL   26 (163)
Q Consensus        10 ~ia~~~~vs~~~vs~~l   26 (163)
                      +||+++|||.+||++|+
T Consensus         2 ~lA~~~gvs~~tvs~~l   18 (52)
T cd01392           2 DIARAAGVSVATVSRVL   18 (52)
T ss_pred             cHHHHHCcCHHHHHHHH
Confidence            79999999999999998

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

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=95.26  E-value=0.012  Score=32.06  Aligned_cols=27  Identities=22%  Similarity=0.331  Sum_probs=21.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|-...++|+.||||..++++.+++|
T Consensus        16 ~~~gn~~~aA~~Lgisr~tL~~klkk~   42 (42)
T PF02954_consen   16 RCGGNVSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_dssp             HTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence            456778899999999999999998775

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=95.21  E-value=0.014  Score=35.92  Aligned_cols=25  Identities=24%  Similarity=0.409  Sum_probs=23.2

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ...|+++.++|+.+|||.++|++|+
T Consensus        15 ~~~~~t~~~lA~~~gis~~tis~~~   39 (78)
T TIGR02607        15 EPLGLSIRALAKALGVSRSTLSRIV   39 (78)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4579999999999999999999997

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

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=95.07  E-value=0.017  Score=33.53  Aligned_cols=32  Identities=25%  Similarity=0.563  Sum_probs=27.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      .|+++.+||+.++++.++|++++++..+-|=+
T Consensus        16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I   47 (59)
T PF01047_consen   16 GGITQSELAEKLGISRSTVTRIIKRLEKKGLI   47 (59)
T ss_dssp             SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCE
Confidence            56899999999999999999999998777755

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PRK00118 putative DNA-binding protein; Validated

Probab=95.07  E-value=0.025  Score=37.19  Aligned_cols=27  Identities=19%  Similarity=0.149  Sum_probs=24.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|++..+||+.+|||.+||++++.+.
T Consensus        31 ~eg~S~~EIAe~lGIS~~TV~r~L~RA   57 (104)
T PRK00118         31 LDDYSLGEIAEEFNVSRQAVYDNIKRT   57 (104)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            368999999999999999999999764

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=95.03  E-value=0.019  Score=32.49  Aligned_cols=25  Identities=32%  Similarity=0.449  Sum_probs=22.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..+..+||+.+|||..||.+|+.++
T Consensus        27 ~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   27 SRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            3688999999999999999999775

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=95.01  E-value=0.055  Score=29.90  Aligned_cols=31  Identities=13%  Similarity=0.085  Sum_probs=24.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      ++..|+|+.+||+..||..|.    +.|-+.|...
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~----~~g~l~~~~~   31 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYE----RIGLLSPART   31 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHH----HCCCCCCCcC
Confidence            467899999999999999986    4476665433

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

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

Probab=95.00  E-value=0.026  Score=32.40  Aligned_cols=46  Identities=20%  Similarity=0.427  Sum_probs=35.7

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGT  149 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnr  149 (163)
                      +++|..+|-++-..+-..++...     ...+||..+|++..+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            46788999999888888888886     57789999999999999999885

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.

>PHA02535 P terminase ATPase subunit; Provisional

Probab=95.00  E-value=0.047  Score=46.22  Aligned_cols=26  Identities=15%  Similarity=0.143  Sum_probs=24.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +|.++.+||+.|||+.+||++|.+++
T Consensus        17 ~G~sv~eIA~~LGv~~~Tl~~W~kr~   42 (581)
T PHA02535         17 QGWTVAEIAEELGLKSRTIYSWKERD   42 (581)
T ss_pred             cCCCHHHHHHHhCCChhHHHHHhccc
Confidence            59999999999999999999998776

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=94.97  E-value=0.056  Score=33.50  Aligned_cols=41  Identities=24%  Similarity=0.370  Sum_probs=36.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR   46 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p~   46 (163)
                      +.-..||+.+++|.+||...+..+.+.|-+.  |++.||..|.
T Consensus        24 VgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT   66 (78)
T PF03444_consen   24 VGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPT   66 (78)
T ss_pred             cCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcC
Confidence            6778999999999999999999999999993  8888888775

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>TIGR01764 excise DNA binding domain, excisionase family

Probab=94.96  E-value=0.026  Score=31.03  Aligned_cols=32  Identities=19%  Similarity=0.276  Sum_probs=24.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      ++..|+|+.||||.++|.+|++    .|.+.+-..|
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~----~g~i~~~~~g   33 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIH----EGELPAYRVG   33 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH----cCCCCeEEeC
Confidence            4678999999999999999984    3655443344

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PRK11050 manganese transport regulator MntR; Provisional

Probab=94.90  E-value=0.03  Score=39.34  Aligned_cols=35  Identities=29%  Similarity=0.378  Sum_probs=31.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++++.+||+.|+||+++|+++++++.+.|-+...
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            56999999999999999999999999999877543

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.88  E-value=0.024  Score=32.56  Aligned_cols=30  Identities=27%  Similarity=0.365  Sum_probs=27.8

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +..+||+.|+||.++|.+.+++..+.|-+.
T Consensus        22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~   51 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEAEGLVQ   51 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            788999999999999999999999988774

>PHA00738 putative HTH transcription regulator

Probab=94.87  E-value=0.02  Score=37.62  Aligned_cols=38  Identities=26%  Similarity=0.183  Sum_probs=33.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg   42 (163)
                      ++..|+|+..|++|+++||+=|+-.++.|-+.-...|-
T Consensus        26 ~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr   63 (108)
T PHA00738         26 ILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGR   63 (108)
T ss_pred             CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECC
Confidence            48899999999999999999999999999987766553

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=94.83  E-value=0.024  Score=38.13  Aligned_cols=54  Identities=17%  Similarity=0.174  Sum_probs=41.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE   58 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~   58 (163)
                      ++..+|||+.|++++++||+=|+-.++.|=+.....|...-....+...+++..
T Consensus        30 ~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~   83 (117)
T PRK10141         30 ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAK   83 (117)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHH
Confidence            488999999999999999999999999999987766654333333444444444

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=94.82  E-value=0.023  Score=36.46  Aligned_cols=26  Identities=27%  Similarity=0.193  Sum_probs=19.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|+++.|||+++|.|.+.|++.|.-.
T Consensus         2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll   27 (93)
T PF08535_consen    2 FGWTQEEIAKRLGKSRSWVSNHLALL   27 (93)
T ss_dssp             TT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            59999999999999999999999654

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=94.81  E-value=0.019  Score=34.07  Aligned_cols=36  Identities=14%  Similarity=0.167  Sum_probs=30.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .+++..|||..+|||..+|.++|......|-+..-+
T Consensus        14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~   49 (62)
T PF04703_consen   14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVERSP   49 (62)
T ss_dssp             S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            458889999999999999999999999999886433

>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators

Probab=94.81  E-value=0.18  Score=30.07  Aligned_cols=31  Identities=6%  Similarity=0.088  Sum_probs=23.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++..|+|+.+|||..++..|.+..   |-+.|..
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~~~---gl~~~~r   31 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWEREF---GLLKPQR   31 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCc
Confidence            367899999999999999885333   6666644

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=94.77  E-value=0.025  Score=34.75  Aligned_cols=24  Identities=13%  Similarity=0.174  Sum_probs=21.6

Q ss_pred             cCCCChhhhHHHhh------cchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLR------VSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~------vs~~~vs~~l   26 (163)
                      ..|+++.|+|+.+|      +|+++|++|.
T Consensus        22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~E   51 (75)
T smart00352       22 KLGFTQADVGLALGALYGPDFSQTTICRFE   51 (75)
T ss_pred             HcCCCHHHHHHHhcccccCcCCHHHHHHHH
Confidence            36999999999999      4999999984

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=94.76  E-value=0.036  Score=32.07  Aligned_cols=35  Identities=23%  Similarity=0.413  Sum_probs=30.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ...++..+|++.|+||.++|++.|++..+-|-+.-
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~   42 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVES   42 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence            34588999999999999999999999988887753

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=94.74  E-value=0.038  Score=35.66  Aligned_cols=35  Identities=20%  Similarity=0.140  Sum_probs=31.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++++.|||..+|+|..+|++.|+.+.+.|=+..
T Consensus        45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r   79 (95)
T TIGR01610        45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR   79 (95)
T ss_pred             CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            35689999999999999999999999999998863

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.69  E-value=0.037  Score=31.60  Aligned_cols=28  Identities=21%  Similarity=0.373  Sum_probs=25.7

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      +...||+.+|+|..||++.++...+.|-
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~   54 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEKGL   54 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence            7789999999999999999999988773

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=94.64  E-value=0.012  Score=35.39  Aligned_cols=34  Identities=21%  Similarity=0.303  Sum_probs=30.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.+|++.++|++.|+...+.|-+.-
T Consensus        21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~   54 (68)
T PF01978_consen   21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVER   54 (68)
T ss_dssp             CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4488999999999999999999999988887743

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88

Probab=94.64  E-value=0.018  Score=32.64  Aligned_cols=37  Identities=24%  Similarity=0.475  Sum_probs=22.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC-CCCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPR   46 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~-~Pg~~Gg~~p~   46 (163)
                      ++..|+++.+|||.+|++++.+.    |.+ .|-.+|+....
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~----g~FP~pvklg~r~~~   41 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKD----GKFPKPVKLGGRAVR   41 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHH----HH---SEESSS----
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhc----ccCCCCEEECCCccc
Confidence            46789999999999999999863    444 44445654433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=94.58  E-value=0.045  Score=30.97  Aligned_cols=26  Identities=23%  Similarity=0.187  Sum_probs=24.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..+||+.|+||.++|.+++.+.
T Consensus        14 ~~~s~~eia~~l~~s~~tv~~~~~~~   39 (57)
T cd06170          14 EGKTNKEIADILGISEKTVKTHLRNI   39 (57)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            68999999999999999999999775

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=94.54  E-value=0.021  Score=35.67  Aligned_cols=21  Identities=19%  Similarity=0.116  Sum_probs=19.9

Q ss_pred             CChhhhHHHhhcchhhHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +...|||+.||||.+||++.|
T Consensus        20 ~ti~dvA~~~gvS~~TVsr~L   40 (80)
T TIGR02844        20 ATVRETAKVFGVSKSTVHKDV   40 (80)
T ss_pred             CCHHHHHHHhCCCHHHHHHHh
Confidence            788999999999999999988

Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=94.53  E-value=0.056  Score=34.07  Aligned_cols=35  Identities=23%  Similarity=0.424  Sum_probs=31.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+++..|||+.++|+.++|+++|....+.|-+...
T Consensus        19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~   53 (91)
T smart00346       19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD   53 (91)
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence            35999999999999999999999999999988654

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=94.50  E-value=0.062  Score=36.52  Aligned_cols=40  Identities=30%  Similarity=0.381  Sum_probs=33.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC--CCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSK   44 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P--g~~Gg~~   44 (163)
                      .++..+||+.++||.++|+++|....+.|-+.-  |..||-.
T Consensus        25 ~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~   66 (130)
T TIGR02944        25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYT   66 (130)
T ss_pred             CccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChh
Confidence            389999999999999999999999999998853  3444443

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=94.50  E-value=0.043  Score=37.96  Aligned_cols=40  Identities=20%  Similarity=0.311  Sum_probs=34.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-.....+
T Consensus        53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~D   92 (144)
T PRK11512         53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPND   92 (144)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCccc
Confidence            5699999999999999999999999999998865544333

>KOG3623|consensus

Probab=94.49  E-value=0.022  Score=48.91  Aligned_cols=51  Identities=14%  Similarity=0.166  Sum_probs=45.3

Q ss_pred             CCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         105 FTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       105 ~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      |+.. +..|...|..|..|+..+...+|.+.||+..-|+.||++++++..+.
T Consensus       564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv  614 (1007)
T KOG3623|consen  564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV  614 (1007)
T ss_pred             cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence            4443 78889999999999999999999999999999999999999987653

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=94.42  E-value=0.024  Score=32.14  Aligned_cols=27  Identities=26%  Similarity=0.423  Sum_probs=20.3

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      -+.|++-.+||++++-|..||.++|+-
T Consensus        17 ~qlG~s~~~isr~i~RSr~~Ir~yl~d   43 (50)
T PF11427_consen   17 HQLGMSLREISRRIGRSRTCIRRYLKD   43 (50)
T ss_dssp             HHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred             HHhchhHHHHHHHhCccHHHHHHHhcC
Confidence            357999999999999999999999853

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

Probab=94.41  E-value=0.049  Score=31.25  Aligned_cols=26  Identities=23%  Similarity=0.262  Sum_probs=22.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+++..|||+.||||.++|+.-|.+-
T Consensus        22 R~~tl~elA~~lgis~st~~~~LRra   47 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHLRRA   47 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            46788999999999999999998764

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

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=94.40  E-value=0.041  Score=36.25  Aligned_cols=26  Identities=19%  Similarity=0.267  Sum_probs=24.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +|+++.+.|++.|||.+|+.++|..-
T Consensus        56 egl~QeeaA~~MgVSR~T~~ril~~A   81 (106)
T PF02001_consen   56 EGLSQEEAAERMGVSRPTFQRILESA   81 (106)
T ss_pred             cCCCHHHHHHHcCCcHHHHHHHHHHH
Confidence            79999999999999999999999765

>PRK09726 antitoxin HipB; Provisional

Probab=94.32  E-value=0.035  Score=35.21  Aligned_cols=24  Identities=8%  Similarity=0.278  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|+
T Consensus        23 ~~gltq~elA~~~gvs~~tis~~e   46 (88)
T PRK09726         23 QNGWTQSELAKKIGIKQATISNFE   46 (88)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            469999999999999999999997

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=94.30  E-value=0.14  Score=31.14  Aligned_cols=51  Identities=12%  Similarity=0.213  Sum_probs=37.2

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY   59 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~   59 (163)
                      ++--|++..+|+|.+||+++++.-   .-..|-.+|+........++++++...
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~---~FPkpvklG~r~v~W~~SEI~~Wi~~~   64 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDG---TFPKPVKLGGRSVAWPESEIDEWIASR   64 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHccC---CCCCCeecCcccccccHHHHHHHHHHH
Confidence            566789999999999999998553   333566678766666667777766443

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=94.28  E-value=0.048  Score=37.68  Aligned_cols=27  Identities=26%  Similarity=0.367  Sum_probs=24.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|+++.+||++||+|.++|+.++++.
T Consensus        19 ~~GlTq~EIAe~LgiS~stV~~~e~ra   45 (137)
T TIGR00721        19 EKGLSQKEIAKELKTTRANVSAIEKRA   45 (137)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence            379999999999999999999888664

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=94.26  E-value=0.049  Score=37.82  Aligned_cols=27  Identities=30%  Similarity=0.257  Sum_probs=24.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|++..+||+.||+|.++|+.++++.
T Consensus        19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra   45 (141)
T PRK03975         19 ERGLTQQEIADILGTSRANVSSIEKRA   45 (141)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            379999999999999999999998664

>PHA00675 hypothetical protein

Probab=94.20  E-value=0.042  Score=33.76  Aligned_cols=26  Identities=23%  Similarity=0.436  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      .+|.+..+||+.||||.++|+.|...
T Consensus        37 r~G~s~~~IA~~fGVsrstV~~I~~g   62 (78)
T PHA00675         37 VEGMSYAVLAEKFEQSKGAIAKICRY   62 (78)
T ss_pred             hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence            36889999999999999999998643

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=94.20  E-value=0.069  Score=35.53  Aligned_cols=36  Identities=17%  Similarity=0.151  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhhc-chhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~v-s~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .|.+.++||+.||| +.+.+++|+.++.+.+...+..
T Consensus        23 ~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~   59 (116)
T COG2963          23 GGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSG   59 (116)
T ss_pred             cCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccC
Confidence            57889999999995 9999999999998887666543

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=94.14  E-value=0.05  Score=34.73  Aligned_cols=32  Identities=25%  Similarity=0.419  Sum_probs=27.8

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      ++.+||+.|+|+.++|++.+.+..+.|=+.-.
T Consensus         1 ~~~ela~~l~is~stvs~~l~~L~~~glI~r~   32 (96)
T smart00529        1 RTSEIAERLNVSPPTVTQMLKKLEKDGLVEYE   32 (96)
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence            46799999999999999999999888877543

iron dependent repressor

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=94.13  E-value=0.034  Score=32.64  Aligned_cols=34  Identities=24%  Similarity=0.348  Sum_probs=28.9

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ..+++..+||+.|+++.++|+.=|+...+.|=+.
T Consensus        22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~   55 (61)
T PF12840_consen   22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE   55 (61)
T ss_dssp             CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence            4679999999999999999999999998877553

...

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=94.11  E-value=0.055  Score=38.44  Aligned_cols=35  Identities=17%  Similarity=0.282  Sum_probs=31.2

Q ss_pred             ccCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           2 AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         2 ~~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+.| ++..+||+++|+|.++|.+=+++..+.|-+.
T Consensus        24 q~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~   59 (164)
T PRK11169         24 QKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQ   59 (164)
T ss_pred             ccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            3455 8999999999999999999999999999874

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=94.09  E-value=0.3  Score=29.03  Aligned_cols=23  Identities=9%  Similarity=-0.074  Sum_probs=19.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +++.|+|+.+|||.+|+..|-+.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~~   23 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKE   23 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHh
Confidence            46789999999999999998644

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=94.05  E-value=0.058  Score=32.43  Aligned_cols=33  Identities=18%  Similarity=0.140  Sum_probs=28.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      +.-++..+||..|+||.++|++-++...+.|-.
T Consensus        11 ~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~   43 (69)
T TIGR00122        11 DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVD   43 (69)
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence            334678899999999999999999999887764

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

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

Probab=93.97  E-value=0.037  Score=30.37  Aligned_cols=25  Identities=24%  Similarity=0.341  Sum_probs=22.8

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ...|++..++|+.+||+.++|++|+
T Consensus         7 ~~~~~s~~~la~~~~i~~~~i~~~~   31 (56)
T smart00530        7 EEKGLTQEELAEKLGVSRSTLSRIE   31 (56)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            3578999999999999999999997

>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons

Probab=93.91  E-value=0.073  Score=31.73  Aligned_cols=41  Identities=17%  Similarity=0.314  Sum_probs=30.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhh-------hccCCCCCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQ-------ETGSIRPGVIGGSKPR   46 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~-------~tG~~~Pg~~Gg~~p~   46 (163)
                      ++-.|+|+++|+.+++|.+|+..++       .+|.+.+.+--|.+|.
T Consensus        14 ~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~E~RVRLg~r~a   61 (65)
T PF05344_consen   14 ISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHWEARVRLGVRPA   61 (65)
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCChHHHhhcCCCCC
Confidence            5678999999999999999998875       4566665554445544

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=93.90  E-value=0.035  Score=32.25  Aligned_cols=31  Identities=23%  Similarity=0.347  Sum_probs=28.2

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..|+|..|+||..||.+=|....+.|-+.
T Consensus        15 ~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~   45 (57)
T PF08220_consen   15 VSVKELAEEFGVSEMTIRRDLNKLEKQGLIK   45 (57)
T ss_pred             EEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            7889999999999999999999998888753

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=93.90  E-value=0.043  Score=38.48  Aligned_cols=34  Identities=18%  Similarity=0.316  Sum_probs=30.8

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++| ++..+||+.+|+|.++|.+=+++..+.|-+.
T Consensus        20 ~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~   54 (153)
T PRK11179         20 ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT   54 (153)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            445 8999999999999999999999999999875

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=93.81  E-value=0.053  Score=32.19  Aligned_cols=33  Identities=21%  Similarity=0.437  Sum_probs=27.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      +..+++.+||+.++++.++|++++++..+-|=+
T Consensus        16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv   48 (68)
T PF13463_consen   16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV   48 (68)
T ss_dssp             TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            456899999999999999999999999888876

>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=93.79  E-value=0.069  Score=30.92  Aligned_cols=27  Identities=26%  Similarity=0.278  Sum_probs=23.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      -.|.+..+||+.++||..||...+...
T Consensus        16 ~~G~~~~eIA~~l~is~~tV~~~~~~i   42 (58)
T PF00196_consen   16 AQGMSNKEIAEELGISEKTVKSHRRRI   42 (58)
T ss_dssp             HTTS-HHHHHHHHTSHHHHHHHHHHHH
T ss_pred             HhcCCcchhHHhcCcchhhHHHHHHHH
Confidence            379999999999999999999988665

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 ....

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=93.76  E-value=0.044  Score=34.30  Aligned_cols=38  Identities=32%  Similarity=0.456  Sum_probs=32.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~   43 (163)
                      ++..+||++++++...|.+++....+.|=+.  .|..||-
T Consensus        26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy   65 (83)
T PF02082_consen   26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGY   65 (83)
T ss_dssp             BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCce
Confidence            7889999999999999999999999999885  5555654

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=93.68  E-value=0.072  Score=29.43  Aligned_cols=25  Identities=12%  Similarity=0.191  Sum_probs=19.3

Q ss_pred             CC-CChhhhHHHhhcchhhHHHHHhh
Q psy1904           4 AG-VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         4 ~g-~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      .| ++...+|+.|||..+|+++.++.
T Consensus        14 ~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen   14 NGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             TTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            45 99999999999999999988754

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=93.66  E-value=0.046  Score=42.46  Aligned_cols=23  Identities=26%  Similarity=0.239  Sum_probs=20.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      |...|||+..|||.+|||+.|+.
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~   23 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVING   23 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Confidence            46789999999999999999954

>PF14493 HTH_40: Helix-turn-helix domain

Probab=93.66  E-value=0.14  Score=32.59  Aligned_cols=68  Identities=12%  Similarity=0.068  Sum_probs=46.3

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDK   74 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~   74 (163)
                      |.+.|+++.+||+.-+++.+||..-|-.+...|..-+-.      ...+....+.|.+..+..+.....++.+.
T Consensus         9 l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~------~~l~~e~~~~I~~~~~~~~~~~lk~i~e~   76 (91)
T PF14493_consen    9 LFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIE------ELLSEEEIKQIEDAIEKLGSEKLKPIKEA   76 (91)
T ss_pred             HHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHH------HhCCHHHHHHHHHHHHHcCcccHHHHHHH
Confidence            356899999999999999999999999998888732211      22344455556565555554444444443

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=93.65  E-value=0.081  Score=36.27  Aligned_cols=24  Identities=17%  Similarity=0.241  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        16 ~~gltq~~lA~~~gvs~~~is~~E   39 (135)
T PRK09706         16 QLKLSQRSLAKAVKVSHVSISQWE   39 (135)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            368999999999999999999996

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=93.61  E-value=0.087  Score=32.03  Aligned_cols=31  Identities=35%  Similarity=0.467  Sum_probs=28.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..+||..+|+|..+|++.|+.+++.|-+.
T Consensus        29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   29 LTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6789999999999999999999999988775

...

>PRK09492 treR trehalose repressor; Provisional

Probab=93.53  E-value=0.054  Score=41.87  Aligned_cols=23  Identities=30%  Similarity=0.323  Sum_probs=21.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +...|||+.+|||.+|||+.|+.
T Consensus         5 ~ti~dIA~~agVS~~TVSrvLn~   27 (315)
T PRK09492          5 LTIKDIARLSGVGKSTVSRVLNN   27 (315)
T ss_pred             CcHHHHHHHhCCCHHHHhHHhCC
Confidence            57889999999999999999964

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=93.49  E-value=0.4  Score=28.48  Aligned_cols=29  Identities=14%  Similarity=0.067  Sum_probs=24.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +++.|+|+.+|||..++..|.    +.|-+.|.
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~----~~gli~~~   29 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYE----RIGLLPPP   29 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCC
Confidence            468899999999999999986    46888775

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=93.47  E-value=0.045  Score=36.94  Aligned_cols=25  Identities=16%  Similarity=0.090  Sum_probs=23.2

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ...|+++.|+|++.|||.+++++|.
T Consensus        15 ~~~Glsq~eLA~~~Gis~~~is~iE   39 (120)
T PRK13890         15 DERHMTKKELSERSGVSISFLSDLT   39 (120)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            4579999999999999999999997

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=93.45  E-value=0.069  Score=31.79  Aligned_cols=35  Identities=20%  Similarity=0.360  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+++..+||+.|+++.++|+++|+...+.|-+...
T Consensus        19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~   53 (78)
T cd00090          19 GPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESR   53 (78)
T ss_pred             CCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEE
Confidence            34889999999999999999999999888877654

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=93.43  E-value=0.052  Score=42.03  Aligned_cols=23  Identities=30%  Similarity=0.336  Sum_probs=20.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln~   24 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNN   24 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCC
Confidence            46789999999999999999953

This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis

>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=93.39  E-value=0.54  Score=30.49  Aligned_cols=67  Identities=13%  Similarity=0.070  Sum_probs=42.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH--hCCCCCchhhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK--TNPNITSWEVRDKLIK   77 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~--~~p~~~~~e~~~~l~~   77 (163)
                      +++.|+|+.+|||.+|+..|-+.   .|-+.|... ||.  +.-+......+..+..  ..-+++..+++.-+..
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~---~gli~p~r~~~g~--R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~   70 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETE---FPQLKPVKRAGGR--RYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE   70 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHH---cCCCCCcCCCCCC--eeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            36789999999999999998543   365666433 332  3334555555555443  3456777777766553

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=93.38  E-value=0.088  Score=35.43  Aligned_cols=24  Identities=13%  Similarity=0.029  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.++|+.+|+|+++|++|.
T Consensus        76 ~~gltq~~lA~~lg~~~~tis~~e   99 (127)
T TIGR03830        76 KLGLSQREAAELLGGGVNAFSRYE   99 (127)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            468999999999999999999996

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>PRK01381 Trp operon repressor; Provisional

Probab=93.30  E-value=0.029  Score=36.40  Aligned_cols=21  Identities=14%  Similarity=0.180  Sum_probs=19.6

Q ss_pred             CCChhhhHHHhhcchhhHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKI   25 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~   25 (163)
                      ++++.+||+.+|||.+||+|-
T Consensus        55 ~~sQREIa~~lGvSiaTITRg   75 (99)
T PRK01381         55 ELSQREIKQELGVGIATITRG   75 (99)
T ss_pred             CcCHHHHHHHhCCceeeehhh
Confidence            499999999999999999984

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=93.27  E-value=0.16  Score=37.67  Aligned_cols=109  Identities=24%  Similarity=0.258  Sum_probs=64.7

Q ss_pred             CC-CChhhhHHHhhcchhhHHHHHhhhhhc-cCCCCCCCCCCCCCcCChHHHHHHHHH-HHhCCCCCchhhhhhhhhhcc
Q psy1904           4 AG-VRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVEKRIEEY-KKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~t-G~~~Pg~~Gg~~p~~~~~~~~~~i~~~-~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      .| ....|+|-.|++|..||++.++.|++. |-+-|.. |....-..+-.+-..+... .+..+   ..+          
T Consensus       103 gglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtr-G~i~DiGp~~tHK~~ii~~~l~g~~---~~e----------  168 (220)
T PF07900_consen  103 GGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTR-GTIHDIGPGVTHKKIIIRLYLKGKP---TPE----------  168 (220)
T ss_pred             CCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccC-CcccccCCcchHHHHHHHHHHcCCC---HHH----------
Confidence            44 788999999999999999999999655 9999864 2211111111111111111 11100   000          


Q ss_pred             CCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCC--CHHHHHHHHHHhCCCcccccc
Q psy1904          81 LDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYP--DIYTREALANKFGMTETRVQQ  144 (163)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p--~~~~r~~la~~l~l~~~~v~~  144 (163)
                                        =..+|.+|.+.+..--+.|.+-.+.  ....-+++|..+|+++.-|+-
T Consensus       169 ------------------iar~t~HS~~av~rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~e  216 (220)
T PF07900_consen  169 ------------------IARRTNHSPEAVDRYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKE  216 (220)
T ss_pred             ------------------HHHHhccCHHHHHHHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence                              1224666777776666677666554  233456788889988876653

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=93.27  E-value=0.049  Score=34.59  Aligned_cols=26  Identities=15%  Similarity=0.155  Sum_probs=22.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ..|++..+||+.+|||-+||+|.-+-
T Consensus        47 ~~g~syreIa~~tgvS~aTItRvsr~   72 (87)
T PF01371_consen   47 DEGKSYREIAEETGVSIATITRVSRC   72 (87)
T ss_dssp             HTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            47999999999999999999996543

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=93.26  E-value=0.092  Score=36.29  Aligned_cols=39  Identities=23%  Similarity=0.355  Sum_probs=33.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSK   44 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~   44 (163)
                      ++..+||+.++||..+|.++|......|=+  .+|..||-.
T Consensus        26 ~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~   66 (141)
T PRK11014         26 TSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIR   66 (141)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCee
Confidence            677999999999999999999999999987  556556543

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=93.21  E-value=0.18  Score=30.07  Aligned_cols=46  Identities=15%  Similarity=0.113  Sum_probs=31.0

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHH
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE   57 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~   57 (163)
                      +..|+|+.+|||..+|..|.+    .|-+.|....+.. +.=+......+.
T Consensus         2 ti~eva~~~gvs~~tlr~y~~----~gll~~~~~~~g~-r~y~~~dv~~l~   47 (69)
T PF13411_consen    2 TIKEVAKLLGVSPSTLRYYER----EGLLPPPRDENGY-RYYSEEDVERLR   47 (69)
T ss_dssp             EHHHHHHHTTTTHHHHHHHHH----TTSSTTBESTTSS-EEE-HHHHHHHH
T ss_pred             cHHHHHHHHCcCHHHHHHHHH----hcCcccccccCce-eeccHHHHHHHH
Confidence            568999999999999999974    4668777633332 444444544443

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=93.21  E-value=0.075  Score=31.32  Aligned_cols=19  Identities=26%  Similarity=0.281  Sum_probs=16.6

Q ss_pred             ChhhhHHHhhcchhhHHHH
Q psy1904           7 RPCVISRQLRVSHGCVSKI   25 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~   25 (163)
                      +...+|+.||||+++|+.|
T Consensus        11 ~~~~lAkalGVs~~aVs~W   29 (60)
T PF14549_consen   11 GQSKLAKALGVSPQAVSQW   29 (60)
T ss_dssp             SHHHHHHHHTS-HHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHh
Confidence            5678999999999999999

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=93.20  E-value=0.091  Score=36.22  Aligned_cols=40  Identities=10%  Similarity=0.243  Sum_probs=33.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      .|+++.|||+.++++.++|++++++..+-|=+.-.....+
T Consensus        45 ~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~D   84 (144)
T PRK03573         45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASD   84 (144)
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCC
Confidence            3689999999999999999999999999998865544333

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=93.15  E-value=0.1  Score=34.72  Aligned_cols=36  Identities=14%  Similarity=0.167  Sum_probs=31.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .++++.+||+.++++.++|++.+++..+.|=+.--.
T Consensus        41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~   76 (118)
T TIGR02337        41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLK   76 (118)
T ss_pred             CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence            568999999999999999999999999998886443

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>PRK06424 transcription factor; Provisional

Probab=93.13  E-value=0.096  Score=36.51  Aligned_cols=24  Identities=4%  Similarity=0.088  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++||+.++|++|.
T Consensus        95 ~~GLSQ~eLA~~iGvs~stIskiE  118 (144)
T PRK06424         95 RLSMSQADLAAKIFERKNVIASIE  118 (144)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999996

>PF14502 HTH_41: Helix-turn-helix domain

Probab=93.11  E-value=0.097  Score=29.27  Aligned_cols=31  Identities=26%  Similarity=0.376  Sum_probs=27.4

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ...|.++.|+||.|||+.-|+-..+.|.+.-
T Consensus         8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~L   38 (48)
T PF14502_consen    8 TISEYSEKFGVSRGTIQNALKFLEENGAIKL   38 (48)
T ss_pred             CHHHHHHHhCcchhHHHHHHHHHHHCCcEEe
Confidence            5678999999999999999999988887753

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=93.10  E-value=0.11  Score=30.35  Aligned_cols=30  Identities=20%  Similarity=0.298  Sum_probs=27.2

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +..+||..|+||..+|++.|+++.+.|-+.
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~   56 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVE   56 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            378999999999999999999999988764

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=92.98  E-value=0.048  Score=32.90  Aligned_cols=35  Identities=26%  Similarity=0.422  Sum_probs=28.6

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +.| ++..|||+.|+++...|.-.|..+..-|-+.-
T Consensus        11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~   46 (69)
T PF09012_consen   11 ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRK   46 (69)
T ss_dssp             HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEE
T ss_pred             HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            445 88999999999999999999999999998853

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PRK09526 lacI lac repressor; Reviewed

Probab=92.98  E-value=0.081  Score=41.34  Aligned_cols=23  Identities=35%  Similarity=0.365  Sum_probs=21.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +...|||+..|||.+|||+.|+.
T Consensus         6 ~ti~dIA~~aGVS~~TVSrvLn~   28 (342)
T PRK09526          6 VTLYDVARYAGVSYQTVSRVLNQ   28 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhcC
Confidence            67899999999999999999954

>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins

Probab=92.97  E-value=0.026  Score=35.92  Aligned_cols=28  Identities=21%  Similarity=0.350  Sum_probs=21.4

Q ss_pred             ccCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      ...++++...|+ +||.|+|+++.+|...
T Consensus        23 ~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~P   51 (87)
T PF02376_consen   23 KRNNISQRVFAKKVLNRSQGTLSDLLRKP   51 (87)
T ss_dssp             HHTT--HHHHHHHTTSS-HHHHHHHHHSC
T ss_pred             HHcCCCHHHHHHHHhccChhHHHHHhCCC
Confidence            457899999999 8999999999999643

The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.

>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]

Probab=92.89  E-value=0.1  Score=36.99  Aligned_cols=30  Identities=23%  Similarity=0.501  Sum_probs=25.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      -|+++.|+|++-||||+.+-||     |.|.+.|.
T Consensus        17 LGitQ~dLA~~aGVSQ~~IArl-----E~G~vdPr   46 (187)
T COG3620          17 LGITQKDLARRAGVSQPYIARL-----EAGKVDPR   46 (187)
T ss_pred             cCCCHHHHHHHcCccHHHHHHH-----hcCCCCcc
Confidence            4899999999999999999998     56666664

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

Probab=92.86  E-value=0.071  Score=29.38  Aligned_cols=24  Identities=25%  Similarity=0.374  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|++..++|+.++++.++|++|+
T Consensus        10 ~~~~s~~~~a~~~~~~~~~v~~~~   33 (58)
T cd00093          10 EKGLTQEELAEKLGVSRSTISRIE   33 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            468999999999999999999997

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

>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA

Probab=92.79  E-value=0.46  Score=30.92  Aligned_cols=66  Identities=15%  Similarity=0.121  Sum_probs=37.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      +++.|+|+.+|||..|+..|.    ..|-+.|...++..-+.-+......+..+.. ..-+++..++..-+
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye----~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~   67 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYD----EIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL   67 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            467899999999999999875    4588877432221223334444444422211 11356655555443

Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip

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

Probab=92.68  E-value=0.096  Score=30.77  Aligned_cols=24  Identities=25%  Similarity=0.365  Sum_probs=19.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+||+.+++++|.
T Consensus        10 ~~~lt~~~~a~~~~i~~~~i~~~e   33 (64)
T PF12844_consen   10 EKGLTQKDLAEKLGISRSTISKIE   33 (64)
T ss_dssp             HCT--HHHHHHHHTS-HHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999997

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=92.65  E-value=0.068  Score=41.68  Aligned_cols=23  Identities=17%  Similarity=0.150  Sum_probs=20.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +...|||+..|||.+|||+.|+.
T Consensus         6 ~ti~dIA~~agVS~~TVSrvLn~   28 (331)
T PRK14987          6 PVLQDVADRVGVTKMTVSRFLRN   28 (331)
T ss_pred             CcHHHHHHHhCCCHHHhhhhhCC
Confidence            57889999999999999999943

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=92.61  E-value=0.08  Score=41.39  Aligned_cols=23  Identities=22%  Similarity=0.143  Sum_probs=21.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus         7 ~Ti~dIA~~agVS~~TVSr~Ln~   29 (342)
T PRK10014          7 ITIHDVALAAGVSVSTVSLVLSG   29 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHCC
Confidence            78899999999999999999975

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=92.59  E-value=0.1  Score=36.68  Aligned_cols=24  Identities=21%  Similarity=0.249  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++|||+++|++|.
T Consensus        36 ~lGmTq~eLAerlGVS~~tIs~iE   59 (150)
T TIGR02612        36 ALGMSGAQLAGRLGVTPQRVEALE   59 (150)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            369999999999999999999996

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

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=92.53  E-value=0.12  Score=31.26  Aligned_cols=24  Identities=17%  Similarity=0.203  Sum_probs=22.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.-||..|-
T Consensus        12 ~~~ltQ~elA~~vgVsRQTi~~iE   35 (68)
T COG1476          12 ELGLTQEELAKLVGVSRQTIIAIE   35 (68)
T ss_pred             HhCcCHHHHHHHcCcCHHHHHHHH
Confidence            478999999999999999999984

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=92.52  E-value=0.097  Score=34.18  Aligned_cols=32  Identities=19%  Similarity=0.379  Sum_probs=29.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|+|.++|.+.+++..+.|-+.
T Consensus        17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344       17 RISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            48899999999999999999999998888775

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PRK08359 transcription factor; Validated

Probab=92.46  E-value=0.13  Score=37.08  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=22.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|..+||+.++|++|-
T Consensus        96 ~kglSQeeLA~~lgvs~stI~~iE  119 (176)
T PRK08359         96 KSGLSYEELSHEVGLSVNDLRRIA  119 (176)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999984

>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators

Probab=92.14  E-value=0.7  Score=29.22  Aligned_cols=68  Identities=19%  Similarity=0.058  Sum_probs=39.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      ++++.|+|+.+|||..++..|-    +.|-+.|....+..-+.=+......+..... ..-+++..+++.-+.
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye----~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~   69 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWE----EKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR   69 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            4688999999999999999884    4587777543221122223334333322211 124566655555544

Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PF13309 HTH_22: HTH domain

Probab=92.03  E-value=0.1  Score=31.13  Aligned_cols=20  Identities=20%  Similarity=0.283  Sum_probs=17.4

Q ss_pred             hhhhHHHhhcchhhHHHHHh
Q psy1904           8 PCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ...+|+.||||..||++.|+
T Consensus        45 v~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   45 VEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             HHHHHHHHCCCHHHHHHHcC
Confidence            35789999999999999874

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=92.03  E-value=0.11  Score=40.88  Aligned_cols=23  Identities=35%  Similarity=0.403  Sum_probs=20.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+..|||.+|||+.|+.
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~   24 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNN   24 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCC
Confidence            46789999999999999999954

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=91.98  E-value=0.67  Score=30.51  Aligned_cols=67  Identities=10%  Similarity=0.024  Sum_probs=40.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+..|-    +.|-+.|....+..-+.-++.....+..+..- .-++...++..-+.
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye----~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~   68 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWE----KEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVE   68 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            578899999999999999885    55888875532222233344444444333222 22456656655443

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=91.98  E-value=0.11  Score=40.66  Aligned_cols=22  Identities=23%  Similarity=0.305  Sum_probs=20.0

Q ss_pred             ChhhhHHHhhcchhhHHHHHhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ...|||+..|||.+|||+.|+.
T Consensus         3 Ti~dIA~~agVS~~TVSrvLn~   24 (341)
T PRK10703          3 TIKDVAKRAGVSTTTVSHVINK   24 (341)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC
Confidence            5789999999999999999964

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=91.93  E-value=0.63  Score=30.57  Aligned_cols=41  Identities=10%  Similarity=0.208  Sum_probs=34.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~   44 (163)
                      .++++.+||..++++.++|++.+++..+-|=+.=.....++
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~   82 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDE   82 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence            35999999999999999999999999999988654444443

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=91.90  E-value=0.15  Score=35.94  Aligned_cols=38  Identities=29%  Similarity=0.427  Sum_probs=32.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      ++..|||+.|+|+.+||+..+++..+-|=+.--+-+|-
T Consensus        25 ~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi   62 (154)
T COG1321          25 ARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGV   62 (154)
T ss_pred             ccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCe
Confidence            88899999999999999999999999998865444443

>TIGR01481 ccpA catabolite control protein A

Probab=91.86  E-value=0.11  Score=40.36  Aligned_cols=23  Identities=30%  Similarity=0.377  Sum_probs=20.2

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +...|||+..|||.+|||+.|+.
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn~   24 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVNG   24 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCC
Confidence            35679999999999999999954

Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=91.75  E-value=0.1  Score=40.43  Aligned_cols=19  Identities=32%  Similarity=0.361  Sum_probs=17.7

Q ss_pred             hhhHHHhhcchhhHHHHHh
Q psy1904           9 CVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         9 ~~ia~~~~vs~~~vs~~l~   27 (163)
                      .|||+..|||.+|||+.|+
T Consensus         2 ~dIA~~agVS~~TVSrvLn   20 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVIN   20 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhC
Confidence            5899999999999999995

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=91.74  E-value=0.18  Score=37.65  Aligned_cols=34  Identities=15%  Similarity=0.267  Sum_probs=30.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +++..+||+.+++|+++|+++|++..+.|=+.-.
T Consensus        21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~   54 (217)
T PRK14165         21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRT   54 (217)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            5889999999999999999999999999888544

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=91.72  E-value=0.19  Score=35.49  Aligned_cols=24  Identities=13%  Similarity=0.218  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|..+||++++|++|.
T Consensus        80 ~~glSqeeLA~~lgvs~s~IsriE  103 (154)
T TIGR00270        80 KRGWSQEQLAKKIQEKESLIKKIE  103 (154)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999995

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=91.62  E-value=0.21  Score=29.49  Aligned_cols=30  Identities=23%  Similarity=0.309  Sum_probs=25.4

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +..+||++|+||..+|.+-|....+.|-+.
T Consensus        26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~   55 (64)
T PF00392_consen   26 SERELAERYGVSRTTVREALRRLEAEGLIE   55 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence            678999999999999999999998888764

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>TIGR00180 parB_part ParB-like partition proteins

Probab=91.52  E-value=0.12  Score=37.44  Aligned_cols=25  Identities=8%  Similarity=0.187  Sum_probs=23.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      .|+++.+||+.||+|.++|++.|.-
T Consensus       119 ~g~s~~~iA~~lg~s~~~V~r~l~l  143 (187)
T TIGR00180       119 FSMTQEDLAKKIGKSRAHITNLLRL  143 (187)
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5899999999999999999999855

This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.

>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D

Probab=91.37  E-value=0.15  Score=31.71  Aligned_cols=21  Identities=19%  Similarity=0.120  Sum_probs=16.3

Q ss_pred             CChhhhHHHhhcchhhHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ....++|+.||||.|||.+=+
T Consensus        20 aTVR~~Ak~FGvSKSTVHkDv   40 (82)
T PF12116_consen   20 ATVRQAAKVFGVSKSTVHKDV   40 (82)
T ss_dssp             --HHHHHHHHTS-HHHHHHHH
T ss_pred             cHHHHHHHHHCCcHHHHHHHH
Confidence            456789999999999999976

It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=91.34  E-value=0.13  Score=40.25  Aligned_cols=21  Identities=29%  Similarity=0.290  Sum_probs=19.4

Q ss_pred             ChhhhHHHhhcchhhHHHHHh
Q psy1904           7 RPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ...|||+..|||.+|||+.|+
T Consensus         3 ti~dIA~~aGVS~~TVSrvLn   23 (343)
T PRK10727          3 TIKDVARLAGVSVATVSRVIN   23 (343)
T ss_pred             CHHHHHHHhCCCHHHHHHHhC
Confidence            578999999999999999994

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=91.21  E-value=0.12  Score=40.23  Aligned_cols=24  Identities=29%  Similarity=0.195  Sum_probs=20.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +...|||+..|||.+|||+.|+..
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~~   25 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDD   25 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcCC
Confidence            357899999999999999999643

>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator

Probab=91.19  E-value=0.98  Score=29.09  Aligned_cols=64  Identities=19%  Similarity=0.238  Sum_probs=38.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH---HHHhCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE---YKKTNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~---~~~~~p~~~~~e~~~~l   75 (163)
                      +++.++|+++|||.+|+..|.    +.|-+.|....+. .+.=+......+..   +.++ -+++..++..-+
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye----~~Gll~p~r~~~g-~R~Y~~~dv~~l~~I~~L~~~-~G~~l~ei~~~l   67 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYE----EIGLVSPERSEGR-YRLYSEEDLKRLERILRLREV-LGFSLQEVTHFL   67 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCC-CEEECHHHHHHHHHHHHHHHH-cCCCHHHHHHHH
Confidence            467899999999999999986    4588877554322 22233334444433   3321 356665555443

Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=91.13  E-value=0.66  Score=33.31  Aligned_cols=54  Identities=17%  Similarity=0.200  Sum_probs=39.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEE   58 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~   58 (163)
                      ++.+.|||+.++++.++|++++++..+-|=+.-.....++-.   ..++.-.+.+..
T Consensus        71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~  127 (176)
T PRK10870         71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE  127 (176)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            488999999999999999999999999998866554444323   234444444433

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=91.12  E-value=0.25  Score=37.35  Aligned_cols=34  Identities=9%  Similarity=0.153  Sum_probs=31.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.+|++.+||+++|.-+.+.|=+..
T Consensus        23 ~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        23 PRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            5699999999999999999999999999998864

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=90.93  E-value=0.27  Score=33.93  Aligned_cols=32  Identities=19%  Similarity=0.246  Sum_probs=29.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.|+||.++|++.|++..+.|-+.
T Consensus        22 ~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~   53 (142)
T PRK03902         22 YARVSDIAEALSVHPSSVTKMVQKLDKDEYLI   53 (142)
T ss_pred             CcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence            38889999999999999999999999988775

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=90.93  E-value=0.17  Score=31.17  Aligned_cols=25  Identities=8%  Similarity=0.103  Sum_probs=20.1

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .++..|||+..+||.+||.|..+..
T Consensus        34 ~~si~elA~~~~vS~sti~Rf~kkL   58 (77)
T PF01418_consen   34 FMSISELAEKAGVSPSTIVRFCKKL   58 (77)
T ss_dssp             T--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred             HccHHHHHHHcCCCHHHHHHHHHHh
Confidence            4688999999999999999998775

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]

Probab=90.87  E-value=0.12  Score=40.20  Aligned_cols=31  Identities=26%  Similarity=0.311  Sum_probs=26.9

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG   33 (163)
                      ++|+|..+||++||..++||++=|++-.-.+
T Consensus        21 ~~~~S~reIA~~LgRh~sTIsRElkRn~~~~   51 (318)
T COG2826          21 KAKMSIREIAKQLNRHHSTISRELKRNRTRD   51 (318)
T ss_pred             HcCCCHHHHHHHhCCCcchhhHHHhcCCccc
Confidence            5799999999999999999999998864433

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=90.78  E-value=0.18  Score=27.35  Aligned_cols=24  Identities=17%  Similarity=0.250  Sum_probs=19.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ++..+||+.+|||.++|.+=+++.
T Consensus        18 ~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen   18 RSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHHh
Confidence            788999999999999998866553

...

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=90.76  E-value=0.16  Score=39.40  Aligned_cols=21  Identities=24%  Similarity=0.199  Sum_probs=18.9

Q ss_pred             hhhhHHHhhcchhhHHHHHhh
Q psy1904           8 PCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ..|||+..|||.+|||+.|+.
T Consensus         2 i~dIA~~aGVS~~TVSrvLn~   22 (327)
T TIGR02417         2 LSDIAKLAGVSKTTASYVING   22 (327)
T ss_pred             HHHHHHHhCCCHHHHHHHHcC
Confidence            579999999999999999954

Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=90.69  E-value=0.2  Score=29.23  Aligned_cols=19  Identities=26%  Similarity=0.240  Sum_probs=16.3

Q ss_pred             hHHHhhcchhhHHHHHhhh
Q psy1904          11 ISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus        11 ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|+.|+|+..+|.+|+++-
T Consensus        31 aarkf~V~r~~Vr~W~kqe   49 (58)
T PF09607_consen   31 AARKFNVSRRQVRKWRKQE   49 (58)
T ss_dssp             HHHHTTS-HHHHHHHHTTH
T ss_pred             HHHHhCccHHHHHHHHHHH
Confidence            8999999999999999654

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator

Probab=90.68  E-value=1.3  Score=28.52  Aligned_cols=64  Identities=14%  Similarity=0.187  Sum_probs=37.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|...  +|.+  .=+......+..... ..-+++..++..-+
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye----~~Gll~p~~~~~~gyR--~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l   67 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYD----KIGLFKPEIVKENGYR--YYTLEQFEQLDIILLLKELGISLKEIKDYL   67 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCc--cCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            467899999999999988874    5699988532  3332  233333333322211 12256666666543

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=90.66  E-value=0.19  Score=34.81  Aligned_cols=30  Identities=20%  Similarity=0.387  Sum_probs=28.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ++..+||+.+|+|.++|.+.+++..+.|-+
T Consensus        23 ~~~~eia~~lglS~~~v~~Ri~~L~~~GiI   52 (154)
T COG1522          23 ISNAELAERVGLSPSTVLRRIKRLEEEGVI   52 (154)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence            889999999999999999999999988855

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=90.63  E-value=0.25  Score=31.77  Aligned_cols=27  Identities=11%  Similarity=0.185  Sum_probs=24.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .|+++-|.|.+.|||.+|+.++|+.-+
T Consensus        48 ~~l~QeeAA~rMgISr~Tfwr~l~sAR   74 (99)
T COG1342          48 EGLTQEEAALRMGISRQTFWRLLTSAR   74 (99)
T ss_pred             hhccHHHHHHHhcccHHHHHHHHHHHH
Confidence            689999999999999999999997653

>PRK01905 DNA-binding protein Fis; Provisional

Probab=90.33  E-value=0.22  Score=30.79  Aligned_cols=26  Identities=19%  Similarity=0.270  Sum_probs=22.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|-...++|++||||.+++++.++++
T Consensus        49 ~~gn~s~aAr~LGIsrstL~rklkk~   74 (77)
T PRK01905         49 AGGNQSLAAEYLGINRNTLRKKLQQH   74 (77)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            45667889999999999999999886

>PRK00215 LexA repressor; Validated

Probab=90.27  E-value=0.29  Score=35.83  Aligned_cols=34  Identities=24%  Similarity=0.226  Sum_probs=30.1

Q ss_pred             CChhhhHHHhhc-chhhHHHHHhhhhhccCCCCCC
Q psy1904           6 VRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         6 ~~~~~ia~~~~v-s~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++..|||+.||+ +.+||+++|++..+.|-+....
T Consensus        24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215         24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCC
Confidence            467799999999 9999999999999999886554

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=90.24  E-value=0.38  Score=33.79  Aligned_cols=39  Identities=33%  Similarity=0.340  Sum_probs=33.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSK   44 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~   44 (163)
                      ++..+||++++||..++.||+...+..|=+  ..|+.||-.
T Consensus        25 ~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~   65 (153)
T PRK11920         25 SRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVR   65 (153)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCee
Confidence            688999999999999999999999999977  446666653

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=90.19  E-value=0.23  Score=35.82  Aligned_cols=24  Identities=17%  Similarity=0.227  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.++|+.+|||+++|++|.
T Consensus        18 ~~glt~~elA~~~gis~~~is~~E   41 (185)
T PRK09943         18 QQGLSQRRAAELSGLTHSAISTIE   41 (185)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            479999999999999999999997

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=90.19  E-value=0.3  Score=28.45  Aligned_cols=25  Identities=20%  Similarity=0.361  Sum_probs=22.0

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      +....|+.++||+++|++.++...+
T Consensus        15 s~~~AA~~l~is~~~vs~~i~~LE~   39 (60)
T PF00126_consen   15 SISAAAEELGISQSAVSRQIKQLEE   39 (60)
T ss_dssp             SHHHHHHHCTSSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhhccchHHHHHHHHHHH
Confidence            6778999999999999999988843

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=90.16  E-value=0.5  Score=29.80  Aligned_cols=36  Identities=25%  Similarity=0.400  Sum_probs=31.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .++.+.+||+.+++|.++|++.++...+.|-+.-..
T Consensus        23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~   58 (101)
T smart00347       23 GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLP   58 (101)
T ss_pred             CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecC
Confidence            358999999999999999999999999999886443

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=90.08  E-value=1.4  Score=28.31  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=39.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|..  .+|.+  .=+......+..... ..-+++..++..-+
T Consensus         1 m~i~eva~~~gvs~~tlR~ye----~~Gll~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l   67 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYD----HIGLLSPSQRTEGGHR--LYDRADIRRLHQIIALRRLGFSLREIGRAL   67 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCce--eeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            578899999999999998875    568888843  23333  233444433322221 12256666666544

Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=90.00  E-value=0.32  Score=34.92  Aligned_cols=26  Identities=19%  Similarity=0.193  Sum_probs=23.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..|||..||||.++|...+.+-
T Consensus       121 ~g~~~~EIA~~lgis~~tV~~~l~Ra  146 (181)
T PRK09637        121 EGLSQKEIAEKLGLSLSGAKSRVQRG  146 (181)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            79999999999999999999988554

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=89.99  E-value=0.27  Score=30.47  Aligned_cols=36  Identities=19%  Similarity=0.371  Sum_probs=31.9

Q ss_pred             CccCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           1 MAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         1 ~~~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      |+..| ++..+||+.|+.+...|.-.|.++..-|.+.
T Consensus        11 l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkve   47 (78)
T PRK15431         11 LALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAV   47 (78)
T ss_pred             HHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            45667 8999999999999999999999998888774

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=89.92  E-value=0.29  Score=32.83  Aligned_cols=26  Identities=19%  Similarity=0.236  Sum_probs=23.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .++...|||+.||||.++|++.|+++
T Consensus        70 pd~tl~Ela~~l~Vs~~ti~~~Lkrl   95 (119)
T PF01710_consen   70 PDATLRELAERLGVSPSTIWRALKRL   95 (119)
T ss_pred             CCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence            45777899999999999999999887

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=89.92  E-value=0.36  Score=37.11  Aligned_cols=33  Identities=15%  Similarity=0.114  Sum_probs=30.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..|||+.+|++.+||+++|+.+.+.|=+.
T Consensus        39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~   71 (271)
T PRK10163         39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY   71 (271)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            468999999999999999999999999999883

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=89.90  E-value=0.38  Score=34.26  Aligned_cols=41  Identities=22%  Similarity=0.297  Sum_probs=35.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR   46 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p~   46 (163)
                      ++..+||+.++|+...+.++|....+.|=+.  .|..||-.+.
T Consensus        26 vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~La   68 (164)
T PRK10857         26 VPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLG   68 (164)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeecc
Confidence            8999999999999999999999999999886  4656665544

>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein

Probab=89.82  E-value=0.34  Score=31.96  Aligned_cols=28  Identities=18%  Similarity=0.351  Sum_probs=21.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      .|....++|+.+|+|...|.+|+++.+.
T Consensus        71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~   98 (108)
T PF08765_consen   71 NGMNVRELARKYGLSERQIYRIIKRVRR   98 (108)
T ss_dssp             -SS-HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4889999999999999999999988743

It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.

>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator

Probab=89.79  E-value=1.3  Score=28.05  Aligned_cols=48  Identities=13%  Similarity=0.089  Sum_probs=32.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE   58 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~   58 (163)
                      +++.++|+.+|||..|+..|.    +.|-+.|....+. .+.-++.....+..
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye----~~Gli~p~r~~~g-~R~y~~~dv~~l~~   49 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYE----RLGLLSPSRTDGG-TRRYSERDIERLRR   49 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHH----HCCCcCCCcCCCC-CeeECHHHHHHHHH
Confidence            467899999999999999986    4588888543222 23334444444433

Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB

Probab=89.79  E-value=1.6  Score=28.81  Aligned_cols=67  Identities=12%  Similarity=0.035  Sum_probs=40.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+..|-    +.|-+.|..-.....+.-+......+..+.. ..-+++..++..-+.
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye----~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYE----KEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAE   68 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            468899999999999998874    5588855332212223344444444432221 123677777776554

Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=89.76  E-value=0.29  Score=25.95  Aligned_cols=25  Identities=16%  Similarity=0.112  Sum_probs=19.4

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ++.|+|+.+|||..|+..|-    +.|-+
T Consensus         1 ti~e~A~~~gvs~~tlR~ye----~~Gll   25 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYE----REGLL   25 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHH----HTTSS
T ss_pred             CHHHHHHHHCCCHHHHHHHH----HCCCC
Confidence            36799999999999998885    44766

One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....

>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]

Probab=89.68  E-value=0.44  Score=31.19  Aligned_cols=49  Identities=22%  Similarity=0.391  Sum_probs=37.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCc
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITS   68 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~   68 (163)
                      .|+++.++|+.+||+..+|+.|+              .|.  +..+.+..-.+....+..|.++.
T Consensus        22 ~glt~~~lA~~lgV~r~~is~li--------------ng~--~~iT~dmAlrL~k~fGtspefWl   70 (104)
T COG3093          22 LGLTQTELAEALGVTRNTISELI--------------NGR--RAITADMALRLAKVFGTSPEFWL   70 (104)
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHH--------------cCC--cCCCHHHHHHHHHHhCCCHHHHH
Confidence            48999999999999999999998              222  34566777777777777776653

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=89.64  E-value=1.3  Score=31.99  Aligned_cols=62  Identities=13%  Similarity=0.106  Sum_probs=38.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRD   73 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~   73 (163)
                      +++.++|+.+|||..||.+|-++    |.+.+... +|.  +.-+.....++..+.. .+-++...++..
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~----g~L~~~R~~~G~--R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~   64 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQ----LNLPCEKNEYGH--YIFTEEDLQLLEYVKSQIEEGQNMQDTQK   64 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCcCCCCC--EEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence            46789999999999999999754    55544332 333  2334445556654442 233566655544

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=89.61  E-value=0.39  Score=30.49  Aligned_cols=27  Identities=19%  Similarity=0.282  Sum_probs=24.1

Q ss_pred             CCCChhhhHHHhh-cchhhHHHHHhhhh
Q psy1904           4 AGVRPCVISRQLR-VSHGCVSKILNRYQ   30 (163)
Q Consensus         4 ~g~~~~~ia~~~~-vs~~~vs~~l~~~~   30 (163)
                      -|++-.+|++.|| .+++||+.-+++..
T Consensus        43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~   70 (90)
T cd06571          43 TGLSLPEIGRAFGGRDHSTVLHAVRKIE   70 (90)
T ss_pred             hCCCHHHHHHHhCCCCHhHHHHHHHHHH
Confidence            4899999999999 99999999887763

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=89.60  E-value=0.41  Score=32.76  Aligned_cols=41  Identities=20%  Similarity=0.331  Sum_probs=34.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR   46 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p~   46 (163)
                      ++..+||+.++|+...+.++|....+.|=+.  .|..||-.+.
T Consensus        26 ~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~   68 (135)
T TIGR02010        26 VTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLG   68 (135)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEecc
Confidence            7899999999999999999999999999875  3555654443

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>PRK15320 transcriptional activator SprB; Provisional

Probab=89.46  E-value=0.37  Score=35.49  Aligned_cols=29  Identities=10%  Similarity=0.124  Sum_probs=26.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhc
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~t   32 (163)
                      .|.+..|||..|++|.+||++.+.+..+-
T Consensus       178 kG~SNKEIAekL~LS~KTVSTYKnRLLeK  206 (251)
T PRK15320        178 SGHPAIELAKKFGLGTKTVSIYRKKVMYR  206 (251)
T ss_pred             cCCCHHHHHHHhccchhhHHHHHHHHHHH
Confidence            79999999999999999999999887443

>PRK11569 transcriptional repressor IclR; Provisional

Probab=89.46  E-value=0.4  Score=36.88  Aligned_cols=34  Identities=18%  Similarity=0.329  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.+|++.+||+++|..+.+.|=+.-
T Consensus        42 ~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~   75 (274)
T PRK11569         42 GSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQ   75 (274)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4589999999999999999999999999998853

>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators

Probab=89.39  E-value=1.9  Score=27.67  Aligned_cols=64  Identities=14%  Similarity=0.151  Sum_probs=36.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDK   74 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~   74 (163)
                      ++..|+|+.+||+..+|..|.+    .|-+.|...++.. +.-+......+.....- ..++...++..-
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~   65 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSENGY-RLYSEEDLERLRLIRRLRELGLSLKEIREL   65 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCCCC-cccCHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence            4678999999999999999863    4777665543322 22333333333322211 145555554443

Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=89.35  E-value=0.47  Score=33.23  Aligned_cols=40  Identities=25%  Similarity=0.398  Sum_probs=34.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSKP   45 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~p   45 (163)
                      ++..+||++.+||...+.+++...+.-|=+  .+|+.||-.-
T Consensus        26 ~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~L   67 (150)
T COG1959          26 VSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRL   67 (150)
T ss_pred             ccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccC
Confidence            668999999999999999999999999988  4566676643

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=89.34  E-value=0.42  Score=36.47  Aligned_cols=32  Identities=22%  Similarity=0.393  Sum_probs=29.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +++..|||+.+|++.+||+++|..+.+.|=+.
T Consensus        26 ~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~   57 (263)
T PRK09834         26 GATVGLLAELTGLHRTTVRRLLETLQEEGYVR   57 (263)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            48999999999999999999999998888774

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=89.28  E-value=0.28  Score=31.66  Aligned_cols=26  Identities=19%  Similarity=0.293  Sum_probs=22.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|-....+|++||||.+|+.+.|+++
T Consensus        67 ~~gn~s~AAr~LGIsRsTL~rKLkr~   92 (95)
T PRK00430         67 TRGNQTRAALMLGINRGTLRKKLKKY   92 (95)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            45667889999999999999999886

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=89.19  E-value=0.75  Score=31.07  Aligned_cols=41  Identities=24%  Similarity=0.328  Sum_probs=33.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKP   45 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p   45 (163)
                      .++..+||+.++++.++|.++|......|=+.  .|..||-.+
T Consensus        25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l   67 (132)
T TIGR00738        25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRL   67 (132)
T ss_pred             cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccC
Confidence            48999999999999999999999999988775  344455444

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=89.16  E-value=0.43  Score=32.45  Aligned_cols=33  Identities=18%  Similarity=0.187  Sum_probs=29.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      +.++.--+||++++++.|||+|-|+..-+.|-+
T Consensus        40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV   72 (126)
T COG3355          40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLV   72 (126)
T ss_pred             cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCe
Confidence            345888999999999999999999999888766

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=89.13  E-value=0.26  Score=37.53  Aligned_cols=33  Identities=21%  Similarity=0.393  Sum_probs=29.8

Q ss_pred             CC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .| ++..|+|+.|+||..||.|.|+...+.|-+.
T Consensus        17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~   50 (251)
T PRK13509         17 LGFVTVEKVIERLGISPATARRDINKLDESGKLK   50 (251)
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            44 8999999999999999999999998888774

>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator

Probab=89.05  E-value=2  Score=27.93  Aligned_cols=63  Identities=10%  Similarity=0.009  Sum_probs=37.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDK   74 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~   74 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|... +|.+  .=+....+.+.-+.. ..-+++..++..-
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye----~~Gll~~~r~~~g~R--~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~   66 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYE----KLGLITGTRNANGYR--LYPDSDLQRLLLIQQLQAGGLSLKECLAC   66 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCe--eCCHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence            578899999999999998765    5588887543 3332  223334444432211 2235666665553

Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>COG5606 Uncharacterized conserved small protein [Function unknown]

Probab=89.03  E-value=0.17  Score=31.88  Aligned_cols=24  Identities=25%  Similarity=0.279  Sum_probs=22.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.++++.+||..|||+++.||.+.
T Consensus        39 q~~l~Q~qiae~lgV~qprvS~l~   62 (91)
T COG5606          39 QAALSQAQIAELLGVTQPRVSDLA   62 (91)
T ss_pred             HHHHHHHHHHHHhCCCCchHHHHH
Confidence            568899999999999999999986

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=88.99  E-value=0.33  Score=25.35  Aligned_cols=20  Identities=35%  Similarity=0.375  Sum_probs=17.6

Q ss_pred             ChhhhHHHhhcchhhHHHHH
Q psy1904           7 RPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +..++|+-||+++++|++.|
T Consensus        18 Si~eAa~~l~i~~~~I~~~l   37 (37)
T PF07453_consen   18 SIREAARYLGISHSTISKYL   37 (37)
T ss_pred             CHHHHHHHhCCCHHHHHHhC
Confidence            57899999999999998864

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=88.97  E-value=0.51  Score=28.18  Aligned_cols=33  Identities=27%  Similarity=0.420  Sum_probs=27.1

Q ss_pred             CCCCh--hhhHHHhhcc-hhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRP--CVISRQLRVS-HGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~--~~ia~~~~vs-~~~vs~~l~~~~~tG~~~   36 (163)
                      .|.+|  .|||+.||++ .++|...|+...+-|-+.
T Consensus        22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~   57 (65)
T PF01726_consen   22 NGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR   57 (65)
T ss_dssp             HSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred             cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence            46555  6999999996 999999999999888774

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=88.97  E-value=0.39  Score=29.36  Aligned_cols=18  Identities=11%  Similarity=0.062  Sum_probs=16.4

Q ss_pred             hhhhHHHhhcchhhHHHH
Q psy1904           8 PCVISRQLRVSHGCVSKI   25 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~   25 (163)
                      ...+|+.||||++.||.|
T Consensus        13 ~~kvA~aLGIs~~AVsQW   30 (75)
T PRK09744         13 KTKLANAAGVRLASVAAW   30 (75)
T ss_pred             HHHHHHHHCCCHHHHHHH
Confidence            457899999999999999

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=88.87  E-value=0.48  Score=34.74  Aligned_cols=33  Identities=18%  Similarity=0.306  Sum_probs=30.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..+||+.|+|+.++|++.|+.+.+.|-+.
T Consensus        14 ~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~   46 (203)
T TIGR02702        14 GQATAAALAEALAISPQAVRRHLKDLETEGLIE   46 (203)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            459999999999999999999999998888884

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=88.82  E-value=0.44  Score=34.26  Aligned_cols=26  Identities=15%  Similarity=0.171  Sum_probs=23.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +|++..|||+.||||.++|...+.+-
T Consensus       126 eg~s~~EIA~~lgis~~tV~~~l~Ra  151 (182)
T PRK12511        126 EGLSYQEAAAVLGIPIGTLMSRIGRA  151 (182)
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence            79999999999999999999998654

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=88.72  E-value=1.5  Score=29.55  Aligned_cols=64  Identities=20%  Similarity=0.227  Sum_probs=41.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH--hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~--~~p~~~~~e~~~~l   75 (163)
                      +++.++|+.+|||..|+..|-    +.|-+.|...+|.  +.-+......+.-+..  .+.+++..+++.-+
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE----~~GLl~p~r~~G~--R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L   67 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWE----RHGLIKPARRNGQ--RLYSNNDLKRLRFIKKLINEKGLNIAGVKQIL   67 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCcCCCCc--EEECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            578899999999999999875    3488888655444  3334444444433322  22567776666543

Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=88.62  E-value=0.51  Score=35.87  Aligned_cols=34  Identities=15%  Similarity=0.244  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.+|++.+||+++|+.+.+.|=+.-
T Consensus        27 ~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~   60 (257)
T PRK15090         27 REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ   60 (257)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3588999999999999999999999999998854

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

Probab=88.62  E-value=0.22  Score=29.73  Aligned_cols=21  Identities=14%  Similarity=0.172  Sum_probs=16.0

Q ss_pred             ChhhhHHHhhcchhhHH-HHHh
Q psy1904           7 RPCVISRQLRVSHGCVS-KILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs-~~l~   27 (163)
                      +..|+|+.||||+++|+ .|.+
T Consensus        14 ~~~~lA~~lgis~st~s~~~~~   35 (66)
T PF07022_consen   14 SDKELAERLGISKSTLSNNWKK   35 (66)
T ss_dssp             SCHHHHCCTT--HHHHH-HHHH
T ss_pred             CHHHHHHHhCcCHHHhhHHHHh
Confidence            45699999999999999 7764

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

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=88.59  E-value=0.25  Score=37.61  Aligned_cols=40  Identities=25%  Similarity=0.309  Sum_probs=32.6

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      +.| ++..|||+.|+||..||.|-|....+.|-+. ...||-
T Consensus        16 ~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~-r~~GGa   56 (252)
T PRK10906         16 QQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL-RHHGGA   56 (252)
T ss_pred             HcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCCE
Confidence            345 8899999999999999999999998888874 334443

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=88.57  E-value=0.47  Score=34.25  Aligned_cols=26  Identities=15%  Similarity=0.126  Sum_probs=24.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +|++..|||+.||||.++|...|.+-
T Consensus       131 ~g~s~~EIA~~Lgis~~tVk~~l~Ra  156 (187)
T PRK12516        131 SGFAYEEAAEICGCAVGTIKSRVNRA  156 (187)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            79999999999999999999998664

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=88.48  E-value=0.36  Score=34.32  Aligned_cols=28  Identities=36%  Similarity=0.377  Sum_probs=24.8

Q ss_pred             ccCCCChhhhHHHhh-cchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISRQLR-VSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~-vs~~~vs~~l~~~   29 (163)
                      -.+|++..+||++|| ||.+.|.=.+.++
T Consensus        15 w~~G~SasqIA~~lg~vsRnAViGk~hRl   43 (162)
T PF07750_consen   15 WAEGLSASQIARQLGGVSRNAVIGKAHRL   43 (162)
T ss_pred             HHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence            358999999999999 9999998887766

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=88.38  E-value=0.55  Score=34.14  Aligned_cols=35  Identities=11%  Similarity=0.091  Sum_probs=31.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.+++..+||++++++..+-|=+.=.
T Consensus        58 ~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~   92 (185)
T PRK13777         58 KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS   92 (185)
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence            67999999999999999999999999999988633

>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=88.32  E-value=3  Score=26.89  Aligned_cols=61  Identities=18%  Similarity=0.180  Sum_probs=35.8

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEV   71 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~   71 (163)
                      ++.|+|+.+|||..|+..|.    +.|-+.|..-....-+.=+......+.-+..-..++...++
T Consensus         2 ~i~e~A~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i   62 (99)
T cd04772           2 RTVDLARAIGLSPQTVRNYE----SLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVA   62 (99)
T ss_pred             CHHHHHHHHCcCHHHHHHHH----HcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHH
Confidence            57899999999999998874    56888774322112233344555555333322234444443

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators

Probab=88.26  E-value=2.3  Score=27.41  Aligned_cols=63  Identities=11%  Similarity=0.146  Sum_probs=37.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH--hCCCCCchhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK--TNPNITSWEVRDK   74 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~--~~p~~~~~e~~~~   74 (163)
                      +++.++|+.+|||.+++..|.    +.|-+.|... +|.  +.-+......+.....  ..-+++..++..-
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye----~~Gli~p~r~~~g~--R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~   67 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYD----RLGLVSPARTNGGG--RRYSNNDLELLRQVQRLSQDEGFNLAGIKRI   67 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCC--eeECHHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence            467899999999999999885    4587777432 333  2234444444433322  2235555544443

Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=88.19  E-value=0.5  Score=33.77  Aligned_cols=33  Identities=9%  Similarity=0.166  Sum_probs=29.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      ++..|||..+|+|.-+|+++|+++++.|-+.-.
T Consensus       144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~  176 (193)
T TIGR03697       144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH  176 (193)
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            578999999999999999999999999887644

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=88.17  E-value=0.5  Score=35.07  Aligned_cols=27  Identities=22%  Similarity=0.101  Sum_probs=24.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+|++..|||+.||||.++|...|.+-
T Consensus       148 ~eg~s~~EIAe~LgiS~~tVk~~L~RA  174 (216)
T PRK12533        148 LEDMSYREIAAIADVPVGTVMSRLARA  174 (216)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            379999999999999999999988654

>PRK06474 hypothetical protein; Provisional

Probab=88.16  E-value=0.44  Score=34.39  Aligned_cols=32  Identities=16%  Similarity=0.323  Sum_probs=29.9

Q ss_pred             CChhhhHHHh-hcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +++++|+..+ +|+.+||++-|+.+.+.|-+..
T Consensus        27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~   59 (178)
T PRK06474         27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHV   59 (178)
T ss_pred             CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEE
Confidence            8999999999 7999999999999999998864

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=88.13  E-value=0.49  Score=34.14  Aligned_cols=31  Identities=16%  Similarity=0.255  Sum_probs=29.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..+||..+|++..+|+++|+++++.|-+.
T Consensus       150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~  180 (202)
T PRK13918        150 ATHDELAAAVGSVRETVTKVIGELSREGYIR  180 (202)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence            5688999999999999999999999999987

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=88.10  E-value=2.4  Score=27.26  Aligned_cols=66  Identities=14%  Similarity=0.156  Sum_probs=39.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh--CCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT--NPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~--~p~~~~~e~~~~l   75 (163)
                      ++..|+|+.+|||..++.-|.    +.|-+.|....+..-+.-+......+.....-  .-++...++..-+
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye----~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l   68 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYL----REGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVL   68 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            567899999999999998886    45888874322122233455555555443322  1245555555443

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators

Probab=88.04  E-value=2.4  Score=27.55  Aligned_cols=64  Identities=16%  Similarity=0.059  Sum_probs=37.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDK   74 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~   74 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|....+ .-+.=+......+..... ..-+++..+++.-
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye----~~Gll~~~r~~~-g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~   66 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYE----SIGLIPSARSEA-NYRLYSEADLSRLEKIVFLQAGGLPLEEIAGC   66 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence            478899999999999996664    458885543322 122233334433332221 2236777666654

Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=87.96  E-value=0.51  Score=26.44  Aligned_cols=22  Identities=32%  Similarity=0.374  Sum_probs=19.6

Q ss_pred             ChhhhHHHhhcchhhHHHHHhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +..++|+.||+++++|++.++.
T Consensus        19 S~~eAa~~lg~~~~~I~~~~~~   40 (53)
T smart00497       19 SIREAAKYLGISHSSISKYLNT   40 (53)
T ss_pred             CHHHHHHHhCCCHHHHHHHHhC
Confidence            6789999999999999999854

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=87.78  E-value=0.3  Score=36.93  Aligned_cols=32  Identities=28%  Similarity=0.381  Sum_probs=28.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..|||+.|+||..||.|.|+...+.|.+.
T Consensus        18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~   49 (240)
T PRK10411         18 SLTTEALAEQLNVSKETIRRDLNELQTQGKIL   49 (240)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            48999999999999999999999998877764

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=87.68  E-value=0.6  Score=35.42  Aligned_cols=35  Identities=17%  Similarity=0.347  Sum_probs=31.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      |++..|||+++|++.+||+++|....+.|=+.--.
T Consensus        19 ~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~   53 (246)
T COG1414          19 GLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP   53 (246)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            46799999999999999999999999999887654

>TIGR00498 lexA SOS regulatory protein LexA

Probab=87.62  E-value=0.54  Score=34.25  Aligned_cols=35  Identities=20%  Similarity=0.352  Sum_probs=29.3

Q ss_pred             CCCChh--hhHHHhhcc-hhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPC--VISRQLRVS-HGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~--~ia~~~~vs-~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|..|.  |||+.||++ .+||++.|++..+.|-+...
T Consensus        22 ~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~   59 (199)
T TIGR00498        22 TGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD   59 (199)
T ss_pred             cCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence            344454  999999998 99999999999999887654

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PRK15043 transcriptional regulator MirA; Provisional

Probab=87.62  E-value=2  Score=32.59  Aligned_cols=67  Identities=18%  Similarity=0.196  Sum_probs=42.5

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKLI   76 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l~   76 (163)
                      -+++.++|+.+|||..|+..|-+++   |-+.|... ||.+  .=+....+.+..+..- .-++...+++.-+.
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wErr~---GLL~P~Rt~~G~R--~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~   71 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQRRY---GLLKPQRTDGGHR--LFNDADIDRIREIKRWIDNGVQVSKVKMLLS   71 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHhc---CCCCCccCCCCCE--EECHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            3688999999999999999987655   88888654 4333  3344444444332221 23566656555443

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=87.53  E-value=0.41  Score=37.89  Aligned_cols=21  Identities=29%  Similarity=0.319  Sum_probs=19.0

Q ss_pred             ChhhhHHHhhcchhhHHHHHh
Q psy1904           7 RPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ..-|||+..|||.+|||+.|+
T Consensus         2 TikDVA~~AGVS~sTVSrvln   22 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVLN   22 (333)
T ss_pred             CHHHHHHHhCCCHHHHHHHHc
Confidence            467999999999999999994

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=87.47  E-value=0.51  Score=30.83  Aligned_cols=26  Identities=19%  Similarity=0.252  Sum_probs=20.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +..|-.+||..+|||...|+.++++-
T Consensus        32 eDlSlsEIAe~~~iSRqaV~d~ikr~   57 (101)
T PF04297_consen   32 EDLSLSEIAEELGISRQAVYDSIKRA   57 (101)
T ss_dssp             S---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            56889999999999999999999774

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=87.22  E-value=0.66  Score=32.81  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=23.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+..|||+.||+|.++|...|.+-
T Consensus       115 ~g~s~~eIA~~lgis~~tV~~~l~Ra  140 (170)
T TIGR02959       115 EGLSQQEIAEKLGLSLSGAKSRVQRG  140 (170)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            78999999999999999999998664

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).

>PRK04140 hypothetical protein; Provisional

Probab=87.20  E-value=0.6  Score=36.85  Aligned_cols=24  Identities=25%  Similarity=0.264  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus       137 ~~GlSq~eLA~~lGVSr~tIskyE  160 (317)
T PRK04140        137 ELGLSLGELASELGVSRRTISKYE  160 (317)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999997

>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]

Probab=87.04  E-value=0.88  Score=34.82  Aligned_cols=43  Identities=26%  Similarity=0.416  Sum_probs=38.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCCCCcC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSKPRVA   48 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~p~~~   48 (163)
                      ++=.|||..++...|||...++.++..|-+  .||+.||..|...
T Consensus        26 IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~PT~k   70 (294)
T COG2524          26 IKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPTSK   70 (294)
T ss_pred             cchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCCccccHH
Confidence            677899999999999999999999999988  7899999988744

>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]

Probab=86.88  E-value=0.86  Score=33.07  Aligned_cols=48  Identities=23%  Similarity=0.339  Sum_probs=34.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI   56 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i   56 (163)
                      .+.|.+.|+++|||..|+.+|.    .-|-+.+-..-+.+-+...++....+
T Consensus         1 ~m~~~e~~~~lgis~~Tl~rw~----r~G~i~~~~~~~gr~~~~ee~v~~~~   48 (193)
T COG2452           1 LLRPKEACQLLGISYSTLLRWI----REGKIRVVTTEGGKYRIPEEEIKKYL   48 (193)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHH----HcCcccceEecCceEeccHhHHHHHh
Confidence            3689999999999999999997    44888776655555555444444433

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=86.83  E-value=0.63  Score=34.51  Aligned_cols=33  Identities=21%  Similarity=0.370  Sum_probs=29.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      ++..+||..+|+|..+|+|+|+++++.|-+.-.
T Consensus       185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~  217 (235)
T PRK11161        185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK  217 (235)
T ss_pred             ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            567899999999999999999999999988744

>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator

Probab=86.66  E-value=2.6  Score=28.43  Aligned_cols=65  Identities=17%  Similarity=0.144  Sum_probs=38.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC-CCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP-GVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P-g~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+++|||..|+.-|    .+.|-+.| ... +|.  +.-+......+.-+.. ..-+++..++..-+.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~gy--R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYY----QRRGLLPEPPRPEGGY--RRYPEETVTRLRFIKRAQELGFTLDEIAELLE   68 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            57889999999999999544    56788874 332 332  3334444444322221 123566766665543

Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=86.64  E-value=0.72  Score=33.10  Aligned_cols=27  Identities=19%  Similarity=0.132  Sum_probs=24.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+|++..|||+.||+|.++|...|.+-
T Consensus       125 ~~g~s~~EIA~~Lgis~~tV~~~l~RA  151 (182)
T PRK12540        125 ASGFSYEDAAAICGCAVGTIKSRVNRA  151 (182)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            379999999999999999999998664

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=86.52  E-value=0.6  Score=31.91  Aligned_cols=37  Identities=19%  Similarity=0.083  Sum_probs=30.4

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +..|.++.++|+.++|+.++|.+|..+..+.....++
T Consensus        86 ~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~~~  122 (129)
T COG3677          86 YMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGLRL  122 (129)
T ss_pred             HHcCCCcccHHHHhcccHHHHHHHHHhhcchhhccCC
Confidence            4567999999999999999999999888665555444

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=86.50  E-value=0.69  Score=34.43  Aligned_cols=31  Identities=26%  Similarity=0.302  Sum_probs=28.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..|||..+|++..+|+|+|+.+++.|-+.
T Consensus       180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~  210 (230)
T PRK09391        180 MSRRDIADYLGLTIETVSRALSQLQDRGLIG  210 (230)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            4568999999999999999999999999875

>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=86.44  E-value=3.4  Score=27.28  Aligned_cols=65  Identities=18%  Similarity=0.187  Sum_probs=39.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l   75 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|....+. -+.=+..+...+..+..- .-++...++..-+
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye----~~GLl~p~r~~~g-~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l   66 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYE----EQGLLVPERSANG-YRDYDEAAVDRVRQIRRLLAAGLTLEEIREFL   66 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHH----HCCCCCCCcCCCC-CeecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            578899999999999988875    4588888543222 233334444444332221 2356666666544

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=86.20  E-value=1  Score=26.03  Aligned_cols=27  Identities=30%  Similarity=0.272  Sum_probs=24.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      -.|.+..+||..+++|..||...+...
T Consensus        17 ~~G~s~~eia~~l~is~~tV~~h~~~i   43 (65)
T COG2771          17 AQGKSNKEIARILGISEETVKTHLRNI   43 (65)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            368999999999999999999988665

>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator

Probab=86.20  E-value=3.2  Score=28.63  Aligned_cols=66  Identities=18%  Similarity=0.156  Sum_probs=42.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|....+. -+.=+......+..+.. ..-+++..++..-+.
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE----~~GLl~p~r~~~g-~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYE----QKGLIASWRNAGN-QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA   68 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCC-CeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            678999999999999988875    4488877544322 23334455555533322 234677777776543

Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=85.98  E-value=0.79  Score=34.71  Aligned_cols=26  Identities=19%  Similarity=0.202  Sum_probs=23.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +|++..|||.+||||.+||...|.+-
T Consensus       176 eg~S~~EIA~~Lgis~~TVk~rl~RA  201 (244)
T TIGR03001       176 DGLSMDRIGAMYQVHRSTVSRWVAQA  201 (244)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            78999999999999999999988554

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=85.96  E-value=3.1  Score=28.60  Aligned_cols=65  Identities=14%  Similarity=0.163  Sum_probs=40.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.++|+.+|||..|+..|-    +.|-+.|... +|.+  .=+......+..+.. ..-+++..++.+-+.
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~g~R--~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   67 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDSNYR--YYDETALDRLQLIEHLKGQRLSLAEIKDQLE   67 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCCe--eECHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            467899999999999998885    5699988664 3332  223334333322221 133577777776543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=85.93  E-value=1  Score=23.98  Aligned_cols=26  Identities=15%  Similarity=0.128  Sum_probs=20.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..++..|||..+|+|.+..+++.++.
T Consensus         7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~   32 (42)
T PF00165_consen    7 QKLTLEDIAEQAGFSPSYFSRLFKKE   32 (42)
T ss_dssp             SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            56889999999999999999998775

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=85.86  E-value=1.1  Score=29.52  Aligned_cols=37  Identities=22%  Similarity=0.251  Sum_probs=31.5

Q ss_pred             CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      ..+++.||...+     +||.+||++.|+.+.+-|-+.--..
T Consensus        15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~   56 (116)
T cd07153          15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIEL   56 (116)
T ss_pred             CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence            348999999988     6999999999999999998875443

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators

Probab=85.84  E-value=3.8  Score=27.37  Aligned_cols=67  Identities=15%  Similarity=0.175  Sum_probs=39.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+++|||..|+.-    |.+.|-+.|..-....-+.=+......+..+.. ..-+++..++..-+.
T Consensus         1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~   68 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLS   68 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            4788999999999999854    456799986432212223334444444432211 233677777766543

Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=85.69  E-value=2.4  Score=33.46  Aligned_cols=27  Identities=22%  Similarity=0.270  Sum_probs=24.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .|++..|||+.||+|.++|...|.+-+
T Consensus       168 ~g~s~~EIA~~lgis~~tVk~~l~RAr  194 (339)
T PRK08241        168 LGWSAAEVAELLDTSVAAVNSALQRAR  194 (339)
T ss_pred             hCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            799999999999999999999886653

>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species

Probab=85.59  E-value=0.75  Score=32.76  Aligned_cols=33  Identities=21%  Similarity=0.322  Sum_probs=28.4

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ..| .+-.|||..||||.+.|.+.-++|....+-
T Consensus        16 ~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~s   49 (181)
T PF04645_consen   16 KEGRLSDAEIAKELGVSRVNVWKMRQKWESSEDS   49 (181)
T ss_pred             hcCCccHHHHHHHHCchHHHHHHHHHHHHhcCCc
Confidence            467 889999999999999999999998655544

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=85.54  E-value=3.7  Score=26.27  Aligned_cols=30  Identities=13%  Similarity=0.138  Sum_probs=24.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|..
T Consensus         1 ~ti~eva~~~gvs~~tLRyye----~~Gll~p~~   30 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYD----DIGLFKPAK   30 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCc
Confidence            367899999999999988875    458888854

Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator

Probab=85.44  E-value=5  Score=26.32  Aligned_cols=64  Identities=17%  Similarity=0.094  Sum_probs=39.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC-C-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-I-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~-~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      .++.|+|+.+|||..|+.-|-    ..|-+.|.. . +|.  +.=+......+.-+.. ..-++...++..-+
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye----~~GLl~p~~r~~~g~--R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l   67 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYL----LRGLLHPVARTEGGY--GLFDDCALQRLRFVRAAFEAGIGLDELARLC   67 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            367899999999999998875    459998853 2 333  3334444444433332 23356666665544

Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=85.35  E-value=3.6  Score=28.03  Aligned_cols=65  Identities=18%  Similarity=0.189  Sum_probs=40.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+++|||..|+.-|-    +.|-+.|..  .+|.+  .=+......+..+.. ..-+++..++..-+.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye----~~GLl~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~   69 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYE----KNGLIKPAGRTDSGYR--LYTDEDQKRLRFILKAKELGFTLDEIKELLS   69 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCce--ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578999999999999988875    558888853  23333  223344444432221 234677777766543

This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=85.31  E-value=0.67  Score=30.51  Aligned_cols=33  Identities=27%  Similarity=0.542  Sum_probs=30.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      |.|..||.+|+|+-|.+.++|+.+.+.|.+.+-
T Consensus        60 ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V   92 (105)
T PF03297_consen   60 ITPSVLSERLKINGSLARKALRELESKGLIKPV   92 (105)
T ss_dssp             ECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEE
T ss_pred             eeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEE
Confidence            678999999999999999999999999999875

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=85.25  E-value=3.9  Score=27.60  Aligned_cols=65  Identities=15%  Similarity=0.162  Sum_probs=40.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      |++.|+|+++|||..|+.-|-    +.|-+.|..  .+|.+  .=+......+..+.. ..-+++..++..-+.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYE----EKGLIPPPLRSEGGYR--TYTQQHLDELRLISRARQVGFSLEECKELLN   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCe--ecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            578899999999999987664    669888743  24433  233444444432221 234677777765443

This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.

>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor

Probab=85.16  E-value=0.96  Score=24.82  Aligned_cols=23  Identities=26%  Similarity=0.294  Sum_probs=20.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||++.|||.+++++..
T Consensus        15 ~~~s~~~Ia~~~gvs~~~~y~~f   37 (47)
T PF00440_consen   15 EAVSIRDIARRAGVSKGSFYRYF   37 (47)
T ss_dssp             TTSSHHHHHHHHTSCHHHHHHHC
T ss_pred             HhCCHHHHHHHHccchhhHHHHc
Confidence            56899999999999999999864

Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=85.07  E-value=0.79  Score=35.15  Aligned_cols=45  Identities=22%  Similarity=0.383  Sum_probs=39.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVA   48 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~   48 (163)
                      .|+.+.||.+..|.|.+|||..|..+.+.|-+.=...+|..-++.
T Consensus        19 ~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsGKs~rVw   63 (321)
T COG3888          19 EGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSGKSKRVW   63 (321)
T ss_pred             CCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeecCcceEEe
Confidence            689999999999999999999999999999998777777654443

>PRK12423 LexA repressor; Provisional

Probab=85.04  E-value=0.74  Score=33.79  Aligned_cols=34  Identities=24%  Similarity=0.278  Sum_probs=29.3

Q ss_pred             CCC--ChhhhHHHhh-cchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGV--RPCVISRQLR-VSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~--~~~~ia~~~~-vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+  +..|||+.|| +|.++|++.|+.+.+.|-+.-
T Consensus        22 ~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~   58 (202)
T PRK12423         22 AGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEV   58 (202)
T ss_pred             cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence            455  7889999999 599999999999999888754

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=85.03  E-value=0.69  Score=29.27  Aligned_cols=33  Identities=15%  Similarity=0.304  Sum_probs=30.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      |.|..||.+|+|+-|-+.++|+.+.+.|.+.+-
T Consensus        42 ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V   74 (86)
T PRK09334         42 VTPYTLASKYGIKISVAKKVLRELEKRGVLVLY   74 (86)
T ss_pred             EcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence            679999999999999999999999999998775

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=84.96  E-value=0.97  Score=29.34  Aligned_cols=28  Identities=7%  Similarity=0.058  Sum_probs=23.1

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhh-hccC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQ-ETGS   34 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~-~tG~   34 (163)
                      +....|+.|+||+++|++-++... ..|.
T Consensus        18 Sis~AA~~L~iS~stvs~~I~~LE~~lg~   46 (99)
T TIGR00637        18 SISQAAKDAGISYKSAWDYIRAMNNLSGE   46 (99)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            567889999999999999998883 3444

ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=84.84  E-value=1.2  Score=31.74  Aligned_cols=31  Identities=10%  Similarity=0.019  Sum_probs=27.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      ++++...+|..+|||.+|+.+|-..-++.|+
T Consensus        18 ~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GD   48 (165)
T PF08822_consen   18 DRLSLEQAAAKCGVSYATARRWKREAKAKGD   48 (165)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence            5788899999999999999999888777775

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=84.79  E-value=0.53  Score=35.90  Aligned_cols=35  Identities=11%  Similarity=0.148  Sum_probs=30.5

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +.| ++..|+|+.|+||..||.|=|....+.|-+.=
T Consensus        16 ~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r   51 (256)
T PRK10434         16 KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIR   51 (256)
T ss_pred             HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            345 88999999999999999999999988887643

>PHA02943 hypothetical protein; Provisional

Probab=84.71  E-value=0.98  Score=31.71  Aligned_cols=41  Identities=27%  Similarity=0.342  Sum_probs=34.0

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      +.| .+..+||+.||+|++-|.-+|.-...-|-+.--..|..
T Consensus        21 k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~   62 (165)
T PHA02943         21 ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRA   62 (165)
T ss_pred             hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecce
Confidence            456 66889999999999999999999988898876555644

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=84.66  E-value=0.9  Score=30.79  Aligned_cols=29  Identities=28%  Similarity=0.382  Sum_probs=25.2

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      |-..|.++.+||++||-+.+.||-|-++.
T Consensus        19 lRekG~tQ~eIA~~L~TTraNvSaIEkrA   47 (143)
T COG1356          19 LREKGLTQSEIARILKTTRANVSAIEKRA   47 (143)
T ss_pred             hhhccccHHHHHHHHccchhhHHHHHHHH
Confidence            34579999999999999999999987664

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=84.64  E-value=1  Score=33.63  Aligned_cols=26  Identities=15%  Similarity=0.119  Sum_probs=23.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+..+||+.||||.++|...+.+.
T Consensus       164 ~g~s~~EIAe~lgis~~tVk~~l~Ra  189 (231)
T PRK11922        164 EELSVEETAQALGLPEETVKTRLHRA  189 (231)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            78999999999999999999988554

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=84.53  E-value=0.74  Score=34.96  Aligned_cols=26  Identities=23%  Similarity=0.239  Sum_probs=24.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .||+-.|||..||||..||.+|-.++
T Consensus        18 ~gmk~~dIAeklGvspntiksWKrr~   43 (279)
T COG5484          18 KGMKLKDIAEKLGVSPNTIKSWKRRD   43 (279)
T ss_pred             hhccHHHHHHHhCCChHHHHHHHHhc
Confidence            68999999999999999999998765

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=84.41  E-value=0.82  Score=29.85  Aligned_cols=32  Identities=19%  Similarity=0.305  Sum_probs=28.5

Q ss_pred             hhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           9 CVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         9 ~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      .+||+.++|+.++|++++++..+-|-+.-...
T Consensus        40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~   71 (126)
T COG1846          40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRD   71 (126)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence            89999999999999999999999998865443

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=84.28  E-value=0.91  Score=33.64  Aligned_cols=33  Identities=15%  Similarity=0.220  Sum_probs=29.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+..|||..+|+|.-+|+|.|+++.+.|-+...
T Consensus       170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~  202 (226)
T PRK10402        170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS  202 (226)
T ss_pred             chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence            467999999999999999999999999988754

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=84.26  E-value=2  Score=31.40  Aligned_cols=38  Identities=26%  Similarity=0.347  Sum_probs=31.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      ++-.++|+.||||.++|..-|.+....|=+.-.+..|.
T Consensus        35 L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~   72 (212)
T TIGR03338        35 LNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGV   72 (212)
T ss_pred             ecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCe
Confidence            45678999999999999999999999999855443444

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.

>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators

Probab=84.21  E-value=4.4  Score=27.35  Aligned_cols=65  Identities=15%  Similarity=0.110  Sum_probs=39.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC-C-CCCCCCCcCChHHHHHHHHHH-HhCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG-V-IGGSKPRVATPDVEKRIEEYK-KTNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg-~-~Gg~~p~~~~~~~~~~i~~~~-~~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|. . .+|.+  .=+......+..+. -..-+++..+++.-+.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~~~~r~~~g~R--~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYE----EIGLIPPPSRSDNGYR--VYNQRDIEELRFIRRARDLGFSLEEIRELLA   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCce--ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578899999999999988764    55888753 3 23333  23344444443222 1234677777776443

Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements

>PRK11013 DNA-binding transcriptional regulator LysR; Provisional

Probab=84.13  E-value=0.67  Score=35.89  Aligned_cols=26  Identities=35%  Similarity=0.425  Sum_probs=22.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +.| +....|+.|+||+++||+.++++
T Consensus        17 ~~g-S~s~AAe~L~isqsavS~~Ik~L   42 (309)
T PRK11013         17 TAG-SLTEAARLLHTSQPTVSRELARF   42 (309)
T ss_pred             HhC-cHHHHHHHHCCCcHHHHHHHHHH
Confidence            444 77889999999999999999888

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=83.96  E-value=6.6  Score=26.41  Aligned_cols=65  Identities=15%  Similarity=0.082  Sum_probs=41.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      .+++.|+|+.+|||..||.-|-    +.|-+.|..-  +|.+  .=++.+...+.-+.. ..-++...+++.-+
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye----~~GLL~p~~r~~~gyR--~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll   70 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYL----LRGLLHPVRRTTSGYG--IFDDASLQRLRFVRAAFEAGIGLGELARLC   70 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCe--eCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            5789999999999999988775    5588888643  4433  334555555533332 23456666666543

This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.

>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth

Probab=83.95  E-value=1.1  Score=26.13  Aligned_cols=21  Identities=29%  Similarity=0.395  Sum_probs=17.8

Q ss_pred             hhhhHHHhhcchhhHHHHHhh
Q psy1904           8 PCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +.+.|+.|||+++.|||-|+.
T Consensus        15 Q~kaA~~lGV~Q~AIsKAlr~   35 (59)
T PF09048_consen   15 QAKAARALGVTQSAISKALRA   35 (59)
T ss_dssp             HHHHHHHHTS-HHHHHHHHHC
T ss_pred             hHHHHHHcCCcHHHHHHHHHc
Confidence            678999999999999999854

Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....

>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators

Probab=83.89  E-value=4.4  Score=26.90  Aligned_cols=65  Identities=15%  Similarity=0.091  Sum_probs=39.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      ++..++|+.+|||..|+.-|-    +.|-+.|....+ .-+.-+......+..+.. ..-+++..++..-+
T Consensus         1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l   66 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIF   66 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            467899999999999987764    669998854333 223334444444322211 12356666666543

Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK09954 putative kinase; Provisional

Probab=83.89  E-value=1  Score=35.86  Aligned_cols=30  Identities=20%  Similarity=0.283  Sum_probs=27.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ++..+||+.|+||.++|.+.+++..+.|-+
T Consensus        18 ~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954         18 IQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            899999999999999999999999887765

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=83.78  E-value=1.2  Score=32.23  Aligned_cols=27  Identities=26%  Similarity=0.176  Sum_probs=24.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..|||+.||||.++|...|.+-
T Consensus       127 ~~g~s~~EIA~~LgiS~~tVk~~l~Ra  153 (188)
T PRK12546        127 ASGFSYEEAAEMCGVAVGTVKSRANRA  153 (188)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            379999999999999999999998664

>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional

Probab=83.54  E-value=0.69  Score=35.37  Aligned_cols=26  Identities=8%  Similarity=0.059  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +.| +...+|+.|+||+++||+.++..
T Consensus        14 ~~g-s~s~AA~~L~isQ~avSr~i~~L   39 (296)
T PRK09906         14 EEL-NFTKAAEKLHTAQPSLSQQIKDL   39 (296)
T ss_pred             hhC-CHHHHHHHhCCCCcHHHHHHHHH
Confidence            444 67889999999999999999887

>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator

Probab=83.53  E-value=5.5  Score=26.04  Aligned_cols=65  Identities=11%  Similarity=0.120  Sum_probs=38.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDK   74 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~   74 (163)
                      +++.|+|+.+|||.+|+.-|.    +.|-+.|... +....+.=+......+..+..- .-++...++..-
T Consensus         1 ~~i~eva~~~gis~~tlR~ye----~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l   67 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYD----KIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEI   67 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence            467899999999999998875    4588888442 2122233344444444332221 124555555543

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=83.47  E-value=4.3  Score=27.98  Aligned_cols=65  Identities=22%  Similarity=0.248  Sum_probs=40.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|..  .+|.  +.=+......+..+.. ..-+++..++..-+.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye----~~GLl~p~~r~~~gy--R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   69 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYE----KQGLMDPEVRTEGGY--RLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS   69 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHH----HCCCCCCcccCCCCC--eeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578899999999999998875    558888853  2333  3334444444433221 233677777776543

>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators

Probab=83.47  E-value=5  Score=27.01  Aligned_cols=67  Identities=10%  Similarity=0.103  Sum_probs=39.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+++|||..|+.-|-    +.|-+.|..-....-+.=+......+..+.. ..-+++..++..-+.
T Consensus         1 m~IgevA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYE----KEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQ   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578899999999999987764    6688876432112223334444443322211 122577777776543

Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

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

Probab=83.44  E-value=1.2  Score=25.47  Aligned_cols=38  Identities=29%  Similarity=0.481  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHhccCCCC--CCHHHHHHHHHHhCCCcccc
Q psy1904         105 FTSAQLEELEKSFQRSHY--PDIYTREALANKFGMTETRV  142 (163)
Q Consensus       105 ~t~~q~~~Le~~F~~~~~--p~~~~r~~la~~l~l~~~~v  142 (163)
                      +|+.|.+.|..+|+..-|  |-.....+||..+|++...+
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~   40 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV   40 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence            578899999999887754  55567789999999987654

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

>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

Probab=83.44  E-value=1.1  Score=31.83  Aligned_cols=31  Identities=19%  Similarity=0.388  Sum_probs=26.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +.|+|+.|+|+.++++.+.|.+|     |.|.+.|.
T Consensus        90 ~~G~SqedLA~ki~ek~svI~~i-----E~g~~~P~  120 (165)
T COG1813          90 KRGLSQEDLAAKLKEKVSVIRRI-----ERGEATPN  120 (165)
T ss_pred             HcCCCHHHHHHHhcccHHHHHHH-----HhcccCcc
Confidence            57999999999999999999998     55655554

>PRK12682 transcriptional regulator CysB-like protein; Reviewed

Probab=83.35  E-value=0.78  Score=35.46  Aligned_cols=28  Identities=18%  Similarity=0.148  Sum_probs=24.8

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ++.|-+-..+|+.|+||+++||+-++..
T Consensus        13 ~~~~~s~s~AA~~L~isq~avSr~I~~L   40 (309)
T PRK12682         13 VRRNLNLTEAAKALHTSQPGVSKAIIEL   40 (309)
T ss_pred             HHccCCHHHHHHHhcCccHHHHHHHHHH
Confidence            4466788899999999999999999888

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=83.32  E-value=0.96  Score=32.73  Aligned_cols=29  Identities=14%  Similarity=0.099  Sum_probs=25.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      -+|.+-.|||+.|+||.+||...+.+..+
T Consensus       146 AqGkTnKEIAe~L~IS~rTVkth~srImk  174 (198)
T PRK15201        146 ASGYHLSETAALLSLSEEQTKSLRRSIMR  174 (198)
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999877633

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=83.22  E-value=5.8  Score=26.82  Aligned_cols=65  Identities=15%  Similarity=0.147  Sum_probs=39.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.++|+.+|||..|+.-|-    +.|-+.|..  .+|.+  .=+......+..+.. ..-+++..++..-+.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye----~~GLl~~~~r~~~gyR--~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~   68 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYE----KQGLLPPPARTDNNYR--VYTVGHVERLAFIRNCRTLDMSLAEIRQLLR   68 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCC--cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578899999999999988774    568887643  23333  233444433432221 233677777766543

This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=83.22  E-value=1.2  Score=33.39  Aligned_cols=60  Identities=20%  Similarity=0.222  Sum_probs=37.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhc-cCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNI   66 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~t-G~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~   66 (163)
                      .|++-.|||+.+|+|.++|...|.+-++. ...-+.  |+..+. ...+..-.+....+++|..
T Consensus       131 eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~--~~~~~~-~~~~~~~~~~~~~~~~~~~  191 (228)
T PRK06704        131 FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE--GIEIVE-FTDDMEVVVTSIREERPEL  191 (228)
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh--cCCCCC-ccccHHHHHHHHHhcCHHH
Confidence            68999999999999999999987554221 111111  111111 1344555666777788743

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=83.21  E-value=1.1  Score=35.00  Aligned_cols=26  Identities=27%  Similarity=0.284  Sum_probs=23.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..|||+.||||.++|...|.+-
T Consensus       157 ~g~s~~EIA~~lgis~~tV~~~l~Ra  182 (324)
T TIGR02960       157 LGWRAAETAELLGTSTASVNSALQRA  182 (324)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            68999999999999999999998665

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=83.14  E-value=5.7  Score=27.08  Aligned_cols=65  Identities=12%  Similarity=0.094  Sum_probs=39.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      |++.|+|+++|||..|+.-|-    +.|-+.|..-  +|.  +.=+......+.-+.. ..-+++..++..-+.
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gy--R~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~   68 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGY--RDYPPETVWVLEIISSAQQAGFSLDEIRQLLP   68 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            578899999999999987764    5688877432  333  2223444444432222 223577777776553

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su

>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator

Probab=83.09  E-value=0.85  Score=34.34  Aligned_cols=23  Identities=13%  Similarity=0.148  Sum_probs=21.1

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +-..+|+.|+||+++||+.+++.
T Consensus        13 s~~~AA~~L~isqsavS~~i~~L   35 (279)
T TIGR03339        13 SFTRAAERLGLSQPTVTDQVRKL   35 (279)
T ss_pred             CHHHHHHHhcCCchHHHHHHHHH
Confidence            67789999999999999999887

This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=83.02  E-value=7  Score=26.80  Aligned_cols=65  Identities=11%  Similarity=0.132  Sum_probs=41.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      |++.|+|+++|||..|+.-|    .+.|-+.|..-  +|.  +.=+......+..+.. ..-++...++.+-+.
T Consensus         1 m~Ige~a~~~gvs~~tlRyY----E~~GLl~p~~r~~~gy--R~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~   68 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFY----EEKGLVTPPMRSENGY--RTYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCc--ccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            57889999999999998776    46688877532  333  3334455555543332 233677777766543

>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH

Probab=82.97  E-value=1  Score=26.48  Aligned_cols=19  Identities=21%  Similarity=0.281  Sum_probs=17.8

Q ss_pred             hhhhHHHhhcchhhHHHHH
Q psy1904           8 PCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+|++|+++.+||.|++
T Consensus        19 qtEvaR~l~c~R~TVrKY~   37 (64)
T PF06322_consen   19 QTEVARRLGCNRATVRKYS   37 (64)
T ss_pred             HHHHHHHhcccHHHHHHHh
Confidence            5799999999999999998

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=82.96  E-value=0.64  Score=35.42  Aligned_cols=36  Identities=22%  Similarity=0.256  Sum_probs=31.7

Q ss_pred             ccCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           2 AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         2 ~~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+.| ++..|+|+.|+||..||.|=|....+.|-+.=
T Consensus        15 ~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R   51 (253)
T COG1349          15 KEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLR   51 (253)
T ss_pred             HHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence            3466 88999999999999999999999999998853

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=82.93  E-value=1.2  Score=34.82  Aligned_cols=24  Identities=17%  Similarity=0.245  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.++|+.+|||.++|++|.
T Consensus        39 ~~gltq~~lA~~~gvs~~~i~~~E   62 (309)
T PRK08154         39 RRGMSRKVLAQASGVSERYLAQLE   62 (309)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999995

>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators

Probab=82.84  E-value=5.9  Score=26.69  Aligned_cols=65  Identities=15%  Similarity=0.173  Sum_probs=39.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.++|+.+|||..|+.-|-    +.|-+.|..  .+|.  +.=+......+..+.. ..-+++..++..-+.
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~--R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYE----SIGLLPEPARTAGGY--RLYGAAHVERLRFIRRARDLGFSLEEIRALLA   68 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCc--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            468899999999999988764    568887643  2333  3334444444433222 233567766665443

Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=82.76  E-value=0.92  Score=33.34  Aligned_cols=27  Identities=26%  Similarity=0.214  Sum_probs=24.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      -+|.+-.|||+.|+||..||...+++.
T Consensus       150 a~G~snkeIA~~L~iS~~TVk~h~~~I  176 (207)
T PRK15411        150 MAGQGTIQISDQMNIKAKTVSSHKGNI  176 (207)
T ss_pred             HcCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence            479999999999999999999988765

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=82.74  E-value=1.6  Score=33.01  Aligned_cols=36  Identities=14%  Similarity=0.377  Sum_probs=32.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      ++..+||+++|||.+.|..-++++.+.|-+...+.|
T Consensus       199 lse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG  234 (251)
T TIGR02787       199 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG  234 (251)
T ss_pred             ccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            899999999999999999999999999999766533

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=82.40  E-value=1.4  Score=31.13  Aligned_cols=32  Identities=22%  Similarity=0.143  Sum_probs=29.5

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      -++..|||+.|||+...|.++|..+.+-|=+.
T Consensus        28 ~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~   59 (158)
T TIGR00373        28 EFTDEEISLELGIKLNEVRKALYALYDAGLAD   59 (158)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence            38899999999999999999999999999884

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>PRK11233 nitrogen assimilation transcriptional regulator; Provisional

Probab=82.27  E-value=0.86  Score=35.20  Aligned_cols=23  Identities=9%  Similarity=0.125  Sum_probs=20.8

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +-..+|+.|+||+++||+-+++.
T Consensus        17 S~s~AA~~L~isQ~avS~~I~~L   39 (305)
T PRK11233         17 SLTQAAEVLHIAQPALSQQVATL   39 (305)
T ss_pred             CHHHHHHHhCCCchHHHHHHHHH
Confidence            67889999999999999999776

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=81.96  E-value=1.2  Score=28.44  Aligned_cols=21  Identities=24%  Similarity=0.381  Sum_probs=18.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .|++  ++|++.|||.+++++|.
T Consensus        44 ~glS--qLAe~~GIs~stLs~iE   64 (89)
T TIGR02684        44 RGMT--QLARKTGLSRESLYKAL   64 (89)
T ss_pred             CChH--HHHHHHCCCHHHHHHHH
Confidence            4776  59999999999999997

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

>COG3655 Predicted transcriptional regulator [Transcription]

Probab=81.78  E-value=0.68  Score=28.34  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=23.4

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      |++.+++--|+|++.|||.++++++.
T Consensus        11 l~~r~~~~~eLa~~igis~~~ls~l~   36 (73)
T COG3655          11 LADRKISLKELAEAIGISEANLSKLK   36 (73)
T ss_pred             HHHHhhhHHHHHHHHcccHHHHHHHH
Confidence            46778999999999999999999984

>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional

Probab=81.60  E-value=0.94  Score=34.87  Aligned_cols=27  Identities=11%  Similarity=0.043  Sum_probs=23.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      +.| +....|++|+||+++||+-++..+
T Consensus        14 ~~g-S~s~AA~~L~itQpavS~~i~~LE   40 (305)
T PRK11151         14 EHR-HFRRAADSCHVSQPTLSGQIRKLE   40 (305)
T ss_pred             HhC-CHHHHHHHhCCCchHHHHHHHHHH
Confidence            445 778899999999999999998773

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=81.56  E-value=1.2  Score=31.68  Aligned_cols=34  Identities=21%  Similarity=0.236  Sum_probs=29.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++..+||..+++|..||++.++.+.+.+-+.-..
T Consensus        76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~  109 (165)
T PF05732_consen   76 ATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR  109 (165)
T ss_pred             eeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc
Confidence            4678999999999999999999999998886553

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=81.32  E-value=6.5  Score=26.25  Aligned_cols=65  Identities=17%  Similarity=0.200  Sum_probs=42.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|...+|.  +.=++.....+..... ..-+++..++..-+.
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe----~~GLl~p~r~~gy--R~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~   66 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYE----DKGLLSPERRGQT--RVYSRRDRARLKLILRGKRLGFSLEEIRELLD   66 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCcCCCCc--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            467899999999999987764    5699998766543  3334445544432221 234677777666544

Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK13832 plasmid partitioning protein; Provisional

Probab=81.27  E-value=1.1  Score=37.45  Aligned_cols=28  Identities=18%  Similarity=0.110  Sum_probs=24.1

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      |...|+++.+||++||+|.++|++++..
T Consensus       114 Lie~G~T~EeIA~~lG~S~~~V~rlllL  141 (520)
T PRK13832        114 LVALGWTEEAIAVALALPVRQIRKLRLL  141 (520)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3468999999999999999999996643

>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences []

Probab=81.14  E-value=1  Score=29.03  Aligned_cols=28  Identities=18%  Similarity=0.306  Sum_probs=21.6

Q ss_pred             hhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           8 PCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ...||+.||+|.+||.||-    ..|-+.+..
T Consensus        48 ~~GlAklfgcSv~Ta~RiK----~sG~id~AI   75 (96)
T PF12964_consen   48 LKGLAKLFGCSVPTANRIK----KSGKIDPAI   75 (96)
T ss_pred             HHHHHHHhCCCchhHHHHH----hcCCccHHH
Confidence            3579999999999999985    446665543

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=80.87  E-value=2  Score=32.01  Aligned_cols=43  Identities=19%  Similarity=0.262  Sum_probs=33.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC--CCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSKPR   46 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P--g~~Gg~~p~   46 (163)
                      .+++.-|||++||||.-.|.+=|..+...|-+.-  ...|-.+|.
T Consensus        24 g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~   68 (218)
T COG2345          24 GPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPA   68 (218)
T ss_pred             CCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCc
Confidence            3499999999999999999999999998885522  223444555

>PRK09791 putative DNA-binding transcriptional regulator; Provisional

Probab=80.86  E-value=1.1  Score=34.43  Aligned_cols=26  Identities=23%  Similarity=0.250  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +.| +-..+|+.|+||+++||+-++.+
T Consensus        18 ~~g-s~s~AA~~L~isQ~avS~~i~~L   43 (302)
T PRK09791         18 RQG-SIRGASRMLNMSQPALTKSIQEL   43 (302)
T ss_pred             HcC-CHHHHHHHhCCChHHHHHHHHHH
Confidence            445 67789999999999999999888

>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators

Probab=80.78  E-value=6.5  Score=26.75  Aligned_cols=67  Identities=12%  Similarity=0.076  Sum_probs=40.2

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      |++.|+|+.+|||..|+.-|    .+.|=+.|.......-+.=+......+..+.. ..-+++..++..-+.
T Consensus         1 m~IgE~A~~~gvs~~TLRyY----E~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   68 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFY----TRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILS   68 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            57889999999999998544    56698988654211123333444444422211 234677777776543

Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c

>PRK12684 transcriptional regulator CysB-like protein; Reviewed

Probab=80.69  E-value=1.1  Score=34.83  Aligned_cols=28  Identities=18%  Similarity=0.105  Sum_probs=24.6

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ++.|-+-...|+.|+||+++||+.++.+
T Consensus        13 ~~~g~S~s~AA~~L~isQpavS~~ik~L   40 (313)
T PRK12684         13 VRQNFNLTEAAKALYTSQPGVSKAIIEL   40 (313)
T ss_pred             HHcCCCHHHHHHHhcCCChHHHHHHHHH
Confidence            3456688899999999999999999888

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=80.52  E-value=1.7  Score=33.68  Aligned_cols=26  Identities=23%  Similarity=0.158  Sum_probs=24.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..|||+.||+|.++|...|.+-
T Consensus       130 ~g~s~~EIA~~lg~s~~tVk~~l~RA  155 (293)
T PRK09636        130 FGVPFDEIASTLGRSPAACRQLASRA  155 (293)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            68999999999999999999998765

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=80.39  E-value=2.2  Score=24.29  Aligned_cols=25  Identities=16%  Similarity=0.104  Sum_probs=20.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .++..|+|+.||||..++.++-.++
T Consensus        15 hlp~~eAA~~Lgv~~T~LKr~CR~~   39 (52)
T PF02042_consen   15 HLPIKEAAKELGVSVTTLKRRCRRL   39 (52)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHc
Confidence            4788899999999999888876543

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development

Probab=80.31  E-value=1.7  Score=27.82  Aligned_cols=21  Identities=14%  Similarity=0.202  Sum_probs=18.3

Q ss_pred             ChhhhHHHhhcchhhHHHHHh
Q psy1904           7 RPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      .+..+|+..||+.|+||||..
T Consensus        25 gq~~vA~~~Gv~eStISR~k~   45 (91)
T PF05269_consen   25 GQKKVAEAMGVDESTISRWKN   45 (91)
T ss_dssp             HHHHHHHHHTSSTTTHHHHHH
T ss_pred             hhHHHHHHhCCCHHHHHHHHh
Confidence            467899999999999999963

CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=80.25  E-value=1.8  Score=33.41  Aligned_cols=27  Identities=11%  Similarity=0.027  Sum_probs=24.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .|++..|||+.||+|.++|...+.+-+
T Consensus       123 ~g~s~~EIA~~lg~s~~tVr~~l~RAr  149 (281)
T TIGR02957       123 FDYPYEEIASIVGKSEANCRQLVSRAR  149 (281)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            689999999999999999999987763

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=80.21  E-value=1.7  Score=32.18  Aligned_cols=29  Identities=14%  Similarity=0.240  Sum_probs=26.2

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ++..|||..+|++.-+|+++|+.+++.| +
T Consensus       174 ~t~~~iA~~lG~tretvsR~l~~L~~~g-l  202 (236)
T PRK09392        174 YEKRVLASYLGMTPENLSRAFAALASHG-V  202 (236)
T ss_pred             CCHHHHHHHhCCChhHHHHHHHHHHhCC-e
Confidence            3457899999999999999999999999 5

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=80.12  E-value=2.9  Score=27.26  Aligned_cols=65  Identities=11%  Similarity=0.131  Sum_probs=39.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.++|+++|||..|+.-+    .+.|=+.|...+|.+-.  +......+.-+.. ..=+++..++.+-+.
T Consensus         1 m~Ige~a~~~gvs~~tlRyY----e~~GLl~p~~~~g~r~Y--~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   66 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHY----IDLGLLIPEKKGGQYFF--DEKCQDDLEFILELKGLGFSLIEIQKIFS   66 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCcCCccCCCcccc--CHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            57889999999999987665    56798888654444322  2233333322211 122677777776543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=80.10  E-value=6.3  Score=27.75  Aligned_cols=65  Identities=15%  Similarity=0.108  Sum_probs=41.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+++|||..|+.-|-    +.|-+.|... +|.  +.=+......+.-+.. ..-+++..+++.-+.
T Consensus        12 ~~IgevAk~~gvs~~TlRyYE----~~GLi~~~r~~~g~--R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~   78 (154)
T PRK15002         12 LTPGEVAKRSGVAVSALHFYE----SKGLITSIRNSGNQ--RRYKRDVLRYVAIIKIAQRIGIPLATIGEAFG   78 (154)
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCC--EEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            788999999999999987764    6698888543 333  3334444544433221 233577777766544

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=80.03  E-value=1.9  Score=31.35  Aligned_cols=26  Identities=19%  Similarity=0.132  Sum_probs=23.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+-.+||+.|+||.+||...+.+.
T Consensus       164 ~G~s~~eIA~~l~iS~~TV~~h~~~i  189 (216)
T PRK10840        164 EGFLVTEIAKKLNRSIKTISSQKKSA  189 (216)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            79999999999999999999988665

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=80.02  E-value=7.7  Score=27.75  Aligned_cols=64  Identities=14%  Similarity=0.173  Sum_probs=38.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      +++.|+|+.+|||..|+.-|-    +.|-+.|..  .+|.+-  =+......+..+.. ..-++...++..-+
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~--Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll   68 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYE----RIGLLSPSARSESNYRL--YGERDLERLEQICAYRSAGVSLEDIRSLL   68 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCcc--CCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            478899999999999988875    569888853  233332  23333333322221 12355666655544

Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	163
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		3e-34
1k78_A	149	Pax5(1-149)+ets-1(331-440)+dna Length = 149		7e-29
2k27_A	159	Solution Structure Of Human Pax8 Paired Box Domain		4e-28
6pax_A	133	Crystal Structure Of The Human Pax-6 Paired Domain-		4e-23
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		5e-20
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		1e-15
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		5e-14
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		6e-13
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		6e-13
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		6e-12
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		8e-10
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		2e-09
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		1e-08
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		8e-08
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		1e-06
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		7e-04

>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations Length = 128

Iteration: 1
 Score =  140 bits (354), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 76/88 (86%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 29  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 88
Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTES 88
           +++P + SWE+R+KLI+    D S   S
Sbjct: 89  RSSPGMFSWEIREKLIREGVCDRSTAPS 116

>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149

Iteration: 1
 Score =  122 bits (307), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 58/86 (67%), Positives = 71/86 (82%), Gaps = 1/86 (1%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PGVIGGSKP+VATP V ++I EYK
Sbjct: 44  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYK 103
Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDT 86
           + NP + +WE+RD+L+   R+ D+DT
Sbjct: 104 RQNPTMFAWEIRDRLL-AERVCDNDT 128

>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159

Iteration: 1
 Score =  120 bits (301), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 56/88 (63%), Positives = 68/88 (77%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSIRPGVIGGSKP+VATP V ++I +YK
Sbjct: 37  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYK 96
Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTES 88
           + NP + +WE+RD+L+     D+    S
Sbjct: 97  RQNPTMFAWEIRDRLLAEGVCDNDTVPS 124

>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions Length = 133

Iteration: 1
 Score =  103 bits (258), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/76 (63%), Positives = 61/76 (80%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A +G RPC ISR L+VS+GCVSKIL RY  TGSIRP  IGGSKPRVATP+V  +I +YK
Sbjct: 29  LAHSGARPCDISRILQVSNGCVSKILGRYYATGSIRPRAIGGSKPRVATPEVVSKIAQYK 88
Query: 61  KTNPNITSWEVRDKLI 76
           +  P+I +WE+RD+L+
Sbjct: 89  QECPSIFAWEIRDRLL 104

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 46/80 (57%), Positives = 58/80 (72%)
Query: 82  DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
           D SD ESEPGI LKRKQRRSRTTF+++QL+ELE++F+R+ YPDIYTRE LA +  +TE R
Sbjct: 2   DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61
Query: 142 VQQFVLGTAGFLLSCLPSVS 161
           +Q +       L     SVS
Sbjct: 62  IQVWFQNRRARLRKQHTSVS 81

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 36/49 (73%), Positives = 42/49 (85%)
Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           KRKQRR RTTFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 3   KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 51

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 40/46 (86%)
Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           QRRSRTTFT+ QLEELE++F+R+HYPDIYTRE LA +  +TE RVQ
Sbjct: 2   QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQ 47

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 37/44 (84%)
Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R RTTFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 1   RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 32/47 (68%), Positives = 39/47 (82%)
Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           K+RR+RTTFTS QLEELEK FQ++HYPD+Y RE LA +  +TE RVQ
Sbjct: 8   KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQ 54

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 35/43 (81%)
Query: 101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           S  TFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 28/45 (62%), Positives = 34/45 (75%)
Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           QRR RT FTS QL+ELE +FQR+HYPD+ TRE +A    +TE RV
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARV 47

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 33/44 (75%)
Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R+RT+FT  Q+E LEK F+R+HYPD++ RE LA K  + E R+Q
Sbjct: 9   RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 33/45 (73%)
Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           QRR RT FTS QL+ELE +FQR+ YPD+ TRE +A    +TE RV
Sbjct: 3   QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARV 47

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 32/45 (71%)
Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RR RTTFT AQL+ LE  F ++ YPDI+ RE +A K  + E+RVQ
Sbjct: 8   RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 29/45 (64%)
Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RR RT FT  QLE LE  FQ + YPD+ TRE LA K  + E +V+
Sbjct: 8   RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 52

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 89  EPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQF 145
           EPG   K K RRSRT FT  QL  LEK F++  Y     R  LA   G+++ +V+ +
Sbjct: 9   EPGTKAK-KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTW 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	163
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	5e-32
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	1e-26
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	5e-26
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	1e-25
2k27_A	159	Paired box protein PAX-8; paired domain, solution	2e-25
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	3e-25
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	4e-25
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	9e-25
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-23
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	9e-23
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	1e-22
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	7e-22
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	5e-21
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-19
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	4e-18
1uhs_A	72	HOP, homeodomain only protein; structural genomics	7e-18
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	6e-17
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	9e-17
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	3e-16
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-14
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	3e-14
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	4e-14
1lfb_A	99	Liver transcription factor (LFB1); transcription r	3e-13
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	3e-13
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-12
1e3o_C	160	Octamer-binding transcription factor 1; transcript	6e-12
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	7e-12
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-11
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	4e-11
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	8e-11
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	8e-11
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	9e-11
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	2e-10
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-10
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-10
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	3e-10
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	4e-10
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	4e-10
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	4e-10
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	8e-10
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-09
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	8e-09
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	2e-08
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-08
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-08
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-07
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-07
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	5e-07
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	9e-07
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	3e-06
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	3e-06
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	5e-06
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	2e-05
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-05
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	4e-05
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	3e-04
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	3e-04
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	5e-04
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	6e-04
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	7e-04

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

 Score =  108 bits (272), Expect = 5e-32
 Identities = 42/62 (67%), Positives = 53/62 (85%)

Query: 82  DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
           D SD ESEPGI LKRKQRRSRTTF+++QL+ELE++F+R+ YPDIYTRE LA +  +TE R
Sbjct: 2   DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61

Query: 142 VQ 143
           +Q
Sbjct: 62  IQ 63

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Length = 128

 Score = 96.7 bits (240), Expect = 1e-26
 Identities = 66/100 (66%), Positives = 81/100 (81%), Gaps = 2/100 (2%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 29  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 88

Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI--VLKRKQ 98
           +++P + SWE+R+KLI+    D S   S   I  +++ + 
Sbjct: 89  RSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGRD 128

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

 Score = 93.2 bits (232), Expect = 5e-26
 Identities = 24/49 (48%), Positives = 34/49 (69%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
               +R+RT+FT  Q+E LEK F+R+HYPD++ RE LA K  + E R+Q
Sbjct: 4   GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52

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

 Score = 92.4 bits (230), Expect = 1e-25
 Identities = 24/49 (48%), Positives = 29/49 (59%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
               RR RT FT  QLE LE  FQ + YPD+ TRE LA K  + E +V+
Sbjct: 4   GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 52

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159

 Score = 94.5 bits (234), Expect = 2e-25
 Identities = 57/92 (61%), Positives = 69/92 (75%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSIRPGVIGGSKP+VATP V ++I +YK
Sbjct: 37  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYK 96

Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
           + NP + +WE+RD+L+     D+    S   I
Sbjct: 97  RQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSI 128

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Length = 149

 Score = 93.7 bits (232), Expect = 3e-25
 Identities = 58/103 (56%), Positives = 75/103 (72%), Gaps = 2/103 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PGVIGGSKP+VATP V ++I EYK
Sbjct: 44  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYK 103

Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI--VLKRKQRRS 101
           + NP + +WE+RD+L+     D+    S   I  +++ K ++ 
Sbjct: 104 RQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQQP 146

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

 Score = 91.3 bits (227), Expect = 4e-25
 Identities = 25/49 (51%), Positives = 32/49 (65%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
               RR RTTFT AQL+ LE  F ++ YPDI+ RE +A K  + E+RVQ
Sbjct: 4   GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52

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

 Score = 89.7 bits (223), Expect = 9e-25
 Identities = 26/47 (55%), Positives = 34/47 (72%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
            QRR RT FTS QL++LE +FQR+ YPD+ TRE +A    +TE RV+
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 48

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

 Score = 86.7 bits (215), Expect = 2e-23
 Identities = 16/49 (32%), Positives = 25/49 (51%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
               +R RT+F   QL  ++  F  +H PD    + LA K G+T+  +Q
Sbjct: 4   GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52

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

 Score = 84.7 bits (210), Expect = 9e-23
 Identities = 20/45 (44%), Positives = 25/45 (55%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RR RT FT  Q+E LE  F+ + YP I   E LA K  +   R+Q
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46

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

 Score = 83.8 bits (208), Expect = 1e-22
 Identities = 29/43 (67%), Positives = 35/43 (81%)

Query: 101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           S  TFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 2   SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44

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

 Score = 82.4 bits (204), Expect = 7e-22
 Identities = 15/49 (30%), Positives = 20/49 (40%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
               R SRT FT  QL  L+  F  + YP     E L+N   +    + 
Sbjct: 4   GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV 52

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

 Score = 80.1 bits (198), Expect = 5e-21
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           K  R RT     QL  L   +  +  PD   +E L    G++   ++
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48

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

 Score = 76.4 bits (188), Expect = 2e-19
 Identities = 16/60 (26%), Positives = 28/60 (46%)

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           S +    G    ++ +R RTT T  QLE L + +     P     + +A++ G+ +  VQ
Sbjct: 3   SGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62

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

 Score = 76.5 bits (187), Expect = 4e-18
 Identities = 17/138 (12%), Positives = 36/138 (26%), Gaps = 53/138 (38%)

Query: 50  PDVEKRIEEYKKTNPNITSWEVRDKLIK------------------VSRL---------- 81
              +  +E   + +P   +  V+  L +                  +S+           
Sbjct: 14  AHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQ 73

Query: 82  -------------------------DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKS 116
                                         E     +  +K RR+R  +  A  + L ++
Sbjct: 74  KRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQA 133

Query: 117 FQRSHYPDIYTREALANK 134
           ++R   P    RE L  +
Sbjct: 134 YERQKNPSKEERETLVEE 151

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

 Score = 72.4 bits (178), Expect = 7e-18
 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSH-YPDIYTREALANKFGMTETRVQ 143
                T T  Q+E LE +F + + +PD  T   +A + G+TE + Q
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 47

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

 Score = 70.1 bits (172), Expect = 6e-17
 Identities = 12/49 (24%), Positives = 23/49 (46%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
               +R RT  T  QL  L + F  ++ P     + +A+K G+ +  ++
Sbjct: 4   GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52

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

 Score = 69.4 bits (170), Expect = 9e-17
 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSH-YPDIYTREALANKFGMTETRVQ 143
            ++ +  T  Q+E LE +F + + +PD  T   +A + G+TE + Q
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 48

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

 Score = 68.9 bits (168), Expect = 3e-16
 Identities = 16/64 (25%), Positives = 22/64 (34%), Gaps = 15/64 (23%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG---------------MTE 139
               R SR T+    L  +E  F  + YPD   RE +AN                  +T 
Sbjct: 4   GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTS 63

Query: 140 TRVQ 143
            +V 
Sbjct: 64  LKVY 67

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

 Score = 63.2 bits (154), Expect = 2e-14
 Identities = 11/49 (22%), Positives = 19/49 (38%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
                  +   +  QL  L+ SF R+ +P     E L    G++   V+
Sbjct: 5   SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVR 53

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

 Score = 65.1 bits (158), Expect = 3e-14
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 3/85 (3%)

Query: 59  YKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQ 118
            +K  P +  W    +L       +             K+R+ RT+FT   +E L   F+
Sbjct: 57  AQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGE---PSKKRKRRTSFTPQAIEALNAYFE 113

Query: 119 RSHYPDIYTREALANKFGMTETRVQ 143
           ++  P       +A +       V+
Sbjct: 114 KNPLPTGQEITEMAKELNYDREVVR 138

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

 Score = 62.5 bits (152), Expect = 4e-14
 Identities = 10/47 (21%), Positives = 18/47 (38%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
                    T  Q+  L+ SF +S +PD      L    G+  + ++
Sbjct: 3   HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIK 49

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

 Score = 61.4 bits (148), Expect = 3e-13
 Identities = 11/40 (27%), Positives = 20/40 (50%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANK 134
            +K RR+R  +  A  + L ++++R   P    RE L  +
Sbjct: 6   TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE 45

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

 Score = 63.9 bits (154), Expect = 3e-13
 Identities = 17/75 (22%), Positives = 28/75 (37%)

Query: 83  DSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
              ++        +K RR+R  +  A  + L +++ R   P    REAL  +    E   
Sbjct: 127 PGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQ 186

Query: 143 QQFVLGTAGFLLSCL 157
           +      A  L S L
Sbjct: 187 RGVSPSKAHGLGSNL 201

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

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 11/67 (16%), Positives = 25/67 (37%)

Query: 77  KVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG 136
            +   +         +    ++R+ RTT + A  + LE+ F     P       +A +  
Sbjct: 66  WLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELN 125

Query: 137 MTETRVQ 143
           + +  V+
Sbjct: 126 LEKEVVR 132

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

 Score = 59.2 bits (143), Expect = 6e-12
 Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 2/85 (2%)

Query: 61  KTNPNITSW--EVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQ 118
           K  P +  W  +    L   S L      + PGI    ++R+ RT+  +     LEKSF 
Sbjct: 62  KLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFM 121

Query: 119 RSHYPDIYTREALANKFGMTETRVQ 143
            +  P       +A +  M +  ++
Sbjct: 122 ENQKPTSEDITLIAEQLNMEKEVIR 146

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

 Score = 59.0 bits (142), Expect = 7e-12
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           +  E      L + ++R RT+  +     LE  F +S  P +     +AN+ G+ +  V+
Sbjct: 82  NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141

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

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 81  LDDSDTE-----SEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKF 135
           L+++D+      +   I  + ++R+ RT+        LE  F +   P  +    LA+  
Sbjct: 77  LEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSL 136

Query: 136 GMTETRVQ 143
            + +  V+
Sbjct: 137 QLEKEVVR 144

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

 Score = 54.5 bits (132), Expect = 4e-11
 Identities = 12/49 (24%), Positives = 25/49 (51%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           K K  + +++ +      LE+ F+R    +   +E +A K G+T  +V+
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVR 50

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

 Score = 53.8 bits (130), Expect = 8e-11
 Identities = 16/45 (35%), Positives = 27/45 (60%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           +R+ R  F+ AQ+ ELE+ F++  Y     R+ LA+   +T T+V
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQV 46

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

 Score = 54.4 bits (131), Expect = 8e-11
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
            K+R+ R  FT AQ  ELE+ F++  Y     RE LA+   +T T+V
Sbjct: 7   NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQV 53

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

 Score = 54.0 bits (130), Expect = 9e-11
 Identities = 15/61 (24%), Positives = 31/61 (50%)

Query: 82  DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
              ++ ++    +  K++++RT F+S QL  L   FQR  Y  +   + L+N   ++  +
Sbjct: 6   SAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQ 65

Query: 142 V 142
           V
Sbjct: 66  V 66

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

 Score = 53.0 bits (128), Expect = 2e-10
 Identities = 18/44 (40%), Positives = 27/44 (61%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           R+ RT FT+AQL  LE+ F++  Y  I  R   ++   +TET+V
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQV 44

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

 Score = 52.7 bits (127), Expect = 2e-10
 Identities = 12/46 (26%), Positives = 25/46 (54%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
            +++ RT F+ AQL  L+  FQ+  Y  +   + L++   ++  +V
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47

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

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 21/59 (35%), Positives = 29/59 (49%)

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           S +         +K RRSRT FT  QL  LEK F++  Y     R  LA   G+++ +V
Sbjct: 3   SGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61

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

 Score = 52.4 bits (126), Expect = 3e-10
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
              R+ RT ++S QL  L++ FQ++ Y  +  R  LA   G+T+T+V
Sbjct: 5   SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQV 51

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

 Score = 52.0 bits (125), Expect = 4e-10
 Identities = 17/45 (37%), Positives = 27/45 (60%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           +R+ R  F+ AQ+ ELE+ F++  Y     RE LA+   +T T+V
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQV 46

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

 Score = 52.0 bits (125), Expect = 4e-10
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
                 +  +  Q+ ELE+ F    Y     R  LA    +TET+V
Sbjct: 3   HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQV 48

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

 Score = 52.7 bits (126), Expect = 4e-10
 Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 5/62 (8%)

Query: 82  DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
               + + P    ++ + +     T  Q++ LE SF +S +P     + L  +  ++   
Sbjct: 2   SSGSSGAYPDFAPQKFKEK-----TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRRE 56

Query: 142 VQ 143
           + 
Sbjct: 57  ID 58

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

 Score = 51.4 bits (123), Expect = 8e-10
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQF 145
              RSRT  +   L  L+        YPD      L+ +  + +  + +F
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKF 55

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

 Score = 51.8 bits (124), Expect = 1e-09
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
            K+++ RT+FT  Q+ ELEK F +  Y     R ALA    MT+ +V
Sbjct: 15  PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQV 61

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

 Score = 49.2 bits (117), Expect = 8e-09
 Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 5/60 (8%)

Query: 84  SDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           S   S P    ++ + +     T+ QL  L+ SF  S          L  +  +T   + 
Sbjct: 2   SSGSSGPDFTPQKFKEK-----TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID 56

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

 Score = 47.8 bits (114), Expect = 2e-08
 Identities = 13/47 (27%), Positives = 22/47 (46%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
              +  +  F++ Q  ELEK F+   Y     R+ LA    ++E +V
Sbjct: 5   SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV 51

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

 Score = 49.9 bits (118), Expect = 2e-08
 Identities = 15/92 (16%), Positives = 29/92 (31%)

Query: 54  KRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEEL 113
           K   E  +            ++  +        E E G       ++ R  FT  Q   L
Sbjct: 53  KSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTL 112

Query: 114 EKSFQRSHYPDIYTREALANKFGMTETRVQQF 145
              F+ +  P    +  ++ + G+  + V  F
Sbjct: 113 HAIFKENKRPSKELQITISQQLGLELSTVSNF 144

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

 Score = 46.5 bits (111), Expect = 4e-08
 Identities = 16/40 (40%), Positives = 23/40 (57%)

Query: 103 TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           T+F+ +Q+ ELE+ F R  Y     R ALA    MT+ +V
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQV 41

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

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 2/48 (4%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
              +         QL  LE SF ++  P     + L ++  MT   + 
Sbjct: 7   GPTKYKERA--PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREID 52

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

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 14/45 (31%), Positives = 27/45 (60%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           ++R RT F+S QL  L++ F  + Y     R+ L+++ G+ E ++
Sbjct: 3   EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 47

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

 Score = 43.9 bits (104), Expect = 5e-07
 Identities = 17/45 (37%), Positives = 25/45 (55%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
            RR+RTTFTS+Q+ ELE+ F +  Y        L+ K  +   +V
Sbjct: 2   PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQV 46

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

 Score = 43.1 bits (102), Expect = 9e-07
 Identities = 17/44 (38%), Positives = 23/44 (52%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           RR RT FT  QL  LEK F + +Y     R  LA +  + E+ +
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTI 45

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

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 17/46 (36%), Positives = 22/46 (47%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
                RT FT+ QL ELEK F  + Y     R  +A    + ET+V
Sbjct: 33  SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQV 78

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

 Score = 42.5 bits (99), Expect = 3e-06
 Identities = 13/63 (20%), Positives = 21/63 (33%)

Query: 82  DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
                    G   K          T  QL  L+ +F R+ +P     + LA + G+  T 
Sbjct: 9   SSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTD 68

Query: 142 VQQ 144
           +  
Sbjct: 69  IVS 71

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

 Score = 41.2 bits (97), Expect = 5e-06
 Identities = 18/46 (39%), Positives = 24/46 (52%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
             +R+RT +T AQL ELEK F  + Y     R  LA    +TE  +
Sbjct: 2   SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHI 47

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

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           + +R RT++T  Q  ELEK F  + Y     R  +A+   +TE ++
Sbjct: 27  ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 72

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

 Score = 39.4 bits (92), Expect = 3e-05
 Identities = 17/47 (36%), Positives = 25/47 (53%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
             +RR R T+T  Q  ELEK F  +HY     R  +A+   +TE ++
Sbjct: 18  GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQI 64

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

 Score = 38.9 bits (91), Expect = 4e-05
 Identities = 15/45 (33%), Positives = 24/45 (53%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           ++R R T+T  Q  ELEK F  + Y     R  +A+   +TE ++
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 46

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

 Score = 36.9 bits (85), Expect = 3e-04
 Identities = 9/45 (20%), Positives = 15/45 (33%)

Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQ 144
            S    T  QL  L+  F +  +      + L    G+    + Q
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQ 49

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

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 9/47 (19%), Positives = 22/47 (46%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
              R+ R  ++  QL ELE+ +  + +     R  ++    ++E ++
Sbjct: 5   SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQI 51

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

 Score = 36.0 bits (83), Expect = 5e-04
 Identities = 16/47 (34%), Positives = 22/47 (46%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
           R  R+ R  +T  Q  ELEK F  + Y     R  +A    +TE +V
Sbjct: 11  RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQV 57

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

 Score = 35.6 bits (82), Expect = 6e-04
 Identities = 11/47 (23%), Positives = 24/47 (51%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
            + R+ R  +T  QL+ELE+ +  + +     R  ++    ++E +V
Sbjct: 5   LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQV 51

>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} Length = 102

 Score = 36.4 bits (83), Expect = 7e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALAN 133
               R+R  +  A  + L +++ R   P    REAL  
Sbjct: 4   GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVE 41

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	163
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.9
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.89
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.89
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.88
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.88
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.88
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.88
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.87
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.87
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.87
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.87
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.87
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.86
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.86
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.86
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.85
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.85
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.85
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.85
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.85
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.85
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.85
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.85
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.85
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.85
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.85
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.85
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.85
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.85
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.84
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.84
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.84
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.84
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.84
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.84
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.84
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.84
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.84
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.84
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.83
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.83
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.83
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.83
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.83
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.83
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.83
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.83
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.83
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.82
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.82
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.82
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.82
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.82
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.82
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.81
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.81
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.81
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.81
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.81
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.8
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.79
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.79
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.79
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.79
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.79
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.79
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.78
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.78
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.77
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.77
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.77
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.77
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.7
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.52
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.5
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.46
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	99.03
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	98.95
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	98.94
2k27_A	159	Paired box protein PAX-8; paired domain, solution	98.84
1u78_A	141	TC3 transposase, transposable element TC3 transpos	98.38
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	98.0
3hot_A	345	Transposable element mariner, complete CDS; protei	97.66
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	97.38
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	97.22
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	97.17
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	97.01
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	96.93
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	96.9
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	96.9
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	96.66
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	96.57
3jth_A	98	Transcription activator HLYU; transcription factor	96.48
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	96.38
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	96.3
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	96.18
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.16
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.13
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.11
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	96.11
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.11
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	96.07
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	96.03
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.01
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	96.0
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	95.99
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	95.97
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.96
2kko_A	108	Possible transcriptional regulatory protein (possi	95.94
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	95.93
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	95.93
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.89
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	95.79
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	95.79
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	95.79
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	95.78
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	95.77
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	95.77
2hin_A	71	GP39, repressor protein; transcription factor, dim	95.77
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	95.74
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	95.67
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	95.66
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	95.65
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	95.63
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	95.63
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	95.63
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	95.63
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	95.59
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	95.59
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	95.58
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	95.56
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	95.54
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	95.52
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	95.46
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	95.45
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	95.44
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	95.42
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	95.41
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	95.4
4ghj_A	101	Probable transcriptional regulator; structural gen	95.4
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	95.39
4ich_A	311	Transcriptional regulator; structural genomics, PS	95.39
3t76_A	88	VANU, transcriptional regulator vanug; structural	95.38
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.37
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	95.36
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	95.34
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	95.3
3trb_A	104	Virulence-associated protein I; mobIle and extrach	95.27
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	95.26
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	95.25
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	95.25
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	95.23
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.22
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	95.19
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	95.17
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	95.14
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	95.13
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	95.12
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	95.12
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	95.1
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	95.1
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	95.09
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	95.09
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	95.08
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.06
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	95.06
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	95.06
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	95.05
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.02
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	94.91
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	94.9
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	94.9
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	94.9
2w25_A	150	Probable transcriptional regulatory protein; trans	94.9
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.89
1sfx_A	109	Conserved hypothetical protein AF2008; structural	94.88
3r0a_A	123	Putative transcriptional regulator; structural gen	94.83
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	94.8
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	94.77
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	94.74
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	94.74
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	94.74
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	94.73
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	94.7
3cec_A	104	Putative antidote protein of plasmid maintenance;	94.69
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	94.67
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	94.63
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.63
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	94.6
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	94.59
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	94.58
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	94.48
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	94.48
3c57_A	95	Two component transcriptional regulatory protein;	94.45
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.44
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	94.44
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	94.44
2gxg_A	146	146AA long hypothetical transcriptional regulator;	94.41
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	94.41
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	94.4
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	94.36
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	94.36
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	94.34
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	94.33
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	94.32
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	94.29
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	94.29
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	94.29
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	94.28
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	94.27
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	94.26
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	94.25
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.25
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	94.21
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	94.21
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.2
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	94.19
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	94.16
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	94.16
2nnn_A	140	Probable transcriptional regulator; structural gen	94.12
1b0n_A	111	Protein (SINR protein); transcription regulator, a	94.12
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	94.08
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	94.06
2wus_R	112	RODZ, putative uncharacterized protein; structural	94.0
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.99
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	93.98
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	93.96
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	93.96
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.94
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	93.92
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	93.91
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	93.9
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	93.9
2h09_A	155	Transcriptional regulator MNTR; transcription regu	93.87
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	93.84
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	93.84
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	93.84
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	93.81
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	93.81
3s2w_A	159	Transcriptional regulator, MARR family; structural	93.75
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	93.74
3ivp_A	126	Putative transposon-related DNA-binding protein; A	93.72
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.72
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	93.7
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.66
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	93.66
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	93.64
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	93.57
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	93.57
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	93.54
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	93.53
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	93.53
3mlf_A	111	Transcriptional regulator; structural genomics, he	93.48
2eth_A	154	Transcriptional regulator, putative, MAR family; M	93.48
2pex_A	153	Transcriptional regulator OHRR; transcription regu	93.47
3nqo_A	189	MARR-family transcriptional regulator; structural	93.45
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	93.4
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.39
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	93.39
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	93.39
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	93.34
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	93.34
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	93.3
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	93.29
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	93.28
1yyv_A	131	Putative transcriptional regulator; reductive meth	93.25
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	93.24
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	93.22
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.21
3bja_A	139	Transcriptional regulator, MARR family, putative;	93.16
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	93.1
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	93.1
1p6r_A	82	Penicillinase repressor; transcription regulation,	93.02
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	92.99
3df8_A	111	Possible HXLR family transcriptional factor; APC89	92.96
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	92.89
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	92.88
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	92.78
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	92.77
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	92.68
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	92.65
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	92.64
3f3x_A	144	Transcriptional regulator, MARR family, putative;	92.61
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	92.59
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	92.55
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	92.53
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	92.5
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	92.46
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	92.4
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	92.34
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	92.3
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	92.29
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	92.17
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	92.15
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	92.13
1z91_A	147	Organic hydroperoxide resistance transcriptional;	92.13
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	92.11
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	91.96
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	91.92
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	91.86
3cta_A	230	Riboflavin kinase; structural genomics, transferas	91.86
1okr_A	123	MECI, methicillin resistance regulatory protein ME	91.84
2g7u_A	257	Transcriptional regulator; ICLR family, structural	91.83
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	91.82
3jvd_A	333	Transcriptional regulators; structural genomics, P	91.61
1mkm_A	249	ICLR transcriptional regulator; structural genomic	91.6
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	91.55
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	91.47
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	91.45
1x2l_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, hu	91.36
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	91.28
3k69_A	162	Putative transcription regulator; putative transcr	91.26
2jml_A	81	DNA binding domain/transcriptional regulator; anti	91.22
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	91.11
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	91.11
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	90.98
2obp_A	96	Putative DNA-binding protein; structural genomics,	90.83
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	90.69
4g6q_A	182	Putative uncharacterized protein; structural genom	90.69
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	90.67
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	90.33
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	90.3
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	90.25
3frw_A	107	Putative Trp repressor protein; structural genomic	90.25
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	90.24
2vn2_A	128	DNAD, chromosome replication initiation protein; D	90.14
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	90.05
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	89.97
1ylf_A	149	RRF2 family protein; structural genomics, transcri	89.97
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	89.94
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	89.91
2fxa_A	207	Protease production regulatory protein HPR; protea	89.9
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	89.89
2o0m_A	345	Transcriptional regulator, SORC family; structural	89.85
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	89.62
3e3m_A	355	Transcriptional regulator, LACI family; structural	89.61
3bil_A	348	Probable LACI-family transcriptional regulator; st	89.59
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	89.57
1jye_A	349	Lactose operon repressor; gene regulation, protein	89.56
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	89.54
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	89.47
1wh8_A	111	CUT-like 2, homeobox protein CUX-2; CUT domain, st	89.34
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	89.3
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	89.28
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	89.26
1wh6_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, st	89.19
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	89.16
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	89.14
3by6_A	126	Predicted transcriptional regulator; structural ge	88.94
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	88.92
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	88.88
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	88.82
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	88.79
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	88.78
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	88.73
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	88.69
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	88.54
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	88.44
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	88.41
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	88.4
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	88.32
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	88.24
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	88.16
1u78_A	141	TC3 transposase, transposable element TC3 transpos	88.08
2o4a_A	93	DNA-binding protein SATB1; protein-DNA complex, tr	88.08
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	88.04
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	87.96
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	87.95
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	87.93
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	87.92
3b02_A	195	Transcriptional regulator, CRP family; structural	87.86
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	87.8
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	87.71
1ft9_A	222	Carbon monoxide oxidation system transcription reg	87.66
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	87.41
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	87.41
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	87.12
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	87.06
1xd7_A	145	YWNA; structural genomics, protein structure initi	86.99
1z05_A	429	Transcriptional regulator, ROK family; structural	86.98
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	86.62
2k27_A	159	Paired box protein PAX-8; paired domain, solution	86.43
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	86.08
3iwf_A	107	Transcription regulator RPIR family; transcription	86.03
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	85.9
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	85.82
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	85.44
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	85.21
1bia_A	321	BIRA bifunctional protein; transcription regulatio	85.21
3gp4_A	142	Transcriptional regulator, MERR family; structural	85.2
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	84.83
3hh0_A	146	Transcriptional regulator, MERR family; protein st	84.48
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	84.24
1q06_A	135	Transcriptional regulator CUER; MERR family transc	84.15
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	84.11
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	83.98
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	83.58
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	83.42
1wiz_A	101	DNA-binding protein SATB2; helix bundle, KIAA1034	83.39
3c7j_A	237	Transcriptional regulator, GNTR family; structural	83.03
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	82.99
4fcy_A	529	Transposase; rnaseh, DDE transposase, DNA binding	82.87
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	81.94
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	81.68
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	81.28
3gpv_A	148	Transcriptional regulator, MERR family; protein st	81.24
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	81.23
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	80.99
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	80.91
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	80.8
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	80.78
1hsj_A	487	Fusion protein consisting of staphylococcus access	80.72
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	80.58
2w57_A	150	Ferric uptake regulation protein; gene regulation,	80.49
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	80.23
3pxp_A	292	Helix-turn-helix domain protein; DNA-binding, basi	80.14

>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=99.90  E-value=1.4e-24  Score=136.33  Aligned_cols=67  Identities=33%  Similarity=0.426  Sum_probs=63.3

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      .++.++.||.||..|+..||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..++-|
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~ssg   80 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPSSG   80 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccCCCC
Confidence            4567889999999999999999999999999999999999999999999999999999999988765

>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=99.89  E-value=6.2e-24  Score=130.11  Aligned_cols=65  Identities=17%  Similarity=0.281  Sum_probs=61.9

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      +.++.|+.||..|+..||..|+.++||+..++.+||..+||++.+|++||||||+|+|+..++-|
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~G   70 (70)
T 2cra_A            6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPSSG   70 (70)
T ss_dssp             CCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCTTCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCCCCC
Confidence            46789999999999999999999999999999999999999999999999999999999988765

>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=99.89  E-value=4.8e-24  Score=133.96  Aligned_cols=67  Identities=25%  Similarity=0.294  Sum_probs=62.9

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      +.+.++.||.||.+|+..||..|..++||+..++.+||..|||++.+|++||||||+|+|+...+-|
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~sG   80 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPSSG   80 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhccCCC
Confidence            4567889999999999999999999999999999999999999999999999999999999887754

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

Probab=99.88  E-value=2.3e-23  Score=147.18  Aligned_cols=68  Identities=16%  Similarity=0.233  Sum_probs=53.5

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSG  162 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~~  162 (163)
                      ..+++|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+||.....||
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~g  163 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAAGA  163 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC----
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCCCCC
Confidence            45678899999999999999999999999999999999999999999999999999999999887765

>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=99.88  E-value=1.9e-23  Score=130.84  Aligned_cols=60  Identities=18%  Similarity=0.169  Sum_probs=57.5

Q ss_pred             cccccccCcCCHHHHHHHHHhccC----CCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQR----SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~----~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      .+.+|.||.||.+|+..||..|+.    ++||+..++++||..|||++.+|+|||||||+|+++
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            467889999999999999999999    999999999999999999999999999999999986

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

Probab=99.88  E-value=2.1e-23  Score=127.69  Aligned_cols=65  Identities=29%  Similarity=0.478  Sum_probs=61.5

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      +.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..++-|
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ssg   70 (70)
T 2djn_A            6 SGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPSSG   70 (70)
T ss_dssp             CCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCCCCC
Confidence            46789999999999999999999999999999999999999999999999999999999887654

>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=99.88  E-value=2.1e-23  Score=130.44  Aligned_cols=60  Identities=20%  Similarity=0.214  Sum_probs=56.7

Q ss_pred             ccccccccCcCCHHHHHHHHHhccC-----CCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQR-----SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~-----~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ..+.+|.||.||.+|+..|| .|..     ++||+..++++||..|+|++.+|+|||||||+|+++
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            34578899999999999999 8999     999999999999999999999999999999999986

>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=3.9e-23  Score=130.90  Aligned_cols=65  Identities=23%  Similarity=0.320  Sum_probs=60.8

Q ss_pred             cccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        94 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      ...+.++.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+...
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            34567889999999999999999999999999999999999999999999999999999998754

>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=99.87  E-value=2.1e-24  Score=135.84  Aligned_cols=71  Identities=55%  Similarity=0.845  Sum_probs=60.5

Q ss_pred             CccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          90 PGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        90 ~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      ++....++.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|++..++
T Consensus        10 ~~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~~~   80 (81)
T 1fjl_A           10 PGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTSV   80 (81)
T ss_dssp             -------CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcccC
Confidence            33334567788999999999999999999999999999999999999999999999999999999876543

>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=1.9e-23  Score=127.98  Aligned_cols=66  Identities=26%  Similarity=0.282  Sum_probs=62.2

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      .+.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..++-|
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~~g   70 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPSSG   70 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhccccCC
Confidence            356789999999999999999999999999999999999999999999999999999999988765

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

Probab=99.87  E-value=5.6e-23  Score=145.60  Aligned_cols=143  Identities=16%  Similarity=0.240  Sum_probs=85.6

Q ss_pred             ccCCCChhhhHH-HhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904           2 AAAGVRPCVISR-QLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      ...++++...|. +||+|+++++.+|....+...+..|    ..+   ....-.++    . .|.    +-+........
T Consensus        18 ~~~~i~q~~fa~~ilg~sq~~ls~~l~~pkpw~~l~~g----~~~---y~rm~~WL----~-~pe----~~r~~~l~~~~   81 (164)
T 2d5v_A           18 KRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSG----RET---FRRMWKWL----Q-EPE----FQRMSALRLAA   81 (164)
T ss_dssp             HHTTCCHHHHHHHHTSCCHHHHHHHHHSCCCGGGCSTT----HHH---HHHHHHHH----H-SCH----HHHHHHTTC--
T ss_pred             HHcCCchHHHHHHHhcCCchhHHHHcCCCCCHHHHccc----chH---HHHHHHHH----h-ccc----hhhhhhhhccc
Confidence            457889999998 8899999999999766544444321    100   00011111    0 000    00000000000


Q ss_pred             CCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          81 LDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      +..  ...........+.+|.||.||..|+..|+..|+.++||+..++.+||..+||++.||+|||||||+|+|+....+
T Consensus        82 ~~~--~~~~~~~~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~~  159 (164)
T 2d5v_A           82 CKR--KEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEH  159 (164)
T ss_dssp             --------------------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC----
T ss_pred             ccc--cccccCCcCCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCCC
Confidence            000  001111122345678999999999999999999999999999999999999999999999999999999988766


Q ss_pred             CC
Q psy1904         161 SG  162 (163)
Q Consensus       161 ~~  162 (163)
                      ++
T Consensus       160 ~~  161 (164)
T 2d5v_A          160 HH  161 (164)
T ss_dssp             --
T ss_pred             CC
Confidence            54

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

Probab=99.87  E-value=2.5e-23  Score=127.40  Aligned_cols=65  Identities=40%  Similarity=0.538  Sum_probs=61.4

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      +.++.|+.||.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..++-|
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~~~G   70 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPSSG   70 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTSTTCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCCCCC
Confidence            46788999999999999999999999999999999999999999999999999999999887654

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

Probab=99.86  E-value=4.4e-23  Score=123.41  Aligned_cols=60  Identities=20%  Similarity=0.317  Sum_probs=52.9

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            357889999999999999999999999999999999999999999999999999999874

>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=99.86  E-value=4.3e-23  Score=126.36  Aligned_cols=65  Identities=23%  Similarity=0.264  Sum_probs=60.8

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      .+.++.||.||.+|+..||..|+.++||+..++.+||..+||++.+|++||||||+|+|+....-
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPSS   69 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcccC
Confidence            35678999999999999999999999999999999999999999999999999999999987643

>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=99.86  E-value=4.5e-23  Score=122.96  Aligned_cols=58  Identities=24%  Similarity=0.500  Sum_probs=53.2

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      .++.||.||..|+..||..|+.++||+..++.+||..+||++.+|++||||||+|+|+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4788999999999999999999999999999999999999999999999999999987

>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=99.86  E-value=5.8e-23  Score=148.13  Aligned_cols=127  Identities=18%  Similarity=0.252  Sum_probs=80.8

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhh------h
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDK------L   75 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~------l   75 (163)
                      .+.|+++.++|+.+|||+++||+|++.    |         ..+.   ......          ++.|-++..      +
T Consensus        40 ~~~gitQ~~lA~~~GiSqs~ISr~l~~----~---------~~~~---~~kraa----------ly~W~~~~~~~i~~~~   93 (194)
T 1ic8_A           40 QQHNIPQREVVDTTGLNQSHLSQHLNK----G---------TPMK---TQKRAA----------LYTWYVRKQREVAQQF   93 (194)
T ss_dssp             HHTTCCHHHHHHHHCCCHHHHHHHHHS----B---------CCCC---HHHHHH----------HHHHHHHHTTTTHHHH
T ss_pred             HHcCCCHHHHHHHhCCChHHHHHHHhc----C---------cccc---cccccc----------chhhHHHhhhhhhccc
Confidence            357999999999999999999999732    1         1111   110111          111211110      0


Q ss_pred             hhhccCCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhC-------------------
Q psy1904          76 IKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG-------------------  136 (163)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~-------------------  136 (163)
                      .. ...+....+........++.||.|+.|++.|+.+|++.|+.++||+..+|++||..++                   
T Consensus        94 ~~-~~~~~~~~~~~~~~~~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~  172 (194)
T 1ic8_A           94 TH-AGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS  172 (194)
T ss_dssp             CC-C--------------------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGG
T ss_pred             cC-CCCCCCCCCCcccccccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccc
Confidence            00 0000001111111223466789999999999999999999999999999999999999                   


Q ss_pred             --CCccccccccccccccccc
Q psy1904         137 --MTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus       137 --l~~~~v~~WFqnrR~k~kr  155 (163)
                        |++.+|++||||||++.|.
T Consensus       173 ~~lte~~V~~WFqNRR~~~k~  193 (194)
T 1ic8_A          173 NLVTEVRVYNWFANRRKEEAF  193 (194)
T ss_dssp             GCCCHHHHHHHHHHHHHHCC-
T ss_pred             cccCccccchhchhhhhhhhc
Confidence              9999999999999999863

>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=99.85  E-value=1.5e-22  Score=122.58  Aligned_cols=62  Identities=19%  Similarity=0.236  Sum_probs=58.5

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      +.++.||.||.+|+..||..|+.++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            35788999999999999999999999999999999999999999999999999999998653

>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=99.85  E-value=6.9e-23  Score=125.42  Aligned_cols=65  Identities=23%  Similarity=0.315  Sum_probs=60.8

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      +.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+..++-|
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~~sG   70 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPSSG   70 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCCCCC
Confidence            35678999999999999999999999999999999999999999999999999999999877654

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

Probab=99.85  E-value=1.5e-22  Score=124.80  Aligned_cols=65  Identities=17%  Similarity=0.285  Sum_probs=60.6

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      .+.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKL   69 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhccc
Confidence            35678999999999999999999999999999999999999999999999999999999976543

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

Probab=99.85  E-value=7.4e-23  Score=122.77  Aligned_cols=59  Identities=31%  Similarity=0.332  Sum_probs=55.6

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            57889999999999999999999999999999999999999999999999999999875

>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=99.85  E-value=6.5e-22  Score=139.42  Aligned_cols=62  Identities=18%  Similarity=0.217  Sum_probs=55.1

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ..+++|.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+||.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            34678899999999999999999999999999999999999999999999999999999985

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

Probab=99.85  E-value=1e-22  Score=126.93  Aligned_cols=62  Identities=31%  Similarity=0.366  Sum_probs=58.4

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +++.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~   67 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhh
Confidence            34567889999999999999999999999999999999999999999999999999999864

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

Probab=99.85  E-value=1e-22  Score=120.24  Aligned_cols=57  Identities=32%  Similarity=0.494  Sum_probs=55.1

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            478999999999999999999999999999999999999999999999999999986

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

Probab=99.85  E-value=1.9e-22  Score=126.58  Aligned_cols=64  Identities=39%  Similarity=0.548  Sum_probs=59.8

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      .+.++.|+.||..|+..||..|+.++||+..++.+||..++|++.+|++||||||+|+|+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            3567899999999999999999999999999999999999999999999999999999886543

>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=99.85  E-value=6e-23  Score=124.96  Aligned_cols=64  Identities=23%  Similarity=0.270  Sum_probs=59.7

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      .++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.....+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   65 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG   65 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccccC
Confidence            4688999999999999999999999999999999999999999999999999999998766544

>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=99.85  E-value=1.3e-21  Score=135.78  Aligned_cols=62  Identities=18%  Similarity=0.253  Sum_probs=55.8

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .+++++.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+||.
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            44667889999999999999999999999999999999999999999999999999999985

>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=2.4e-22  Score=124.61  Aligned_cols=65  Identities=51%  Similarity=0.671  Sum_probs=60.7

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      ..+.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+....
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            34567889999999999999999999999999999999999999999999999999999987664

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

Probab=99.85  E-value=1.1e-22  Score=120.84  Aligned_cols=58  Identities=29%  Similarity=0.350  Sum_probs=55.5

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5789999999999999999999999999999999999999999999999999999875

>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=99.85  E-value=1.7e-22  Score=125.87  Aligned_cols=62  Identities=26%  Similarity=0.285  Sum_probs=58.4

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .++.++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   71 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI   71 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            34567899999999999999999999999999999999999999999999999999999874

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

Probab=99.85  E-value=2.4e-22  Score=126.12  Aligned_cols=60  Identities=40%  Similarity=0.672  Sum_probs=57.3

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +.++.||.||..|+..||..|..++||+..++.+||..++|++.+|++||||||+|+|+.
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (80)
T 2cue_A            6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE   65 (80)
T ss_dssp             SSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHH
Confidence            467889999999999999999999999999999999999999999999999999999864

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

Probab=99.84  E-value=1.5e-22  Score=124.22  Aligned_cols=63  Identities=17%  Similarity=0.203  Sum_probs=59.1

Q ss_pred             ccccCcCCHHHHHHHHHhc-cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          99 RRSRTTFTSAQLEELEKSF-QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F-~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      .+.|..++..|+..||..| ..++||+..++.+||..+||++.||+|||||||+|+|+.+.+.|
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~~s~g   72 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGPSSG   72 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCCCCCC
Confidence            4566778899999999999 99999999999999999999999999999999999999998876

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

Probab=99.84  E-value=2.9e-22  Score=121.95  Aligned_cols=59  Identities=29%  Similarity=0.363  Sum_probs=56.6

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .++.||.||..|+..||..|..++||+..++..||..+||++.+|++||||||+|+|++
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~   60 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   60 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999999999999874

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

Probab=99.84  E-value=3.4e-22  Score=125.61  Aligned_cols=61  Identities=30%  Similarity=0.388  Sum_probs=54.9

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      +.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|++.
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            4678899999999999999999999999999999999999999999999999999999875

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

Probab=99.84  E-value=4.6e-22  Score=126.98  Aligned_cols=62  Identities=24%  Similarity=0.287  Sum_probs=55.6

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+.++.||.||..|+..||..|+.++||+..++.+||..+||++.+|+|||||||+|+|+..
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            35678999999999999999999999999999999999999999999999999999999864

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

Probab=99.84  E-value=3e-22  Score=121.83  Aligned_cols=62  Identities=27%  Similarity=0.364  Sum_probs=58.6

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      .++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~   63 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhH
Confidence            46889999999999999999999999999999999999999999999999999999987653

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

Probab=99.84  E-value=5.5e-22  Score=117.05  Aligned_cols=57  Identities=28%  Similarity=0.402  Sum_probs=54.6

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      .++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            467899999999999999999999999999999999999999999999999999975

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

Probab=99.84  E-value=3.5e-22  Score=128.68  Aligned_cols=62  Identities=31%  Similarity=0.429  Sum_probs=58.5

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +.+.++.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|++
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~   75 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ   75 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhh
Confidence            34567899999999999999999999999999999999999999999999999999999875

>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=99.84  E-value=3e-22  Score=119.35  Aligned_cols=59  Identities=19%  Similarity=0.274  Sum_probs=48.5

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      .+.++.|+.||..|+..||..|..++||+..++.+||..+||++.||++||||||+|+|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            45678899999999999999999999999999999999999999999999999999975

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

Probab=99.84  E-value=7.1e-22  Score=119.89  Aligned_cols=60  Identities=35%  Similarity=0.468  Sum_probs=57.4

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      ++.|+.||..|+..||..|..++||+..++..||..+||++.+|++||||||+|+|+...
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            678999999999999999999999999999999999999999999999999999998654

>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=99.84  E-value=1.3e-22  Score=123.44  Aligned_cols=63  Identities=41%  Similarity=0.528  Sum_probs=58.9

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      +.++.||.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+....
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            357889999999999999999999999999999999999999999999999999999886543

>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=99.83  E-value=8e-22  Score=117.38  Aligned_cols=55  Identities=20%  Similarity=0.182  Sum_probs=51.8

Q ss_pred             HHHHHHHHHhc-cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904         107 SAQLEELEKSF-QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus       107 ~~q~~~Le~~F-~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      +.|+.+||..| ..++||+..++.+||.+|||++.||+|||||||+|+|++.||-|
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~~~~~   64 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGPSSG   64 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSSCCCC
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCCCCCC
Confidence            45799999999 67999999999999999999999999999999999999999865

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

Probab=99.83  E-value=2.3e-22  Score=126.18  Aligned_cols=61  Identities=16%  Similarity=0.124  Sum_probs=57.9

Q ss_pred             cccccccCcCCHHHHHHHHHhccCC----CCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRS----HYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~----~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .+.++.||.||.+|+..||..|+.+    +||+..++.+||..+||++.+|+|||||||+|+|+.
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            4567899999999999999999999    999999999999999999999999999999999873

>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=99.83  E-value=5.2e-22  Score=124.59  Aligned_cols=61  Identities=28%  Similarity=0.388  Sum_probs=57.9

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      +.++.||.||.+|+..||..|+.++||+..++.+||..+||++.+|++||||||+|+|++.
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (80)
T 2dmq_A            6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL   66 (80)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999999999999999998753

>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=99.83  E-value=4.3e-22  Score=129.32  Aligned_cols=65  Identities=26%  Similarity=0.247  Sum_probs=56.7

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      .+.++.||.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+...-+
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~g   96 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREG   96 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC-
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhccC
Confidence            45678899999999999999999999999999999999999999999999999999999876543

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

Probab=99.83  E-value=5.3e-22  Score=117.89  Aligned_cols=57  Identities=51%  Similarity=0.718  Sum_probs=50.7

Q ss_pred             ccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904         101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus       101 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|++.
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            479999999999999999999999999999999999999999999999999999864

>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=99.83  E-value=7.4e-22  Score=121.31  Aligned_cols=58  Identities=19%  Similarity=0.124  Sum_probs=54.2

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ..|+.||.+|+.+|+..|..++||+..++++||..+||++.||+|||||+|+|+|+..
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            3467799999999999999999999999999999999999999999999999998753

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

Probab=99.83  E-value=9.6e-22  Score=127.39  Aligned_cols=63  Identities=21%  Similarity=0.201  Sum_probs=56.2

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      ....++.|+.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|++-
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            345668899999999999999999999999999999999999999999999999999999863

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

Probab=99.83  E-value=4.1e-22  Score=116.72  Aligned_cols=54  Identities=30%  Similarity=0.396  Sum_probs=50.9

Q ss_pred             CcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         103 TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       103 t~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      |.||..|+..||..|..++||+..++.+||..+||++.+|++||||||+|+||+
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            689999999999999999999999999999999999999999999999999874

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

Probab=99.83  E-value=3e-21  Score=116.11  Aligned_cols=59  Identities=20%  Similarity=0.218  Sum_probs=56.5

Q ss_pred             cccccCcCCHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          98 QRRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .++.|+.|+..|+..|+..|   ..++||+..++.+||..+||++.||++||||+|+|+|++
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   64 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   64 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSCC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhccC
Confidence            46889999999999999999   999999999999999999999999999999999999874

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

Probab=99.82  E-value=2.1e-21  Score=120.61  Aligned_cols=61  Identities=20%  Similarity=0.226  Sum_probs=57.1

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      .+.|+.||.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+....
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~   69 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS   69 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSS
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhccc
Confidence            3458999999999999999999999999999999999999999999999999999986654

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

Probab=99.82  E-value=2.5e-21  Score=119.68  Aligned_cols=62  Identities=19%  Similarity=0.195  Sum_probs=58.5

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      .++.|+.||.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+.-.+
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   67 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSN   67 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCS
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcC
Confidence            46789999999999999999999999999999999999999999999999999999987654

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

Probab=99.82  E-value=9e-21  Score=138.05  Aligned_cols=61  Identities=26%  Similarity=0.336  Sum_probs=53.7

Q ss_pred             ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhC---------------------CCccccccccccccc
Q psy1904          93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG---------------------MTETRVQQFVLGTAG  151 (163)
Q Consensus        93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~---------------------l~~~~v~~WFqnrR~  151 (163)
                      ...++.||.|+.|++.|+.+|+..|+.++||+..+|++||..++                     |++.+|++||+|||+
T Consensus       137 ~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             -----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            34567889999999999999999999999999999999999987                     899999999999998


Q ss_pred             cc
Q psy1904         152 FL  153 (163)
Q Consensus       152 k~  153 (163)
                      ..
T Consensus       217 ~~  218 (221)
T 2h8r_A          217 EE  218 (221)
T ss_dssp             TC
T ss_pred             hh
Confidence            75

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

Probab=99.82  E-value=1.9e-21  Score=119.65  Aligned_cols=59  Identities=25%  Similarity=0.269  Sum_probs=55.5

Q ss_pred             ccccCcCCHHHHHHHHHhccC-CCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+.|+.||..|+..||..|+. ++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            467899999999999999996 99999999999999999999999999999999998754

>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=99.82  E-value=2.7e-21  Score=119.24  Aligned_cols=65  Identities=14%  Similarity=0.227  Sum_probs=59.7

Q ss_pred             cccccccCcCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      .+.++.|+.|+..|+..|+..|..   ++||+..++.+||..+||++.||++||||+|+|+|+.+..-
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   72 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPSS   72 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTSC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccccc
Confidence            346788999999999999999976   99999999999999999999999999999999999887643

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

Probab=99.82  E-value=2.5e-21  Score=119.38  Aligned_cols=59  Identities=24%  Similarity=0.200  Sum_probs=55.5

Q ss_pred             ccccCcCCHHHHHHHHHhcc-CCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQ-RSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~-~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+.|+.||..|+..||..|+ .++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            46789999999999999999 599999999999999999999999999999999998753

>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=99.81  E-value=4.6e-21  Score=118.70  Aligned_cols=60  Identities=17%  Similarity=0.122  Sum_probs=55.7

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      ++|+.||.+|+..||..|..++||+..++.+||..+||++.+|++||||||+|+|+....
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            456779999999999999999999999999999999999999999999999999886544

>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=99.81  E-value=9.1e-21  Score=132.87  Aligned_cols=61  Identities=20%  Similarity=0.254  Sum_probs=57.4

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .+++|.||.|+..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            3567889999999999999999999999999999999999999999999999999999985

>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=2e-21  Score=135.81  Aligned_cols=60  Identities=22%  Similarity=0.339  Sum_probs=57.5

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      .+++|.|+.|+..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+||
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            456789999999999999999999999999999999999999999999999999999987

>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=99.81  E-value=7e-21  Score=112.77  Aligned_cols=65  Identities=20%  Similarity=0.263  Sum_probs=59.0

Q ss_pred             cccccccCcCCHHHHHHHHHhccC-CCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      +..+|.||.|+.+|+..|+..|+. ++||+...+..||.++||++.+|+|||||+|.-.+-.-++-
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~~~~~~~   70 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSGPSS   70 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSSCSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeecCCCCCC
Confidence            356899999999999999999999 99999999999999999999999999999998776555543

>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=99.81  E-value=9.5e-21  Score=116.78  Aligned_cols=62  Identities=26%  Similarity=0.343  Sum_probs=58.6

Q ss_pred             ccccCcCCHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904          99 RRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      ++.|+.|+..|+..|+..|   ..++||+..++..||..+||++.||++||||+|+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   66 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccc
Confidence            5789999999999999999   9999999999999999999999999999999999999877643

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

Probab=99.80  E-value=1.4e-20  Score=122.02  Aligned_cols=63  Identities=25%  Similarity=0.331  Sum_probs=53.8

Q ss_pred             ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHH------------------hC---CCccccccccccccccc
Q psy1904          95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANK------------------FG---MTETRVQQFVLGTAGFL  153 (163)
Q Consensus        95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~------------------l~---l~~~~v~~WFqnrR~k~  153 (163)
                      .++.+|.|+.|+..|+..||..|+.++||+..+|++||..                  ||   |++.+|++||||||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4567889999999999999999999999999999999999                  88   99999999999999999


Q ss_pred             ccCC
Q psy1904         154 LSCL  157 (163)
Q Consensus       154 kr~~  157 (163)
                      |+..
T Consensus        86 k~k~   89 (99)
T 1lfb_A           86 AFRH   89 (99)
T ss_dssp             SCCC
T ss_pred             HHhc
Confidence            7653

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

Probab=99.79  E-value=1.5e-20  Score=111.62  Aligned_cols=55  Identities=18%  Similarity=0.239  Sum_probs=53.4

Q ss_pred             cCcCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         102 RTTFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       102 Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      |+.|+..|+..||..|..   ++||+..++.+||..+||++.||++||||||+|+|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            689999999999999999   9999999999999999999999999999999999986

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

Probab=99.79  E-value=8.2e-21  Score=122.80  Aligned_cols=62  Identities=26%  Similarity=0.334  Sum_probs=58.5

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhC---------------CCcccccccccccccccccCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG---------------MTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~---------------l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .+.+|.|+.|+..|+.+||..|+.++||+..++++||..++               |++.+|++||||||+|+|+..
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999999               999999999999999998754

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

Probab=99.79  E-value=7.9e-21  Score=112.88  Aligned_cols=50  Identities=20%  Similarity=0.273  Sum_probs=48.7

Q ss_pred             CHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904         106 TSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus       106 t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      |.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|+|+
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kk   61 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR   61 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhc
Confidence            68999999999999999999999999999999999999999999999986

>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=3.1e-20  Score=112.69  Aligned_cols=57  Identities=25%  Similarity=0.271  Sum_probs=53.5

Q ss_pred             CcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904         103 TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus       103 t~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      ..+|..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|+...+
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~   65 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS   65 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhh
Confidence            467999999999999999999999999999999999999999999999999887654

>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=99.79  E-value=2.2e-20  Score=120.62  Aligned_cols=60  Identities=23%  Similarity=0.243  Sum_probs=56.9

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHh---------------------CCCcccccccccccccccc
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKF---------------------GMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l---------------------~l~~~~v~~WFqnrR~k~k  154 (163)
                      ++.+|.||.|++.|+.+||..|+.++||+..+|++||..+                     .|++.+|++||||||+++|
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~k   83 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA   83 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHHH
Confidence            4578899999999999999999999999999999999999                     7999999999999999997


Q ss_pred             c
Q psy1904         155 S  155 (163)
Q Consensus       155 r  155 (163)
                      +
T Consensus        84 r   84 (102)
T 2da6_A           84 F   84 (102)
T ss_dssp             H
T ss_pred             H
Confidence            6

>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=99.79  E-value=2.1e-20  Score=119.06  Aligned_cols=60  Identities=27%  Similarity=0.354  Sum_probs=56.6

Q ss_pred             ccccCcCCHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          99 RRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      |+.|+.|+..|+..|+..|   ..++||+..++.+||..+||++.||++||||||+|+|+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   64 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccc
Confidence            5789999999999999999   99999999999999999999999999999999999998754

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

Probab=99.78  E-value=2.6e-20  Score=118.22  Aligned_cols=53  Identities=17%  Similarity=0.058  Sum_probs=51.1

Q ss_pred             cCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         104 TFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       104 ~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .||.+|+.+||..|..++||+..++.+||..|||++.||+|||||||+||++.
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~   69 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   69 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHH
Confidence            78999999999999999999999999999999999999999999999999763

>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=9.4e-20  Score=109.21  Aligned_cols=54  Identities=11%  Similarity=0.070  Sum_probs=50.8

Q ss_pred             CcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         103 TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       103 t~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ..++..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|.++.
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            456789999999999999999999999999999999999999999999998774

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

Probab=99.77  E-value=5.6e-20  Score=117.00  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=55.7

Q ss_pred             ccccccCcCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ++++.|+.|+..|+..|+..|..   ++||+..++.+||..+||++.||++||||||+|+|.
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            45667999999999999999999   999999999999999999999999999999999874

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

Probab=99.77  E-value=6.6e-20  Score=115.63  Aligned_cols=59  Identities=17%  Similarity=0.204  Sum_probs=54.7

Q ss_pred             cccCcCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904         100 RSRTTFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      +.|+.|+..|+..|+..|..   ++||+..++.+||..+||++.||++||||||+|+|+...
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            44667999999999999999   999999999999999999999999999999999998754

>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=99.77  E-value=8.7e-20  Score=116.46  Aligned_cols=54  Identities=19%  Similarity=0.205  Sum_probs=51.3

Q ss_pred             cCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904         104 TFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus       104 ~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      .||.+|+.+||..|..++||+..++.+||..+||++.+|+|||||||+|+++.-
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            489999999999999999999999999999999999999999999999997644

>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=99.77  E-value=5.2e-20  Score=116.05  Aligned_cols=61  Identities=10%  Similarity=0.276  Sum_probs=56.3

Q ss_pred             ccccccCcCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      +.++.|+.|+.+|+..|+..|..   ++||+..++.+||..+||++.||++||||+|+|+|+.+
T Consensus         6 ~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            46788999999999999999876   69999999999999999999999999999999998654

>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=99.70  E-value=2.9e-18  Score=103.70  Aligned_cols=57  Identities=14%  Similarity=0.225  Sum_probs=50.9

Q ss_pred             cCCHHHHHHHHHhcc---CCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904         104 TFTSAQLEELEKSFQ---RSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV  160 (163)
Q Consensus       104 ~~t~~q~~~Le~~F~---~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~  160 (163)
                      .|+.+|+..|+..|.   .++||+..++.+||..+||++.||++||||+|+|+|+.+-.-
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   63 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQ   63 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC---
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHH
Confidence            689999999999999   999999999999999999999999999999999999887543

>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=99.52  E-value=1.7e-15  Score=90.31  Aligned_cols=47  Identities=9%  Similarity=0.141  Sum_probs=44.8

Q ss_pred             HHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccc
Q psy1904         107 SAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFL  153 (163)
Q Consensus       107 ~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~  153 (163)
                      .+|+..|+..|..|++|+..++..||..+||+...|+|||||||+..
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~   60 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ   60 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccccc
Confidence            56899999999999999999999999999999999999999999864

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

Probab=99.50  E-value=1.8e-15  Score=95.33  Aligned_cols=54  Identities=13%  Similarity=0.220  Sum_probs=50.2

Q ss_pred             CcCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         103 TTFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       103 t~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .-|+.++..+|+..|..   ++||+..++.+||..+||++.||++||+|+|+|+++.
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~   66 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPD   66 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhH
Confidence            45889999999999977   9999999999999999999999999999999999764

>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=99.46  E-value=8.1e-15  Score=116.68  Aligned_cols=58  Identities=19%  Similarity=0.232  Sum_probs=54.7

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      ..++.++.|+..|+..|++.|+.++||+..+|.+||.++||+++||++||||||+|+|
T Consensus       364 ~~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          364 AQTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            3456788999999999999999999999999999999999999999999999999986

>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=99.03  E-value=2.6e-11  Score=63.54  Aligned_cols=17  Identities=0%  Similarity=-0.115  Sum_probs=15.4

Q ss_pred             ccccccccccccccccC
Q psy1904         140 TRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       140 ~~v~~WFqnrR~k~kr~  156 (163)
                      +||+|||||||+|||+.
T Consensus         1 rQVkIWFQNRRaK~Kk~   17 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKR   17 (37)
T ss_dssp             CCTTTTTTCSHHHHTSS
T ss_pred             CCceeccHHHHHHHHHH
Confidence            58999999999999874

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=98.95  E-value=2.1e-09  Score=74.15  Aligned_cols=75  Identities=71%  Similarity=1.233  Sum_probs=64.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIK   77 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~   77 (163)
                      ..|.+..+||+.||||.+||++|+++|.+.|.+.+...+|..+...++...+.|.++..++|..+.+++...+..
T Consensus        46 ~~G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~  120 (149)
T 1k78_A           46 HQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLA  120 (149)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCCCCCHHHHHHHHHHHHhCcchhHHHHHHHHHH
Confidence            479999999999999999999999999999998887666655666677778888888889999999988888754

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=98.94  E-value=1.1e-09  Score=72.95  Aligned_cols=75  Identities=80%  Similarity=1.391  Sum_probs=63.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIK   77 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~   77 (163)
                      ..|.+..+||+.||||.+||++|+++|+++|.+.+...++.++...++...+.|.++..++|..+.+++...+..
T Consensus        31 ~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~~~~i~~~~~~~~~~s~~~i~~~l~~  105 (128)
T 1pdn_C           31 ADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIR  105 (128)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTTCTTCCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHHHHHHHHHHHhCcchHHHHHHHHHHH
Confidence            479999999999999999999999999999988776655545666666677778788888999999988888764

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=98.84  E-value=3.8e-09  Score=73.64  Aligned_cols=75  Identities=71%  Similarity=1.234  Sum_probs=62.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIK   77 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~   77 (163)
                      ..|.+..+||+.||||.+||++|+++|+++|.+.+...++..+...++...+.|.++..++|.++.+++...+..
T Consensus        39 ~~G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~  113 (159)
T 2k27_A           39 HQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLA  113 (159)
T ss_dssp             HHTCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCHHHHHHHHHHHHHCccchHHHHHHHHHH
Confidence            468999999999999999999999999999998887656554555666677778788888999999888887754

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=98.38  E-value=6e-07  Score=60.70  Aligned_cols=68  Identities=18%  Similarity=0.267  Sum_probs=51.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKL   75 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l   75 (163)
                      ..|.+..+||+.||||.+||++|++++.+.|...+    ..+|...++.....+... ..+|..+..++...+
T Consensus        20 ~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~----~gr~~~l~~~~~~~i~~~-~~~~~~s~~~i~~~l   87 (141)
T 1u78_A           20 LLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----APRRKALSVRDERNVIRA-ASNSCKTARDIRNEL   87 (141)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCC----CCCCCSSCHHHHHHHHHH-HHHCCCCHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHcccccCCcCC----CCCCCcCCHHHHHHHHHH-HhCCCCCHHHHHHHH
Confidence            57999999999999999999999999988876543    234455566666666665 566777776666654

>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=98.00  E-value=2.2e-06  Score=47.21  Aligned_cols=32  Identities=22%  Similarity=0.282  Sum_probs=28.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      ..|++..+||+.||||.+||++|++++.+.|.
T Consensus        19 ~~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g~   50 (51)
T 1tc3_C           19 LLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT   50 (51)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHCSTTTTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHhhHHhcCC
Confidence            47999999999999999999999999877663

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=97.66  E-value=9.3e-05  Score=57.05  Aligned_cols=69  Identities=12%  Similarity=0.163  Sum_probs=52.8

Q ss_pred             ccCCCChhhhHHHhh-------cchhhHHHHHhhhhhccC--CCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhh
Q psy1904           2 AAAGVRPCVISRQLR-------VSHGCVSKILNRYQETGS--IRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVR   72 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~-------vs~~~vs~~l~~~~~tG~--~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~   72 (163)
                      ...|.+..+||+.|+       ||.+||++|++++++ |.  +.+.+.+| +|+..+.   +.+.++.+.+|..+..++.
T Consensus        19 ~~~G~s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~-g~~~l~~~~r~g-rp~~~~~---~~i~~~v~~~~~~t~~~ia   93 (345)
T 3hot_A           19 FHLKKTAAESHRMLVEAFGEQVPTVKTCERWFQRFKS-GDFDVDDKEHGK-PPKRYED---AELQALLDEDDAQTQKQLA   93 (345)
T ss_dssp             HHTTCCHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTT-CCCCCSCCCCCC-CCCSSCH---HHHHHHHHHCSCCCHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhC-CCccccCCCCCC-CCCcccH---HHHHHHHHhCccchHHHHH
Confidence            358999999999988       999999999999987 54  56666555 4554443   3455677889999887777


Q ss_pred             hhh
Q psy1904          73 DKL   75 (163)
Q Consensus        73 ~~l   75 (163)
                      ..+
T Consensus        94 ~~l   96 (345)
T 3hot_A           94 EQL   96 (345)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            665

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

Probab=97.38  E-value=0.00016  Score=45.73  Aligned_cols=30  Identities=13%  Similarity=0.235  Sum_probs=27.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      |.+..+||+.||||.+||++|+++|...|.
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~~~~~~~g~   52 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWIIKYGSNHN   52 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHHHHCCCST
T ss_pred             CChHHHHHHHHCcCHHHHHHHHHHHhhcCc
Confidence            899999999999999999999999987664

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=97.22  E-value=0.00031  Score=45.02  Aligned_cols=30  Identities=20%  Similarity=0.346  Sum_probs=27.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhc
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~t   32 (163)
                      .+|+++.|||+.||||..+|+++|++.++.
T Consensus        32 v~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~   61 (101)
T 2w7n_A           32 VDGKPQATFATSLGLTRGAVSQAVHRVWAA   61 (101)
T ss_dssp             TTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            479999999999999999999999998765

>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=97.17  E-value=7.9e-05  Score=41.11  Aligned_cols=27  Identities=4%  Similarity=0.015  Sum_probs=24.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|++..+||+.||||.+||++|++.+
T Consensus        19 ~~g~s~~~ia~~lgvs~~Tv~r~l~~~   45 (52)
T 1jko_C           19 EKGHPRQQLAIIFGIGVSTLYRYFPAS   45 (52)
T ss_dssp             HTTCCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence            468999999999999999999999664

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=97.01  E-value=0.00023  Score=40.10  Aligned_cols=26  Identities=27%  Similarity=0.243  Sum_probs=23.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ..|.+..+||+.||||.+||++++++
T Consensus        29 ~~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           29 KMGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            47899999999999999999999853

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

Probab=96.93  E-value=0.00039  Score=39.88  Aligned_cols=30  Identities=10%  Similarity=0.062  Sum_probs=25.9

Q ss_pred             CCCC----hhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904           4 AGVR----PCVISRQLRVSHGCVSKILNRYQETG   33 (163)
Q Consensus         4 ~g~~----~~~ia~~~~vs~~~vs~~l~~~~~tG   33 (163)
                      .|.+    ..+||+.|||+.++|++|++++.+.+
T Consensus        20 ~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~~~   53 (59)
T 2glo_A           20 NDNDCKGNQRATARKYNIHRRQIQKWLQCESNLR   53 (59)
T ss_dssp             HCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHHHH
T ss_pred             cCCCcchHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4667    89999999999999999998886544

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

Probab=96.90  E-value=0.00065  Score=42.17  Aligned_cols=29  Identities=10%  Similarity=0.177  Sum_probs=26.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhc
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~t   32 (163)
                      .|.+..+||+.||||.+||++|++++.+.
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k~~~~~   65 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCKNEDKL   65 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHhc
Confidence            58899999999999999999999988653

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=96.90  E-value=0.00016  Score=47.84  Aligned_cols=72  Identities=11%  Similarity=0.074  Sum_probs=60.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKL   75 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l   75 (163)
                      .+.++.|+|..|+|+...+..||+...++|.+.+-..+.--.........+.+.++.++++.++..+.++.+
T Consensus        19 ~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~Rd~l   90 (121)
T 2pjp_A           19 EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRL   90 (121)
T ss_dssp             SCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETTEEEEHHHHHHHHHHHHHHHHHHSSEEHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceECHHHHHHHHHHHHHHHHHCCCccHHHHHHHH
Confidence            567889999999999999999999999999999876554444445566677777888889999999999886

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=96.66  E-value=0.0011  Score=38.94  Aligned_cols=22  Identities=27%  Similarity=0.265  Sum_probs=19.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      +++.|||+.+|||.+|||++|+
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLn   22 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVIN   22 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            4678999999999999999994

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=96.57  E-value=0.00084  Score=43.17  Aligned_cols=31  Identities=6%  Similarity=0.075  Sum_probs=27.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      |.+..+||+.||||.+||++|++++...|..
T Consensus        30 g~s~~~va~~~gIs~~tl~~W~~~~~~~~~~   60 (108)
T 2rn7_A           30 WATICSIAPKIGCTPETLRVWVRQHERDTGG   60 (108)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHTTSCC
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHHHHhcccc
Confidence            4788999999999999999999999887754

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.48  E-value=0.0022  Score=40.32  Aligned_cols=42  Identities=12%  Similarity=0.168  Sum_probs=35.0

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg   42 (163)
                      |++.+++.+|||+.+|||+++|++-|+...+.|-+.-...|.
T Consensus        32 L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~   73 (98)
T 3jth_A           32 LHNQELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEAQ   73 (98)
T ss_dssp             TTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTT
T ss_pred             HhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            445558999999999999999999999999999886544443

>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=96.38  E-value=0.0064  Score=40.19  Aligned_cols=56  Identities=13%  Similarity=0.095  Sum_probs=35.4

Q ss_pred             CCCCh-hhhHHHhhcchhhHHHHHhhhhh-------ccCCCCCCCCCCCCCcCChHHHHHHHHHHH
Q psy1904           4 AGVRP-CVISRQLRVSHGCVSKILNRYQE-------TGSIRPGVIGGSKPRVATPDVEKRIEEYKK   61 (163)
Q Consensus         4 ~g~~~-~~ia~~~~vs~~~vs~~l~~~~~-------tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~   61 (163)
                      .|.+. .+||+.|||+.+||++|++....       .+...|.. . .......+..++.+..+..
T Consensus        23 ~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~~~~~~~~~~~~~~-k-r~r~~~~~~~E~~L~~Wi~   86 (131)
T 1hlv_A           23 NPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCR-K-TNKLSPYDKLEGLLIAWFQ   86 (131)
T ss_dssp             CTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHHHHHHHGGGGGTC-C-CCCCCTTHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHhchhhhcchhhhccccchhh-c-ccCCCCCHHHHHHHHHHHH
Confidence            56554 49999999999999999988744       34333311 1 1112345666666655553

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=96.30  E-value=0.0011  Score=40.02  Aligned_cols=25  Identities=16%  Similarity=0.197  Sum_probs=23.1

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .+.|++..++|+.+|||.++|++|+
T Consensus        19 ~~~glT~~~LA~~~Gvs~stls~~~   43 (74)
T 1neq_A           19 KKRKLSLSALSRQFGYAPTTLANAL   43 (74)
T ss_dssp             HTTSCCHHHHHHHHSSCHHHHHHTT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            4679999999999999999999986

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=96.18  E-value=0.0018  Score=38.25  Aligned_cols=21  Identities=24%  Similarity=0.218  Sum_probs=20.1

Q ss_pred             CChhhhHHHhhcchhhHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +++.|||+..|||.+|||++|
T Consensus        10 ~t~~diA~~aGVS~sTVSr~l   30 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRAL   30 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHH
Confidence            689999999999999999998

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=96.16  E-value=0.0024  Score=38.76  Aligned_cols=32  Identities=13%  Similarity=0.274  Sum_probs=29.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++++.|||+.||||.++|.+.|.+..+.|-+.
T Consensus        31 ~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~   62 (77)
T 1qgp_A           31 ATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   62 (77)
T ss_dssp             CEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            68999999999999999999999999888774

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.13  E-value=0.0028  Score=37.30  Aligned_cols=32  Identities=13%  Similarity=0.263  Sum_probs=29.2

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..|||+.||||.++|.++++.+++.|-+.
T Consensus        25 ~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~   56 (67)
T 2heo_A           25 PVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVS   56 (67)
T ss_dssp             CEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEe
Confidence            48899999999999999999999999888764

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.11  E-value=0.0044  Score=37.65  Aligned_cols=33  Identities=18%  Similarity=0.216  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..|||+.||||.++|++.|+...+.|-+.
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~   45 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQ   45 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            348999999999999999999999999999886

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=96.11  E-value=0.0038  Score=37.12  Aligned_cols=24  Identities=8%  Similarity=-0.082  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        22 ~~gltq~elA~~~gvs~~tis~~E   45 (73)
T 3fmy_A           22 KLSLTQKEASEIFGGGVNAFSRYE   45 (73)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            369999999999999999999996

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.11  E-value=0.002  Score=39.61  Aligned_cols=37  Identities=22%  Similarity=0.314  Sum_probs=33.1

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      ...|++..+||+.||||.++|.+.|....+.|-+.-.
T Consensus        27 ~~~g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           27 GIEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             SSSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            3567899999999999999999999999999988654

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=96.07  E-value=0.0027  Score=45.29  Aligned_cols=28  Identities=18%  Similarity=0.186  Sum_probs=25.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|+++.+||+.||||+++|+++|+..+
T Consensus        22 ~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           22 NDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            4799999999999999999999997753

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=96.03  E-value=0.0039  Score=39.84  Aligned_cols=25  Identities=8%  Similarity=0.154  Sum_probs=22.4

Q ss_pred             CC-CChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AG-VRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .| +++.+||+.+|||.+||||+ ++.
T Consensus        56 ~ge~TQREIA~~lGiS~stISRi-~r~   81 (101)
T 1jhg_A           56 RGEMSQRELKNELGAGIATITRG-SNS   81 (101)
T ss_dssp             HCCSCHHHHHHHHCCCHHHHHHH-HHH
T ss_pred             cCCcCHHHHHHHHCCChhhhhHH-HHH
Confidence            57 99999999999999999998 544

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.01  E-value=0.0022  Score=39.90  Aligned_cols=34  Identities=18%  Similarity=0.365  Sum_probs=30.4

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +.| ++..|||+.|+||..||.+-|..+.+.|-+.
T Consensus        13 ~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~   47 (87)
T 2k02_A           13 LQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVV   47 (87)
T ss_dssp             HSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSE
T ss_pred             HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            345 8899999999999999999999998888774

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=96.00  E-value=0.0029  Score=38.55  Aligned_cols=25  Identities=20%  Similarity=0.292  Sum_probs=23.2

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ...|+++.++|+.+|||.++|++|+
T Consensus        28 ~~~glsq~elA~~~gis~~~is~~e   52 (83)
T 2a6c_A           28 RNSGLTQFKAAELLGVTQPRVSDLM   52 (83)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3579999999999999999999997

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=95.99  E-value=0.0024  Score=39.97  Aligned_cols=35  Identities=23%  Similarity=0.298  Sum_probs=31.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +++..|||+.||||.++|++.|+...+.|-+.-..
T Consensus        38 ~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~   72 (99)
T 3cuo_A           38 GTSAGELTRITGLSASATSQHLARMRDEGLIDSQR   72 (99)
T ss_dssp             SEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            58999999999999999999999999999885443

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=95.97  E-value=0.0037  Score=39.54  Aligned_cols=35  Identities=14%  Similarity=0.202  Sum_probs=31.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++++.|||+.||||.++|+++|+...+.|-+.-
T Consensus        34 ~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~   68 (109)
T 2d1h_A           34 EKPITSEELADIFKLSKTTVENSLKKLIELGLVVR   68 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            35689999999999999999999999999888754

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=95.96  E-value=0.0024  Score=38.91  Aligned_cols=33  Identities=18%  Similarity=0.372  Sum_probs=30.3

Q ss_pred             cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      +.| ++..|||+.|+||..||.+-|..+.+.|-+
T Consensus        13 ~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l   46 (78)
T 1xn7_A           13 LRGRMEAAQISQTLNTPQPMINAMLQQLESMGKA   46 (78)
T ss_dssp             HSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSE
T ss_pred             HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            345 899999999999999999999999999987

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=95.94  E-value=0.0026  Score=40.92  Aligned_cols=40  Identities=15%  Similarity=0.077  Sum_probs=33.6

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      +..+++.+|||+.||||+++|++.|+...+.|-+.....|
T Consensus        35 ~~~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~g   74 (108)
T 2kko_A           35 AQGERAVEAIATATGMNLTTASANLQALKSGGLVEARREG   74 (108)
T ss_dssp             TTCCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEET
T ss_pred             HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            3445889999999999999999999999999988654433

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=95.93  E-value=0.0032  Score=40.27  Aligned_cols=37  Identities=22%  Similarity=0.184  Sum_probs=32.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +.+++.+|||+.+|||+++|++.|+...+.|-+.-..
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~   73 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKR   73 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            3458999999999999999999999999999886443

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=95.93  E-value=0.0045  Score=35.45  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        12 ~~g~s~~~lA~~~gis~~~i~~~e   35 (66)
T 2xi8_A           12 KKKISQSELAALLEVSRQTINGIE   35 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=95.89  E-value=0.0044  Score=38.83  Aligned_cols=34  Identities=18%  Similarity=0.075  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.|+||.++|++.|+...+.|-+.-
T Consensus        42 ~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~   75 (96)
T 1y0u_A           42 KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIER   75 (96)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4589999999999999999999999998887754

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=95.79  E-value=0.0054  Score=35.69  Aligned_cols=24  Identities=13%  Similarity=0.115  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        14 ~~glsq~~lA~~~gis~~~i~~~e   37 (71)
T 1zug_A           14 ALKMTQTELATKAGVKQQSIQLIE   37 (71)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999997

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=95.79  E-value=0.0068  Score=34.43  Aligned_cols=28  Identities=21%  Similarity=0.120  Sum_probs=25.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|.+..|||+.||||.+||+..+.+..
T Consensus        11 ~~g~s~~eIA~~l~is~~tV~~~~~~~~   38 (61)
T 2jpc_A           11 DEGYTNHGISEKLHISIKTVETHRMNMM   38 (61)
T ss_dssp             HTSCCSHHHHHHTCSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3799999999999999999999987763

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=95.79  E-value=0.0055  Score=35.44  Aligned_cols=24  Identities=4%  Similarity=0.279  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        12 ~~glsq~~lA~~~gis~~~i~~~e   35 (69)
T 1r69_A           12 QLGLNQAELAQKVGTTQQSIEQLE   35 (69)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=95.78  E-value=0.0035  Score=36.38  Aligned_cols=25  Identities=16%  Similarity=0.395  Sum_probs=22.4

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ...| +..++|+.+|||+++|++|++
T Consensus        11 ~~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A           11 EEHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             HHTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            3468 999999999999999999984

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=95.77  E-value=0.0047  Score=36.20  Aligned_cols=22  Identities=23%  Similarity=0.357  Sum_probs=20.3

Q ss_pred             ChhhhHHHhhcchhhHHHHHhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +..++|+.||||+++||+|++.
T Consensus        15 sq~~~A~~Lgvsq~aVS~~~~~   36 (65)
T 2cw1_A           15 NQEYAARALGLSQKLIEEVLKR   36 (65)
T ss_dssp             CHHHHHHHSSSCHHHHHHHHHT
T ss_pred             CHHHHHHHhCCCHHHHHHHHHh
Confidence            8899999999999999999844

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=95.77  E-value=0.0053  Score=36.97  Aligned_cols=24  Identities=8%  Similarity=0.281  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|+
T Consensus        23 ~~gltq~~lA~~~gvs~~~is~~e   46 (80)
T 3kz3_A           23 ELGLSYESVADKMGMGQSAVAALF   46 (80)
T ss_dssp             HHTCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            368999999999999999999997

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=95.77  E-value=0.0059  Score=36.44  Aligned_cols=21  Identities=19%  Similarity=0.131  Sum_probs=19.2

Q ss_pred             ChhhhHHHhhcchhhHHHHHh
Q psy1904           7 RPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ++.++|+.||||+++|++|+.
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~   32 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQ   32 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHh
Confidence            478999999999999999984

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=95.74  E-value=0.0073  Score=36.77  Aligned_cols=22  Identities=14%  Similarity=0.345  Sum_probs=21.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      |+++.++|+..|||++|+|.|.
T Consensus        32 GikQ~eLAK~iGIsqsTLSaIe   53 (83)
T 2l1p_A           32 DMNQSSLAKECPLSQSMISSIV   53 (83)
T ss_dssp             TSCHHHHHHHSSSCHHHHHHHH
T ss_pred             hcCHHHHHHHcCCCHHHHHHHH
Confidence            9999999999999999999996

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=95.67  E-value=0.0085  Score=37.84  Aligned_cols=34  Identities=6%  Similarity=-0.108  Sum_probs=30.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|+|++|+||.+.+..|.+.|.+.|.-..
T Consensus        48 g~~s~~e~arry~Is~s~i~~W~r~~~~~G~~~L   81 (95)
T 2jrt_A           48 GLITEREALDRYSLSEEEFALWRSAVAAHGEKAL   81 (95)
T ss_dssp             TSSCHHHHHHHTTCCHHHHHHHHHHTTTCCTTSC
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHH
Confidence            4589999999999999999999999988886554

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=95.66  E-value=0.0078  Score=36.85  Aligned_cols=33  Identities=12%  Similarity=0.259  Sum_probs=30.2

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +++..+||+.||||.++|.+.|.+..+.|-+.-
T Consensus        27 ~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~   59 (81)
T 1qbj_A           27 ATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQK   59 (81)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            488999999999999999999999999998853

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=95.65  E-value=0.0065  Score=40.02  Aligned_cols=38  Identities=16%  Similarity=0.111  Sum_probs=32.5

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++.+++.++||+.||||+++|++.|+...+.|-+.-..
T Consensus        56 ~~~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~   93 (122)
T 1r1t_A           56 ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK   93 (122)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            34458999999999999999999999999988875443

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=95.63  E-value=0.0031  Score=36.35  Aligned_cols=23  Identities=17%  Similarity=0.115  Sum_probs=20.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .|.++.++|+.+|||+++|++|.
T Consensus         9 ~~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            9 HFGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HHSSHHHHHHHHTCCHHHHHHCC
T ss_pred             HcCCHHHHHHHhCCCHHHHHHHH
Confidence            34589999999999999999995

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

Probab=95.63  E-value=0.0099  Score=34.59  Aligned_cols=27  Identities=11%  Similarity=0.065  Sum_probs=24.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..+||+.+|||.++|.+++.+.
T Consensus        29 ~~g~s~~eIA~~lgis~~tv~~~~~ra   55 (70)
T 2o8x_A           29 LLGLSYADAAAVCGCPVGTIRSRVARA   55 (70)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478999999999999999999998765

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=95.63  E-value=0.014  Score=34.12  Aligned_cols=51  Identities=16%  Similarity=0.121  Sum_probs=36.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC-CCCCCCCCCCCcCChHHHHHHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVEKRIEEYKK   61 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~-~Pg~~Gg~~p~~~~~~~~~~i~~~~~   61 (163)
                      ++..|+|+.||||.+||++|.+.    |.+ .|-..|+.. .....++++++.+...
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~----g~fP~piklG~~~-~w~~~ev~~Wl~~~~~   62 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKS----GDLPKAKVIHGRA-RWLYRDHCEFKNKLLS   62 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHH----HHCCCSEESSSCE-EEEHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC----CCCCCCEEeCCCe-EEeHHHHHHHHHHHHH
Confidence            67889999999999999999865    544 444466554 5555777777755443

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=95.63  E-value=0.0091  Score=36.58  Aligned_cols=24  Identities=21%  Similarity=0.344  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|.
T Consensus        25 ~~gltq~elA~~~gis~~~is~~E   48 (86)
T 3eus_A           25 DAGLTQADLAERLDKPQSFVAKVE   48 (86)
T ss_dssp             HTTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            379999999999999999999996

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=95.59  E-value=0.0077  Score=40.15  Aligned_cols=36  Identities=19%  Similarity=0.385  Sum_probs=31.9

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ...|+++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        48 ~~~~~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r   83 (146)
T 3tgn_A           48 SEESLTNSELARRLNVSQAAVTKAIKSLVKEGMLET   83 (146)
T ss_dssp             TTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEe
Confidence            345599999999999999999999999999998854

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=95.58  E-value=0.0078  Score=34.59  Aligned_cols=24  Identities=17%  Similarity=0.243  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        16 ~~g~s~~~lA~~~gis~~~i~~~e   39 (68)
T 2r1j_L           16 KLKIRQAALGKMVGVSNVAISQWE   39 (68)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            368999999999999999999997

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=95.56  E-value=0.0064  Score=38.10  Aligned_cols=34  Identities=15%  Similarity=0.213  Sum_probs=31.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ..|+.+.|||+++++++++|.++|+++.+-|-+.
T Consensus        34 ~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIk   67 (91)
T 2dk5_A           34 NKGIWSRDVRYKSNLPLTEINKILKNLESKKLIK   67 (91)
T ss_dssp             TTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            4589999999999999999999999998887775

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=95.54  E-value=0.0075  Score=35.53  Aligned_cols=24  Identities=21%  Similarity=0.160  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        19 ~~glsq~~lA~~~gis~~~is~~e   42 (73)
T 3omt_A           19 EKGKTNLWLTETLDKNKTTVSKWC   42 (73)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            468999999999999999999997

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=95.52  E-value=0.0038  Score=39.30  Aligned_cols=24  Identities=29%  Similarity=0.289  Sum_probs=21.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      .|++..|||+.+|||.+||++.|.
T Consensus        19 ~~~ti~dlA~~~gVS~~TVsR~L~   42 (93)
T 2l0k_A           19 TKKTVRVIAKEFGVSKSTVHKDLT   42 (93)
T ss_dssp             HCCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHc
Confidence            468899999999999999999993

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=95.46  E-value=0.0085  Score=35.11  Aligned_cols=24  Identities=13%  Similarity=0.124  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        24 ~~g~s~~~lA~~~gis~~~i~~~e   47 (74)
T 1y7y_A           24 AKGLSQETLAFLSGLDRSYVGGVE   47 (74)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=95.45  E-value=0.0085  Score=35.45  Aligned_cols=24  Identities=13%  Similarity=0.159  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        21 ~~glsq~~lA~~~gis~~~i~~~e   44 (77)
T 2b5a_A           21 QKGVSQEELADLAGLHRTYISEVE   44 (77)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            479999999999999999999997

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=95.44  E-value=0.011  Score=37.21  Aligned_cols=24  Identities=13%  Similarity=0.093  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        41 ~~glsq~elA~~lgvs~~~is~~E   64 (99)
T 2ppx_A           41 ALKLTQEEFSARYHIPLGTLRDWE   64 (99)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            369999999999999999999995

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=95.42  E-value=0.0088  Score=35.94  Aligned_cols=24  Identities=17%  Similarity=0.206  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        21 ~~gltq~elA~~~gis~~~is~~E   44 (78)
T 3qq6_A           21 EKGYSLSELAEKAGVAKSYLSSIE   44 (78)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            379999999999999999999997

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=95.41  E-value=0.0091  Score=35.83  Aligned_cols=23  Identities=17%  Similarity=0.251  Sum_probs=21.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      .| ++.++|+.+|||+++|++|.+
T Consensus        11 ~g-sq~~lA~~lgvs~~~is~~e~   33 (79)
T 3bd1_A           11 LG-SVSALAASLGVRQSAISNWRA   33 (79)
T ss_dssp             HS-SHHHHHHHHTCCHHHHHHHHH
T ss_pred             hC-CHHHHHHHHCCCHHHHHHHHH
Confidence            58 999999999999999999974

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=95.40  E-value=0.0082  Score=35.62  Aligned_cols=24  Identities=4%  Similarity=0.108  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        18 ~~g~sq~~lA~~~gis~~~i~~~e   41 (78)
T 3b7h_A           18 QQNLTINRVATLAGLNQSTVNAMF   41 (78)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=95.40  E-value=0.0077  Score=38.45  Aligned_cols=24  Identities=4%  Similarity=0.016  Sum_probs=22.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++|||.++|++|-
T Consensus        47 ~~glTQ~eLA~~~gvs~~~is~~E   70 (101)
T 4ghj_A           47 NRDLTQSEVAEIAGIARKTVLNAE   70 (101)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHcCCCHHHHHHHH
Confidence            369999999999999999999994

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=95.39  E-value=0.0078  Score=37.43  Aligned_cols=24  Identities=13%  Similarity=0.072  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        20 ~~glsq~~lA~~~gis~~~is~~e   43 (94)
T 2kpj_A           20 KSEKTQLEIAKSIGVSPQTFNTWC   43 (94)
T ss_dssp             TSSSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            579999999999999999999997

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=95.39  E-value=0.0011  Score=50.27  Aligned_cols=24  Identities=13%  Similarity=0.051  Sum_probs=0.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++|||+++|++|.
T Consensus        41 ~~g~t~~~la~~~g~s~~~is~~e   64 (311)
T 4ich_A           41 SRPGAQREFAAAIGLDESKLSKSL   64 (311)
T ss_dssp             ------------------------
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999996

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=95.37  E-value=0.0067  Score=39.42  Aligned_cols=34  Identities=12%  Similarity=0.160  Sum_probs=30.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..+||+.|+||+++|++.|+...+.|-+.-
T Consensus        44 ~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~   77 (119)
T 2lkp_A           44 GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVG   77 (119)
T ss_dssp             CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4689999999999999999999999988887743

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=95.36  E-value=0.0096  Score=35.13  Aligned_cols=24  Identities=13%  Similarity=0.072  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        21 ~~g~s~~~lA~~~gis~~~i~~~e   44 (76)
T 3bs3_A           21 EKQRTNRWLAEQMGKSENTISRWC   44 (76)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

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

Probab=95.34  E-value=0.014  Score=34.34  Aligned_cols=27  Identities=15%  Similarity=0.108  Sum_probs=24.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..+||+.+|||.++|+..+.+.
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~   50 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNA   50 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            478999999999999999999999875

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=95.30  E-value=0.011  Score=35.24  Aligned_cols=24  Identities=8%  Similarity=0.158  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        13 ~~glsq~~lA~~~gis~~~i~~~e   36 (77)
T 2k9q_A           13 RLSLTAKSVAEEMGISRQQLCNIE   36 (77)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            368999999999999999999997

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=95.27  E-value=0.0077  Score=38.57  Aligned_cols=24  Identities=17%  Similarity=0.292  Sum_probs=22.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|+
T Consensus        25 ~~gltq~eLA~~lGis~~~is~ie   48 (104)
T 3trb_A           25 LDKMSANQLAKHLAIPTNRVTAIL   48 (104)
T ss_dssp             TTSCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            579999999999999999999997

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=95.26  E-value=0.0087  Score=39.29  Aligned_cols=38  Identities=21%  Similarity=0.214  Sum_probs=31.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      .+++.++||+.||||+++|++.|+...+.|-+.-...|
T Consensus        55 ~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~g   92 (122)
T 1u2w_A           55 EELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEG   92 (122)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEC
Confidence            45889999999999999999999999999988654434

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=95.25  E-value=0.0068  Score=38.92  Aligned_cols=36  Identities=25%  Similarity=0.300  Sum_probs=31.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .+++..+||+.|+||.++|++.|+...+.|-+.-..
T Consensus        33 ~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~   68 (114)
T 2oqg_A           33 ADQSASSLATRLPVSRQAIAKHLNALQACGLVESVK   68 (114)
T ss_dssp             SCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEe
Confidence            458999999999999999999999999999886543

>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3

Probab=95.25  E-value=0.012  Score=37.54  Aligned_cols=32  Identities=9%  Similarity=0.035  Sum_probs=28.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      .+++..|+|++|+||.++|..|.+.|.+.|.-
T Consensus        49 g~lS~~EAa~ry~Is~~ei~~W~r~y~~~G~~   80 (101)
T 2oa4_A           49 GLITLAEAKQTYGLSDEEFNSWVSALAEHGKD   80 (101)
T ss_dssp             TTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSS
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHH
Confidence            45999999999999999999999999888754

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=95.23  E-value=0.012  Score=34.67  Aligned_cols=24  Identities=17%  Similarity=0.243  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        16 ~~gls~~~lA~~~gis~~~i~~~e   39 (76)
T 1adr_A           16 KLKIRQAALGKMVGVSNVAISQWE   39 (76)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999997

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=95.22  E-value=0.0078  Score=40.15  Aligned_cols=35  Identities=29%  Similarity=0.391  Sum_probs=31.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++++.|||+.+|++.++|+++|++..+.|=+.-
T Consensus        39 ~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r   73 (152)
T 1ku9_A           39 DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRK   73 (152)
T ss_dssp             SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            45699999999999999999999999999998854

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=95.19  E-value=0.011  Score=39.27  Aligned_cols=24  Identities=8%  Similarity=-0.082  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        82 ~~glsq~~la~~~g~s~~~i~~~E  105 (133)
T 3o9x_A           82 KLSLTQKEASEIFGGGVNAFSRYE  105 (133)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            479999999999999999999996

>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=95.17  E-value=0.016  Score=35.22  Aligned_cols=28  Identities=21%  Similarity=0.341  Sum_probs=25.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|++..|||+.||||.+||...+.+.+
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l~r~~   61 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHVKHML   61 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4799999999999999999999987763

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=95.14  E-value=0.014  Score=35.42  Aligned_cols=24  Identities=8%  Similarity=0.278  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        23 ~~glsq~~lA~~~gis~~~i~~~e   46 (88)
T 2wiu_B           23 QNGWTQSELAKKIGIKQATISNFE   46 (88)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999997

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=95.13  E-value=0.0095  Score=37.63  Aligned_cols=40  Identities=13%  Similarity=0.128  Sum_probs=33.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg   42 (163)
                      ...++.+|||+.+|||+++|++-|+...+.|-+.-...|.
T Consensus        34 ~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~   73 (102)
T 3pqk_A           34 EGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIK   73 (102)
T ss_dssp             TCCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSSS
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            3448999999999999999999999999999885544443

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=95.12  E-value=0.014  Score=35.14  Aligned_cols=24  Identities=25%  Similarity=0.230  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        21 ~~glsq~~lA~~~gis~~~i~~~e   44 (84)
T 2ef8_A           21 EASLSQSELAIFLGLSQSDISKIE   44 (84)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999997

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=95.12  E-value=0.016  Score=34.00  Aligned_cols=45  Identities=18%  Similarity=0.188  Sum_probs=29.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CC--CCCCcCChHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GG--SKPRVATPDVEKRI   56 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg--~~p~~~~~~~~~~i   56 (163)
                      ++..|+|+.||||.+|+.+|.+.    |.  |... ||  ...+....++..++
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~----G~--P~~~~~g~~~~~~y~~~dv~~wl   50 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQ----GM--PVLRGGGKGNEVLYDSAAVIKWY   50 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTT----TC--CCSSCCCSSSCCEEEHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC----CC--CeEeeCCCcceEEECHHHHHHHH
Confidence            35679999999999999999744    65  4432 33  23333344454444

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

Probab=95.10  E-value=0.017  Score=35.77  Aligned_cols=27  Identities=22%  Similarity=0.273  Sum_probs=24.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|++..+||+.||||.++|...+.+.
T Consensus        51 ~~g~s~~eIA~~lgis~~tV~~~l~ra   77 (92)
T 3hug_A           51 YRGWSTAQIATDLGIAEGTVKSRLHYA   77 (92)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            479999999999999999999998665

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=95.10  E-value=0.015  Score=37.32  Aligned_cols=25  Identities=16%  Similarity=0.266  Sum_probs=23.2

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ...|+++.++|+.+|||.++|++|+
T Consensus        21 ~~~glsq~~lA~~~gis~~~is~~e   45 (113)
T 2eby_A           21 EPLDLKINELAELLHVHRNSVSALI   45 (113)
T ss_dssp             TTTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3579999999999999999999997

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=95.09  E-value=0.016  Score=39.19  Aligned_cols=32  Identities=19%  Similarity=0.359  Sum_probs=30.1

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +++..+||+.+|||.++|++.|++..+.|-+.
T Consensus        17 ~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   48 (150)
T 2pn6_A           17 KYSLDEIAREIRIPKATLSYRIKKLEKDGVIK   48 (150)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            48999999999999999999999999999885

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=95.09  E-value=0.011  Score=37.79  Aligned_cols=38  Identities=16%  Similarity=0.270  Sum_probs=32.7

Q ss_pred             ccCCCChhhhHHHh-hcchhhHHHHHhhhhhccCCCCCC
Q psy1904           2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         2 ~~~g~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +..+++.+|||+.+ +||+++|++.|++..+.|=+.-..
T Consensus        24 ~~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~   62 (107)
T 2hzt_A           24 THGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIV   62 (107)
T ss_dssp             TTCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence            34458999999999 999999999999999999886433

>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=95.08  E-value=0.019  Score=33.41  Aligned_cols=27  Identities=11%  Similarity=0.135  Sum_probs=24.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..|||+.+|||.++|..++.+.
T Consensus        23 ~~g~s~~eIA~~lgis~~tV~~~~~ra   49 (68)
T 2p7v_B           23 NTDYTLEEVGKQFDVTRERIRQIEAKA   49 (68)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            378999999999999999999998765

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=95.06  E-value=0.0076  Score=37.58  Aligned_cols=33  Identities=12%  Similarity=0.230  Sum_probs=30.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..+||+.++||+++|++.|++..+.|-+.
T Consensus        29 ~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~   61 (100)
T 1ub9_A           29 RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVK   61 (100)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            458899999999999999999999999998885

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=95.06  E-value=0.0096  Score=45.53  Aligned_cols=41  Identities=20%  Similarity=0.297  Sum_probs=35.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      ..|++..|||++||||..||+|.|...++.|-+.-...|+.
T Consensus        19 ~~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri~g~~   59 (315)
T 2w48_A           19 EQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDY   59 (315)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEecCCc
Confidence            36799999999999999999999999999999875544543

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=95.06  E-value=0.014  Score=35.16  Aligned_cols=24  Identities=29%  Similarity=0.304  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        25 ~~gltq~elA~~~gis~~~is~~e   48 (83)
T 3f6w_A           25 AAGITQKELAARLGRPQSFVSKTE   48 (83)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999997

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=95.05  E-value=0.0092  Score=37.28  Aligned_cols=30  Identities=20%  Similarity=0.326  Sum_probs=29.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      +++.+||+.++|+.++|++++++..+.|=+
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCcCc
Confidence            889999999999999999999999999988

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=95.02  E-value=0.012  Score=36.73  Aligned_cols=32  Identities=16%  Similarity=0.157  Sum_probs=30.6

Q ss_pred             CCChhhhHHHhhcchhh-HHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGC-VSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~-vs~~l~~~~~tG~~~   36 (163)
                      ++++.+||+.++|+.++ |++++++..+.|-+.
T Consensus        30 ~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           30 EPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             CCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCCCchHHHHHHHHHHHHCCCee
Confidence            69999999999999999 999999999999887

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

Probab=94.91  E-value=0.0071  Score=35.69  Aligned_cols=40  Identities=10%  Similarity=0.129  Sum_probs=36.6

Q ss_pred             HHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy1904         109 QLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLG  148 (163)
Q Consensus       109 q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqn  148 (163)
                      -.+.|++.|...+.+.......|..+..|+-.||+-||-.
T Consensus        17 ~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           17 DIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             cchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            3478999999999999999999999999999999999954

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=94.90  E-value=0.0037  Score=40.82  Aligned_cols=40  Identities=13%  Similarity=0.178  Sum_probs=33.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg   42 (163)
                      ...++.++||+.||||+++|++-|+...+.|-+.-...|.
T Consensus        29 ~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~gr   68 (118)
T 3f6o_A           29 RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQGR   68 (118)
T ss_dssp             TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecCC
Confidence            3458899999999999999999999999999886544443

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=94.90  E-value=0.017  Score=35.74  Aligned_cols=24  Identities=17%  Similarity=0.288  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        19 ~~gltq~~lA~~~gis~~~is~~e   42 (94)
T 2ict_A           19 ELNVSLREFARAMEIAPSTASRLL   42 (94)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            468999999999999999999998

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=94.90  E-value=0.012  Score=39.57  Aligned_cols=33  Identities=15%  Similarity=0.304  Sum_probs=29.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ..++..+||+.+|||.++|++.|++..+.|-+.
T Consensus        18 ~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   50 (144)
T 2cfx_A           18 SRLSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (144)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            348999999999999999999999998888774

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=94.90  E-value=0.013  Score=39.78  Aligned_cols=33  Identities=12%  Similarity=0.216  Sum_probs=30.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ..++..+||+.+|+|.++|++.|++..+.|-+.
T Consensus        20 ~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A           20 GRATLSELATRAGLSVSAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            348999999999999999999999999999883

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=94.89  E-value=0.021  Score=38.13  Aligned_cols=33  Identities=18%  Similarity=0.240  Sum_probs=30.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++++.+||+.|+||.++|+++|++..+.|-+.
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~   53 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLI   53 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            569999999999999999999999998888774

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=94.88  E-value=0.02  Score=35.95  Aligned_cols=34  Identities=29%  Similarity=0.399  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..+||+.++|+.++|++.|+...+.|-+.-
T Consensus        33 ~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~   66 (109)
T 1sfx_A           33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRR   66 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4689999999999999999999999999888754

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=94.83  E-value=0.015  Score=38.29  Aligned_cols=32  Identities=13%  Similarity=0.315  Sum_probs=29.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +++.+||+.+++|.+||++.|+++.+.|-+.-
T Consensus        43 ~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r   74 (123)
T 3r0a_A           43 IDTDALSKSLKLDVSTVQRSVKKLHEKEILQR   74 (123)
T ss_dssp             EEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999998843

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=94.80  E-value=0.021  Score=37.87  Aligned_cols=33  Identities=18%  Similarity=0.406  Sum_probs=30.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..+||+.|+|+.++|++.|++..+.|-+.
T Consensus        30 ~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~   62 (139)
T 2x4h_A           30 EGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVK   62 (139)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEE
Confidence            468999999999999999999999998888764

>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=94.77  E-value=0.023  Score=36.92  Aligned_cols=27  Identities=22%  Similarity=0.199  Sum_probs=24.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..+||+.+|||.+||++++.+.
T Consensus        36 ~~g~s~~EIA~~lgiS~~tV~~~l~ra   62 (113)
T 1s7o_A           36 ADDYSLAEIADEFGVSRQAVYDNIKRT   62 (113)
T ss_dssp             HTCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            379999999999999999999999765

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=94.74  E-value=0.022  Score=35.00  Aligned_cols=24  Identities=4%  Similarity=0.122  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        24 ~~glsq~~lA~~~gis~~~is~~e   47 (91)
T 1x57_A           24 SKGLTQKDLATKINEKPQVIADYE   47 (91)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=94.74  E-value=0.011  Score=38.25  Aligned_cols=37  Identities=14%  Similarity=0.231  Sum_probs=32.5

Q ss_pred             cCCCChhhhHHHh-hcchhhHHHHHhhhhhccCCCCCC
Q psy1904           3 AAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         3 ~~g~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +.+++..+||+.+ +|+.++|++.|++..+.|-+.-..
T Consensus        33 ~~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~   70 (112)
T 1z7u_A           33 QGTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRES   70 (112)
T ss_dssp             HSCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             hCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEee
Confidence            4468999999999 999999999999999999886443

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

Probab=94.74  E-value=0.025  Score=35.01  Aligned_cols=28  Identities=14%  Similarity=0.100  Sum_probs=25.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|++..+||+.||||.+||...+.+.+
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l~r~~   69 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHVSNIL   69 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3799999999999999999999997764

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=94.73  E-value=0.015  Score=39.50  Aligned_cols=32  Identities=16%  Similarity=0.272  Sum_probs=29.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|+|.++|++.|++..+.|-+.
T Consensus        21 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (151)
T 2cyy_A           21 KAPLREISKITGLAESTIHERIRKLRESGVIK   52 (151)
T ss_dssp             TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            48999999999999999999999999999875

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=94.70  E-value=0.019  Score=34.54  Aligned_cols=24  Identities=13%  Similarity=0.141  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        22 ~~glsq~~lA~~~gis~~~i~~~e   45 (82)
T 3s8q_A           22 EKGMTQEDLAYKSNLDRTYISGIE   45 (82)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            479999999999999999999996

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=94.69  E-value=0.019  Score=36.30  Aligned_cols=24  Identities=13%  Similarity=0.275  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        29 ~~gltq~~lA~~~gis~~~is~~e   52 (104)
T 3cec_A           29 DLDINTANFAEILGVSNQTIQEVI   52 (104)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999997

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=94.67  E-value=0.02  Score=35.19  Aligned_cols=24  Identities=8%  Similarity=0.277  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|+
T Consensus        28 ~~glsq~~lA~~~gis~~~is~~e   51 (92)
T 1lmb_3           28 ELGLSQESVADKMGMGQSGVGALF   51 (92)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            469999999999999999999997

>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=94.63  E-value=0.031  Score=33.00  Aligned_cols=26  Identities=12%  Similarity=0.051  Sum_probs=23.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..|||+.+|||.++|..++.+.
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra   54 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKA   54 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            78999999999999999999988654

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=94.63  E-value=0.016  Score=39.82  Aligned_cols=32  Identities=16%  Similarity=0.295  Sum_probs=29.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|+|.++|++.|++..+.|-+.
T Consensus        24 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   55 (162)
T 2p5v_A           24 RLTNVELSERVALSPSPCLRRLKQLEDAGIVR   55 (162)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            48999999999999999999999998888774

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=94.60  E-value=0.019  Score=38.08  Aligned_cols=34  Identities=6%  Similarity=0.200  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-
T Consensus        49 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r   82 (140)
T 3hsr_A           49 EKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVR   82 (140)
T ss_dssp             CEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEe
Confidence            4589999999999999999999999999888753

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=94.59  E-value=0.023  Score=34.40  Aligned_cols=34  Identities=18%  Similarity=0.386  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..||++.|     +||.+||++.|+.+.+.|-+.-
T Consensus        32 ~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~   70 (83)
T 2fu4_A           32 HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR   70 (83)
T ss_dssp             SSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEE
Confidence            358999999999     9999999999999999988753

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=94.58  E-value=0.021  Score=33.10  Aligned_cols=24  Identities=8%  Similarity=-0.007  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhh--cchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLR--VSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~--vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|  ||.++|++|.
T Consensus        19 ~~glsq~~lA~~~g~~is~~~i~~~e   44 (71)
T 2ewt_A           19 QQGLSLHGVEEKSQGRWKAVVVGSYE   44 (71)
T ss_dssp             HTTCCHHHHHHHTTTSSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCcCCHHHHHHHH
Confidence            46999999999999  9999999997

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=94.48  E-value=0.02  Score=37.81  Aligned_cols=34  Identities=21%  Similarity=0.259  Sum_probs=31.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-
T Consensus        46 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r   79 (139)
T 3eco_A           46 DGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYR   79 (139)
T ss_dssp             TCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEee
Confidence            3799999999999999999999999999988853

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=94.48  E-value=0.024  Score=37.63  Aligned_cols=35  Identities=11%  Similarity=0.227  Sum_probs=28.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        50 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   84 (142)
T 3ech_A           50 RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   84 (142)
T ss_dssp             TTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC-
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeec
Confidence            46999999999999999999999999999888543

>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=94.45  E-value=0.031  Score=34.94  Aligned_cols=28  Identities=14%  Similarity=0.253  Sum_probs=25.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|++..+||+.||||.+||...+.+.+
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~r~~   67 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVSRLL   67 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4799999999999999999999987763

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=94.44  E-value=0.016  Score=39.30  Aligned_cols=32  Identities=16%  Similarity=0.250  Sum_probs=29.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|+|.++|++.|++..+.|-+.
T Consensus        22 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   53 (152)
T 2cg4_A           22 RTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   53 (152)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcc
Confidence            48999999999999999999999998888774

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=94.44  E-value=0.029  Score=36.82  Aligned_cols=34  Identities=24%  Similarity=0.502  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        42 ~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~   75 (138)
T 3bpv_A           42 PGIKQDELATFFHVDKGTIARTLRRLEESGFIER   75 (138)
T ss_dssp             TTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            5699999999999999999999999999888754

>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=94.44  E-value=0.082  Score=35.65  Aligned_cols=59  Identities=14%  Similarity=0.007  Sum_probs=37.6

Q ss_pred             CCCChhhhHH----Hh--hcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHHh
Q psy1904           4 AGVRPCVISR----QL--RVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKKT   62 (163)
Q Consensus         4 ~g~~~~~ia~----~~--~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~~   62 (163)
                      .+++..+||+    .|  +||.+|||+||+.....-+...+.  ..-.......++.++.+..+..+
T Consensus        29 ~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~~~~~~~~~~kr~r~~~~~~le~~L~~Wi~~   95 (144)
T 1iuf_A           29 NRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLDNTVEKPWDVKRNRPPKYPLLEAALFEWQVQ   95 (144)
T ss_dssp             SCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTTTSCSSSSSSSCCCCCSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhhhcccccccccCCCCCCCHHHHHHHHHHHHH
Confidence            4589999999    99  999999999998764422221111  01112224457777777666655

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=94.41  E-value=0.027  Score=37.31  Aligned_cols=35  Identities=9%  Similarity=0.208  Sum_probs=31.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r   82 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVR   82 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEe
Confidence            35689999999999999999999999999888853

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=94.41  E-value=0.03  Score=34.86  Aligned_cols=24  Identities=13%  Similarity=-0.002  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        15 ~~gltq~~lA~~~gis~~~is~~e   38 (99)
T 2l49_A           15 SEYLSRQQLADLTGVPYGTLSYYE   38 (99)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            469999999999999999999996

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

Probab=94.40  E-value=0.031  Score=33.26  Aligned_cols=28  Identities=21%  Similarity=0.137  Sum_probs=25.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|++..+||+.||||.++|...+.+..
T Consensus        29 ~~g~s~~eIA~~l~is~~tV~~~~~r~~   56 (79)
T 1x3u_A           29 VAGLPNKSIAYDLDISPRTVEVHRANVM   56 (79)
T ss_dssp             TTTCCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4799999999999999999999987763

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=94.36  E-value=0.03  Score=36.88  Aligned_cols=33  Identities=9%  Similarity=0.125  Sum_probs=30.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        50 ~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r   82 (141)
T 3bro_A           50 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLYR   82 (141)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEe
Confidence            699999999999999999999999999887743

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=94.34  E-value=0.022  Score=36.37  Aligned_cols=34  Identities=26%  Similarity=0.233  Sum_probs=30.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++.++||+.||||.++|++.|+...+.|-+.-.
T Consensus        33 ~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           33 EMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             CBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3789999999999999999999999999988543

>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, PR structure initiative; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13

Probab=94.33  E-value=0.024  Score=37.22  Aligned_cols=24  Identities=17%  Similarity=0.191  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++|||+++|++|.
T Consensus        51 ~~glTQ~eLA~~lGis~~~Is~iE   74 (120)
T 2o38_A           51 RARLSQAAAAARLGINQPKVSALR   74 (120)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            469999999999999999999997

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=94.32  E-value=0.031  Score=37.22  Aligned_cols=34  Identities=21%  Similarity=0.237  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|++++|++++++..+.|=+.-
T Consensus        53 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r   86 (148)
T 3nrv_A           53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEV   86 (148)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4699999999999999999999999999887753

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

Probab=94.29  E-value=0.039  Score=33.83  Aligned_cols=26  Identities=8%  Similarity=0.014  Sum_probs=24.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..+||..+|||.++|..++.+-
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra   62 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKA   62 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            78999999999999999999998765

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=94.29  E-value=0.032  Score=38.37  Aligned_cols=32  Identities=16%  Similarity=0.282  Sum_probs=29.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|||.++|.+-++++.+.|-+.
T Consensus        17 ~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~   48 (162)
T 3i4p_A           17 TLAVADLAKKVGLSTTPCWRRIQKMEEDGVIR   48 (162)
T ss_dssp             CSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            38999999999999999999999999999775

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=94.29  E-value=0.025  Score=37.91  Aligned_cols=34  Identities=12%  Similarity=0.205  Sum_probs=31.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ..|+++.+||+.++|++++|++++++..+-|=+.
T Consensus        49 ~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~   82 (151)
T 3kp7_A           49 IEALTVGQITEKQGVNKAAVSRRVKKLLNAELVK   82 (151)
T ss_dssp             HSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEE
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            3579999999999999999999999999999885

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.28  E-value=0.035  Score=36.75  Aligned_cols=35  Identities=11%  Similarity=0.255  Sum_probs=31.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++++.+||+.++|+.++|++++++..+-|-+.-
T Consensus        50 ~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r   84 (146)
T 2fbh_A           50 RDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRR   84 (146)
T ss_dssp             SSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeee
Confidence            35699999999999999999999999998887754

>2ovg_A Phage lambda CRO; transcription factor, helix-turn-helix, bacteriophage, flexi transcription; 1.35A {Enterobacteria phage lambda} PDB: 2ecs_A 1cop_D 4cro_A* 5cro_O 1orc_A 2orc_A 2a63_A 1d1l_A 6cro_A* 3orc_A* 1d1m_B

Probab=94.27  E-value=0.028  Score=32.89  Aligned_cols=21  Identities=10%  Similarity=0.213  Sum_probs=19.5

Q ss_pred             ChhhhHHHhhcchhhHHHHHh
Q psy1904           7 RPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      +...+|+.||||+++||++++
T Consensus        15 s~t~aA~~L~vtQ~AVS~~ir   35 (66)
T 2ovg_A           15 GQTKTAKDLGVYPSSINQAIH   35 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHHHH
Confidence            778999999999999999984

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=94.26  E-value=0.037  Score=37.63  Aligned_cols=35  Identities=14%  Similarity=0.202  Sum_probs=31.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        59 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   93 (162)
T 3k0l_A           59 PNLSNAKLAERSFIKPQSANKILQDLLANGWIEKA   93 (162)
T ss_dssp             TTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEec
Confidence            56999999999999999999999999999988543

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.25  E-value=0.032  Score=37.05  Aligned_cols=35  Identities=17%  Similarity=0.302  Sum_probs=31.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++++.+||+.++|++++|++++++..+.|-+.-
T Consensus        48 ~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r   82 (147)
T 2hr3_A           48 GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR   82 (147)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEee
Confidence            35699999999999999999999999999888743

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=94.25  E-value=0.022  Score=39.71  Aligned_cols=32  Identities=22%  Similarity=0.310  Sum_probs=29.6

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|||.++|.+.|++..+.|-+.
T Consensus        31 ~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~   62 (171)
T 2ia0_A           31 RLTISELSEQLKKPESTIHFRIKKLQERGVIE   62 (171)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            48999999999999999999999998888874

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=94.21  E-value=0.036  Score=35.70  Aligned_cols=24  Identities=21%  Similarity=0.191  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        32 ~~gltq~elA~~~gis~~~is~~E   55 (114)
T 3vk0_A           32 NKGWSQEELARQCGLDRTYVSAVE   55 (114)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999996

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=94.21  E-value=0.01  Score=40.60  Aligned_cols=57  Identities=14%  Similarity=0.160  Sum_probs=40.9

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE   58 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~   58 (163)
                      +...++.++||+.|+||+++|++-|+...+.|-+.-...|...-...++.....+.+
T Consensus        68 ~~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~lt~~~~~~l~~  124 (151)
T 3f6v_A           68 TSGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDGRFRYYRLDPQGLAQLRA  124 (151)
T ss_dssp             GGCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHH
Confidence            444588999999999999999999999999998865544433333344444444434

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=94.20  E-value=0.019  Score=38.91  Aligned_cols=32  Identities=13%  Similarity=0.266  Sum_probs=29.6

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|+|.++|++.+++..+.|-+.
T Consensus        23 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   54 (151)
T 2dbb_A           23 RLTYRELADILNTTRQRIARRIDKLKKLGIIR   54 (151)
T ss_dssp             TCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            48999999999999999999999998888775

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=94.19  E-value=0.039  Score=37.37  Aligned_cols=34  Identities=12%  Similarity=0.292  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+.+.+||+.++|+.++|++++++..+-|=+.-
T Consensus        45 ~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R   78 (151)
T 4aik_A           45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITR   78 (151)
T ss_dssp             TTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEe
Confidence            4688899999999999999999999999998853

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=94.16  E-value=0.018  Score=36.75  Aligned_cols=38  Identities=16%  Similarity=0.107  Sum_probs=32.2

Q ss_pred             ccCCCChhhhHHHh-hcchhhHHHHHhhhhhccCCCCCC
Q psy1904           2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         2 ~~~g~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ...+++..|||+.+ |||+++|++.|++..+.|-+.-..
T Consensus        35 ~~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~   73 (107)
T 2fsw_A           35 NRRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQ   73 (107)
T ss_dssp             TTSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HhCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEee
Confidence            33458999999999 599999999999999999886443

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=94.16  E-value=0.023  Score=32.77  Aligned_cols=27  Identities=0%  Similarity=-0.022  Sum_probs=23.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|-....+|+.||||.+|+++.+++|
T Consensus        30 ~~~gn~~~aA~~LGisr~tL~rklkk~   56 (63)
T 3e7l_A           30 EYDYDLKRTAEEIGIDLSNLYRKIKSL   56 (63)
T ss_dssp             HTTTCHHHHHHHHTCCHHHHHHHHHHT
T ss_pred             HhCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            345677899999999999999999887

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=94.12  E-value=0.031  Score=36.74  Aligned_cols=34  Identities=12%  Similarity=0.235  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        51 ~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r   84 (140)
T 2nnn_A           51 GPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQR   84 (140)
T ss_dssp             SSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999998887753

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=94.12  E-value=0.032  Score=35.43  Aligned_cols=24  Identities=17%  Similarity=0.206  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        12 ~~gltq~~lA~~~gis~~~i~~~e   35 (111)
T 1b0n_A           12 EKGYSLSELAEKAGVAKSYLSSIE   35 (111)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=94.08  E-value=0.047  Score=34.86  Aligned_cols=24  Identities=4%  Similarity=0.117  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        47 ~~glsq~elA~~~gis~~~is~~E   70 (107)
T 2jvl_A           47 EPTMTQAELGKEIGETAATVASYE   70 (107)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            579999999999999999999996

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=94.06  E-value=0.036  Score=38.11  Aligned_cols=25  Identities=4%  Similarity=0.028  Sum_probs=23.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      .|++..+||+.||||.+|+++|.+.
T Consensus        47 ~~lTv~eIA~~LGIS~~TLyrW~k~   71 (155)
T 2ao9_A           47 EKRTQDEMANELGINRTTLWEWRTK   71 (155)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHc
Confidence            3799999999999999999999874

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=94.00  E-value=0.035  Score=35.98  Aligned_cols=24  Identities=8%  Similarity=-0.046  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++|||.++|++|.
T Consensus        18 ~~glSq~eLA~~~gis~~~is~iE   41 (112)
T 2wus_R           18 ERRITLLDASLFTNINPSKLKRIE   41 (112)
T ss_dssp             TTTCCHHHHHHHSSCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999984

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=93.99  E-value=0.078  Score=34.66  Aligned_cols=36  Identities=11%  Similarity=-0.052  Sum_probs=32.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-..
T Consensus        52 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~   87 (127)
T 2frh_A           52 KEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKR   87 (127)
T ss_dssp             SEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBC
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            468999999999999999999999999999886543

>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=93.98  E-value=0.041  Score=35.67  Aligned_cols=27  Identities=19%  Similarity=0.143  Sum_probs=24.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|++..+||+.||||.++|...+.+.
T Consensus        39 ~~g~s~~EIA~~lgiS~~tV~~~l~ra   65 (113)
T 1xsv_A           39 LEDYSLSEIADTFNVSRQAVYDNIRRT   65 (113)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            479999999999999999999998665

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=93.96  E-value=0.045  Score=37.01  Aligned_cols=34  Identities=26%  Similarity=0.352  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        62 ~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r   95 (162)
T 2fa5_A           62 PGSSASEVSDRTAMDKVAVSRAVARLLERGFIRR   95 (162)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEee
Confidence            5699999999999999999999999999988854

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=93.96  E-value=0.016  Score=36.50  Aligned_cols=32  Identities=16%  Similarity=0.263  Sum_probs=27.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++.+|||+.+|+|+++||+-|+...+. -+.
T Consensus        40 ~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~   71 (99)
T 2zkz_A           40 KALNVTQIIQILKLPQSTVSQHLCKMRGK-VLK   71 (99)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhh
Confidence            45889999999999999999999999777 444

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=93.94  E-value=0.044  Score=39.53  Aligned_cols=34  Identities=12%  Similarity=0.185  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.|+||.++|++.+++..+.|=+.-
T Consensus        19 ~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r   52 (214)
T 3hrs_A           19 NKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIK   52 (214)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEE
Confidence            4599999999999999999999999999987743

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=93.92  E-value=0.04  Score=36.26  Aligned_cols=34  Identities=21%  Similarity=0.368  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++||.++|++.+++..+.|-+.-
T Consensus        44 ~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~   77 (142)
T 3bdd_A           44 APLHQLALQERLQIDRAAVTRHLKLLEESGYIIR   77 (142)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999999887743

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=93.91  E-value=0.041  Score=36.11  Aligned_cols=34  Identities=24%  Similarity=0.461  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.+++++++|++++++..+.|=+.-
T Consensus        47 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r   80 (138)
T 1jgs_A           47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVER   80 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999999988854

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=93.90  E-value=0.044  Score=34.51  Aligned_cols=24  Identities=13%  Similarity=0.141  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        39 ~~gltq~elA~~~gis~~~is~iE   62 (99)
T 3g5g_A           39 EKGMTQEDLAYKSNLDRTYISGIE   62 (99)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999996

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=93.90  E-value=0.047  Score=36.52  Aligned_cols=35  Identities=11%  Similarity=0.250  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        53 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~   87 (150)
T 3fm5_A           53 EGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRT   87 (150)
T ss_dssp             TCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-
T ss_pred             CCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            35899999999999999999999999998888543

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=93.87  E-value=0.047  Score=36.92  Aligned_cols=33  Identities=30%  Similarity=0.418  Sum_probs=29.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++++.+||+.|+||.++|++.|++..+.|-+.
T Consensus        53 ~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~   85 (155)
T 2h09_A           53 GEARQVDMAARLGVSQPTVAKMLKRLATMGLIE   85 (155)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEE
T ss_pred             CCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEE
Confidence            458999999999999999999999998888664

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=93.84  E-value=0.039  Score=35.39  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=22.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        20 ~~glsq~~lA~~~gis~~~i~~~e   43 (114)
T 3op9_A           20 EHGLKNHQIAELLNVQTRTVAYYM   43 (114)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999997

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=93.84  E-value=0.031  Score=36.97  Aligned_cols=34  Identities=21%  Similarity=0.362  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        42 ~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r   75 (144)
T 1lj9_A           42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYR   75 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999999888754

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=93.84  E-value=0.033  Score=37.75  Aligned_cols=35  Identities=14%  Similarity=0.122  Sum_probs=31.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+++..||++.++||+++|++.|++..+.|-+.-.
T Consensus        36 g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~   70 (146)
T 2f2e_A           36 GLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAV   70 (146)
T ss_dssp             TCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEE
Confidence            44899999999999999999999999999988543

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=93.81  E-value=0.04  Score=36.70  Aligned_cols=34  Identities=9%  Similarity=0.274  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        55 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r   88 (150)
T 2rdp_A           55 GDLTVGELSNKMYLACSTTTDLVDRMERNGLVAR   88 (150)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeee
Confidence            4689999999999999999999999999887753

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=93.81  E-value=0.031  Score=37.08  Aligned_cols=34  Identities=12%  Similarity=0.047  Sum_probs=31.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r   83 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVR   83 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeec
Confidence            5689999999999999999999999999998853

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=93.75  E-value=0.032  Score=37.76  Aligned_cols=35  Identities=14%  Similarity=0.368  Sum_probs=31.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        63 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   97 (159)
T 3s2w_A           63 DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQ   97 (159)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            56899999999999999999999999999888543

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=93.74  E-value=0.029  Score=37.47  Aligned_cols=36  Identities=11%  Similarity=0.256  Sum_probs=26.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-..
T Consensus        56 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~   91 (148)
T 3jw4_A           56 SGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRI   91 (148)
T ss_dssp             TCCCHHHHHHC------CHHHHHHHHHHTTSBCCC-
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeC
Confidence            579999999999999999999999999999886443

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=93.72  E-value=0.05  Score=35.53  Aligned_cols=24  Identities=8%  Similarity=0.191  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        23 ~~glsq~~lA~~~gis~~~is~~E   46 (126)
T 3ivp_A           23 KQGLTREQVGAMIEIDPRYLTNIE   46 (126)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            379999999999999999999996

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=93.72  E-value=0.047  Score=32.73  Aligned_cols=31  Identities=13%  Similarity=0.349  Sum_probs=28.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +..-+||+.||++...|-+.|..+.+.|-+.
T Consensus        30 ~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~   60 (75)
T 1sfu_A           30 TTAISLSNRLKINKKKINQQLYKLQKEDTVK   60 (75)
T ss_dssp             ECHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence            7788999999999999999999999999884

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=93.70  E-value=0.037  Score=39.32  Aligned_cols=35  Identities=11%  Similarity=0.169  Sum_probs=31.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +.+++..+||+.+|||.++|++.|++..+.|-+.-
T Consensus        31 ~~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~   65 (192)
T 1uly_A           31 NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV   65 (192)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            34589999999999999999999999988888754

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=93.66  E-value=0.035  Score=34.66  Aligned_cols=34  Identities=9%  Similarity=0.173  Sum_probs=30.1

Q ss_pred             CCCChhhh----HHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVI----SRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~i----a~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+|    |+.++|+.++|++++++..+.|=+.-
T Consensus        21 ~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r   58 (99)
T 1tbx_A           21 EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKE   58 (99)
T ss_dssp             TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEE
Confidence            46899999    89999999999999999988887754

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=93.66  E-value=0.047  Score=36.22  Aligned_cols=34  Identities=15%  Similarity=0.100  Sum_probs=31.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        44 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   77 (145)
T 3g3z_A           44 GSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEW   77 (145)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEee
Confidence            4699999999999999999999999999998853

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=93.64  E-value=0.047  Score=36.65  Aligned_cols=34  Identities=6%  Similarity=0.190  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        56 ~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r   89 (155)
T 3cdh_A           56 DAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTR   89 (155)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4699999999999999999999999999988853

>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=93.57  E-value=0.06  Score=33.38  Aligned_cols=26  Identities=19%  Similarity=0.217  Sum_probs=24.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+..+||+.|+||.+||...+.+.
T Consensus        43 ~G~s~~eIA~~L~iS~~TV~~~~~~i   68 (90)
T 3ulq_B           43 KGFTNQEIADALHLSKRSIEYSLTSI   68 (90)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            79999999999999999999998776

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=93.57  E-value=0.042  Score=40.57  Aligned_cols=34  Identities=12%  Similarity=0.179  Sum_probs=31.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..+||+.++++.+||+++|+...+.|=+.-
T Consensus       165 ~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r  198 (244)
T 2wte_A          165 KGTGITELAKMLDKSEKTLINKIAELKKFGILTQ  198 (244)
T ss_dssp             TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5799999999999999999999999999998753

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=93.54  E-value=0.053  Score=34.90  Aligned_cols=24  Identities=29%  Similarity=0.351  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        39 ~~glsq~~lA~~~gis~~~is~~E   62 (117)
T 3f52_A           39 DKGVTLRELAEASRVSPGYLSELE   62 (117)
T ss_dssp             HHTCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999999999999999996

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=93.53  E-value=0.032  Score=42.49  Aligned_cols=23  Identities=26%  Similarity=0.213  Sum_probs=21.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus        11 ~ti~diA~~agVS~~TVSr~Ln~   33 (344)
T 3kjx_A           11 LTLRDVSEASGVSEMTVSRVLRN   33 (344)
T ss_dssp             CCHHHHHHHHCCCSHHHHHHHTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcC
Confidence            67899999999999999999954

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=93.53  E-value=0.05  Score=35.95  Aligned_cols=34  Identities=24%  Similarity=0.364  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        46 ~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r   79 (145)
T 2a61_A           46 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR   79 (145)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeee
Confidence            4689999999999999999999999998887754

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=93.48  E-value=0.052  Score=34.90  Aligned_cols=24  Identities=13%  Similarity=0.203  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        34 ~~gltq~elA~~~gis~~~is~~E   57 (111)
T 3mlf_A           34 DYGLTQKELGDLFKVSSRTIQNME   57 (111)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            469999999999999999999996

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=93.48  E-value=0.047  Score=36.71  Aligned_cols=34  Identities=12%  Similarity=0.200  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        57 ~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r   90 (154)
T 2eth_A           57 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVR   90 (154)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999999888754

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=93.47  E-value=0.039  Score=37.01  Aligned_cols=34  Identities=18%  Similarity=0.281  Sum_probs=30.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        60 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r   93 (153)
T 2pex_A           60 DERSVSEIGERLYLDSATLTPLLKRLQAAGLVTR   93 (153)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEee
Confidence            4589999999999999999999999999887753

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=93.45  E-value=0.048  Score=38.28  Aligned_cols=35  Identities=11%  Similarity=0.208  Sum_probs=31.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        56 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   90 (189)
T 3nqo_A           56 EETTLNNIARKMGTSKQNINRLVANLEKNGYVDVI   90 (189)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            47999999999999999999999999999988543

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=93.40  E-value=0.041  Score=36.74  Aligned_cols=34  Identities=24%  Similarity=0.383  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        53 ~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r   86 (152)
T 3bj6_A           53 PGATAPQLGAALQMKRQYISRILQEVQRAGLIER   86 (152)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence            4689999999999999999999999999988854

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=93.39  E-value=0.053  Score=36.58  Aligned_cols=32  Identities=13%  Similarity=0.281  Sum_probs=28.0

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++++.+||+.++|+.++|++++++..+-|=+.
T Consensus        52 ~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr   83 (148)
T 4fx0_A           52 DLTMSELAARIGVERTTLTRNLEVMRRDGLVR   83 (148)
T ss_dssp             --CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEE
Confidence            38999999999999999999999998888763

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=93.39  E-value=0.037  Score=36.44  Aligned_cols=34  Identities=15%  Similarity=0.305  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        49 ~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r   82 (142)
T 2fbi_A           49 GEMESYQLANQACILRPSMTGVLARLERDGIVRR   82 (142)
T ss_dssp             CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999998887743

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=93.39  E-value=0.049  Score=36.71  Aligned_cols=24  Identities=13%  Similarity=0.199  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        79 ~~glTq~elA~~lGis~s~is~~E  102 (141)
T 3kxa_A           79 KKGFTQSELATAAGLPQPYLSRIE  102 (141)
T ss_dssp             HTTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=93.34  E-value=0.038  Score=37.04  Aligned_cols=35  Identities=20%  Similarity=0.344  Sum_probs=31.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-.
T Consensus        54 ~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   88 (149)
T 4hbl_A           54 NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRE   88 (149)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeC
Confidence            56899999999999999999999999999988543

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=93.34  E-value=0.043  Score=37.62  Aligned_cols=35  Identities=9%  Similarity=0.274  Sum_probs=31.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        67 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~  101 (166)
T 3deu_A           67 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ  101 (166)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEee
Confidence            56999999999999999999999999998888533

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=93.30  E-value=0.044  Score=36.75  Aligned_cols=34  Identities=9%  Similarity=0.221  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        54 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           54 PGISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4589999999999999999999999999888854

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=93.29  E-value=0.038  Score=33.38  Aligned_cols=32  Identities=19%  Similarity=0.187  Sum_probs=29.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..|||+.||||.+||.+-|..+.+.|-+.-
T Consensus        25 psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R   56 (77)
T 2jt1_A           25 VKTRDIADAAGLSIYQVRLYLEQLHDVGVLEK   56 (77)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            56889999999999999999999999999853

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

Probab=93.28  E-value=0.065  Score=33.87  Aligned_cols=28  Identities=21%  Similarity=0.139  Sum_probs=25.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .+|++..|||+.|+||.+||...+.+..
T Consensus        47 ~~G~s~~EIA~~L~iS~~TV~~~l~ri~   74 (99)
T 1p4w_A           47 AEGFLVTEIAKKLNRSIKTISSQKKSAM   74 (99)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3699999999999999999999987763

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=93.25  E-value=0.033  Score=37.08  Aligned_cols=45  Identities=16%  Similarity=0.156  Sum_probs=35.0

Q ss_pred             ccCCCChhhhHHHh-hcchhhHHHHHhhhhhccCCCCCCCCCCCCC
Q psy1904           2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (163)
Q Consensus         2 ~~~g~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~   46 (163)
                      ...+++..+|++.+ |||+++|++.|++..+.|-+.-......++.
T Consensus        45 ~~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~   90 (131)
T 1yyv_A           45 RDGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPH   90 (131)
T ss_dssp             GGCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCE
T ss_pred             HcCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCe
Confidence            33458999999999 7999999999999999998864433333333

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=93.22  E-value=0.077  Score=35.22  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=29.6

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.||||.++|++.|++..+.|-+.
T Consensus        18 ~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   49 (141)
T 1i1g_A           18 RTPFTEIAKKLGISETAVRKRVKALEEKGIIE   49 (141)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            48999999999999999999999999888874

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=93.21  E-value=0.045  Score=37.06  Aligned_cols=34  Identities=21%  Similarity=0.271  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        65 ~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r   98 (162)
T 3cjn_A           65 DGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRR   98 (162)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEe
Confidence            4589999999999999999999999999988853

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=93.16  E-value=0.032  Score=36.59  Aligned_cols=34  Identities=9%  Similarity=0.206  Sum_probs=30.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        46 ~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r   79 (139)
T 3bja_A           46 GKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMT   79 (139)
T ss_dssp             CSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeee
Confidence            4589999999999999999999999999887743

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=93.10  E-value=0.053  Score=39.24  Aligned_cols=27  Identities=11%  Similarity=0.277  Sum_probs=24.2

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ...|+++.++|+.+|||+++|++|++.
T Consensus        27 ~~~g~t~~~lA~~~gis~~~i~~~~~g   53 (236)
T 3bdn_A           27 NELGLSQESVADKMGMGQSGVGALFNG   53 (236)
T ss_dssp             TTTTCCSHHHHHHHTSCHHHHHHHTTT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            457999999999999999999999743

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=93.10  E-value=0.041  Score=34.17  Aligned_cols=27  Identities=11%  Similarity=0.010  Sum_probs=23.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|-...++|+.||||.+|+++.|++|
T Consensus        62 ~~~gn~~~aA~~LGIsr~tL~rklkk~   88 (91)
T 1ntc_A           62 HTQGHKQEAARLLGWGAATLTAKLKEL   88 (91)
T ss_dssp             HTTTCTTHHHHHTTCCHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            345567789999999999999999887

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=93.02  E-value=0.056  Score=32.53  Aligned_cols=34  Identities=15%  Similarity=0.280  Sum_probs=29.8

Q ss_pred             CCCChhhhHHHhh----cchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~----vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.|||+.|+    ++.+||+++|++..+-|-+.-
T Consensus        22 ~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r   59 (82)
T 1p6r_A           22 SSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNH   59 (82)
T ss_dssp             SSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEE
Confidence            4589999999998    699999999999998887753

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=92.99  E-value=0.054  Score=35.90  Aligned_cols=24  Identities=8%  Similarity=0.140  Sum_probs=22.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.|+|+++|||.+++++|.
T Consensus        14 ~~gltq~elA~~~gis~~~is~iE   37 (130)
T 3fym_A           14 RLGMTLTELEQRTGIKREMLVHIE   37 (130)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            379999999999999999999994

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=92.96  E-value=0.052  Score=34.93  Aligned_cols=33  Identities=15%  Similarity=0.211  Sum_probs=29.8

Q ss_pred             CC--hhhhHHHh-hcchhhHHHHHhhhhhccCCCCC
Q psy1904           6 VR--PCVISRQL-RVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         6 ~~--~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+  .+||++.+ |||++++++.|+...+.|=+.-.
T Consensus        41 ~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~   76 (111)
T 3df8_A           41 TRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERR   76 (111)
T ss_dssp             SCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEe
Confidence            56  99999999 99999999999999999988644

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=92.89  E-value=0.054  Score=41.15  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=19.9

Q ss_pred             ChhhhHHHhhcchhhHHHHHhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ...|||+..|||.+|||+.|+.
T Consensus         2 ti~diA~~agVS~~TVSrvLn~   23 (340)
T 1qpz_A            2 TIKDVAKRANVSTTTVSHVINK   23 (340)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCCCHHHHHHHHcC
Confidence            5679999999999999999963

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=92.88  E-value=0.073  Score=30.26  Aligned_cols=26  Identities=15%  Similarity=0.129  Sum_probs=23.0

Q ss_pred             CCCChhhhHHHh-----hcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQL-----RVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~   29 (163)
                      ..++..||++.|     +||.+||++.|+..
T Consensus        18 ~~~t~~el~~~l~~~~~~vs~~Tv~R~L~~l   48 (64)
T 2p5k_A           18 EIETQDELVDMLKQDGYKVTQATVSRDIKEL   48 (64)
T ss_dssp             CCCSHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhCCCcCHHHHHHHHHHc
Confidence            348999999999     99999999999843

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=92.78  E-value=0.02  Score=39.22  Aligned_cols=24  Identities=13%  Similarity=0.185  Sum_probs=0.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.+||+.+|||.++|++|.
T Consensus        12 ~~gltq~elA~~lgis~~~vs~~e   35 (158)
T 2p5t_A           12 THDLTQLEFARIVGISRNSLSRYE   35 (158)
T ss_dssp             ------------------------
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            478999999999999999999994

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=92.77  E-value=0.042  Score=36.97  Aligned_cols=35  Identities=17%  Similarity=0.227  Sum_probs=31.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++++.+||+.++|+.++|++++++..+.|=+.-..
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~   85 (147)
T 4b8x_A           51 ELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRP   85 (147)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEee
Confidence            38999999999999999999999999999885443

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=92.68  E-value=0.077  Score=33.00  Aligned_cols=24  Identities=8%  Similarity=0.126  Sum_probs=22.0

Q ss_pred             cCCCChhhhHHHhhcchhh----HHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGC----VSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~----vs~~l   26 (163)
                      ..|+++.++|+.+|||.++    |++|.
T Consensus        12 ~~glsq~~lA~~~gis~~~~~~~is~~E   39 (98)
T 3lfp_A           12 RAGISQEKLGVLAGIDEASASARMNQYE   39 (98)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCcchhhhHHHHHH
Confidence            3689999999999999999    99986

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=92.65  E-value=0.041  Score=37.34  Aligned_cols=35  Identities=6%  Similarity=0.080  Sum_probs=31.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.=.
T Consensus        66 ~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~  100 (161)
T 3e6m_A           66 GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARS  100 (161)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            46899999999999999999999999999988533

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=92.64  E-value=0.045  Score=36.68  Aligned_cols=34  Identities=15%  Similarity=0.302  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        50 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r   83 (155)
T 1s3j_A           50 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIAR   83 (155)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEee
Confidence            4588999999999999999999999999887743

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=92.61  E-value=0.038  Score=36.63  Aligned_cols=31  Identities=10%  Similarity=0.314  Sum_probs=28.6

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++.+||+.++|+.++|++++++..+.|-+.=
T Consensus        52 ~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r   82 (144)
T 3f3x_A           52 SMVYLANRYFVTQSAITAAVDKLEAKGLVRR   82 (144)
T ss_dssp             EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHCCChhHHHHHHHHHHHCCCEEe
Confidence            8999999999999999999999999888753

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=92.59  E-value=0.055  Score=40.90  Aligned_cols=23  Identities=30%  Similarity=0.388  Sum_probs=20.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+..|||.+|||+.|+.
T Consensus         3 ~ti~dvA~~agVS~~TVSrvln~   25 (332)
T 2hsg_A            3 VTIYDVAREASVSMATVSRVVNG   25 (332)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Confidence            56789999999999999999954

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=92.55  E-value=0.057  Score=36.98  Aligned_cols=34  Identities=12%  Similarity=0.213  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++++++..+.|=+.-
T Consensus        58 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r   91 (168)
T 2nyx_A           58 GPINLATLATLLGVQPSATGRMVDRLVGAELIDR   91 (168)
T ss_dssp             CSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            4689999999999999999999999999988853

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=92.53  E-value=0.017  Score=37.91  Aligned_cols=28  Identities=29%  Similarity=0.348  Sum_probs=24.5

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      |-+.|+++.++|+.+|||+++|++|.+-
T Consensus         1 lR~~glTQ~eLA~~~Gvs~~~is~~E~G   28 (122)
T 1nr3_A            1 MRERGWSQKKIARELKTTRQNVSAIERK   28 (122)
T ss_dssp             CCCCSCSSCSTHHHHHHCCSSSCCHHHH
T ss_pred             CcccCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            3458999999999999999999999754

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=92.50  E-value=0.063  Score=33.82  Aligned_cols=32  Identities=22%  Similarity=0.233  Sum_probs=29.1

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +..+||+.|+||.++|++-|+.+.+.|-+.-.
T Consensus        37 s~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           37 SVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            78899999999999999999999999988543

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=92.46  E-value=0.1  Score=34.26  Aligned_cols=38  Identities=16%  Similarity=0.345  Sum_probs=30.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC--CCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P--g~~Gg~   43 (163)
                      ++..+||+.++|+.++|.++|....+.|=+.-  |..||-
T Consensus        27 ~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~g~~ggy   66 (129)
T 2y75_A           27 TSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIRGAYGGY   66 (129)
T ss_dssp             BCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC----CCE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecCCCCCce
Confidence            78899999999999999999999999997743  434544

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=92.40  E-value=0.041  Score=39.44  Aligned_cols=35  Identities=26%  Similarity=0.246  Sum_probs=31.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +.+++.++||+.++||+++|+..|+...+.|-+.-
T Consensus        26 ~~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~   60 (202)
T 2p4w_A           26 KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIES   60 (202)
T ss_dssp             HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence            35588999999999999999999999999998854

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=92.34  E-value=0.047  Score=36.03  Aligned_cols=34  Identities=24%  Similarity=0.357  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++++.+||+.++|+.++|++.+++..+.|-+.-
T Consensus        50 ~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r   83 (142)
T 2bv6_A           50 SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKR   83 (142)
T ss_dssp             SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEe
Confidence            3488999999999999999999999999888854

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=92.30  E-value=0.084  Score=35.84  Aligned_cols=28  Identities=14%  Similarity=0.169  Sum_probs=25.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .+|++..|||+.||||.++|...|.+-+
T Consensus       107 ~~g~s~~EIA~~lgis~~tV~~~l~rar  134 (157)
T 2lfw_A          107 MEGFSPEDAAYLIEVDTSEVETLVTEAL  134 (157)
T ss_dssp             SSCCCHHHHHHTTTSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4799999999999999999999997653

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=92.29  E-value=0.031  Score=36.26  Aligned_cols=33  Identities=21%  Similarity=0.371  Sum_probs=30.7

Q ss_pred             CCChhhhHHHh--hcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQL--RVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~--~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++.+||+.+  +||..+|++-|+...+.|-+..
T Consensus        27 ~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~   61 (111)
T 3b73_A           27 NGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQP   61 (111)
T ss_dssp             CBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEe
Confidence            48999999999  9999999999999999998864

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=92.17  E-value=0.026  Score=42.76  Aligned_cols=28  Identities=21%  Similarity=0.216  Sum_probs=0.0

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ...-++..|||+.+|||.+|||+.|+..
T Consensus         2 ~~~~~ti~diA~~agVS~~TVSrvln~~   29 (332)
T 2o20_A            2 VESTTTIYDVARVAGVSMATVSRVVNGN   29 (332)
T ss_dssp             ----------------------------
T ss_pred             CCCCCcHHHHHHHHCCCHHHHHHHHcCC
Confidence            3444778999999999999999999753

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=92.15  E-value=0.052  Score=37.09  Aligned_cols=35  Identities=14%  Similarity=0.310  Sum_probs=28.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-.
T Consensus        61 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   95 (168)
T 3u2r_A           61 EGMATLQIADRLISRAPDITRLIDRLDDRGLVLRT   95 (168)
T ss_dssp             SCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeec
Confidence            47999999999999999999999999998888543

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=92.13  E-value=0.043  Score=37.03  Aligned_cols=34  Identities=29%  Similarity=0.450  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        61 ~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r   94 (160)
T 3boq_A           61 DGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVK   94 (160)
T ss_dssp             TCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEE
T ss_pred             CCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEe
Confidence            5699999999999999999999999999888853

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=92.13  E-value=0.041  Score=36.55  Aligned_cols=35  Identities=20%  Similarity=0.333  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++++.+||+.++|+.++|++++++..+.|-+.-.
T Consensus        53 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~   87 (147)
T 1z91_A           53 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRK   87 (147)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECC
T ss_pred             CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEec
Confidence            35889999999999999999999999998888543

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=92.11  E-value=0.053  Score=39.45  Aligned_cols=34  Identities=32%  Similarity=0.489  Sum_probs=30.5

Q ss_pred             CCCCh--hhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRP--CVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~--~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++  .+||+.|+||.++|++.|++..+.|-+.-
T Consensus        21 ~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r   56 (230)
T 1fx7_A           21 EGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRV   56 (230)
T ss_dssp             HTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            47888  99999999999999999999999987743

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=91.96  E-value=0.11  Score=38.54  Aligned_cols=34  Identities=3%  Similarity=0.028  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.+|++.+||+++|+.+.+.|-+.-
T Consensus        37 ~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~   70 (260)
T 2o0y_A           37 PTRSLKELVEGTKLPKTTVVRLVATMCARSVLTS   70 (260)
T ss_dssp             SSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5799999999999999999999999999887754

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=91.92  E-value=0.058  Score=39.14  Aligned_cols=33  Identities=30%  Similarity=0.453  Sum_probs=29.4

Q ss_pred             CCCCh--hhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRP--CVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~--~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .|+.+  .+||+.|+|+.++|++++++..+.|=+.
T Consensus        21 ~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~   55 (226)
T 2qq9_A           21 EGVTPLRARIAERLEQSGPTVSQTVARMERDGLVV   55 (226)
T ss_dssp             HTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            46666  9999999999999999999999888774

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=91.86  E-value=0.063  Score=41.20  Aligned_cols=23  Identities=30%  Similarity=0.307  Sum_probs=20.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +...|||+.+|||.+|||+.|+.
T Consensus        10 ~Ti~diA~~aGVS~~TVSrvLn~   32 (366)
T 3h5t_A           10 GTLASIAAKLGISRTTVSNAYNR   32 (366)
T ss_dssp             THHHHHHHHHTSCHHHHHHHHHC
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCC
Confidence            56789999999999999999964

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=91.86  E-value=0.094  Score=38.02  Aligned_cols=32  Identities=22%  Similarity=0.322  Sum_probs=28.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      .|++..++|+.|+||+++||+.+++..+.|=+
T Consensus        26 ~~~s~s~aA~~L~isq~avSr~I~~LE~~~L~   57 (230)
T 3cta_A           26 AYLTSSKLADMLGISQQSASRIIIDLEKNGYI   57 (230)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            45889999999999999999999999885544

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=91.84  E-value=0.076  Score=34.28  Aligned_cols=35  Identities=14%  Similarity=0.156  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhh----cchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~----vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++++.+||+.++    |+.+||+++|++..+-|-+.-.
T Consensus        23 ~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~   61 (123)
T 1okr_A           23 KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRK   61 (123)
T ss_dssp             SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEE
Confidence            4689999999999    8899999999999998888543

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=91.83  E-value=0.12  Score=38.21  Aligned_cols=33  Identities=18%  Similarity=0.226  Sum_probs=29.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..|||+.+|++.+||+++|+.+.+.|-+.
T Consensus        28 ~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~   60 (257)
T 2g7u_A           28 PNPTLAELATEAGLSRPAVRRILLTLQKLGYVA   60 (257)
T ss_dssp             SSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            469999999999999999999999998888774

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=91.82  E-value=0.12  Score=32.72  Aligned_cols=33  Identities=12%  Similarity=0.299  Sum_probs=29.6

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +..+||+.|+||.++|.+-|+.+.+.|-+.-..
T Consensus        45 s~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           45 VASKIADRVGITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            788999999999999999999999999885443

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=91.61  E-value=0.033  Score=42.34  Aligned_cols=23  Identities=13%  Similarity=0.036  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus         7 ~ti~diA~~agVS~~TVSr~Ln~   29 (333)
T 3jvd_A            7 SSLKEVAELAGVGYATASRALSG   29 (333)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            67889999999999999999963

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=91.60  E-value=0.11  Score=38.07  Aligned_cols=34  Identities=18%  Similarity=0.167  Sum_probs=30.7

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +++..|||+.+|++.+||+++|+.+.+.|-+.-.
T Consensus        23 ~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           23 DVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            5899999999999999999999999998887543

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=91.55  E-value=0.041  Score=38.18  Aligned_cols=33  Identities=30%  Similarity=0.382  Sum_probs=30.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      |+++.+||+.++|+.++|++++++..+.|-+.-
T Consensus        86 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r  118 (181)
T 2fbk_A           86 GLRPTELSALAAISGPSTSNRIVRLLEKGLIER  118 (181)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEe
Confidence            599999999999999999999999999888753

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=91.47  E-value=0.13  Score=36.48  Aligned_cols=32  Identities=19%  Similarity=0.319  Sum_probs=27.7

Q ss_pred             CCC--ChhhhHHHhhcc-hhhHHHHHhhhhhccCC
Q psy1904           4 AGV--RPCVISRQLRVS-HGCVSKILNRYQETGSI   35 (163)
Q Consensus         4 ~g~--~~~~ia~~~~vs-~~~vs~~l~~~~~tG~~   35 (163)
                      .|+  ++.++|+.+||+ +++|++|++...+.|-+
T Consensus        22 ~g~~ps~~elA~~lgiss~~tv~~~~~~l~~~~~l   56 (202)
T 1jhf_A           22 TGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVI   56 (202)
T ss_dssp             HSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSE
T ss_pred             hCCCccHHHHHHHhCCCChHHHHHHHHHHHHCCCc
Confidence            588  899999999999 99999999988765544

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=91.45  E-value=0.089  Score=38.53  Aligned_cols=33  Identities=18%  Similarity=0.335  Sum_probs=30.1

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +++..|||+.+|++.+||+++|+.+.+.|=+.-
T Consensus        21 ~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~   53 (241)
T 2xrn_A           21 GLSLAAIAQLVGLPRSTVQRIINALEEEFLVEA   53 (241)
T ss_dssp             CEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            589999999999999999999999998887743

>1x2l_A CUT-like 2, homeobox protein CUX-2; CUT domain, human homeobox protein CUX-2, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=91.36  E-value=0.067  Score=34.03  Aligned_cols=33  Identities=27%  Similarity=0.337  Sum_probs=26.0

Q ss_pred             cCCCChhhhHH-HhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAGVRPCVISR-QLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ..++++...|+ +||+|+++++.+|...+....+
T Consensus        32 ~~~isQ~~FA~~VLgrsQgtlS~lL~~PkpW~~L   65 (101)
T 1x2l_A           32 KHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKL   65 (101)
T ss_dssp             HTTCCHHHHHHHTTCSCHHHHHHHHHCCCCGGGC
T ss_pred             HcCCCHHHHHHHHHccccchHHHHhcCCCCHHHH
Confidence            46788889998 6999999999999765444443

>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15

Probab=91.28  E-value=0.11  Score=36.44  Aligned_cols=24  Identities=17%  Similarity=0.170  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        22 ~~gltq~~lA~~~gis~~~is~~e   45 (192)
T 1y9q_A           22 SRGLSLDATAQLTGVSKAMLGQIE   45 (192)
T ss_dssp             HTTCCHHHHHHHHSSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=91.26  E-value=0.12  Score=35.72  Aligned_cols=39  Identities=21%  Similarity=0.341  Sum_probs=33.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSK   44 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~   44 (163)
                      ++..+||+.++||...|.|++...++.|-+.  .|..||-.
T Consensus        29 ~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~rG~~GGy~   69 (162)
T 3k69_A           29 VASRELAQSLHLNPVMIRNILSVLHKHGYLTGTVGKNGGYQ   69 (162)
T ss_dssp             BCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEECSTTCEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeE
Confidence            7899999999999999999999999999884  35556553

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=91.22  E-value=0.36  Score=28.97  Aligned_cols=66  Identities=14%  Similarity=0.126  Sum_probs=39.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHH---HHHHhCCCCCchhhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIE---EYKKTNPNITSWEVRDKLI   76 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~---~~~~~~p~~~~~e~~~~l~   76 (163)
                      -+++.|+|+.+|||..|+..|-+.   .|-+.|...  +|.+  .=+......+.   .+.. .-+++..+++.-+.
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~~---~gl~~p~r~~~~g~R--~Y~~~dl~~l~~I~~l~~-~~G~sl~ei~~~l~   75 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWERR---YGFPRPLRSEGNNYR--VYSREEVEAVRRVARLIQ-EEGLSVSEAIAQVK   75 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHHH---TCCSCCBSSSCSSSC--EECHHHHHHHHHHHHHHH-HTSTHHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHh---CCCCCCcCCCCCCee--ecCHHHHHHHHHHHHHHH-HCCCCHHHHHHHHH
Confidence            467899999999999999988643   266666543  3332  23333443332   3221 23566666665554

>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12

Probab=91.11  E-value=0.13  Score=29.33  Aligned_cols=23  Identities=26%  Similarity=0.492  Sum_probs=20.8

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ...++|+.||||.+|+++.+++|
T Consensus        35 n~~~aA~~LGIsr~tL~rklkk~   57 (61)
T 1g2h_A           35 STRKLAQRLGVSHTAIANKLKQY   57 (61)
T ss_dssp             SHHHHHHHTTSCTHHHHHHHHTT
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHh
Confidence            56789999999999999999887

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=91.11  E-value=0.082  Score=37.44  Aligned_cols=31  Identities=19%  Similarity=0.185  Sum_probs=28.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+..|||+.||+|.++|++.|+...+.|-+.
T Consensus        25 ~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~   55 (196)
T 3k2z_A           25 PSVREIARRFRITPRGALLHLIALEKKGYIE   55 (196)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHcCCCcHHHHHHHHHHHHCCCEE
Confidence            6888999999999999999999999999874

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=90.98  E-value=0.16  Score=32.06  Aligned_cols=26  Identities=12%  Similarity=0.144  Sum_probs=23.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+..|||..+|||.++|..++.+-
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rA   63 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKA   63 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            67999999999999999999998553

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=90.83  E-value=0.23  Score=31.22  Aligned_cols=32  Identities=13%  Similarity=0.205  Sum_probs=29.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++.+||++++++.+++++.|.+....|=+.
T Consensus        36 ~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~   67 (96)
T 2obp_A           36 PWSLPKIAKRAQLPMSVLRRVLTQLQAAGLAD   67 (96)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHhCCchhhHHHHHHHHHHCCCEE
Confidence            38999999999999999999999998888774

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=90.69  E-value=0.1  Score=38.67  Aligned_cols=34  Identities=15%  Similarity=0.271  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+++..|||+.+|++.+||+++|+.+.+.|=+.-
T Consensus        20 ~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~   53 (260)
T 3r4k_A           20 LEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQ   53 (260)
T ss_dssp             SEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4589999999999999999999999999998854

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=90.69  E-value=0.11  Score=36.37  Aligned_cols=36  Identities=8%  Similarity=0.148  Sum_probs=31.2

Q ss_pred             CccCCCChhhhHHHhh-cchhhHHHHHhhhhhccCCC
Q psy1904           1 MAAAGVRPCVISRQLR-VSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~-vs~~~vs~~l~~~~~tG~~~   36 (163)
                      |++.+...|+||+.|+ +++++||.=|+..++.|-+.
T Consensus        32 L~~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~aglv~   68 (182)
T 4g6q_A           32 LIGRSLTTRELAELLPDVATTTLYRQVGILVKAGVLM   68 (182)
T ss_dssp             TTTSCEEHHHHHHHCTTBCHHHHHHHHHHHHHHTSEE
T ss_pred             HHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCeE
Confidence            4566689999999996 99999999999998888774

>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A

Probab=90.67  E-value=0.14  Score=35.99  Aligned_cols=24  Identities=8%  Similarity=0.022  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        21 ~~g~s~~~la~~~gis~~~ls~~e   44 (198)
T 2bnm_A           21 QVKMDHAALASLLGETPETVAAWE   44 (198)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999997

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=90.33  E-value=0.15  Score=33.88  Aligned_cols=45  Identities=13%  Similarity=0.158  Sum_probs=35.4

Q ss_pred             ccCCCChhhhHHHh-hcchhhHHHHHhhhhhccCCCCCCCCCCCCC
Q psy1904           2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (163)
Q Consensus         2 ~~~g~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~   46 (163)
                      +...++..||++.+ +||.+++++.|++..+.|=+.-......++.
T Consensus        36 ~~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~   81 (131)
T 4a5n_A           36 IDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPK   81 (131)
T ss_dssp             TTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCE
T ss_pred             hcCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCCe
Confidence            33458999999999 9999999999999999998864443433333

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=90.30  E-value=0.14  Score=34.54  Aligned_cols=39  Identities=21%  Similarity=0.353  Sum_probs=33.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSK   44 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~   44 (163)
                      ++..+||+.++|+..+|.++|....+.|-+.  .|..||-.
T Consensus        29 ~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy~   69 (143)
T 3t8r_A           29 ISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVRGAKGGYQ   69 (143)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECSSSSSEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecCCCCCCee
Confidence            7889999999999999999999999999884  56556653

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=90.25  E-value=0.13  Score=38.14  Aligned_cols=33  Identities=12%  Similarity=0.153  Sum_probs=29.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..|||+.+|++.+||+++|+.+.+.|-+.
T Consensus        35 ~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~   67 (265)
T 2ia2_A           35 QRRTLSDVARATDLTRATARRFLLTLVELGYVA   67 (265)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            468999999999999999999999998887664

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=90.25  E-value=0.24  Score=31.76  Aligned_cols=27  Identities=15%  Similarity=0.070  Sum_probs=24.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+|.+..+||+.+|+|.+||+|+-+-+
T Consensus        56 ~~G~SyreIa~~tG~StaTIsRv~r~L   82 (107)
T 3frw_A           56 TDKRTYLDISEKTGASTATISRVNRSL   82 (107)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCccHHHHHHHHHHH
Confidence            479999999999999999999987554

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=90.24  E-value=0.1  Score=34.08  Aligned_cols=27  Identities=15%  Similarity=0.218  Sum_probs=23.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..+||+.+|+|.+||++.-+-.
T Consensus        73 ~~G~syreIA~~~g~S~aTIsRv~r~L   99 (119)
T 3kor_A           73 KQGYTYATIEQESGASTATISRVKRSL   99 (119)
T ss_dssp             HHTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            468999999999999999999976544

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=90.14  E-value=0.2  Score=33.02  Aligned_cols=34  Identities=18%  Similarity=0.235  Sum_probs=30.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+.++.+||+++++|.++|.+.|+.+.+-|-+.-
T Consensus        50 ~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~   83 (128)
T 2vn2_A           50 LFPTPAELAERMTVSAAECMEMVRRLLQKGMIAI   83 (128)
T ss_dssp             SSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3489999999999999999999999999887743

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=90.05  E-value=0.057  Score=41.01  Aligned_cols=23  Identities=30%  Similarity=0.314  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus         5 ~ti~diA~~agVS~~TVSr~Ln~   27 (339)
T 3h5o_A            5 VTMHDVAKAAGVSAITVSRVLNQ   27 (339)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Confidence            67889999999999999999964

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=89.97  E-value=0.15  Score=34.21  Aligned_cols=26  Identities=12%  Similarity=0.162  Sum_probs=24.3

Q ss_pred             CCCChhhhHHHhhc-chhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRV-SHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~v-s~~~vs~~l~~~   29 (163)
                      .|.+..+|++.+|| |.+||++|+...
T Consensus        27 ~G~sl~~i~~~~~~ps~~T~~~W~~~~   53 (140)
T 4dyq_A           27 SGESLLKVCKRPGMPDKSTVFRWLAKH   53 (140)
T ss_dssp             TTCCHHHHHTSTTCCCHHHHHHHHHHC
T ss_pred             CCCcHHHHHhcCCCCCHHHHHHHHHcC
Confidence            79999999999999 999999999775

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=89.97  E-value=0.25  Score=33.31  Aligned_cols=37  Identities=16%  Similarity=0.335  Sum_probs=30.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~   43 (163)
                      ++..+||+.++|+..+|.+++....+.|-+.  .| .||-
T Consensus        31 ~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG-~GGy   69 (149)
T 1ylf_A           31 CTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG-PGGA   69 (149)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----CCE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC-CCce
Confidence            7889999999999999999999999999874  35 5554

>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein STRU initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1

Probab=89.94  E-value=0.18  Score=35.17  Aligned_cols=24  Identities=17%  Similarity=0.091  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.++|+.||||++++++|.
T Consensus       101 ~~glTQ~elA~~LGvsr~tis~yE  124 (170)
T 2auw_A          101 RNNLSLTTAAEALGISRRMVSYYR  124 (170)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            479999999999999999999996

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=89.91  E-value=0.23  Score=31.87  Aligned_cols=32  Identities=19%  Similarity=0.130  Sum_probs=28.7

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      +..++|+.||||.++|.+.|......|-+.-.
T Consensus        35 s~~~La~~~~vSr~tvr~al~~L~~~Gli~~~   66 (113)
T 3tqn_A           35 SIRKISTEYQINPLTVSKAYQSLLDDNVIEKR   66 (113)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            56799999999999999999999999988544

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=89.90  E-value=0.13  Score=36.71  Aligned_cols=59  Identities=12%  Similarity=0.020  Sum_probs=39.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHHHHHh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEEYKKT   62 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~~~~~   62 (163)
                      .|+++.+||+.++|+.++|++++++..+-|=+.-......+..   ..++.-...+......
T Consensus        61 ~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~  122 (207)
T 2fxa_A           61 NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEE  122 (207)
T ss_dssp             TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHHHHHH
Confidence            4689999999999999999999999999998854332222211   3445555555444433

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=89.89  E-value=0.06  Score=40.82  Aligned_cols=23  Identities=22%  Similarity=0.316  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      +...|||+..|||.+|||+.|+.
T Consensus         4 ~ti~diA~~agVS~~TVSrvln~   26 (338)
T 3dbi_A            4 TTMLEVAKRAGVSKATVSRVLSG   26 (338)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHCC
Confidence            45789999999999999999964

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=89.85  E-value=0.06  Score=41.63  Aligned_cols=34  Identities=9%  Similarity=0.174  Sum_probs=0.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.|||+.|+||.+||++.|++..+.|-+.-
T Consensus        33 ~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~   66 (345)
T 2o0m_A           33 QPIGRRSLSETMGITERVLRTETDVLKQLNLIEP   66 (345)
T ss_dssp             ----------------------------------
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5799999999999999999999999999998853

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=89.62  E-value=0.2  Score=34.48  Aligned_cols=38  Identities=16%  Similarity=0.376  Sum_probs=33.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~   43 (163)
                      ++..+||+.++|+...|.++|....+.|-+.  .|..||-
T Consensus        45 ~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy   84 (159)
T 3lwf_A           45 ISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRGAHGGY   84 (159)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSTTCEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCCCce
Confidence            7899999999999999999999999999885  4555654

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=89.61  E-value=0.065  Score=41.02  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus        13 ~ti~diA~~agVS~~TVSr~Ln~   35 (355)
T 3e3m_A           13 VTMRDVAKAAGVSRMTVSRALKK   35 (355)
T ss_dssp             -----------------------
T ss_pred             CcHHHHHHHhCCCHHHHHHHHCC
Confidence            56789999999999999999963

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=89.59  E-value=0.065  Score=40.97  Aligned_cols=23  Identities=26%  Similarity=0.153  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.+|||.+|||+.|+.
T Consensus         9 ~ti~dvA~~aGVS~~TVSrvLn~   31 (348)
T 3bil_A            9 PTLKDVARQAGVSIATASRALAD   31 (348)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
Confidence            47889999999999999999975

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=89.57  E-value=0.81  Score=29.01  Aligned_cols=66  Identities=12%  Similarity=0.026  Sum_probs=40.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      ++++.|+|+.+|||..|+..|-    +.|-+.|..  .+|.+  .=+......+..... ..-+++..++..-+.
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye----~~Gll~p~~r~~~g~R--~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~   69 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYD----DIGLLVPSERSHAGHR--RYSDADLDRLQQILFYRELGFPLDEVAALLD   69 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHH----HHTSSCCSEECSSCCE--EBCHHHHHHHHHHHHHHHTTCCHHHHHHHHT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCe--ecCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            4688999999999999999885    348888754  24433  233444433322221 123566666665543

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=89.56  E-value=0.065  Score=40.93  Aligned_cols=24  Identities=25%  Similarity=0.229  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +...|||+.+|||.+|||+.|+..
T Consensus         4 ~ti~diA~~aGVS~~TVSrvLn~~   27 (349)
T 1jye_A            4 VTLYDVAEYAGVSYQTVSRVVNQA   27 (349)
T ss_dssp             ------------------------
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Confidence            467899999999999999999754

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=89.54  E-value=0.15  Score=35.88  Aligned_cols=27  Identities=15%  Similarity=0.230  Sum_probs=23.9

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.++.+||++||+|.++|+++|.-.
T Consensus        50 ~~G~t~eeiA~~lG~s~s~V~~~LrLl   76 (178)
T 1r71_A           50 AKGKKKGDIAKEIGKSPAFITQHVTLL   76 (178)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            358999999999999999999998553

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=89.47  E-value=0.25  Score=34.38  Aligned_cols=32  Identities=16%  Similarity=0.248  Sum_probs=29.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  178 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIRS  178 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            67899999999999999999999999998863

>1wh8_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=89.34  E-value=0.13  Score=33.16  Aligned_cols=33  Identities=18%  Similarity=0.289  Sum_probs=26.5

Q ss_pred             cCCCChhhhHH-HhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAGVRPCVISR-QLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ..++++...|+ +||+++++|+.+|...+....+
T Consensus        42 ~~~isQ~~FA~~ILgrsQgtlSdlL~~PkpW~~L   75 (111)
T 1wh8_A           42 DNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKL   75 (111)
T ss_dssp             HTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTS
T ss_pred             HCCCcHHHHHHHHhccCcCcHHHHHcCCCCHHHH
Confidence            46788999999 9999999999999775444443

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=89.30  E-value=0.07  Score=40.32  Aligned_cols=24  Identities=25%  Similarity=0.227  Sum_probs=0.0

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ++..|||+.+|||.+|||+.|+..
T Consensus         3 ~ti~diA~~agVS~~TVSrvln~~   26 (330)
T 3ctp_A            3 ANIREIAKRAGISIATVSRHLNNT   26 (330)
T ss_dssp             ------------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCC
Confidence            357899999999999999999753

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=89.28  E-value=0.26  Score=34.59  Aligned_cols=33  Identities=15%  Similarity=0.325  Sum_probs=29.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      -++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  201 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVKL  201 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            367899999999999999999999999998853

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=89.26  E-value=0.28  Score=35.10  Aligned_cols=59  Identities=17%  Similarity=0.172  Sum_probs=44.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNI   66 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~   66 (163)
                      ..++..+||+.|+||.++|+..+++..+.|-+.-.. +|   -..|+.-.+....+.+.+...
T Consensus        29 ~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~~-~G---v~LTe~G~~~A~~i~~rhr~~   87 (200)
T 2p8t_A           29 EPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ-RG---HFLTLKGKEIRDKLLSMFSEP   87 (200)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---C---EEECHHHHHHHHHHHTTBCCC
T ss_pred             CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC-CC---eEECHHHHHHHHHHHHHHHHh
Confidence            458899999999999999999999999999885544 33   345666666666666655543

>1wh6_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=89.19  E-value=0.17  Score=32.13  Aligned_cols=28  Identities=32%  Similarity=0.479  Sum_probs=24.3

Q ss_pred             ccCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      ...++++...|+ +||+++++++.+|...
T Consensus        31 ~~~~isQ~~FA~~ILgrsqgtlSdlL~~P   59 (101)
T 1wh6_A           31 AKNGICQRIFGEKVLGLSQGSVSDMLSRP   59 (101)
T ss_dssp             HTTTCCHHHHHHHTTCCCHHHHHHHHHSC
T ss_pred             HHcCCcHHHHHHHHHccCcCcHHHHhcCC
Confidence            356789999999 9999999999999664

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=89.16  E-value=0.17  Score=37.87  Aligned_cols=35  Identities=11%  Similarity=0.178  Sum_probs=29.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+++..|||+.+|++.+||+++|..+.+.|=+.-.
T Consensus        44 ~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~   78 (275)
T 3mq0_A           44 RDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARS   78 (275)
T ss_dssp             SCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            45889999999999999999999999999988543

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=89.14  E-value=0.27  Score=34.39  Aligned_cols=32  Identities=25%  Similarity=0.365  Sum_probs=29.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       164 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  195 (216)
T 4ev0_A          164 IRHHELAALAGTSRETVSRVLHALAEEGVVRL  195 (216)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            67899999999999999999999999998863

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=88.94  E-value=0.3  Score=32.08  Aligned_cols=33  Identities=15%  Similarity=0.081  Sum_probs=29.3

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +-.++|+.||||..+|.+-|..+...|-+.-.+
T Consensus        37 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   69 (126)
T 3by6_A           37 SVRETALQEKINPNTVAKAYKELEAQKVIRTIP   69 (126)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            678999999999999999999999999885443

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=88.92  E-value=0.18  Score=33.08  Aligned_cols=33  Identities=18%  Similarity=0.186  Sum_probs=29.3

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +..++|+.||||..+|.+.|..+...|-+...+
T Consensus        39 s~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   71 (125)
T 3neu_A           39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKR   71 (125)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEec
Confidence            478999999999999999999999999886543

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=88.88  E-value=0.39  Score=32.24  Aligned_cols=38  Identities=24%  Similarity=0.253  Sum_probs=32.6

Q ss_pred             CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      ..+++.||...|     +||.+||++.|+.+.+.|-+.--..+
T Consensus        36 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~   78 (145)
T 2fe3_A           36 AHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYG   78 (145)
T ss_dssp             SCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeC
Confidence            458999999999     89999999999999999988654443

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=88.82  E-value=0.24  Score=32.00  Aligned_cols=34  Identities=18%  Similarity=0.274  Sum_probs=29.9

Q ss_pred             CCCChhhhHHHhh----cchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~----vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.|||+.|+    ++.+||+.+|++..+-|=+.=
T Consensus        23 ~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R   60 (126)
T 1sd4_A           23 KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKR   60 (126)
T ss_dssp             SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEE
Confidence            4689999999998    599999999999988888753

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=88.79  E-value=0.24  Score=32.83  Aligned_cols=35  Identities=11%  Similarity=0.068  Sum_probs=31.0

Q ss_pred             CCCChhhhHHHhh----cchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~----vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++++.||++.|+    |+.+||+++|++..+-|-+.=-
T Consensus        23 ~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~   61 (138)
T 2g9w_A           23 EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI   61 (138)
T ss_dssp             SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEE
Confidence            4699999999998    8999999999999998888543

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=88.78  E-value=0.32  Score=33.16  Aligned_cols=31  Identities=3%  Similarity=0.014  Sum_probs=29.3

Q ss_pred             CChhhhHHHhh-cchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLR-VSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~-vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ...++|+..++ ||++||++-|+.+.+.|-+.
T Consensus        46 ~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~   77 (151)
T 3u1d_A           46 LSVEELLYRNPDETEANLRYHVDELVDRGIVE   77 (151)
T ss_dssp             BCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeE
Confidence            68899999999 99999999999999999986

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=88.73  E-value=0.3  Score=34.66  Aligned_cols=32  Identities=19%  Similarity=0.214  Sum_probs=29.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       176 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  207 (231)
T 3e97_A          176 LGTQDIMARTSSSRETVSRVLKRLEAHNILEV  207 (231)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            67899999999999999999999999998864

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=88.69  E-value=0.26  Score=34.52  Aligned_cols=29  Identities=17%  Similarity=0.245  Sum_probs=27.6

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      ++..+||+.|+||..||++-++..++.|-
T Consensus        37 ~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~   65 (187)
T 1j5y_A           37 VSGAQLAEELSVSRQVIVQDIAYLRSLGY   65 (187)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence            89999999999999999999999988886

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=88.54  E-value=0.12  Score=38.15  Aligned_cols=53  Identities=9%  Similarity=-0.004  Sum_probs=37.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIE   57 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~   57 (163)
                      ++++.|||+.++|+.++|++++++..+-|=+.=.....++..   ..++.-.+.+.
T Consensus       174 ~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~  229 (250)
T 1p4x_A          174 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAE  229 (250)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHH
Confidence            389999999999999999999999999998854333333322   33444444443

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=88.44  E-value=0.27  Score=29.45  Aligned_cols=20  Identities=15%  Similarity=0.087  Sum_probs=18.9

Q ss_pred             ChhhhHHHhhcchhhHHHHH
Q psy1904           7 RPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++.++|+.+|||.++|++|.
T Consensus        29 sq~~lA~~~gis~~~is~~E   48 (86)
T 2ofy_A           29 SMVTVAFDAGISVETLRKIE   48 (86)
T ss_dssp             CHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHHH
Confidence            77899999999999999996

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=88.41  E-value=0.32  Score=34.29  Aligned_cols=33  Identities=24%  Similarity=0.384  Sum_probs=29.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       167 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          167 GLNTEEIALMLGTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             SSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            368899999999999999999999999998753

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=88.40  E-value=0.89  Score=28.87  Aligned_cols=65  Identities=11%  Similarity=0.052  Sum_probs=39.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.++|+.+|||..|+..|-    +.|-+.|..  .+|.+  .=+......+..... ..-+++..++..-+.
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye----~~Gll~p~~~~~~g~R--~Y~~~dl~~l~~I~~l~~~G~~l~~I~~~l~   70 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYD----NIELLNPSALTDAGYR--LYSDADLERLQQILFFKEIGFRLDEIKEMLD   70 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHH----HTTSSCCSEECTTCCE--EBCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HCCCCCCCeECCCCCe--eeCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            578999999999999999885    458888754  24433  334444443332221 122566666655543

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=88.32  E-value=0.13  Score=37.69  Aligned_cols=36  Identities=19%  Similarity=0.266  Sum_probs=31.7

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +...++.++||+.+|||+++|++.|+...+.|-+.-
T Consensus        22 ~~g~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A           22 TCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             TTTTTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            344589999999999999999999999999998865

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=88.24  E-value=0.34  Score=34.29  Aligned_cols=32  Identities=25%  Similarity=0.301  Sum_probs=29.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       178 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          178 LTQEEIAQLVGASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            67889999999999999999999999997764

>1zs4_A Regulatory protein CII; helix-turn-helix, transcription activator, transcription-DNA; HET: DNA; 1.70A {Enterobacteria phage lambda} SCOP: a.35.1.9

Probab=88.16  E-value=0.21  Score=30.49  Aligned_cols=22  Identities=9%  Similarity=0.072  Sum_probs=19.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      +.+..||+..||+.++||||-.
T Consensus        25 ~gQ~~vAe~~GvdeStISR~k~   46 (83)
T 1zs4_A           25 LGTEKTAEAVGVDKSQISRWKR   46 (83)
T ss_dssp             HCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HhhHHHHHHhCCCHHHHhhhhh
Confidence            4578899999999999999964

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=88.08  E-value=0.33  Score=31.79  Aligned_cols=26  Identities=15%  Similarity=0.212  Sum_probs=22.9

Q ss_pred             CCCChhhhHHHhh--cchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLR--VSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~--vs~~~vs~~l~~~   29 (163)
                      .++++.+|+..||  ||.+||++||.+.
T Consensus        76 ~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           76 SCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             CCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            3588999999999  8999999999765

>2o4a_A DNA-binding protein SATB1; protein-DNA complex, transcription, transcription/DNA complex; HET: DNA; 1.75A {Homo sapiens} SCOP: a.35.1.7 PDB: 2o49_A*

Probab=88.08  E-value=0.096  Score=32.78  Aligned_cols=26  Identities=31%  Similarity=0.562  Sum_probs=23.0

Q ss_pred             CCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      .++++.-.|+ +|+.|++++|.+|...
T Consensus        23 ~~isQ~~FA~~VL~rsQgtLs~lL~~P   49 (93)
T 2o4a_A           23 AGISQAVFARVAFNRTQGLLSEILRKE   49 (93)
T ss_dssp             HTCCHHHHHHHHHSCCHHHHHHHHHHC
T ss_pred             cCCcHHHHHHHHHHHhhhHHHHHHcCC
Confidence            5788899998 9999999999999764

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=88.04  E-value=0.35  Score=34.43  Aligned_cols=29  Identities=17%  Similarity=0.377  Sum_probs=26.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ++..+||..+|+|..+|+++|+++++.| +
T Consensus       179 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g-i  207 (237)
T 3fx3_A          179 YDKMLIAGRLGMKPESLSRAFSRLKAAG-V  207 (237)
T ss_dssp             SCTHHHHHHTTCCHHHHHHHHHHHGGGT-E
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCC-e
Confidence            4578999999999999999999999999 5

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=87.96  E-value=0.21  Score=31.48  Aligned_cols=33  Identities=21%  Similarity=0.175  Sum_probs=28.9

Q ss_pred             CCCChhhhHHHhh----cchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~----vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++++.||++.|+    ++.+||+++|++..+-|-+.
T Consensus        48 ~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~   84 (99)
T 2k4b_A           48 GEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLS   84 (99)
T ss_dssp             SCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCE
T ss_pred             CCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEE
Confidence            4689999999997    57999999999999888774

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=87.95  E-value=0.36  Score=34.77  Aligned_cols=32  Identities=16%  Similarity=0.221  Sum_probs=29.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       194 lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  225 (243)
T 3la7_A          194 LSHQAIAEAIGSTRVTVTRLLGDLREKKMISI  225 (243)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEE
Confidence            67899999999999999999999999998763

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=87.93  E-value=0.28  Score=38.24  Aligned_cols=34  Identities=18%  Similarity=0.296  Sum_probs=29.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..|||+.+|+|.+||+++++.+.+.|-+..
T Consensus        32 ~~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~   65 (380)
T 2hoe_A           32 SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVE   65 (380)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            3489999999999999999999999988776643

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=87.92  E-value=0.36  Score=31.85  Aligned_cols=33  Identities=12%  Similarity=0.062  Sum_probs=29.1

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +-.++|+.||||..+|.+-|......|-+...+
T Consensus        30 se~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~   62 (129)
T 2ek5_A           30 STNELAAFHRINPATARNGLTLLVEAGILYKKR   62 (129)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEET
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence            667999999999999999999999999885443

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=87.86  E-value=0.27  Score=34.05  Aligned_cols=32  Identities=25%  Similarity=0.232  Sum_probs=29.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       140 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  171 (195)
T 3b02_A          140 VSHEEIADATASIRESVSKVLADLRREGLIAT  171 (195)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            67899999999999999999999999998763

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=87.80  E-value=0.31  Score=32.09  Aligned_cols=37  Identities=11%  Similarity=0.060  Sum_probs=31.5

Q ss_pred             CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      ..+++.||.+.+     +||.+||++.|+.+.+.|-+.--..
T Consensus        25 ~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~   66 (131)
T 2o03_A           25 DFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHT   66 (131)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEEC
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEe
Confidence            347899999999     8999999999999999998865443

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=87.71  E-value=0.37  Score=34.73  Aligned_cols=33  Identities=18%  Similarity=0.196  Sum_probs=29.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      -++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       177 ~~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~  209 (250)
T 3e6c_C          177 PLSQKSIGEITGVHHVTVSRVLASLKRENILDK  209 (250)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEe
Confidence            368899999999999999999999999998864

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=87.66  E-value=0.41  Score=33.80  Aligned_cols=32  Identities=22%  Similarity=0.158  Sum_probs=29.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEE
Confidence            68899999999999999999999999998864

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=87.41  E-value=0.38  Score=34.15  Aligned_cols=33  Identities=3%  Similarity=-0.017  Sum_probs=29.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      -++..+||..+|+|..+|+++|+++++.|-+.-
T Consensus       180 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  212 (232)
T 2gau_A          180 YLSREELATLSNMTVSNAIRTLSTFVSERMLAL  212 (232)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEee
Confidence            368899999999999999999999999998753

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=87.41  E-value=0.4  Score=30.79  Aligned_cols=25  Identities=16%  Similarity=0.046  Sum_probs=22.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .++..+||+..+||.+||.|..++.
T Consensus        39 ~~si~elA~~~~vS~aTv~Rf~kkl   63 (111)
T 2o3f_A           39 ESTVNEISALANSSDAAVIRLCXSL   63 (111)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             hcCHHHHHHHHCCCHHHHHHHHHHc
Confidence            5789999999999999999998776

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=87.12  E-value=0.44  Score=31.44  Aligned_cols=31  Identities=16%  Similarity=0.137  Sum_probs=27.7

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      +-.++|+.||||..||.+-|......|-+.-
T Consensus        40 ser~La~~~gVSr~tVReAl~~L~~eGlv~~   70 (134)
T 4ham_A           40 SIREFASRIGVNPNTVSKAYQELERQEVIIT   70 (134)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            4578999999999999999999999998843

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=87.06  E-value=0.38  Score=37.70  Aligned_cols=34  Identities=18%  Similarity=0.259  Sum_probs=30.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..|||+.+|+|.+||+++++.+.+.|-+..
T Consensus        29 ~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~   62 (406)
T 1z6r_A           29 GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   62 (406)
T ss_dssp             CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            3499999999999999999999999988777644

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=86.99  E-value=0.56  Score=31.42  Aligned_cols=38  Identities=11%  Similarity=0.281  Sum_probs=32.0

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKP   45 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p   45 (163)
                      +..+||+.++|+...+.+||....+.|-+.  .| .||-.+
T Consensus        25 s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~rG-~GGy~L   64 (145)
T 1xd7_A           25 SSEIIADSVNTNPVVVRRMISLLKKADILTSRAG-VPGASL   64 (145)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS-SSSCEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeecC-CCCcee
Confidence            788999999999999999999999999773  35 565543

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=86.98  E-value=0.36  Score=38.21  Aligned_cols=34  Identities=12%  Similarity=0.200  Sum_probs=30.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..|||+.+|+|.+||+++++.+.+.|-+..
T Consensus        52 ~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~   85 (429)
T 1z05_A           52 GPISRIDLSKESELAPASITKITRELIDAHLIHE   85 (429)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            3489999999999999999999999988887654

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=86.62  E-value=0.35  Score=33.61  Aligned_cols=21  Identities=5%  Similarity=0.205  Sum_probs=19.8

Q ss_pred             ChhhhHHHhhcchhhHHHHHh
Q psy1904           7 RPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ++.++|+.+|||+++|++|++
T Consensus        22 tq~elA~~~Gis~~~i~~~e~   42 (189)
T 2fjr_A           22 QKIQLANHFDIASSSLSNRYT   42 (189)
T ss_dssp             SHHHHHHHTTCCHHHHHHHHH
T ss_pred             CHHHHHHHhCcCHHHHHHHHh
Confidence            889999999999999999984

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=86.43  E-value=0.89  Score=30.64  Aligned_cols=36  Identities=14%  Similarity=0.043  Sum_probs=29.4

Q ss_pred             CCCChhhhHHHh----------hcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQL----------RVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~----------~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .++++.+|+..|          .||.+||.+||.++...|.-.|-.
T Consensus       100 ~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~~~~~~~~  145 (159)
T 2k27_A          100 PTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFNLPMD  145 (159)
T ss_dssp             SSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCCCSCCCCC
T ss_pred             ccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCCCccCccc
Confidence            357888999988          489999999999998887766643

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=86.08  E-value=0.46  Score=34.02  Aligned_cols=33  Identities=15%  Similarity=0.239  Sum_probs=29.4

Q ss_pred             CCChhhhHHHhhcchh-hHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHG-CVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~-~vs~~l~~~~~tG~~~P   37 (163)
                      .++..+||..+|+|.+ +|+++|+++++.|-+.-
T Consensus       169 ~~t~~~lA~~lG~sr~etvsR~l~~l~~~glI~~  202 (238)
T 2bgc_A          169 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY  202 (238)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCChHHHHHHHHHHHHHCCCEEe
Confidence            4678999999999995 99999999999998753

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=86.03  E-value=0.55  Score=29.95  Aligned_cols=25  Identities=16%  Similarity=0.248  Sum_probs=22.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .++..+||+..+||.+||.|..++.
T Consensus        35 ~~si~elA~~~~vS~aTv~Rf~kkL   59 (107)
T 3iwf_A           35 NMTSQEIANQLETSSTSIIRLSKKV   59 (107)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            4788999999999999999998776

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=85.90  E-value=0.21  Score=31.45  Aligned_cols=25  Identities=12%  Similarity=0.045  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      .++.+..+|+.+||+.++||+|-..
T Consensus        22 a~~gq~~vA~~iGV~~StISR~k~~   46 (97)
T 1xwr_A           22 AMLGTEKTAEAVGVDKSQISRWKRD   46 (97)
T ss_dssp             HHHCHHHHHHHHTCCTTTHHHHHHH
T ss_pred             HHHhHHHHHHHhCCCHHHHHHHHhh
Confidence            3467889999999999999998643

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=85.82  E-value=0.02  Score=39.78  Aligned_cols=30  Identities=13%  Similarity=0.037  Sum_probs=21.7

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCH
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDI  125 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~  125 (163)
                      .+.+|.||.|+..|+..|+..|+.++||+.
T Consensus       134 ~~~~rprt~~~~~q~~~l~~~f~~~~~~~~  163 (169)
T 2rgt_A          134 SGGSGGGTPMVAASPERHDGGLQANPVEVQ  163 (169)
T ss_dssp             -------EEEECCCCEECCSSCCCCCCCCC
T ss_pred             CCCcCCCCcccHHHHHHHHHHHhCCCCccc
Confidence            346789999999999999999999999864

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=85.44  E-value=0.57  Score=31.03  Aligned_cols=36  Identities=14%  Similarity=0.247  Sum_probs=31.4

Q ss_pred             CCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           5 GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         5 g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      .+++.||.+.|     +||.+||++.|+.+.+.|-+.--..
T Consensus        34 ~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~   74 (136)
T 1mzb_A           34 HMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNF   74 (136)
T ss_dssp             SBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECS
T ss_pred             CCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            48999999999     8999999999999999998865443

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=85.21  E-value=0.49  Score=28.55  Aligned_cols=33  Identities=6%  Similarity=0.252  Sum_probs=30.1

Q ss_pred             CCCChhhhHHHhhcchh-hHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHG-CVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~-~vs~~l~~~~~tG~~~   36 (163)
                      .+.++.+||+.|||+.. .|.+.|....+-|-+.
T Consensus        24 g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~   57 (79)
T 1xmk_A           24 SDSSALNLAKNIGLTKARDINAVLIDMERQGDVY   57 (79)
T ss_dssp             CCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEE
T ss_pred             CCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEE
Confidence            34789999999999999 9999999999999886

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=85.21  E-value=0.49  Score=36.14  Aligned_cols=31  Identities=13%  Similarity=0.137  Sum_probs=28.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..+||+.|+||..||.+-|+..++.|-+.
T Consensus        20 ~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i   50 (321)
T 1bia_A           20 HSGEQLGETLGMSRAAINKHIQTLRDWGVDV   50 (321)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHTTCCC
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHhCCCcE
Confidence            8999999999999999999999999888664

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=85.20  E-value=2.9  Score=27.91  Aligned_cols=64  Identities=16%  Similarity=0.095  Sum_probs=40.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC-CC-CCCCCCcCChHHHHHH---HHHHHhCCCCCchhhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG-VI-GGSKPRVATPDVEKRI---EEYKKTNPNITSWEVRDKLI   76 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg-~~-Gg~~p~~~~~~~~~~i---~~~~~~~p~~~~~e~~~~l~   76 (163)
                      .+++.++|+.+|||..|+.-|-    +.|-+.|. .. +|.+  .=+......+   ..+.  .-+++..+++.-+.
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye----~~GLl~p~~r~~~g~R--~Y~~~dl~~l~~I~~lr--~~G~sL~eIk~~l~   70 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYE----RIGLIPPIHRNESGVR--KFGAEDLRWILFTRQMR--RAGLSIEALIDYLA   70 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHH----HHTSSCCCCBCTTSCB--CBCHHHHHHHHHHHHHH--HTTCCHHHHHHHHH
T ss_pred             CCcHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCCe--eeCHHHHHHHHHHHHHH--HcCCCHHHHHHHHH
Confidence            3688999999999999998875    44888883 32 3333  2334444433   3332  23677777665543

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=84.83  E-value=0.57  Score=31.20  Aligned_cols=34  Identities=12%  Similarity=0.078  Sum_probs=30.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+.++.+||+++|+|.++|.++|.+..+-|-+.-
T Consensus        50 ~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i   83 (135)
T 2v79_A           50 YFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFI   83 (135)
T ss_dssp             CSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5689999999999999999999999988888764

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=84.48  E-value=1.7  Score=29.16  Aligned_cols=66  Identities=11%  Similarity=0.083  Sum_probs=40.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      ..+++.|+|+.+|||..|+.-|-    +.|-+.|..  .+|.+  .=+......+..+.. ..-+++..+++.-+
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye----~~GLl~p~~r~~~g~R--~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l   71 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYD----KINLLKPSDYTEGGHR--LYTKDDLYVLQQIQSFKHLGFSLGEIQNII   71 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHH----HTTSSCCSEECTTSCE--EBCHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHH----HCCCCCCCeECCCCCE--eeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            35789999999999999988875    559998853  24433  334444444432221 12356666665544

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=84.24  E-value=0.31  Score=35.99  Aligned_cols=131  Identities=8%  Similarity=-0.017  Sum_probs=72.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR   80 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~   80 (163)
                      .|+++.|||+.++++.++|.++|++..+.|=+.=.....++..   ..++.-.+.+.......-     +....+..+ .
T Consensus        49 ~~~~~~el~~~l~~~~~t~t~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~~~-----~~~eq~s~E-~  122 (250)
T 1p4x_A           49 NTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFD-----QIIKQFNLA-D  122 (250)
T ss_dssp             SEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHHHHHHHHH-----HHHHHHHHH-T
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHHHHHHHHHH-----HHHHHHhcc-c
Confidence            4799999999999999999999999999998854433334333   234444444433332221     112333333 1


Q ss_pred             CCCCCCCCCCcccc---cc------ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccc
Q psy1904          81 LDDSDTESEPGIVL---KR------KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV  142 (163)
Q Consensus        81 ~~~~~~~~~~~~~~---~~------~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v  142 (163)
                      .+-+.-.+-.....   ..      ...-...-+|..|...|.........  .....+||..++++...|
T Consensus       123 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~gLt~~q~~vL~~L~~~~~~--~~t~~eLa~~l~i~~~tv  191 (250)
T 1p4x_A          123 QSESQMIPKDSKEFLNLMMYTMYFKNIIKKHLTLSFVEFTILAIITSQNKN--IVLLKDLIETIHHKYPQT  191 (250)
T ss_dssp             TCCSSCSCCSHHHHHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHTTTTC--CEEHHHHHHHSSSCHHHH
T ss_pred             ccccccchHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhCCCC--CcCHHHHHHHHCCChhhH
Confidence            11110000000000   00      00112456888998888877655421  123457888888876543

>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A

Probab=84.15  E-value=2.3  Score=28.12  Aligned_cols=65  Identities=9%  Similarity=0.097  Sum_probs=39.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      +++.|+|+.+|||..|+..|-    +.|-+.|..  .+|.+  .=+......+..+.. ..-+++..++..-+.
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye----~~Gll~p~~r~~~g~R--~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYE----EKGLVTPPMRSENGYR--TYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH----HTTCSCCCEECTTSCE--ECCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCe--eeCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            468899999999999998875    458887752  34433  233444443322211 123677777766554

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=84.11  E-value=0.88  Score=30.68  Aligned_cols=36  Identities=22%  Similarity=0.208  Sum_probs=31.1

Q ss_pred             CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ..+++.||.+.+     +||.+||++.|+.+.+.|-+.--.
T Consensus        41 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~   81 (150)
T 2xig_A           41 THLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLE   81 (150)
T ss_dssp             SCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEE
Confidence            358899999998     799999999999999999886543

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=83.98  E-value=0.66  Score=33.77  Aligned_cols=26  Identities=15%  Similarity=0.259  Sum_probs=23.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ..|+++.+||+.||+|.++|+++|.-
T Consensus       132 ~~g~t~~~iA~~lG~s~~~V~~~l~l  157 (230)
T 1vz0_A          132 EMGLTQEEVARRVGKARSTVANALRL  157 (230)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHG
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46899999999999999999999854

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=83.58  E-value=0.97  Score=28.06  Aligned_cols=51  Identities=16%  Similarity=0.108  Sum_probs=37.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE   58 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~   58 (163)
                      .|+.+.+||..+++|.+++++.+....+.|=+.-.. ++   -..|+.-.+.+..
T Consensus        19 ~~~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~-~~---~~LT~kG~~~l~~   69 (95)
T 1r7j_A           19 SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG-KQ---YMLTKKGEELLED   69 (95)
T ss_dssp             TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TE---EEECHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEC-Ce---eEEChhHHHHHHH
Confidence            358999999999999999999999999999886442 22   4455555544433

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.42  E-value=0.67  Score=29.03  Aligned_cols=33  Identities=15%  Similarity=0.192  Sum_probs=29.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      ..||-..||+.+.++++++|.++|+++..-+-+
T Consensus        51 n~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lI   83 (95)
T 2yu3_A           51 NKGIWSRDVRYKSNLPLTEINKILKNLESKKLI   83 (95)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSE
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCE
Confidence            478999999999999999999999999665544

>1wiz_A DNA-binding protein SATB2; helix bundle, KIAA1034 protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=83.39  E-value=0.21  Score=31.65  Aligned_cols=26  Identities=31%  Similarity=0.487  Sum_probs=22.5

Q ss_pred             CCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      .++++.-.|+ +|+.|+++++.+|+..
T Consensus        33 ~~isQ~~FA~~VL~rsQgtLs~lLr~P   59 (101)
T 1wiz_A           33 ASVSQAVFARVAFNRTQGLLSEILRKE   59 (101)
T ss_dssp             HTCCHHHHHHHHHSCCHHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHHHHhhhHHHHHHcCC
Confidence            5688888888 8999999999999654

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=83.03  E-value=0.75  Score=33.41  Aligned_cols=38  Identities=18%  Similarity=0.207  Sum_probs=32.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      ++..++|+.||||.++|.+-|......|-+.-.+.+|.
T Consensus        50 L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~~~~G~   87 (237)
T 3c7j_A           50 LRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGA   87 (237)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCce
Confidence            67889999999999999999999999998865544444

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=82.99  E-value=0.35  Score=31.71  Aligned_cols=33  Identities=12%  Similarity=-0.007  Sum_probs=28.2

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +..++|+.||||..+|.+.+......|-+...+
T Consensus        37 s~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   69 (126)
T 3ic7_A           37 SVREYASIVEVNANTVMRSYEYLQSQEVIYNKR   69 (126)
T ss_dssp             CTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEET
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEc
Confidence            567899999999999999999999999886543

>4fcy_A Transposase; rnaseh, DDE transposase, DNA binding protein-DNA complex; HET: DNA; 3.71A {Enterobacteria phage MU} PDB: 2ezk_A 2ezl_A 2ezh_A 2ezi_A

Probab=82.87  E-value=2  Score=34.77  Aligned_cols=25  Identities=12%  Similarity=0.166  Sum_probs=21.7

Q ss_pred             hhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904           9 CVISRQLRVSHGCVSKILNRYQETG   33 (163)
Q Consensus         9 ~~ia~~~~vs~~~vs~~l~~~~~tG   33 (163)
                      ..+|+.+|||..|+++|+.+|+..|
T Consensus        56 ~~~a~~~gvS~~Tl~rW~~~y~~~~   80 (529)
T 4fcy_A           56 ATVAGHYQVSASTLRDKYYQVQKFA   80 (529)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHTSC
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhhC
Confidence            4578999999999999999997654

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=81.94  E-value=0.64  Score=31.60  Aligned_cols=24  Identities=17%  Similarity=0.200  Sum_probs=22.5

Q ss_pred             CChhhhHHHh-----hcchhhHHHHHhhh
Q psy1904           6 VRPCVISRQL-----RVSHGCVSKILNRY   29 (163)
Q Consensus         6 ~~~~~ia~~~-----~vs~~~vs~~l~~~   29 (163)
                      .++.|+++.|     +||++||||-|+..
T Consensus        20 ~tq~eL~~~L~~~G~~VtqaTisRDL~eL   48 (149)
T 1b4a_A           20 ETQDELVDRLREAGFNVTQATVSRDIKEM   48 (149)
T ss_dssp             CSHHHHHHHHHHTTCCCCHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHcCCCcCHHHHHHHHHHc
Confidence            7899999999     99999999999877

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=81.68  E-value=1.1  Score=33.23  Aligned_cols=28  Identities=18%  Similarity=0.118  Sum_probs=25.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      .+|.+..|||++|+||..||...+.+..
T Consensus       210 ~~G~s~~eIA~~l~is~~TV~~~~~~~~  237 (265)
T 3qp6_A          210 SRGKTNWEIATILNISERTVKFHVANVI  237 (265)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3799999999999999999999997763

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=81.28  E-value=0.44  Score=34.84  Aligned_cols=35  Identities=9%  Similarity=0.070  Sum_probs=31.3

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +..+..+.+||+.+|++.++|+..|.+..+.|.+.
T Consensus       175 ~~~~~t~~~la~~~~l~~~~V~~~l~~L~~~~~v~  209 (232)
T 2qlz_A          175 LNGRATVEELSDRLNLKEREVREKISEMARFVPVK  209 (232)
T ss_dssp             HSSEEEHHHHHHHHTCCHHHHHHHHHHHTTTSCEE
T ss_pred             hcCCCCHHHHHHHhCcCHHHHHHHHHHHHhcCCeE
Confidence            34568899999999999999999999999999885

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=81.24  E-value=3.1  Score=27.90  Aligned_cols=66  Identities=9%  Similarity=0.002  Sum_probs=41.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC-C-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-I-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI   76 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~-~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~   76 (163)
                      -+++.|+|+.+|||..|+.-|-    +.|-+.|.. . +|.  +.=+......+..+.. ..-+++..+++.-+.
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye----~~Gll~p~~r~~~g~--R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~   84 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYD----KQGLFPFLQRNEKGD--RIFNEEALKYLEMILCLKNTGMPIQKIKQFID   84 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHH----HTTCCTTCEECTTCC--EEBCHHHHHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4679999999999999988774    568887633 2 333  3334444444432222 234677777666554

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=81.23  E-value=0.81  Score=31.10  Aligned_cols=40  Identities=20%  Similarity=0.401  Sum_probs=33.9

Q ss_pred             CC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      +| ++-.+||+.||+|+|-|.-+|.....-|-+.--..|-.
T Consensus        22 ~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~   62 (165)
T 2vxz_A           22 DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNV   62 (165)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTE
T ss_pred             hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccE
Confidence            55 77889999999999999999999999998876555644

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=80.99  E-value=1.5  Score=31.20  Aligned_cols=38  Identities=16%  Similarity=0.210  Sum_probs=31.2

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      ++-.++|+.||||.++|..-|++....|=+.-.+..|.
T Consensus        40 L~E~~La~~lgVSRtpVREAl~~L~~eGlv~~~~~~G~   77 (222)
T 3ihu_A           40 LVETDLVAHFGVGRNSVREALQRLAAEGIVDLQRHRGA   77 (222)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECSTTCE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCe
Confidence            45678999999999999999999999998854443444

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=80.91  E-value=0.72  Score=33.81  Aligned_cols=22  Identities=23%  Similarity=0.303  Sum_probs=20.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .|+++.++|+.+ ||.++||+|.
T Consensus        17 ~~~tq~~la~~~-~s~~~is~~e   38 (293)
T 2qfc_A           17 RGLTQKQLSENI-CHQSEVSRIE   38 (293)
T ss_dssp             HTCCTTTTTTTT-SCHHHHHHHH
T ss_pred             cCCCHHHHHHHH-cCHHHHHHHH
Confidence            589999999999 9999999995

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=80.80  E-value=1  Score=25.35  Aligned_cols=30  Identities=23%  Similarity=0.237  Sum_probs=27.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~   35 (163)
                      +....+|+.|||+.-.|..+|++..+-|-+
T Consensus        26 ldI~~~a~kygV~kdeV~~~LrrLe~KGLI   55 (59)
T 2xvc_A           26 LDIEHFSKVYGVEKQEVVKLLEALKNKGLI   55 (59)
T ss_dssp             EEHHHHHHHHCCCHHHHHHHHHHHHHTTSE
T ss_pred             EeHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence            678899999999999999999999887754

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=80.78  E-value=1.1  Score=29.93  Aligned_cols=25  Identities=8%  Similarity=0.061  Sum_probs=21.9

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      +....|+.|+||+++||+.++...+
T Consensus        40 S~s~AA~~L~iSqsavS~~I~~LE~   64 (135)
T 2ijl_A           40 SISAAGRAMDMSYRRAWLLVDALNH   64 (135)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5667899999999999999999844

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=80.72  E-value=0.49  Score=37.75  Aligned_cols=37  Identities=8%  Similarity=0.054  Sum_probs=32.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~   40 (163)
                      .|+++.+||++++++.++|+++|++..+.|=+.=...
T Consensus       419 ~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~  455 (487)
T 1hsj_A          419 NEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRS  455 (487)
T ss_dssp             SEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEEC
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCC
Confidence            4699999999999999999999999999998854433

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=80.58  E-value=1  Score=33.01  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=21.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+ ||.++|++|.
T Consensus        16 ~~~~tq~~la~~~-~s~~~~s~~e   38 (293)
T 3u3w_A           16 LRGLTQKQLSENI-CHQSEVSRIE   38 (293)
T ss_dssp             HTTCCHHHHHTTT-SCHHHHHHHH
T ss_pred             HCCCCHHHHHHHh-CCHHHHHHHH
Confidence            3799999999999 9999999995

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=80.49  E-value=0.93  Score=30.56  Aligned_cols=34  Identities=15%  Similarity=0.386  Sum_probs=29.8

Q ss_pred             CCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCC
Q psy1904           5 GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         5 g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+++.||.+.|     +||.+||++.|+.+.+.|-+.--
T Consensus        33 h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~   71 (150)
T 2w57_A           33 HISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRH   71 (150)
T ss_dssp             SEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEE
Confidence            47889999988     79999999999999999988643

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=80.23  E-value=2.3  Score=28.78  Aligned_cols=63  Identities=14%  Similarity=0.135  Sum_probs=39.1

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHH---HHHHHHHhCCCCCchhhhhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEK---RIEEYKKTNPNITSWEVRDKL   75 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~---~i~~~~~~~p~~~~~e~~~~l   75 (163)
                      -+++.++|+.+|||..|+..|-    +.|-+.|... +|.+-.  +.....   .|..+.+.  +++..++..-+
T Consensus        11 ~~~i~e~A~~~gvs~~TLR~ye----~~Gll~p~r~~~g~R~Y--~~~dl~~l~~I~~lr~~--G~sl~eI~~~l   77 (154)
T 2zhg_A           11 LLTPGEVAKRSGVAVSALHFYE----SKGLITSIRNSGNQRRY--KRDVLRYVAIIKIAQRI--GIPLATIGEAF   77 (154)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHH----HTTSSCCEECTTSCEEB--CTTHHHHHHHHHHHHHH--TCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHH----HcCCCCcccCCCCCEEe--CHHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            4789999999999999998875    4587877543 443322  223333   33333332  56666665544

>3pxp_A Helix-turn-helix domain protein; DNA-binding, basic helix-loop-helix motif, BHLH motif, lambd repressor-like DNA-binding fold; HET: MSE MYR; 2.30A {Chloroflexus aurantiacus}

Probab=80.14  E-value=1.1  Score=33.85  Aligned_cols=23  Identities=9%  Similarity=0.118  Sum_probs=21.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .|+++.|+|...|||.+++++|.
T Consensus        24 ~gLtqeelA~~~gvS~~~is~iE   46 (292)
T 3pxp_A           24 RVWTQEVLAERTQLPKRTIERIE   46 (292)
T ss_dssp             CBCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHH
Confidence            68999999999999999999985

---

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	163
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	2e-23
d1k78a2	61	a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [Ta	2e-18
d6paxa2	65	a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [Ta	3e-16
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-14
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	5e-14
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	8e-13
d1k78a1	63	a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax	1e-12
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-12
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-12
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-12
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-12
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-12
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	4e-12
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	7e-12
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	1e-11
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-11
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	2e-11
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-11
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-11
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-11
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	5e-11
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	6e-11
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	8e-11
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	8e-11
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	9e-09
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	1e-08
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-08
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-08
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-08
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-08
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	4e-08
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-07
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-07
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-07
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	9e-05
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	9e-04

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 87.3 bits (216), Expect = 2e-23
 Identities = 66/92 (71%), Positives = 77/92 (83%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 28  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 87

Query: 61  KTNPNITSWEVRDKLIKVSRLDDSDTESEPGI 92
           +++P + SWE+R+KLI+    D S   S   I
Sbjct: 88  RSSPGMFSWEIREKLIREGVCDRSTAPSVSAI 119

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.7 bits (179), Expect = 2e-18
 Identities = 23/39 (58%), Positives = 32/39 (82%)

Query: 39 VIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIK 77
          VIGGSKP+VATP V ++I EYK+ NP + +WE+RD+L+ 
Sbjct: 1  VIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLA 39

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (164), Expect = 3e-16
 Identities = 21/37 (56%), Positives = 30/37 (81%)

Query: 41 GGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIK 77
          GGSKPRVATP+V  +I +YK+  P+I +WE+RD+L+ 
Sbjct: 1  GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLS 37

>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 = 62.9 bits (153), Expect = 1e-14
 Identities = 16/48 (33%), Positives = 23/48 (47%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R  R+ R  +T  Q  ELEK F  + Y     R  +A    +TE +V+
Sbjct: 11  RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK 58

>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 = 61.0 bits (148), Expect = 5e-14
 Identities = 24/45 (53%), Positives = 34/45 (75%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           +R+RT+FT  Q+E LEK F+R+HYPD++ RE LA K  + E R+Q
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 46

>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 = 57.9 bits (140), Expect = 8e-13
 Identities = 13/45 (28%), Positives = 23/45 (51%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           +  +  F++ Q  ELEK F+   Y     R+ LA    ++E +V+
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVK 45

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (140), Expect = 1e-12
 Identities = 31/38 (81%), Positives = 33/38 (86%)

Query: 1  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38
          +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PG
Sbjct: 26 LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPG 63

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 57.5 bits (139), Expect = 1e-12
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           K  R RT     QL  L   +  +  PD   +E L    G++   ++
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.1 bits (138), Expect = 1e-12
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R T+T  Q  ELEK F  + Y     R  +A+   +TE +++
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 42

>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 = 57.2 bits (138), Expect = 1e-12
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R RT F+S QL  L++ F  + Y     R+ L+++ G+ E +++
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 44

>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 = 57.2 bits (138), Expect = 1e-12
 Identities = 30/47 (63%), Positives = 41/47 (87%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           KQRRSRTTF+++QL+ELE++F+R+ YPDIYTRE LA +  +TE R+Q
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 47

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 2e-12
 Identities = 9/45 (20%), Positives = 22/45 (48%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R+ R  ++  QL ELE+ +  + +     R  ++    ++E ++ 
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQIT 46

>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 = 56.6 bits (136), Expect = 4e-12
 Identities = 14/45 (31%), Positives = 19/45 (42%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R SR T+    L  +E  F  + YPD   RE +AN       +  
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPG 45

>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 = 55.3 bits (133), Expect = 7e-12
 Identities = 26/46 (56%), Positives = 34/46 (73%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           QRR RT FTS QL++LE +FQR+ YPD+ TRE +A    +TE RV+
Sbjct: 1   QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 46

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.5 bits (131), Expect = 1e-11
 Identities = 10/42 (23%), Positives = 22/42 (52%)

Query: 102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           +++ +      LE+ F+R    +   +E +A K G+T  +V+
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVR 42

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 54.1 bits (130), Expect = 2e-11
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R RT FT  QL  LEK F + +Y     R  LA +  + E+ ++
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIK 44

>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 = 54.2 bits (130), Expect = 2e-11
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 94  LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           L + ++R RT+  +     LE  F +   P +     +AN+ G+ +  V+
Sbjct: 4   LVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVR 53

>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 = 54.2 bits (130), Expect = 2e-11
 Identities = 18/45 (40%), Positives = 28/45 (62%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R+ RT FT+AQL  LE+ F++  Y  I  R   ++   +TET+V+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK 45

>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 = 53.3 bits (128), Expect = 3e-11
 Identities = 9/42 (21%), Positives = 17/42 (40%)

Query: 102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           R  FT  Q   L   F+ +  P    +  ++ + G+  + V 
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVS 43

>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 = 54.6 bits (131), Expect = 3e-11
 Identities = 17/48 (35%), Positives = 23/48 (47%)

Query: 96  RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
                 RT FT+ QL ELEK F  + Y     R  +A    + ET+V+
Sbjct: 25  GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 72

>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 = 53.5 bits (128), Expect = 5e-11
 Identities = 20/50 (40%), Positives = 29/50 (58%)

Query: 94  LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           L  K+R+ R  FT AQ  ELE+ F++  Y     RE LA+   +T T+V+
Sbjct: 5   LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK 54

>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 = 53.0 bits (127), Expect = 6e-11
 Identities = 10/44 (22%), Positives = 19/44 (43%)

Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           + RTT + A  + LE+ F     P       +A +  + +  V+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVR 44

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 52.6 bits (126), Expect = 8e-11
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RR+RTTFTS+Q+ ELE+ F +  Y        L+ K  +   +V+
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK 46

>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 = 53.0 bits (127), Expect = 8e-11
 Identities = 17/46 (36%), Positives = 28/46 (60%)

Query: 98  QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           +R+ R  F+ AQ+ ELE+ F++  Y     RE LA+   +T T+V+
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVK 47

>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 = 47.7 bits (113), Expect = 9e-09
 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 99  RRSRTTFTSAQLEELEKSFQRS-HYPDIYTREALANKFGMTETRVQ 143
                T T  Q+E LE +F +   +PD  T   +A + G+TE + Q
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 47

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 1e-08
 Identities = 10/42 (23%), Positives = 18/42 (42%)

Query: 102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
           RT+  +     LEKSF  +  P       +A +  M +  ++
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR 43

>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 = 46.7 bits (111), Expect = 1e-08
 Identities = 6/48 (12%), Positives = 15/48 (31%), Gaps = 3/48 (6%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSH---YPDIYTREALANKFGMTETRVQ 143
           +  R          +     +     YP    ++ +A +  +T  +V 
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVN 50

>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 = 46.9 bits (111), Expect = 2e-08
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 99  RRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQ 143
           RR R  F     E L + F     + YP    +E LA K G+T ++V 
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVS 49

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 47.1 bits (111), Expect = 2e-08
 Identities = 11/52 (21%), Positives = 19/52 (36%)

Query: 102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFL 153
           R  +  A  + L ++++R   P    RE L  +    E   +      A  L
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGL 52

>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 = 45.9 bits (109), Expect = 2e-08
 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)

Query: 106 TSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQ 143
           T+     LEK F   + +PD    E L+ +       +Q
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ 39

>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 = 45.5 bits (108), Expect = 4e-08
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 100 RSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQ 143
           +          + LEK F   + YPD    + L+ +   +  ++Q
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ 47

>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 = 44.4 bits (105), Expect = 1e-07
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 99  RRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQ 143
           R  R  FT   +  LE  F     + Y D    E L     ++  +++
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIK 46

>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 = 44.2 bits (104), Expect = 2e-07
 Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 95  KRKQRRSRTTFTSAQLEELEKSFQR----SHYPDIYTREALANKFGMTETRVQ 143
               +R RT FT+ Q E++    +R        D    E    + G+    ++
Sbjct: 14  GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLK 66

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-07
 Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 97  KQRRSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQ 143
              RSRT  +   L  L+        YPD      L+ +  + +  + 
Sbjct: 6   SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII 53

>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 = 37.0 bits (85), Expect = 9e-05
 Identities = 9/45 (20%), Positives = 15/45 (33%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
            +     T+ QL  L+ SF  S          L  +  +T   + 
Sbjct: 5   PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID 49

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

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

 Score = 34.3 bits (78), Expect = 9e-04
 Identities = 9/48 (18%), Positives = 16/48 (33%)

Query: 99  RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFV 146
             S    T  QL  L+  F +  +      + L    G+    + Q+ 
Sbjct: 4   GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWF 51

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	163
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.91
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.89
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.89
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.89
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.89
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.89
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.88
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.88
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.88
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.87
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.87
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.87
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.86
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.86
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.86
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.86
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.85
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.84
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.84
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.84
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.83
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.82
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.82
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.81
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	99.77
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.77
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.74
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.74
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.73
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.69
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.65
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.64
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1k78a2	61	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.15
d6paxa2	65	Pax-6 {Human (Homo sapiens) [TaxId: 9606]}	99.05
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	98.01
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	97.65
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	97.51
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	97.21
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.03
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	96.62
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	96.57
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	96.49
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	96.46
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	96.43
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.28
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.25
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.2
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	96.08
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	96.08
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	96.05
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	96.03
d1y7ya1	69	Restriction-modification controller protein C.AhdI	95.99
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	95.98
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	95.78
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	95.75
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	95.75
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	95.61
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	95.39
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	95.37
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	95.35
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	95.29
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	95.28
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.22
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.21
d1s7ea2	80	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	95.17
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	95.0
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	94.96
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	94.89
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.84
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.81
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	94.78
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	94.69
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	94.69
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	94.68
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	94.62
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	94.5
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.49
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.43
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.42
d1zyba1	73	Probable transcription regulator BT4300, C-termina	94.39
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	94.39
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	94.3
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	94.28
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	94.26
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.1
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	94.04
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	93.84
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	93.74
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	93.72
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	93.7
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.67
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	93.59
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	93.58
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	93.45
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	93.44
d1x2la1	87	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	93.43
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	93.23
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	93.22
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	93.19
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	93.13
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	93.13
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	93.12
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	93.07
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	92.95
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	92.83
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	92.81
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	92.62
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	92.57
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	92.48
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	92.45
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	92.27
d1wh6a_	101	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	92.18
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	92.15
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	91.91
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	91.7
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	91.6
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	91.19
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	91.16
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	91.11
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	90.92
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	90.85
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	90.82
d1wh8a_	111	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	90.81
d2o4aa1	83	DNA-binding protein SATB1 {Human (Homo sapiens) [T	90.8
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	90.78
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	90.6
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	90.42
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	90.42
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	90.41
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	90.41
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	90.39
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	90.19
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	89.94
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	89.85
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	89.38
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	88.83
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	88.83
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	88.59
d2csfa1	88	DNA-binding protein SATB2 {Human (Homo sapiens) [T	88.47
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	88.06
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	87.92
d2esna1	89	Probable LysR-type transcriptional regulator PA047	87.77
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	87.46
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	87.46
d1hlva1	66	DNA-binding domain of centromere binding protein B	87.07
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	87.03
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	86.02
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	85.94
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	84.7
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	84.49
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	84.48
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	84.3
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	84.27
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	83.9
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	83.84
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	83.74
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	83.66
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	83.2
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	83.17
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	83.11
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	82.91
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	82.64
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	82.45
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	82.42
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	82.21
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	82.07
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	81.86
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	81.66
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	81.5
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	81.41
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	81.39
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	80.19
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	80.1

>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=99.91  E-value=1.2e-25  Score=130.33  Aligned_cols=57  Identities=16%  Similarity=0.296  Sum_probs=55.3

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ++.||.||.+|+.+||..|..++||+..++.+||..+||++.+|+|||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            678999999999999999999999999999999999999999999999999999986

>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=99.89  E-value=5.1e-25  Score=126.53  Aligned_cols=55  Identities=25%  Similarity=0.279  Sum_probs=53.8

Q ss_pred             cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       102 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ||.||+.|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+||+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7999999999999999999999999999999999999999999999999999986

>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=99.89  E-value=5.1e-25  Score=128.19  Aligned_cols=57  Identities=32%  Similarity=0.494  Sum_probs=55.1

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ||.|+.||++|+.+||..|+.++||+..++.+||..+||++.+|++||||+|+|+||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            468999999999999999999999999999999999999999999999999999886

>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=99.89  E-value=5.8e-25  Score=127.37  Aligned_cols=57  Identities=28%  Similarity=0.328  Sum_probs=55.1

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      |.||.||+.|+..||..|+.++||+..++.+||..+||++.+|+|||||+|+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            578999999999999999999999999999999999999999999999999999875

>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=99.89  E-value=2.9e-24  Score=131.66  Aligned_cols=64  Identities=30%  Similarity=0.346  Sum_probs=59.7

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      .++++.||.||++|+.+||..|+.++||+..++++||..+||++.+|++||||+|+|.|+....
T Consensus         7 ~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   70 (77)
T d1vnda_           7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             SSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhc
Confidence            4567889999999999999999999999999999999999999999999999999999986543

>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=99.89  E-value=1.5e-24  Score=123.89  Aligned_cols=53  Identities=26%  Similarity=0.520  Sum_probs=51.6

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccc
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGF  152 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k  152 (163)
                      |+||.||+.|+..||..|+.++||+..++.+||..+||++.+|+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            57899999999999999999999999999999999999999999999999987

>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=99.88  E-value=1.5e-24  Score=125.65  Aligned_cols=57  Identities=23%  Similarity=0.336  Sum_probs=54.7

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      ++.|+.||+.|+..||..|+.|+||+..++.+||..+||++.||+|||||||+|+||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467899999999999999999999999999999999999999999999999999875

>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=99.88  E-value=2.2e-24  Score=131.97  Aligned_cols=61  Identities=26%  Similarity=0.292  Sum_probs=57.5

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +..++.||.||++|+.+||..|+.++||+..++++||..+||++.+|+|||||||+|+|+.
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~   71 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI   71 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHH
Confidence            3457889999999999999999999999999999999999999999999999999999864

>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=99.88  E-value=2.2e-24  Score=128.81  Aligned_cols=58  Identities=29%  Similarity=0.370  Sum_probs=55.7

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +|.||.||..|+.+||..|+.++||+..++.+||..|||++.+|+|||||||+|+|++
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~   59 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   59 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhh
Confidence            5779999999999999999999999999999999999999999999999999999874

>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=99.87  E-value=9.9e-24  Score=126.24  Aligned_cols=62  Identities=27%  Similarity=0.364  Sum_probs=58.2

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS  159 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~  159 (163)
                      +++.||.||+.|+.+|+..|+.++||+..++.+||..+||++.+|++||||+|+|+|+....
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~   63 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccc
Confidence            36789999999999999999999999999999999999999999999999999999886543

>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=99.87  E-value=8.5e-24  Score=125.58  Aligned_cols=62  Identities=50%  Similarity=0.776  Sum_probs=58.0

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      +.++.||.||++|+.+||..|+.++||+..++.+||..+||++.+|++||||+|+|+|++-.
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            35788999999999999999999999999999999999999999999999999999987543

>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=99.87  E-value=1.4e-23  Score=125.72  Aligned_cols=58  Identities=41%  Similarity=0.701  Sum_probs=55.8

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +|.||.||+.|+.+||..|..|+||+..++.+||..+||++.+|++||||+|+|+|++
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~   59 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE   59 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhh
Confidence            6789999999999999999999999999999999999999999999999999999864

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.5e-23  Score=131.36  Aligned_cols=61  Identities=28%  Similarity=0.300  Sum_probs=54.6

Q ss_pred             cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .++++.|+.||+.|+.+||..|+.|+||+..++++||..|||++.+|+|||||+|+|+|+.
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~   85 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   85 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHh
Confidence            3457889999999999999999999999999999999999999999999999999999874

>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=99.86  E-value=2e-23  Score=125.90  Aligned_cols=58  Identities=26%  Similarity=0.290  Sum_probs=54.9

Q ss_pred             ccccCcCCHHHHHHHHHhccC-CCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ++.|+.||.+|+.+||..|.. ++||+...+++||..+||++.+|+|||||||+|+|++
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            578999999999999999986 7899999999999999999999999999999999875

>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=99.86  E-value=8.3e-23  Score=121.75  Aligned_cols=59  Identities=19%  Similarity=0.248  Sum_probs=56.7

Q ss_pred             cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      +++.||.|+++|+..|+..|..++||+..++++||..+||++.+|++||||+|+++|+.
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            46789999999999999999999999999999999999999999999999999999874

>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=99.86  E-value=1e-23  Score=123.39  Aligned_cols=58  Identities=43%  Similarity=0.592  Sum_probs=55.7

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      ||.||.||++|+.+|+..|..++||+..++..||..+||++.+|++||||+|+|+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            5789999999999999999999999999999999999999999999999999999863

>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=99.85  E-value=1.1e-22  Score=120.93  Aligned_cols=62  Identities=19%  Similarity=0.236  Sum_probs=58.3

Q ss_pred             ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      +.+|.||.||++|+..|+..|..|+||+..++++||..+||++.+|++||||+|++.|+.--
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            35788999999999999999999999999999999999999999999999999999987643

>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=99.84  E-value=2.1e-22  Score=121.73  Aligned_cols=64  Identities=20%  Similarity=0.269  Sum_probs=59.6

Q ss_pred             cccccCcCCHHHHHHHHHhccC-CCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904          98 QRRSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS  161 (163)
Q Consensus        98 ~rr~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~  161 (163)
                      .++.|+.||++|+.+|+..|+. ++||+..++++||..+||++.+|++||||+|++.|+.-|+-|
T Consensus         7 ~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~~p~sg   71 (71)
T d1wi3a_           7 GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSGPSSG   71 (71)
T ss_dssp             CCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSSCSSCC
T ss_pred             CCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcccCCCCC
Confidence            4678999999999999999974 899999999999999999999999999999999999887754

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.84  E-value=1.9e-22  Score=117.08  Aligned_cols=57  Identities=18%  Similarity=0.216  Sum_probs=54.8

Q ss_pred             cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      |.||.|+.+|+..||..|..++||+..++.+||..+||++.+|++||||+|+++|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            568999999999999999999999999999999999999999999999999999874

>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=99.84  E-value=1.9e-22  Score=114.96  Aligned_cols=53  Identities=19%  Similarity=0.270  Sum_probs=51.6

Q ss_pred             cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904         102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus       102 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      ||.||++|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            68999999999999999999999999999999999999999999999999976

>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=99.83  E-value=1.2e-21  Score=120.84  Aligned_cols=60  Identities=20%  Similarity=0.179  Sum_probs=55.2

Q ss_pred             cccccccCcCCHHHHHHHHHhccC----CCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904          96 RKQRRSRTTFTSAQLEELEKSFQR----SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus        96 ~~~rr~Rt~~t~~q~~~Le~~F~~----~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      .+++|.||.||.+|+..|+..|+.    ++||+..++++||..+||++.+|+|||||+|.+.|+
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            356789999999999999888775    899999999999999999999999999999999875

>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=99.82  E-value=3.7e-22  Score=123.78  Aligned_cols=58  Identities=28%  Similarity=0.370  Sum_probs=54.7

Q ss_pred             ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhC---------------CCcccccccccccccccccC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG---------------MTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~---------------l~~~~v~~WFqnrR~k~kr~  156 (163)
                      |+.|+.||++|+.+||..|+.|+||+..++++||..+|               |++.+|++||||||+|+|+.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~   73 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR   73 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHh
Confidence            57899999999999999999999999999999999875               99999999999999999874

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.1e-21  Score=113.35  Aligned_cols=56  Identities=18%  Similarity=0.185  Sum_probs=54.1

Q ss_pred             ccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904         101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC  156 (163)
Q Consensus       101 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~  156 (163)
                      .||.|+++|+..||..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999999874

>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=99.81  E-value=3.1e-21  Score=108.75  Aligned_cols=50  Identities=20%  Similarity=0.384  Sum_probs=48.9

Q ss_pred             ccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy1904         101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTA  150 (163)
Q Consensus       101 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR  150 (163)
                      +||.||++|+..||..|+.++||+..++.+||..+||++.+|++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            58999999999999999999999999999999999999999999999997

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.77  E-value=2e-19  Score=119.66  Aligned_cols=83  Identities=76%  Similarity=1.273  Sum_probs=77.0

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhccC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRL   81 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~~   81 (163)
                      .++|+++|+||++|+||++||++|+++|+++|++.|++.|+++|+..++.+++.|..+.+++|++++||+++.|..+.-+
T Consensus        29 ~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~~~I~~~~~~~P~~t~~El~~~L~~egv~  108 (123)
T d1pdnc_          29 AADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVC  108 (123)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTTCTTCCHHHHHHHHHHTSSS
T ss_pred             HHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCccHHHHHHHHHHcCCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999987655


Q ss_pred             CCC
Q psy1904          82 DDS   84 (163)
Q Consensus        82 ~~~   84 (163)
                      ...
T Consensus       109 ~~~  111 (123)
T d1pdnc_         109 DRS  111 (123)
T ss_dssp             CST
T ss_pred             CCC
Confidence            443

>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=4.8e-20  Score=112.59  Aligned_cols=56  Identities=21%  Similarity=0.228  Sum_probs=53.1

Q ss_pred             cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhC---------------------CCcccccccccccccccccCC
Q psy1904         102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFG---------------------MTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus       102 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~---------------------l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      |+.||++|+..||..|+.++||+..+|+.||..++                     |++.+|++||||||++.|+.+
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999999994                     899999999999999999865

>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=99.75  E-value=9.1e-20  Score=110.53  Aligned_cols=60  Identities=27%  Similarity=0.353  Sum_probs=55.8

Q ss_pred             ccccCcCCHHHHHHHHHhcc---CCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904          99 RRSRTTFTSAQLEELEKSFQ---RSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~---~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      |+.|+.|+++|+.+|+..|.   .++||+..++++||..+||++.||++||+|+|+|.|+..+
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            56789999999999999997   5889999999999999999999999999999999987654

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=1.1e-19  Score=102.72  Aligned_cols=50  Identities=20%  Similarity=0.197  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHhccC-CCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904         106 TSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus       106 t~~q~~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      |.+|..+||..|.. ++||+..++.+||..+||++.+|++||||||++.|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            56799999999976 789999999999999999999999999999999886

>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=99.74  E-value=1.9e-19  Score=109.86  Aligned_cols=55  Identities=16%  Similarity=0.036  Sum_probs=50.7

Q ss_pred             cCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904         104 TFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP  158 (163)
Q Consensus       104 ~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~  158 (163)
                      .+|++|+.+|+..|..++||+..++++||..+||++.+|++||||||++.++...
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            3589999999999999999999999999999999999999999999999765443

>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=99.73  E-value=2.4e-19  Score=109.47  Aligned_cols=56  Identities=18%  Similarity=0.116  Sum_probs=52.3

Q ss_pred             cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904         102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL  157 (163)
Q Consensus       102 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~  157 (163)
                      +..||.+|+.+|+..|..|+||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            34679999999999999999999999999999999999999999999999998743

>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=99.69  E-value=7.2e-19  Score=101.87  Aligned_cols=55  Identities=16%  Similarity=0.216  Sum_probs=50.4

Q ss_pred             cccCcCCHHHHHHHHHhccC-CCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904         100 RSRTTFTSAQLEELEKSFQR-SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL  154 (163)
Q Consensus       100 r~Rt~~t~~q~~~Le~~F~~-~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k  154 (163)
                      +.++.++.++..+||..|.. ++||+..++.+||..+||++.+|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45678888899999999975 68999999999999999999999999999999876

>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=99.65  E-value=8.9e-18  Score=97.72  Aligned_cols=52  Identities=19%  Similarity=0.268  Sum_probs=48.4

Q ss_pred             cCCHHHHHHHHHhccC---CCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904         104 TFTSAQLEELEKSFQR---SHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS  155 (163)
Q Consensus       104 ~~t~~q~~~Le~~F~~---~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr  155 (163)
                      .|+.+|+..|+..|..   ++||+..++++||..+||++.||++||+|+|+|.|+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            4999999999999965   479999999999999999999999999999998775

>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=99.64  E-value=1.9e-17  Score=96.81  Aligned_cols=55  Identities=11%  Similarity=0.207  Sum_probs=51.0

Q ss_pred             ccccCcCCHHHHHHHHHhcc---CCCCCCHHHHHHHHHHhCCCccccccccccccccc
Q psy1904          99 RRSRTTFTSAQLEELEKSFQ---RSHYPDIYTREALANKFGMTETRVQQFVLGTAGFL  153 (163)
Q Consensus        99 rr~Rt~~t~~q~~~Le~~F~---~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~  153 (163)
                      ++.|+.|+++++.+|+..|.   .++||+..++..||..+||+..||++||+|+|.|.
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~   60 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI   60 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHh
Confidence            56678999999999999997   48999999999999999999999999999999875

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1.2e-15  Score=88.37  Aligned_cols=37  Identities=84%  Similarity=1.332  Sum_probs=35.4

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++|+++|+||++|+||++||+||+++|+|||++.||
T Consensus        27 ~~~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i~PG   63 (63)
T d1k78a1          27 AHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPG   63 (63)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCC
Confidence            4589999999999999999999999999999999997

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=4e-11  Score=67.38  Aligned_cols=53  Identities=47%  Similarity=0.846  Sum_probs=47.7

Q ss_pred             CCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhccCCCCCCCCCCc
Q psy1904          39 VIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPG   91 (163)
Q Consensus        39 ~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~~~~~~~~~~~~   91 (163)
                      .+||++|++.++.++..|.+++.+||++++||+++.|..+.-++.++.++.++
T Consensus         1 vIGGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~egiC~~~nvPSvSs   53 (61)
T d1k78a2           1 VIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSS   53 (61)
T ss_dssp             CCCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCcccHHHHHHHHHHcCCCCCCCCCchHH
Confidence            36999999999999999999999999999999999999999988877666543

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.8e-10  Score=65.36  Aligned_cols=52  Identities=44%  Similarity=0.803  Sum_probs=47.0

Q ss_pred             CCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhccCCCCCCCCCCcc
Q psy1904          41 GGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESEPGI   92 (163)
Q Consensus        41 Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~~~~~~~~~~~~~   92 (163)
                      ||++|++.++.++..|.+++.++|+|++||+++.|+.+.-++.++.++.++.
T Consensus         1 GGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~egiC~~~~vPSvSsI   52 (65)
T d6paxa2           1 GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSI   52 (65)
T ss_dssp             SCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTCCCHHHH
T ss_pred             CCCCcCcCCHHHHHHHHHHHHhCCccchHHHHHHHHHcCCCCCCCCCchHHH
Confidence            7899999999999999999999999999999999999999888776665543

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=98.01  E-value=1e-06  Score=45.82  Aligned_cols=28  Identities=25%  Similarity=0.449  Sum_probs=25.2

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      |..+|+.+.+||+.|||+.++|+++|+.
T Consensus        14 L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          14 MWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            3468999999999999999999999963

>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=97.65  E-value=6.4e-06  Score=44.08  Aligned_cols=24  Identities=4%  Similarity=0.063  Sum_probs=22.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .+|.+..+||+.||||.+||+++|
T Consensus        19 ~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_          19 EKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             HCCCCHHHHHHHHCcCHHHHHhhC
Confidence            479999999999999999999997

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=97.51  E-value=4.5e-05  Score=46.33  Aligned_cols=33  Identities=12%  Similarity=0.257  Sum_probs=28.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .|.+..+||+.||||.++|++|+++|...+...
T Consensus        22 ~g~s~~~vA~~lGIs~~tl~~W~k~~~~~~~~~   54 (89)
T d2jn6a1          22 DGASLQQIANDLGINRVTLKNWIIKYGSNHNVQ   54 (89)
T ss_dssp             GGSCHHHHHHHHTSCHHHHHHHHHHHCCCSTTC
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHHHHhhccccc
Confidence            489999999999999999999999996665443

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.21  E-value=0.00012  Score=41.31  Aligned_cols=24  Identities=13%  Similarity=0.093  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|-
T Consensus        10 ~~gltQ~elA~~lGvs~~tvs~~E   33 (62)
T d2ppxa1          10 ALKLTQEEFSARYHIPLGTLRDWE   33 (62)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            469999999999999999999994

>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=97.03  E-value=0.00017  Score=41.03  Aligned_cols=23  Identities=26%  Similarity=0.452  Sum_probs=21.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ++..|||+.|||+.+||+.||+.
T Consensus        26 ~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1          26 LRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             SCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             chHHHHHHHhCCChhHHHHHHHH
Confidence            78999999999999999999965

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=96.62  E-value=0.00076  Score=37.73  Aligned_cols=34  Identities=18%  Similarity=0.190  Sum_probs=29.8

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .++..+||+.||||.++|+.-+++..+.|=+.--
T Consensus        21 ~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~   54 (61)
T d2ev0a1          21 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   54 (61)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEc
Confidence            4889999999999999999999999998876543

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=96.57  E-value=0.0028  Score=34.81  Aligned_cols=22  Identities=32%  Similarity=0.421  Sum_probs=19.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~   27 (163)
                      +...|||+..|||.+|||+.|+
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln   23 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVN   23 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHT
T ss_pred             cCHHHHHHHHCcCHHHHHHHhC
Confidence            4678999999999999999993

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.49  E-value=0.0012  Score=36.67  Aligned_cols=23  Identities=26%  Similarity=0.239  Sum_probs=20.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      |...|||+..|||.+|||+.|+-
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~   23 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVING   23 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            45789999999999999999943

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.46  E-value=0.0014  Score=36.89  Aligned_cols=31  Identities=26%  Similarity=0.317  Sum_probs=28.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..+||+.||||.+||++-+++..+-|=+.
T Consensus        24 v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~   54 (63)
T d2isya1          24 PLRARIAERLDQSGPTVSQTVSRMERDGLLR   54 (63)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            8999999999999999999999998888764

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=96.43  E-value=0.0012  Score=37.29  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.|+|+++|||.++|++|.
T Consensus        12 ~~g~tq~elA~~~gis~~~is~~e   35 (66)
T d1utxa_          12 KKKISQSELAALLEVSRQTINGIE   35 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHhcccCHHHHHHHH
Confidence            479999999999999999999996

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.28  E-value=0.0011  Score=39.65  Aligned_cols=33  Identities=21%  Similarity=0.311  Sum_probs=30.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++++.+||+.+++++++|+++|++..+-|-+.
T Consensus        20 ~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~   52 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQQSASRIIIDLEKNGYIT   52 (85)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence            359999999999999999999999999888874

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.25  E-value=0.0013  Score=36.90  Aligned_cols=29  Identities=14%  Similarity=0.212  Sum_probs=27.4

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      ++..|+|+.||||..||.+-++..++.|-
T Consensus        20 ~s~~eLa~~l~vS~~ti~r~i~~L~~~G~   48 (63)
T d1biaa1          20 HSGEQLGETLGMSRAAINKHIQTLRDWGV   48 (63)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence            89999999999999999999999998885

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=96.20  E-value=0.0016  Score=37.33  Aligned_cols=33  Identities=12%  Similarity=0.211  Sum_probs=30.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .+++..|||+.+|+|.+||++++....+.|-+.
T Consensus        19 g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~   51 (71)
T d1z05a1          19 GPISRIDLSKESELAPASITKITRELIDAHLIH   51 (71)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            358999999999999999999999999888775

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=96.08  E-value=0.0016  Score=36.57  Aligned_cols=24  Identities=13%  Similarity=0.115  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.|+|+.+|||+++|++|.
T Consensus        14 ~~gltq~~lA~~~gvs~~ti~~~E   37 (65)
T d2croa_          14 ALKMTQTELATKAGVKQQSIQLIE   37 (65)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHhHHHHHH
Confidence            479999999999999999999996

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.08  E-value=0.0017  Score=35.65  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=19.3

Q ss_pred             ChhhhHHHhhcchhhHHHHHhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      ...|||+..|||.+|||+.|+.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~   23 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK   23 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC
Confidence            3579999999999999999943

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.05  E-value=0.0063  Score=33.55  Aligned_cols=21  Identities=24%  Similarity=0.213  Sum_probs=19.7

Q ss_pred             CChhhhHHHhhcchhhHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +...|||+..|||.+|||+.|
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l   23 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVV   23 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHH
Confidence            567899999999999999999

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=96.03  E-value=0.0021  Score=36.65  Aligned_cols=24  Identities=21%  Similarity=0.313  Sum_probs=22.8

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.|+|+.+||++++|++|.
T Consensus        17 ~~gltq~elA~~~gv~~~~is~ie   40 (69)
T d2a6ca1          17 NSGLTQFKAAELLGVTQPRVSDLM   40 (69)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHHcCHhHHHHHH
Confidence            579999999999999999999997

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=95.99  E-value=0.0025  Score=36.17  Aligned_cols=24  Identities=13%  Similarity=0.124  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        20 ~~gltq~~lA~~~gis~~~i~~~E   43 (69)
T d1y7ya1          20 AKGLSQETLAFLSGLDRSYVGGVE   43 (69)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHhHhCCCHHHHHHHH
Confidence            479999999999999999999996

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.98  E-value=0.0017  Score=37.23  Aligned_cols=34  Identities=18%  Similarity=0.259  Sum_probs=29.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..|||+.+|+|.+||++++....+.|-+..
T Consensus        18 g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e   51 (70)
T d1z6ra1          18 GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            3499999999999999999999999988887653

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=95.78  E-value=0.0025  Score=38.23  Aligned_cols=24  Identities=17%  Similarity=0.191  Sum_probs=22.9

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +.|+++.++|+.+|||+++|++|+
T Consensus        22 ~~gltq~~lA~~~gis~~~is~ie   45 (89)
T d2o38a1          22 RARLSQAAAAARLGINQPKVSALR   45 (89)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHHhhHhHHHHHH
Confidence            479999999999999999999997

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=95.75  E-value=0.003  Score=37.71  Aligned_cols=24  Identities=17%  Similarity=0.288  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|+
T Consensus        12 ~~glsq~~LA~~lGvs~~~is~ie   35 (87)
T d2icta1          12 ELNVSLREFARAMEIAPSTASRLL   35 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHhhcHHHHHHHH
Confidence            369999999999999999999998

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.75  E-value=0.0038  Score=36.16  Aligned_cols=35  Identities=17%  Similarity=0.167  Sum_probs=32.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .+++..|||+.+|++.+||+++|....+.|-+.-.
T Consensus        19 ~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~   53 (75)
T d1mkma1          19 GDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   53 (75)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            56999999999999999999999999999988654

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.61  E-value=0.0044  Score=36.11  Aligned_cols=24  Identities=4%  Similarity=0.122  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        17 ~~gltq~~lA~~~gis~~~is~~E   40 (78)
T d1x57a1          17 SKGLTQKDLATKINEKPQVIADYE   40 (78)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCChhHHHHcCCCCHHHHHHHH
Confidence            479999999999999999999996

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=95.39  E-value=0.0059  Score=36.32  Aligned_cols=24  Identities=8%  Similarity=0.277  Sum_probs=22.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+++|||.++|++|.
T Consensus        23 ~~gltq~~lA~~lgis~~~is~~E   46 (87)
T d1lmb3_          23 ELGLSQESVADKMGMGQSGVGALF   46 (87)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCccHHHHHHHH
Confidence            369999999999999999999996

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=95.37  E-value=0.005  Score=34.89  Aligned_cols=24  Identities=17%  Similarity=0.091  Sum_probs=22.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.||||..+|++|-
T Consensus        12 ~~gltQ~elA~~LGvs~~ti~~yE   35 (67)
T d2auwa1          12 RNNLSLTTAAEALGISRRMVSYYR   35 (67)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            369999999999999999999984

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=95.35  E-value=0.0046  Score=34.88  Aligned_cols=24  Identities=17%  Similarity=0.206  Sum_probs=22.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        12 ~~gltq~~la~~~gis~~~i~~~E   35 (68)
T d1b0na2          12 EKGYSLSELAEKAGVAKSYLSSIE   35 (68)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            479999999999999999999996

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=95.29  E-value=0.0051  Score=34.13  Aligned_cols=24  Identities=4%  Similarity=0.279  Sum_probs=22.6

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.|+|+.+|||.++|++|.
T Consensus        12 ~~g~sq~elA~~~gvs~~~is~~E   35 (63)
T d1r69a_          12 QLGLNQAELAQKVGTTQQSIEQLE   35 (63)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCcHHHHHHHhCcCHHHHHHHH
Confidence            479999999999999999999996

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=95.28  E-value=0.0072  Score=33.78  Aligned_cols=24  Identities=17%  Similarity=0.243  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        14 ~~g~tq~~lA~~~gvs~~~i~~~e   37 (66)
T d2r1jl1          14 KLKIRQAALGKMVGVSNVAISQWE   37 (66)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            368999999999999999999997

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=95.22  E-value=0.0049  Score=34.42  Aligned_cols=32  Identities=16%  Similarity=0.302  Sum_probs=29.0

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      -++..+||+.+|+|.++|.+=++++.+.|-+.
T Consensus        19 r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~   50 (63)
T d2cfxa1          19 RLSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (63)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            38999999999999999999999999888763

>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=95.21  E-value=0.0065  Score=34.39  Aligned_cols=26  Identities=15%  Similarity=0.149  Sum_probs=24.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..|||+.+|||.++|...+.+-
T Consensus        36 ~~~s~~eIA~~lgis~~tv~~~~~ra   61 (71)
T d1rp3a2          36 EELPAKEVAKILETSVSRVSQLKAKA   61 (71)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            68999999999999999999998765

>d1s7ea2 a.35.1.7 (A:6-85) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.17  E-value=0.0036  Score=36.65  Aligned_cols=28  Identities=18%  Similarity=0.275  Sum_probs=24.6

Q ss_pred             ccCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      ...+|++...|+ .|+.|+|++|.+|.+.
T Consensus        16 ~~~~IsQ~~Fa~~vL~rsQGtlSdLL~kP   44 (80)
T d1s7ea2          16 KRYSIPQAIFAQRVLCRSQGTLSDLLRNP   44 (80)
T ss_dssp             TSSCCCHHHHHHHTSSSCSSHHHHHTTSC
T ss_pred             HHcCCCHHHHHHHHHccChHHHHHHHcCC
Confidence            457899999999 9999999999999643

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=95.00  E-value=0.0088  Score=36.98  Aligned_cols=26  Identities=19%  Similarity=0.176  Sum_probs=23.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      +|++..+||..+|||.++|+..+.+-
T Consensus        31 ~~ls~~EIA~~lgiS~~aV~~~l~RA   56 (106)
T d1s7oa_          31 DDYSLAEIADEFGVSRQAVYDNIKRT   56 (106)
T ss_dssp             TCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            68999999999999999999998664

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=94.96  E-value=0.0051  Score=34.25  Aligned_cols=34  Identities=18%  Similarity=0.296  Sum_probs=29.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ..++..|||+.+|+|.+||+++++.+.+.|-+..
T Consensus        11 ~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e   44 (62)
T d2hoea1          11 SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVE   44 (62)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4589999999999999999999999977777644

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.89  E-value=0.0083  Score=38.69  Aligned_cols=33  Identities=12%  Similarity=0.257  Sum_probs=30.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .|+++.+||+.+++++++|++++++..+.|=+.
T Consensus        49 ~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~   81 (141)
T d1lnwa_          49 RGLNLQDLGRQMCRDKALITRKIRELEGRNLVR   81 (141)
T ss_dssp             TTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCccHhHHHHHHHHHHHhhcee
Confidence            579999999999999999999999999999774

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=94.84  E-value=0.0063  Score=37.56  Aligned_cols=32  Identities=16%  Similarity=0.234  Sum_probs=29.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++++.|||+.++++.++|+++|++..+-|=+.
T Consensus        36 ~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~   67 (109)
T d2d1ha1          36 PITSEELADIFKLSKTTVENSLKKLIELGLVV   67 (109)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCccHhHHHHHHHHHHHCCCEE
Confidence            38999999999999999999999999999763

>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=94.81  E-value=0.011  Score=33.24  Aligned_cols=26  Identities=19%  Similarity=0.164  Sum_probs=24.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|++..|||+.+|||.++|...+.+-
T Consensus        33 ~~~s~~eIA~~lgis~~tv~~~l~ra   58 (68)
T d1or7a1          33 DGLSYEEIAAIMDCPVGTVRSRIFRA   58 (68)
T ss_dssp             TCCCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            68999999999999999999998764

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=94.78  E-value=0.0087  Score=36.42  Aligned_cols=42  Identities=17%  Similarity=0.128  Sum_probs=35.9

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      ++..+..+|||+.||+|+++||.=|+..++.|-+.....|..
T Consensus        33 ~~~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r~G~~   74 (98)
T d1r1ta_          33 ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRH   74 (98)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEECCE
Confidence            445588999999999999999999999999999977665543

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=94.69  E-value=0.012  Score=33.89  Aligned_cols=24  Identities=13%  Similarity=0.159  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||+++|++|.
T Consensus        21 ~~gltq~~lA~~~gis~~~i~~~e   44 (77)
T d2b5aa1          21 QKGVSQEELADLAGLHRTYISEVE   44 (77)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            469999999999999999999996

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.69  E-value=0.012  Score=32.83  Aligned_cols=30  Identities=17%  Similarity=0.220  Sum_probs=27.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~   34 (163)
                      .++..++|+.|+||..||.+-+....+.|-
T Consensus        22 ~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1          22 PVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            389999999999999999999999888774

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=94.68  E-value=0.0095  Score=38.23  Aligned_cols=33  Identities=24%  Similarity=0.384  Sum_probs=30.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.
T Consensus        43 ~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~   75 (139)
T d2a61a1          43 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLT   75 (139)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCCcccchHHHHHHHhcCeee
Confidence            469999999999999999999999999998774

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=94.62  E-value=0.014  Score=33.68  Aligned_cols=24  Identities=17%  Similarity=0.170  Sum_probs=22.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHH
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ..|+++.++|+.+|||.++|++|.
T Consensus        19 ~~g~sq~~lA~~~gis~~~i~~~E   42 (79)
T d1y9qa1          19 SRGLSLDATAQLTGVSKAMLGQIE   42 (79)
T ss_dssp             HTTCCHHHHHHHHSSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcchhHHHHHH
Confidence            469999999999999999999996

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

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: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=94.50  E-value=0.016  Score=32.58  Aligned_cols=29  Identities=21%  Similarity=0.343  Sum_probs=25.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      -+|.+..+||+.|+||..||...+.+..+
T Consensus        19 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1          19 AQGLPNKMIARRLDITESTVKVHVKHMLK   47 (67)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37999999999999999999998877643

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.49  E-value=0.015  Score=32.80  Aligned_cols=31  Identities=19%  Similarity=0.261  Sum_probs=28.3

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..|||..+|+|.-+|+++|+.+++.|-+.
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~   60 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS   60 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6889999999999999999999999888653

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=94.43  E-value=0.011  Score=32.54  Aligned_cols=32  Identities=16%  Similarity=0.272  Sum_probs=29.4

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      -++..+||+.+|+|.++|..=+++..+.|-+.
T Consensus        17 r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1          17 KAPLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            37999999999999999999999999998775

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=94.42  E-value=0.0089  Score=33.25  Aligned_cols=32  Identities=16%  Similarity=0.250  Sum_probs=28.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++..+||+.+|+|.++|..=++++.+.|-+.
T Consensus        19 r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1          19 RTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            38999999999999999999999998888654

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=94.39  E-value=0.016  Score=33.17  Aligned_cols=31  Identities=32%  Similarity=0.339  Sum_probs=28.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..|||..+|+|..+|++.|+.+++.|-+.
T Consensus        28 lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1          28 VKMDDLARCLDDTRLNISKTLNELQDNGLIE   58 (73)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6789999999999999999999999999775

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=94.39  E-value=0.015  Score=36.82  Aligned_cols=39  Identities=13%  Similarity=0.273  Sum_probs=33.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC--CCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGG   42 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P--g~~Gg   42 (163)
                      ..++-.+||+.+++++..|.||+...+..|=+..  |..||
T Consensus        17 ~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG~~GG   57 (127)
T d1xd7a_          17 EKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGA   57 (127)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSSSSSC
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCCCCCc
Confidence            3488999999999999999999999999998743  54454

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=94.30  E-value=0.0087  Score=33.04  Aligned_cols=28  Identities=14%  Similarity=0.233  Sum_probs=24.7

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ...|-...+.|+.||||..|+++.+++|
T Consensus        30 ~~~~gn~~~aA~~LGIsR~TL~rkmkky   57 (60)
T d1umqa_          30 EMCDRNVSETARRLNMHRRTLQRILAKR   57 (60)
T ss_dssp             HHTTSCHHHHHHHHTSCHHHHHHHHHTS
T ss_pred             HHhcCcHHHHHHHHCCCHHHHHHHHHHc
Confidence            3467778899999999999999999887

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=94.28  E-value=0.0045  Score=37.61  Aligned_cols=42  Identities=14%  Similarity=0.257  Sum_probs=33.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~   46 (163)
                      .++..|||+.|+++.++|++.|++..+-|=+.-....+.++.
T Consensus        30 ~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~   71 (100)
T d1ub9a_          30 KAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPR   71 (100)
T ss_dssp             EEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCE
T ss_pred             CeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCcc
Confidence            488999999999999999999999999998865443334433

>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=94.26  E-value=0.019  Score=32.18  Aligned_cols=28  Identities=14%  Similarity=0.093  Sum_probs=25.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      -+|.+..|||+.|+||.+||...+.+..
T Consensus        17 ~~G~s~~eIA~~L~is~~TV~~~~~~i~   44 (67)
T d1fsea_          17 VQDKTTKEIASELFISEKTVRNHISNAM   44 (67)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4799999999999999999999887763

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.10  E-value=0.015  Score=32.01  Aligned_cols=31  Identities=26%  Similarity=0.334  Sum_probs=28.9

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..+||+.+|+|.++|..=+++..+.|-+.
T Consensus        18 ~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1          18 TPFTEIAKKLGISETAVRKRVKALEEKGIIE   48 (60)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            7999999999999999999999999998774

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=94.04  E-value=0.017  Score=35.59  Aligned_cols=27  Identities=19%  Similarity=0.143  Sum_probs=24.3

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .+|++..+||..+|||.++|...+.+-
T Consensus        32 ~e~ls~~EIA~~lgiS~~aV~~~l~Ra   58 (106)
T d1xsva_          32 LEDYSLSEIADTFNVSRQAVYDNIRRT   58 (106)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HhCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            378999999999999999999998664

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.84  E-value=0.011  Score=36.63  Aligned_cols=40  Identities=20%  Similarity=0.174  Sum_probs=32.6

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~   44 (163)
                      ++..|+||+.||+|+++||.=|+..++.|-+.....|...
T Consensus        45 ~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r~G~~~   84 (108)
T d1u2wa1          45 ELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLA   84 (108)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CC
T ss_pred             CccHHHHHHHHccChhHHHHHHHHHHHCCeeEEEEECCEE
Confidence            4789999999999999999999999999999877666543

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=93.74  E-value=0.012  Score=36.58  Aligned_cols=27  Identities=15%  Similarity=0.230  Sum_probs=24.2

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|.+..+||+++|+|.++|++.|.-.
T Consensus        28 ~~g~s~~eiA~~~G~s~~~V~~~l~L~   54 (114)
T d1r71a_          28 AKGKKKGDIAKEIGKSPAFITQHVTLL   54 (114)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             HhCCCHHHHHHHHCCcHHHHHHHHHHh
Confidence            469999999999999999999999554

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.72  E-value=0.012  Score=35.11  Aligned_cols=28  Identities=11%  Similarity=0.195  Sum_probs=24.9

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~   28 (163)
                      |.+..|++..||..-|||+|.||.+|..
T Consensus        37 l~~h~I~Q~~Va~~TGlsQS~iSq~L~~   64 (94)
T d1ic8a2          37 LQQHNIPQREVVDTTGLNQSHLSQHLNK   64 (94)
T ss_dssp             HHHTTCCHHHHHHHHCCCHHHHHHHHHS
T ss_pred             HHHcCCcHHHHHHHHcccHHHHHHHHhC
Confidence            4567899999999999999999999953

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.70  E-value=0.014  Score=35.94  Aligned_cols=33  Identities=30%  Similarity=0.420  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .++++.+||+.+||+.++|+++|++..+-|-+.
T Consensus        33 g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~   65 (109)
T d1sfxa_          33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEE
Confidence            458999999999999999999999999999874

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.67  E-value=0.012  Score=38.02  Aligned_cols=43  Identities=28%  Similarity=0.369  Sum_probs=35.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~   46 (163)
                      .++++.|||+.+|||.++|++.|++..+.|-+.--..++.++.
T Consensus        40 ~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~drr~   82 (151)
T d1ku9a_          40 KPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKN   82 (151)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCSSC
T ss_pred             CCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCCCce
Confidence            4589999999999999999999999999999954433444433

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=93.59  E-value=0.017  Score=37.25  Aligned_cols=38  Identities=18%  Similarity=0.270  Sum_probs=33.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-....
T Consensus        42 ~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~   79 (144)
T d1lj9a_          42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCC
Confidence            57999999999999999999999999999888644433

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

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: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.58  E-value=0.031  Score=31.09  Aligned_cols=27  Identities=22%  Similarity=0.041  Sum_probs=24.4

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      -.|.+..|||+.|+||..||...+.+.
T Consensus        17 ~~G~s~~eIA~~l~iS~~TV~~~~~~i   43 (65)
T d1l3la1          17 AVGKTMEEIADVEGVKYNSVRVKLREA   43 (65)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HhcCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            369999999999999999999988766

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.45  E-value=0.052  Score=33.58  Aligned_cols=53  Identities=13%  Similarity=0.047  Sum_probs=39.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHH
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEE   58 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~   58 (163)
                      +++.+||+.++++.++|++++++..+.|=+.-.....++..   ..++.-.+.+.+
T Consensus        50 ~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~  105 (115)
T d2frha1          50 YYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIES  105 (115)
T ss_dssp             EEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHHHH
Confidence            88999999999999999999999999998866554444322   334555544443

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=93.44  E-value=0.027  Score=35.72  Aligned_cols=35  Identities=11%  Similarity=0.140  Sum_probs=31.0

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      ++++.|||+.++++.++|++++++..+.|=+.--.
T Consensus        45 ~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~   79 (135)
T d3broa1          45 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKV   79 (135)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHh
Confidence            38999999999999999999999998888885443

>d1x2la1 a.35.1.7 (A:9-95) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.43  E-value=0.0095  Score=35.34  Aligned_cols=27  Identities=33%  Similarity=0.418  Sum_probs=24.0

Q ss_pred             cCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      ..+|++...|+ .|+.|+|++|.||.+.
T Consensus        24 ~~~I~Q~~Fa~~VL~rsQGtlSdLL~~P   51 (87)
T d1x2la1          24 KHNIGQRVFGHYVLGLSQGSVSEILARP   51 (87)
T ss_dssp             HTTCCHHHHHHHTTCSCHHHHHHHHHCC
T ss_pred             HcCCCHHHHHHHHHhhChHHHHHHHhCC
Confidence            46899999999 9999999999999654

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

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: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=93.22  E-value=0.037  Score=31.24  Aligned_cols=28  Identities=14%  Similarity=0.084  Sum_probs=25.0

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~   30 (163)
                      ..|.+..+||..|+||..||...+.+..
T Consensus        25 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~   52 (70)
T d1yioa1          25 IRGLMNKQIAGELGIAEVTVKVHRHNIM   52 (70)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3799999999999999999999887763

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.19  E-value=0.033  Score=35.32  Aligned_cols=34  Identities=12%  Similarity=0.268  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.+++++++|++++++..+-|=+.=
T Consensus        42 ~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r   75 (137)
T d2fbha1          42 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRR   75 (137)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccc
Confidence            4699999999999999999999999988887753

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=93.13  E-value=0.033  Score=32.18  Aligned_cols=31  Identities=3%  Similarity=0.050  Sum_probs=28.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..|||..+|+|.-+|+++|+.+++.|-+.
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~   60 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLA   60 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5788999999999999999999999999775

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=93.13  E-value=0.026  Score=36.04  Aligned_cols=38  Identities=11%  Similarity=0.139  Sum_probs=32.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G   41 (163)
                      .++++.+||+.++|+.++|++++++..+.|=+.-....
T Consensus        45 ~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~   82 (140)
T d2etha1          45 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDP   82 (140)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecc
Confidence            45899999999999999999999999999988654433

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=93.12  E-value=0.036  Score=31.99  Aligned_cols=32  Identities=19%  Similarity=0.219  Sum_probs=29.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++.-|||..+|+|..+|+++|+.+++.|-+.-
T Consensus        31 lt~~elA~~~g~sretvsr~l~~l~~~glI~~   62 (80)
T d3e5ua1          31 LSQKSIGEITGVHHVTVSRVLASLKRENILDK   62 (80)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            67889999999999999999999999997753

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.07  E-value=0.021  Score=34.31  Aligned_cols=40  Identities=25%  Similarity=0.219  Sum_probs=34.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      .-+..+|||+.||+|+++||+=|+..++.|-+.-...|..
T Consensus        30 ~~~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~r~G~~   69 (94)
T d1r1ua_          30 SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQS   69 (94)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEEEECCE
Confidence            3478999999999999999999999999998877665543

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=92.95  E-value=0.042  Score=31.70  Aligned_cols=32  Identities=22%  Similarity=0.158  Sum_probs=29.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++..|||..+|+|..||+++|+.+++.|-+.-
T Consensus        31 ~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~   62 (80)
T d1ft9a1          31 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR   62 (80)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            56789999999999999999999999998753

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.83  E-value=0.037  Score=35.54  Aligned_cols=32  Identities=19%  Similarity=0.329  Sum_probs=29.9

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++++.+||+.++|+.++|++++++....|=+.
T Consensus        49 ~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~   80 (145)
T d2hr3a1          49 DVTPSELAAAERMRSSNLAALLRELERGGLIV   80 (145)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeE
Confidence            38999999999999999999999999988885

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.81  E-value=0.015  Score=36.21  Aligned_cols=40  Identities=8%  Similarity=0.009  Sum_probs=33.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~   43 (163)
                      .|+++.+||+.++++.++|++++++..+-|=+.=.....+
T Consensus        47 ~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~~D   86 (115)
T d1hsja1          47 NEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQD   86 (115)
T ss_dssp             SEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSS
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeecCC
Confidence            3599999999999999999999999999998864443333

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.62  E-value=0.057  Score=33.98  Aligned_cols=56  Identities=9%  Similarity=0.005  Sum_probs=40.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEEY   59 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~~   59 (163)
                      .|+++.+||+.++++.++|++++++..+-|=+.=.....++..   ..++.-.+.+.++
T Consensus        48 ~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~l  106 (125)
T d1p4xa2          48 NIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQL  106 (125)
T ss_dssp             CCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHH
T ss_pred             CCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHHH
Confidence            4689999999999999999999999999998853333333322   3345555545443

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.57  E-value=0.031  Score=35.59  Aligned_cols=35  Identities=9%  Similarity=0.274  Sum_probs=31.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|++++|++++++..+.|=+.-.
T Consensus        45 ~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~   79 (140)
T d3deua1          45 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ   79 (140)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEec
Confidence            45899999999999999999999999999987533

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=92.48  E-value=0.026  Score=33.88  Aligned_cols=27  Identities=15%  Similarity=0.250  Sum_probs=24.1

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..|+++.+||++||.|.++|+..|.-.
T Consensus        17 e~g~t~~~iA~~~Gks~~~V~~~LrLl   43 (93)
T d1vz0a1          17 EMGLTQEEVARRVGKARSTVANALRLL   43 (93)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHGG
T ss_pred             HcCCCHHHHHHHHccchHHHHHHHHHH
Confidence            468999999999999999999998554

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=92.45  E-value=0.086  Score=29.52  Aligned_cols=20  Identities=5%  Similarity=-0.031  Sum_probs=17.8

Q ss_pred             hhhhHHHhhcchhhHHHHHh
Q psy1904           8 PCVISRQLRVSHGCVSKILN   27 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~l~   27 (163)
                      ..++|+.||||..||..|.+
T Consensus         5 k~~lA~iFGVS~~TI~~W~~   24 (68)
T d1j9ia_           5 KKQLADIFGASIRTIQNWQE   24 (68)
T ss_dssp             HHHHHHHTTCCHHHHHHHTT
T ss_pred             HHHHHHHhCCCHHHHHHHHH
Confidence            46899999999999999973

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=92.27  E-value=0.043  Score=34.97  Aligned_cols=33  Identities=24%  Similarity=0.484  Sum_probs=30.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      .|+++.|||+.++++.++|++++++..+.|=+.
T Consensus        47 ~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~   79 (138)
T d1jgsa_          47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVE   79 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEE
Confidence            579999999999999999999999999999874

>d1wh6a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.18  E-value=0.023  Score=34.49  Aligned_cols=27  Identities=33%  Similarity=0.535  Sum_probs=24.0

Q ss_pred             ccCCCChhhhHH-HhhcchhhHHHHHhh
Q psy1904           2 AAAGVRPCVISR-QLRVSHGCVSKILNR   28 (163)
Q Consensus         2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~   28 (163)
                      ...+|++...|+ .|+.|++++|.||.+
T Consensus        31 ~~~~IsQ~~Fa~~VL~rSQGtlSdLL~~   58 (101)
T d1wh6a_          31 AKNGICQRIFGEKVLGLSQGSVSDMLSR   58 (101)
T ss_dssp             HTTTCCHHHHHHHTTCCCHHHHHHHHHS
T ss_pred             HHcCCcHHHHHHHHHccChHHHHHHHhC
Confidence            457899999999 899999999999964

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.15  E-value=0.055  Score=30.87  Aligned_cols=30  Identities=17%  Similarity=0.287  Sum_probs=27.2

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      +..++|+.|+||.+||.+-++.+...|-+.
T Consensus        29 s~~eLa~~~~vSr~tvr~Al~~L~~~G~i~   58 (74)
T d1hw1a1          29 AERELSELIGVTRTTLREVLQRLARDGWLT   58 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            568999999999999999999998888774

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=91.91  E-value=0.02  Score=36.53  Aligned_cols=36  Identities=19%  Similarity=0.305  Sum_probs=32.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.=..
T Consensus        46 ~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~   81 (137)
T d1z91a1          46 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKR   81 (137)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCB
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEee
Confidence            578999999999999999999999999998885443

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.70  E-value=0.029  Score=35.67  Aligned_cols=36  Identities=22%  Similarity=0.312  Sum_probs=32.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-..
T Consensus        47 ~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~   82 (136)
T d2bv6a1          47 SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRER   82 (136)
T ss_dssp             SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEee
Confidence            578999999999999999999999999999885443

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=91.60  E-value=0.034  Score=30.58  Aligned_cols=25  Identities=24%  Similarity=0.402  Sum_probs=21.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .| ....+|+.||||..|+++.+++|
T Consensus        33 ~g-n~~~aA~~Lgisr~tL~rKlkk~   57 (61)
T d1g2ha_          33 YP-STRKLAQRLGVSHTAIANKLKQY   57 (61)
T ss_dssp             SC-SHHHHHHHTTSCTHHHHHHHHTT
T ss_pred             CC-CHHHHHHHHCCCHHHHHHHHHHh
Confidence            45 46789999999999999999887

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=91.19  E-value=0.051  Score=30.59  Aligned_cols=34  Identities=12%  Similarity=0.253  Sum_probs=30.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++.+-+||+.|||+...|=+.|-...+.|.+.-
T Consensus        23 ~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~   56 (70)
T d1sfua_          23 DYTTAISLSNRLKINKKKINQQLYKLQKEDTVKM   56 (70)
T ss_dssp             CEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeec
Confidence            4588999999999999999999999999998864

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=91.16  E-value=0.042  Score=35.13  Aligned_cols=35  Identities=14%  Similarity=0.283  Sum_probs=31.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg   38 (163)
                      .|+++.+||+.++|++++|++++++....|=+.--
T Consensus        48 ~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~   82 (143)
T d1s3ja_          48 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   82 (143)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheee
Confidence            46899999999999999999999999999988543

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.11  E-value=0.044  Score=34.75  Aligned_cols=34  Identities=15%  Similarity=0.305  Sum_probs=30.5

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.=
T Consensus        43 ~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r   76 (136)
T d2fbia1          43 GEMESYQLANQACILRPSMTGVLARLERDGIVRR   76 (136)
T ss_dssp             CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4689999999999999999999999988887743

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=90.92  E-value=0.052  Score=32.21  Aligned_cols=27  Identities=15%  Similarity=0.246  Sum_probs=23.7

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..+-....+|+.||||..|+++.+++|
T Consensus        60 ~~~gn~~~aA~~LGisR~tL~~klk~~   86 (89)
T d1etxa_          60 YTRGNATRAALMMGINRGTLRKKLKKY   86 (89)
T ss_dssp             HTTTCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HcCCcHHHHHHHHCCCHHHHHHHHHHh
Confidence            345677899999999999999999987

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=90.85  E-value=0.078  Score=30.85  Aligned_cols=23  Identities=13%  Similarity=0.108  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .|++..++|++.|||.++|++|.
T Consensus        24 ~~~t~~eLA~~~Gvs~~~ls~iE   46 (82)
T d2ofya1          24 GDMSMVTVAFDAGISVETLRKIE   46 (82)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCHHHHHHHHcCCHHHHHHHH
Confidence            47889999999999999999995

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=90.82  E-value=0.086  Score=29.76  Aligned_cols=31  Identities=19%  Similarity=0.237  Sum_probs=27.4

Q ss_pred             ChhhhHHHhhc-chhhHHHHHhhhhhccCCCC
Q psy1904           7 RPCVISRQLRV-SHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         7 ~~~~ia~~~~v-s~~~vs~~l~~~~~tG~~~P   37 (163)
                      +-.|||+.||+ |.++|...|+.+.+-|-+.-
T Consensus        26 s~rei~~~~g~~S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1          26 TRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             CHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHcCCCCHHHHHHHHHHHHHCcCeec
Confidence            44799999999 89999999999999998853

>d1wh8a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.81  E-value=0.032  Score=34.37  Aligned_cols=28  Identities=21%  Similarity=0.360  Sum_probs=24.3

Q ss_pred             ccCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           2 AAAGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      ...+|++...|+ .|+.|+++++.||.+.
T Consensus        41 ~~~~I~Q~~Fa~~VL~rSQGtlSdLL~~P   69 (111)
T d1wh8a_          41 TDNNLGQRLFGESILGLTQGSVSDLLSRP   69 (111)
T ss_dssp             HHTTCCHHHHHHHTTCCCHHHHHHHHHSC
T ss_pred             HHcCchHHHHHHHHHccChHHHHHHHhCC
Confidence            346899999999 8999999999999654

>d2o4aa1 a.35.1.7 (A:370-452) DNA-binding protein SATB1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: DNA-binding protein SATB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.80  E-value=0.044  Score=32.03  Aligned_cols=27  Identities=30%  Similarity=0.534  Sum_probs=23.5

Q ss_pred             cCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISR-QLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~~   29 (163)
                      ..+|++...|+ .|+.|+|++|.+|...
T Consensus        16 ~~~IsQ~~Fak~vL~rSQgtlSdLL~~p   43 (83)
T d2o4aa1          16 RAGISQAVFARVAFNRTQGLLSEILRKE   43 (83)
T ss_dssp             HHTCCHHHHHHHHHSCCHHHHHHHHHHC
T ss_pred             HcCCCHHHHHHHHHccCcHHHHHHHcCC
Confidence            45789999998 9999999999999664

>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]

Probab=90.78  E-value=0.095  Score=31.35  Aligned_cols=28  Identities=18%  Similarity=0.284  Sum_probs=25.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      .|....++|+.+++|..+|.+|+++.+.
T Consensus        65 ~G~n~~eLA~kY~lS~~~I~~Ii~~~rk   92 (94)
T d1rr7a_          65 NGRNVSELTTRYGVTFNTVYKAIRRMRR   92 (94)
T ss_dssp             CSSCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            5889999999999999999999988753

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=90.60  E-value=0.028  Score=37.38  Aligned_cols=36  Identities=28%  Similarity=0.324  Sum_probs=32.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      .|+++.+||+.++|+.++|++++++..+-|-+.-..
T Consensus        78 ~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~  113 (172)
T d2fbka1          78 EGLRPTELSALAAISGPSTSNRIVRLLEKGLIERRE  113 (172)
T ss_dssp             SCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC
T ss_pred             CCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeec
Confidence            579999999999999999999999999999886444

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=90.42  E-value=0.021  Score=35.92  Aligned_cols=31  Identities=29%  Similarity=0.319  Sum_probs=27.1

Q ss_pred             CccCCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      |-..|+++.|||++||-|.+.|+-|-++-+|
T Consensus         1 LR~kGltQ~eIA~~LgTSraNIs~IEk~A~e   31 (122)
T d1nr3a_           1 MRERGWSQKKIARELKTTRQNVSAIERKAME   31 (122)
T ss_dssp             CCCCSCSSCSTHHHHHHCCSSSCCHHHHHHT
T ss_pred             CccccCCHHHHHHHHCccHHHHHHHHHHHHH
Confidence            4578999999999999999999999877644

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=90.42  E-value=0.095  Score=30.02  Aligned_cols=33  Identities=21%  Similarity=0.203  Sum_probs=29.0

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +-.++|+.|+||.+||.+-|..+...|-+...+
T Consensus        24 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          24 VLETLMAQFEVSKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            567999999999999999999999999886543

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.41  E-value=0.058  Score=31.94  Aligned_cols=27  Identities=11%  Similarity=0.010  Sum_probs=23.5

Q ss_pred             cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..+-...+.|+.|||+.+|+++.+++|
T Consensus        62 ~~~Gn~~~AA~~LGI~R~TL~~Klk~~   88 (91)
T d1ntca_          62 HTQGHKQEAARLLGWGAATLTAKLKEL   88 (91)
T ss_dssp             HTTTCTTHHHHHTTCCHHHHHHHHHHH
T ss_pred             HhCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            345667889999999999999999987

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=90.41  E-value=0.048  Score=35.97  Aligned_cols=60  Identities=12%  Similarity=0.002  Sum_probs=41.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHHHHHhC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEEYKKTN   63 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~~~~~~   63 (163)
                      .|+++.+||+.++|+.++|++++++..+.|=+.-.....++..   ..++.-.+.+.+..+..
T Consensus        54 ~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  116 (162)
T d2fxaa1          54 NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  116 (162)
T ss_dssp             TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHHHHHHH
Confidence            5789999999999999999999999999998854333222222   33566665565554443

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

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: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=90.39  E-value=0.11  Score=30.53  Aligned_cols=26  Identities=19%  Similarity=0.132  Sum_probs=24.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      .|.+..+||..|+||..||...+...
T Consensus        36 ~G~s~~eIA~~l~iS~~TV~~~~~~i   61 (87)
T d1p4wa_          36 EGFLVTEIAKKLNRSIKTISSQKKSA   61 (87)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            69999999999999999999988776

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.19  E-value=0.042  Score=34.58  Aligned_cols=33  Identities=9%  Similarity=-0.026  Sum_probs=30.2

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      ++++.+||+.++++.++|++++++..+.|=+.=
T Consensus        50 ~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r   82 (125)
T d1p4xa1          50 TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISK   82 (125)
T ss_dssp             EEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEE
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCcee
Confidence            489999999999999999999999999998843

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=89.94  E-value=0.087  Score=35.30  Aligned_cols=36  Identities=11%  Similarity=0.159  Sum_probs=31.3

Q ss_pred             ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .+..++..+||+.+|+|+++|++-|+...+.|-+..
T Consensus        29 ~~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~   64 (190)
T d1ulya_          29 RNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV   64 (190)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            344489999999999999999999999999998743

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=89.85  E-value=0.1  Score=29.12  Aligned_cols=31  Identities=19%  Similarity=0.144  Sum_probs=27.8

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~   36 (163)
                      ++..++|+.||||..+|.+-+.++...|-+.
T Consensus        26 l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~   56 (69)
T d2hs5a1          26 LSEPDICAALDVSRNTVREAFQILIEDRLVA   56 (69)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            5678999999999999999999999888764

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=89.38  E-value=0.12  Score=30.13  Aligned_cols=25  Identities=16%  Similarity=0.061  Sum_probs=22.6

Q ss_pred             CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           5 GVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      -++..|||+..+||.+||.|..+++
T Consensus        36 ~~si~~lA~~~~vS~sTi~Rf~kkl   60 (83)
T d2o3fa1          36 ESTVNEISALANSSDAAVIRLCKSL   60 (83)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             HccHHHHHHHHCCCHHHHHHHHHHh
Confidence            3688999999999999999998776

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=88.83  E-value=0.065  Score=36.26  Aligned_cols=34  Identities=26%  Similarity=0.258  Sum_probs=30.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P   37 (163)
                      .-++.++||+.||||.++|++-|+...+.|-+..
T Consensus        27 ~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~   60 (194)
T d2p4wa1          27 RPYFVSELSRELGVGQKAVLEHLRILEEAGLIES   60 (194)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            3478899999999999999999999999998853

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=88.83  E-value=0.15  Score=30.73  Aligned_cols=33  Identities=12%  Similarity=0.177  Sum_probs=29.6

Q ss_pred             CCChhhhHHHhhcc-hhhHHHHHhhhhhccCCCC
Q psy1904           5 GVRPCVISRQLRVS-HGCVSKILNRYQETGSIRP   37 (163)
Q Consensus         5 g~~~~~ia~~~~vs-~~~vs~~l~~~~~tG~~~P   37 (163)
                      .++..|||..+|+| .-||+++|+.+++.|-+.-
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~   64 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY   64 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEE
Confidence            47889999999997 7899999999999998864

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=88.59  E-value=0.18  Score=32.01  Aligned_cols=37  Identities=16%  Similarity=0.361  Sum_probs=30.7

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCC
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGS   43 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~   43 (163)
                      ++-.+||+.++|+...+.|++......|=+  ..|. ||.
T Consensus        24 vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~rG~-GG~   62 (138)
T d1ylfa1          24 CTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGP-GGA   62 (138)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----CCE
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecCC-CCc
Confidence            788999999999999999999999999988  4454 555

>d2csfa1 a.35.1.7 (A:8-95) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.47  E-value=0.076  Score=31.30  Aligned_cols=26  Identities=19%  Similarity=0.330  Sum_probs=23.0

Q ss_pred             cCCCChhhhHH-HhhcchhhHHHHHhh
Q psy1904           3 AAGVRPCVISR-QLRVSHGCVSKILNR   28 (163)
Q Consensus         3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~   28 (163)
                      ..+|++...|+ .|+.|+|++|.+|..
T Consensus        25 ~~~IsQ~~Fak~vL~rSQGtlSdLLrk   51 (88)
T d2csfa1          25 RAKVSQALFAKVAANKSQGWLCELLRW   51 (88)
T ss_dssp             HHTCCHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHHccCcHHHHHHHcC
Confidence            45789999998 999999999999965

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=88.06  E-value=0.17  Score=28.02  Aligned_cols=23  Identities=9%  Similarity=0.180  Sum_probs=21.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.++++..-
T Consensus        19 ~~~ti~~Ia~~agvs~~~~Y~~F   41 (69)
T d2i10a1          19 EGTSITDLTKALGINPPSLYAAF   41 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCHHHHHHHhCCChhHHHHHC
Confidence            57999999999999999999985

>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=87.92  E-value=0.18  Score=26.03  Aligned_cols=40  Identities=18%  Similarity=0.415  Sum_probs=34.2

Q ss_pred             CcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccc
Q psy1904         103 TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVL  147 (163)
Q Consensus       103 t~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFq  147 (163)
                      ..+|++|+......+....     ...+||..+|++...|..||.
T Consensus         4 ~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           4 RAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhCC
Confidence            4689999999999998663     367899999999999998884

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=87.77  E-value=0.18  Score=29.54  Aligned_cols=25  Identities=20%  Similarity=0.288  Sum_probs=21.7

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQE   31 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~   31 (163)
                      +...+|+.++||+++|++.|+..++
T Consensus        22 s~t~AA~~l~isq~avs~~l~~lE~   46 (89)
T d2esna1          22 NVGTAASELAISASAFSHALGRLRQ   46 (89)
T ss_dssp             SHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCCcHhhHHHHHHHh
Confidence            5567899999999999999998843

>d1q06a_ a.6.1.3 (A:) Transcriptional regulator CueR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcriptional regulator CueR
species: Escherichia coli [TaxId: 562]

Probab=87.46  E-value=0.55  Score=29.08  Aligned_cols=64  Identities=9%  Similarity=0.113  Sum_probs=40.1

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      |++.|+|+.+|||..|+.-|.    +.|-+.|..  .+|.+  .=+..+...+..+.. ..-++...++.+-+
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye----~~GLl~p~~r~~~gyR--~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l   67 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYE----EKGLVTPPMRSENGYR--TYTQQHLNELTLLRQARQVGFNLEESGELV   67 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH----HTTCSCCCEECTTSCE--ECCHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HcCCCCCCccCCcCcc--cchHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            678999999999999988875    559898853  34443  234444444432221 12356666666543

>d1rzsa_ a.35.1.2 (A:) cro p22 {Bacteriophage p22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro p22
species: Bacteriophage p22 [TaxId: 10754]

Probab=87.46  E-value=0.14  Score=27.95  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=16.1

Q ss_pred             hhhhHHHhhcchhhHHHH
Q psy1904           8 PCVISRQLRVSHGCVSKI   25 (163)
Q Consensus         8 ~~~ia~~~~vs~~~vs~~   25 (163)
                      ..-+|+.||||++.||.|
T Consensus        13 ~~k~A~algis~~AVsqW   30 (61)
T d1rzsa_          13 QRAVAKALGISDAAVSQW   30 (61)
T ss_dssp             HHHHHHHHTCCHHHHHHC
T ss_pred             HHHHHHHhCCCHHHHHHH
Confidence            456899999999999999

>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=87.07  E-value=0.19  Score=27.91  Aligned_cols=46  Identities=9%  Similarity=0.203  Sum_probs=37.4

Q ss_pred             cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccc
Q psy1904         102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTA  150 (163)
Q Consensus       102 Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR  150 (163)
                      |-.+|..+...+-..|+.++-..   ..+||..+|+...+|..|..|+.
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHH
Confidence            34688888888888888886543   56899999999999999998863

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=87.03  E-value=0.18  Score=30.46  Aligned_cols=23  Identities=9%  Similarity=0.147  Sum_probs=20.6

Q ss_pred             CC-CChhhhHHHhhcchhhHHHHH
Q psy1904           4 AG-VRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g-~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .| ++..+||+.+|||.+||+|.-
T Consensus        56 ~G~~s~reI~~~~gvs~aTItR~s   79 (101)
T d1jhga_          56 RGEMSQRELKNELGAGIATITRGS   79 (101)
T ss_dssp             HCCSCHHHHHHHHCCCHHHHHHHH
T ss_pred             cCCcCHHHHHHHhCCChHHHHHHH
Confidence            57 899999999999999998864

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=86.02  E-value=0.19  Score=30.17  Aligned_cols=33  Identities=21%  Similarity=0.193  Sum_probs=29.2

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~   39 (163)
                      +..++|+.|+||..||.+-++.+...|-+....
T Consensus        35 s~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   67 (100)
T d1v4ra1          35 SVADIRAQFGVAAKTVSRALAVLKSEGLVSSRG   67 (100)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEec
Confidence            568999999999999999999999999886443

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.94  E-value=0.25  Score=27.93  Aligned_cols=23  Identities=17%  Similarity=0.128  Sum_probs=21.3

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +|++..+||+..|||.+++++..
T Consensus        23 ~~~ti~~Ia~~agvs~~s~y~~F   45 (79)
T d2fbqa1          23 AETSLRLITSKAGVNLAAVNYHF   45 (79)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHT
T ss_pred             ccccHHHHHHHHCcChhHHHHHC
Confidence            67999999999999999999985

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=84.70  E-value=0.3  Score=27.19  Aligned_cols=23  Identities=22%  Similarity=0.112  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.+++++.-
T Consensus        23 ~~~ti~~Ia~~agvs~~t~y~~F   45 (72)
T d1pb6a1          23 HGTRLEQIAELAGVSKTNLLYYF   45 (72)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHS
T ss_pred             cccCHHHHHHHhCCChHHHHHHC
Confidence            57999999999999999999974

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.49  E-value=0.26  Score=27.40  Aligned_cols=23  Identities=9%  Similarity=0.015  Sum_probs=20.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .+++-.+||+..|||.++++..-
T Consensus        22 ~~~t~~~Ia~~agvs~~t~Y~~F   44 (73)
T d1t56a1          22 ADISVDDLAKGAGISRPTFYFYF   44 (73)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHC
Confidence            46899999999999999999974

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

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: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=84.48  E-value=0.47  Score=25.73  Aligned_cols=26  Identities=12%  Similarity=0.051  Sum_probs=22.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l~~~   29 (163)
                      ..++-.+||+.||||...|+.|..+.
T Consensus        27 ~~~tl~eIa~~lgiS~erVrqi~~~a   52 (61)
T d1ku3a_          27 REHTLEEVGAYFGVTRERIRQIENKA   52 (61)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            45788999999999999999987553

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=84.30  E-value=0.33  Score=27.09  Aligned_cols=23  Identities=4%  Similarity=-0.060  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .|++..+||+..|||.++++..-
T Consensus        23 ~~~s~~~Ia~~agvs~~t~Y~~F   45 (74)
T d1v7ba1          23 ETLSYDSLAEATGLSKSGLIYHF   45 (74)
T ss_dssp             TTCCHHHHHHHHCSCHHHHHHHC
T ss_pred             cccCHHHHHHHhCcCcchHhhhC
Confidence            57999999999999999999974

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.27  E-value=0.32  Score=26.91  Aligned_cols=23  Identities=13%  Similarity=0.043  Sum_probs=21.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.++++..-
T Consensus        20 ~~~s~~~Ia~~agvs~~~~y~~F   42 (71)
T d1jt6a1          20 NATTTGEIVKLSESSKGNLYYHF   42 (71)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             cccCHHHHHHHHCcCHhHHHHHC
Confidence            57899999999999999999985

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=83.90  E-value=0.19  Score=27.19  Aligned_cols=23  Identities=13%  Similarity=0.190  Sum_probs=20.6

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++-.+||++.|||.++++...
T Consensus        18 ~~~s~~~Ia~~agvs~~tiy~~F   40 (62)
T d2vkva1          18 EGLTTRKLAQKLGVEQPTLYWHV   40 (62)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHS
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHC
Confidence            45889999999999999999975

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=83.84  E-value=0.37  Score=26.67  Aligned_cols=23  Identities=13%  Similarity=0.096  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +|++..+||+..|||.++++..-
T Consensus        24 ~~~si~~Ia~~agvs~~~~y~~F   46 (71)
T d1ui5a1          24 ESTTLSEIVAHAGVTKGALYFHF   46 (71)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cccCHHHHHHHHCcCHhHHHHHC
Confidence            57899999999999999999984

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=83.74  E-value=0.21  Score=27.61  Aligned_cols=23  Identities=13%  Similarity=0.112  Sum_probs=20.4

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +|++..+||+..|||.+++++.-
T Consensus        22 ~~~t~~~Ia~~agvs~~~iy~hF   44 (68)
T d1z0xa1          22 EQLSMRKVAKQLGVQAPAIYWYF   44 (68)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHTTC
T ss_pred             cccCHHHHHHHHCcchhHHHHhc
Confidence            46899999999999999999863

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=83.66  E-value=0.38  Score=28.04  Aligned_cols=29  Identities=14%  Similarity=0.322  Sum_probs=23.2

Q ss_pred             ChhhhHHHhhcchhhHHHHHhhh-hhccCC
Q psy1904           7 RPCVISRQLRVSHGCVSKILNRY-QETGSI   35 (163)
Q Consensus         7 ~~~~ia~~~~vs~~~vs~~l~~~-~~tG~~   35 (163)
                      +....|+.|+||+++||+-++.. .+.|..
T Consensus        17 s~~~AA~~L~isq~avs~~i~~LE~~lg~~   46 (89)
T d1ixca1          17 NMAAAAKRLHVSQPPITRQMQALEADLGVV   46 (89)
T ss_dssp             SHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHhcCCce
Confidence            55678999999999999999988 334433

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=83.20  E-value=0.41  Score=26.36  Aligned_cols=23  Identities=22%  Similarity=0.193  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++-.+||++.|||.+++++..
T Consensus        23 ~~~t~~~Ia~~agvs~~~~y~~F   45 (69)
T d2fq4a1          23 KAVTVDKIAERAKVSKATIYKWW   45 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            56899999999999999999985

>d2oi8a1 a.4.1.9 (A:8-86) Putative regulatory protein Sco4313 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulatory protein Sco4313
species: Streptomyces coelicolor [TaxId: 1902]

Probab=83.17  E-value=0.26  Score=27.94  Aligned_cols=23  Identities=9%  Similarity=0.226  Sum_probs=20.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.+++++..
T Consensus        28 ~~~t~~~Ia~~agvs~~~~Y~~F   50 (79)
T d2oi8a1          28 SALSLNAIAKRMGMSGPALYRYF   50 (79)
T ss_dssp             TSCCHHHHHHHTTCCHHHHHTTC
T ss_pred             cccCHHHHHHHhCCCCCchhhhc
Confidence            57899999999999999999864

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=83.11  E-value=0.32  Score=27.54  Aligned_cols=23  Identities=13%  Similarity=0.056  Sum_probs=20.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .+++-.+||+..|||.++++..-
T Consensus        26 ~~~t~~~Ia~~agvs~~t~y~~F   48 (78)
T d2o7ta1          26 DSLTMENIAEQAGVGVATLYRNF   48 (78)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cccCHHHHHHHhCCCHHHHHHHC
Confidence            56899999999999999999874

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=82.91  E-value=0.21  Score=28.01  Aligned_cols=23  Identities=13%  Similarity=0.158  Sum_probs=20.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +|++..+||+..|||.++++..-
T Consensus        22 ~~~ti~~Ia~~agvs~~~iY~~F   44 (75)
T d2id6a1          22 DRATTDEIAEKAGVAKGLIFHYF   44 (75)
T ss_dssp             HHCCHHHHHHHHTCCTHHHHHHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHC
Confidence            45899999999999999999985

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=82.64  E-value=0.41  Score=26.49  Aligned_cols=22  Identities=18%  Similarity=0.071  Sum_probs=20.3

Q ss_pred             CCChhhhHHHhhcchhhHHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      |++..+||+..|||.++++..-
T Consensus        20 ~~t~~~Ia~~agvs~~~~Y~~F   41 (70)
T d2hkua1          20 GVPITQICAAAGAHPNQVTYYY   41 (70)
T ss_dssp             TSCHHHHHHHHTCCHHHHHHHH
T ss_pred             CchHHHHHHHHCCChhhHHhcC
Confidence            5889999999999999999985

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.45  E-value=0.43  Score=26.17  Aligned_cols=23  Identities=13%  Similarity=0.075  Sum_probs=21.1

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.+++++.-
T Consensus        19 ~~~si~~Ia~~agvs~~t~Y~~F   41 (70)
T d2gena1          19 DATTIEMIRDRSGASIGSLYHHF   41 (70)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHT
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            57899999999999999999984

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=82.42  E-value=1.3  Score=26.45  Aligned_cols=64  Identities=13%  Similarity=0.117  Sum_probs=39.5

Q ss_pred             CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904           6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL   75 (163)
Q Consensus         6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l   75 (163)
                      .++.|+|+.+|||..|+.-|-    +.|-+.|..-  +|.  +.=+......+..... ..-+++..++..-+
T Consensus         3 ytI~e~A~~~gvs~~tlR~Ye----~~GLl~p~~r~~~gy--R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l   69 (109)
T d1r8da_           3 YQVKQVAEISGVSIRTLHHYD----NIELLNPSALTDAGY--RLYSDADLERLQQILFFKEIGFRLDEIKEML   69 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHH----HTTSSCCSEECTTCC--EEBCHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HcCCcCCcccCCccc--ccccHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            578899999999999988875    5599987532  443  3334444443322221 12356666666544

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=82.21  E-value=0.33  Score=26.96  Aligned_cols=23  Identities=9%  Similarity=0.128  Sum_probs=20.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +|++..+||+..|||+++++..-
T Consensus        21 ~~~si~~Ia~~agvs~~~iy~~F   43 (73)
T d1sgma1          21 HATGLNQIVKESGAPKGSLYHFF   43 (73)
T ss_dssp             TTCCHHHHHHHHCCCSCHHHHST
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHc
Confidence            67999999999999999999863

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=82.07  E-value=0.35  Score=27.17  Aligned_cols=23  Identities=13%  Similarity=0.241  Sum_probs=20.8

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.+++++.-
T Consensus        25 ~~~s~~~Ia~~agvs~~~lY~~F   47 (77)
T d2gfna1          25 SAVTTRAVAEESGWSTGVLNHYF   47 (77)
T ss_dssp             GGCCHHHHHHHHSSCHHHHHHHT
T ss_pred             cccCHHHHHHHHCCCHHHHHHHC
Confidence            46899999999999999999974

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=81.86  E-value=0.36  Score=26.91  Aligned_cols=23  Identities=9%  Similarity=0.140  Sum_probs=21.0

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      +|++..+||+..|||.+++++..
T Consensus        23 ~~~s~~~Ia~~agvs~~~iY~~F   45 (74)
T d2g7sa1          23 NSFSYADISQVVGIRNASIHHHF   45 (74)
T ss_dssp             GGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             cccCHHHHHHHHCcCcchHHHHC
Confidence            56899999999999999999974

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=81.66  E-value=0.5  Score=26.24  Aligned_cols=23  Identities=17%  Similarity=0.088  Sum_probs=20.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .+++..+||+..|||.+++++..
T Consensus        24 ~~~t~~~Ia~~agvs~~~~y~~F   46 (75)
T d3c07a1          24 DRTTMRAIAQEAGVSVGNAYYYF   46 (75)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            56899999999999999999974

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=81.50  E-value=0.51  Score=26.27  Aligned_cols=23  Identities=17%  Similarity=0.203  Sum_probs=21.2

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      .+++..+||+..|||.+++++.-
T Consensus        23 ~~~si~~Ia~~agvs~~~~Y~~F   45 (73)
T d2fx0a1          23 EGTSIQEIAKEAKVNVAMASYYF   45 (73)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             ccCcHHHHHHHHCcChhHHHHHC
Confidence            56899999999999999999985

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.41  E-value=0.44  Score=27.82  Aligned_cols=41  Identities=17%  Similarity=0.246  Sum_probs=32.2

Q ss_pred             CChhhhHHHhh--cchhhHHHHHhhhhhccCC-CCCCCCCCCCC
Q psy1904           6 VRPCVISRQLR--VSHGCVSKILNRYQETGSI-RPGVIGGSKPR   46 (163)
Q Consensus         6 ~~~~~ia~~~~--vs~~~vs~~l~~~~~tG~~-~Pg~~Gg~~p~   46 (163)
                      ++-.+||+.++  +|.+||...|..+.+.|-+ .|...+|.-|.
T Consensus        24 v~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~h~s~GriPT   67 (87)
T d1stza1          24 VSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHTSAGRIPT   67 (87)
T ss_dssp             BCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSSCSCBEEC
T ss_pred             cCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCCCCCCCCccc
Confidence            56678999855  6899999999999999999 56655665443

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=81.39  E-value=0.41  Score=26.20  Aligned_cols=23  Identities=22%  Similarity=0.310  Sum_probs=20.9

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++..+||+..|||.++++..-
T Consensus        20 ~~~ti~~Ia~~agvs~~~iy~~F   42 (69)
T d2np5a1          20 EGASVREVAKRAGVSIGAVQHHF   42 (69)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cccCHHHHHHHhCCCHHHHHHHC
Confidence            56899999999999999999974

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=80.19  E-value=0.44  Score=25.97  Aligned_cols=21  Identities=19%  Similarity=0.197  Sum_probs=19.2

Q ss_pred             CCChhhhHHHhhcchhhHHHH
Q psy1904           5 GVRPCVISRQLRVSHGCVSKI   25 (163)
Q Consensus         5 g~~~~~ia~~~~vs~~~vs~~   25 (163)
                      +++..+||+..|||.++++..
T Consensus        19 ~~ti~~Ia~~agvs~~~iY~~   39 (65)
T d2g7ga1          19 DFRMPDLARHLNVQVSSIYHH   39 (65)
T ss_dssp             SCCHHHHHHHTTSCHHHHHTT
T ss_pred             CCCHHHHHHHhCccccchhhc
Confidence            588999999999999999875

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=80.10  E-value=0.44  Score=26.09  Aligned_cols=23  Identities=17%  Similarity=0.125  Sum_probs=20.7

Q ss_pred             CCCChhhhHHHhhcchhhHHHHH
Q psy1904           4 AGVRPCVISRQLRVSHGCVSKIL   26 (163)
Q Consensus         4 ~g~~~~~ia~~~~vs~~~vs~~l   26 (163)
                      ++++-.+||+..|||.+++++..
T Consensus        25 ~~~t~~~Ia~~agvs~~~iY~~F   47 (68)
T d2id3a1          25 DALDLGEIARRAGVGKTTVYRRW   47 (68)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            45889999999999999999975