Citrus Sinensis ID: 045349

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
Protein Sequence
MAGANSSAAGSSSRAQRNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKGDDHTEPSVMNITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHVSV
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEcccccEEEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEEEccEEEEEEEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEcccEEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEEcccEEEEc
Coil and Loop (DISEMBL)
maganssaagsssrAQRNINEKHRRMLMKDLISQLAslipsnsklsmpqilDDATSYIMHLQKNKESLERKKALlkgddhtepsvmnittsgsTLEVNLICGLNRNFMFHEIISILEEEAAEVInvtrfnsgdrvIFSVQSKVYITHLHVSV
Flexible Loop (DISEMBL)
maganssaagsssraqrNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALlkgddhtepsvmnittsgstlEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQskvyithlhvsv
Low Complexity Region (SEG)
MaganssaagsssraqrnINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKGDDHTEPSVMNITTSGSTLEVNLICGLNRNFMFHeiisileeeaaeviNVTRFNSGDRVIFSVQSKVYITHLHVSV
Disordered region (IsUnstruct)
********************************************************YI*****************************ITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLH***
Disordered Region (DISOPRED)
************************RMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQ*********************************EVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHVS*
Disordered Region (DISEMBL)
****************RNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKGDDHTEPSVMNITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHVSV
Disordered Region (DISPRO)
**************AQRNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKGDDHTEPSVMNITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHVSV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAGANSSAAGSSSRAQRNINEKHRRMLMKDLISQLASLIPSNSKLSMPQIxxxxxxxxxxxxxxxxxxxxxxxxxxxxDHTEPSVMNITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHVSV
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	152
225425498	189	PREDICTED: uncharacterized protein LOC10	0.921	0.740	0.424	1e-21
225425500	370	PREDICTED: uncharacterized protein LOC10	0.907	0.372	0.417	2e-20
297849398	187	T10O24.22 [Arabidopsis lyrata subsp. lyr	0.940	0.764	0.405	5e-19
224079207	162	predicted protein [Populus trichocarpa]	0.881	0.827	0.418	8e-19
147770000	176	hypothetical protein VITISV_017511 [Viti	0.868	0.75	0.371	3e-18
79340924	181	basic helix-loop-helix domain-containing	0.986	0.828	0.381	6e-18
5091553	188	T10O24.22 [Arabidopsis thaliana]	0.980	0.792	0.389	6e-18
224125352	183	predicted protein [Populus trichocarpa]	0.875	0.726	0.421	1e-17
356508667	190	PREDICTED: uncharacterized protein LOC10	0.953	0.763	0.370	3e-17
147863541	168	hypothetical protein VITISV_038226 [Viti	0.809	0.732	0.386	3e-17

>gi|225425498|ref|XP_002263440.1| PREDICTED: uncharacterized protein LOC100241449 [Vitis vinifera]

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/146 (42%), Positives = 95/146 (65%), Gaps = 6/146 (4%)

Query: 3   GANSSAAGSSSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHL 61
           G+ +  A +S +  RN  EK+RRM MKDL ++LA  IP+  SK S+  +L+ AT+++  L
Sbjct: 22  GSMTRRASNSPKLHRNEIEKNRRMSMKDLYARLAFQIPTAPSKSSLHLLLEHATTHVKRL 81

Query: 62  QKNKESLERKKALLKGDDH-----TEPSVMNITTSGSTLEVNLICGLNRNFMFHEIISIL 116
           Q+  + L++KK LL+G  H     +   V+ +   GSTLEV L  GLN+NF  +E+IS+L
Sbjct: 82  QQRLKMLKQKKQLLEGRTHHITGSSRSPVIIVREMGSTLEVFLTSGLNKNFFLYEVISVL 141

Query: 117 EEEAAEVINVTRFNSGDRVIFSVQSK 142
           EEEAA+V+   +   GDR+I+S+ S+
Sbjct: 142 EEEAAQVVTANQSTVGDRIIYSICSQ 167

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425500|ref|XP_002263481.1| PREDICTED: uncharacterized protein LOC100263706 [Vitis vinifera]

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 63/151 (41%), Positives = 92/151 (60%), Gaps = 13/151 (8%)

Query: 13  SRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLERK 71
           S+  R+  E++RRM MKDL S+LA L+P+  SK S+   LD AT+YI  LQK  E+L++ 
Sbjct: 34  SKLDRSAVERNRRMHMKDLFSRLAFLVPTRPSKSSLHVSLDHATTYIKQLQKRIETLKQT 93

Query: 72  KALLKGD-DHT-----------EPSVMNITTSGSTLEVNLICGLNRNFMFHEIISILEEE 119
           K LL+G  D T              V+ +   GS+LE+ LI G N+ F  HE+IS+LEEE
Sbjct: 94  KQLLQGSTDETGGVRCQMSGASRSPVITVRDMGSSLELLLISGSNKKFRLHEVISVLEEE 153

Query: 120 AAEVINVTRFNSGDRVIFSVQSKVYITHLHV 150
           AA+V+ V +   GDR+ +S+ S+   + + V
Sbjct: 154 AAQVVTVNQCIVGDRICYSIHSEAVSSRIGV 184

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849398|ref|XP_002892580.1| T10O24.22 [Arabidopsis lyrata subsp. lyrata] gi|297338422|gb|EFH68839.1| T10O24.22 [Arabidopsis lyrata subsp. lyrata]

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 62/153 (40%), Positives = 96/153 (62%), Gaps = 10/153 (6%)

Query: 1   MAGANSSAAGSSS--RAQRNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYI 58
           MA A     G+SS  R QRN+ EK RRM MK L S+L+S +    KL +PQ++D ATSY+
Sbjct: 1   MARAREIGEGNSSSLREQRNLREKDRRMRMKHLFSELSSHVSPTRKLPVPQLIDQATSYM 60

Query: 59  MHLQKNKESL-ERKKALLKGD--DHTEPSV----MNITTSGSTLEVNLICGLN-RNFMFH 110
           + L++N   L E+KK L++G+  +  E S     ++I +  ST+E+NLI  LN +  M H
Sbjct: 61  IQLKENVNYLKEKKKTLVQGELGNLYEGSSLLPKLSIRSRDSTIELNLIMDLNMKRVMLH 120

Query: 111 EIISILEEEAAEVINVTRFNSGDRVIFSVQSKV 143
           E++SI EEE A++++    N  DR  +++ ++V
Sbjct: 121 ELVSIFEEEGAQIMSANLQNLNDRTTYTIIAQV 153

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224079207|ref|XP_002305793.1| predicted protein [Populus trichocarpa] gi|222848757|gb|EEE86304.1| predicted protein [Populus trichocarpa]

 Score = 98.6 bits (244), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 64/153 (41%), Positives = 85/153 (55%), Gaps = 19/153 (12%)

Query: 11  SSSRAQRNINEKHRRMLMKDLISQLASLIPSNSK----LSMPQILDDATSYIMHLQKNKE 66
           SSSR  R + E++RR  MK+L SQL SL+P  S     LS+P  LD+A SYI  LQ N E
Sbjct: 6   SSSRTDRKLIERNRRNQMKELYSQLNSLVPHQSSREPVLSVPDQLDEAASYIKRLQTNLE 65

Query: 67  SLERKKALLKGDDHTEPSVMN---------------ITTSGSTLEVNLICGLNRNFMFHE 111
            ++ KK  L G +  + +  N               ++  GSTLEV L+ GL+  FMF E
Sbjct: 66  KMKEKKDSLMGMERADYTCKNSSGGKTAGLRSPQIEVSEMGSTLEVVLMNGLDSRFMFIE 125

Query: 112 IISILEEEAAEVINVTRFNSGDRVIFSVQSKVY 144
           II +L EE AE+IN +     D V  ++ SKVY
Sbjct: 126 IIRVLHEEGAEIINASLSVVQDTVFHTIHSKVY 158

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147770000|emb|CAN72144.1| hypothetical protein VITISV_017511 [Vitis vinifera]

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 55/148 (37%), Positives = 87/148 (58%), Gaps = 16/148 (10%)

Query: 11  SSSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLE 69
           SSSR  R   E+ RR   K+L S+L  L+P+  SK S+P++LD AT+++  L +  E L+
Sbjct: 7   SSSRVDRKALERDRRQCTKELFSRLGFLLPTPLSKRSLPEMLDQATTHVKQLGQRVEMLK 66

Query: 70  RKKALLKG----DDHTEP-----------SVMNITTSGSTLEVNLICGLNRNFMFHEIIS 114
           +KK LL+G    DD T              V+ ++  GS LEV +  G N+ FM H++I 
Sbjct: 67  QKKQLLEGSSSIDDQTTGIRDHMMGGAWLPVLTVSDLGSMLEVCVKSGSNKKFMLHQVIQ 126

Query: 115 ILEEEAAEVINVTRFNSGDRVIFSVQSK 142
           +L EEAA+V+ ++  N GDR+ + + ++
Sbjct: 127 VLVEEAAQVVALSYSNVGDRIFYKINAQ 154

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79340924|ref|NP_563873.2| basic helix-loop-helix domain-containing protein [Arabidopsis thaliana] gi|332190477|gb|AEE28598.1| basic helix-loop-helix domain-containing protein [Arabidopsis thaliana]

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 61/160 (38%), Positives = 96/160 (60%), Gaps = 10/160 (6%)

Query: 1   MAGANSSAAGSSS--RAQRNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYI 58
           M  A     G+SS  R QRN+ EK RRM MK L S L+S +    KL +P ++D ATSY+
Sbjct: 1   MGRAREIGEGNSSSLREQRNLREKDRRMRMKHLFSILSSHVSPTRKLPVPHLIDQATSYM 60

Query: 59  MHLQKNKESL-ERKKALLKGD--DHTEPSV----MNITTSGSTLEVNLICGLN-RNFMFH 110
           + L++N   L E+K+ LL+G+  +  E S     ++I +  ST+E+NLI  LN +  M H
Sbjct: 61  IQLKENVNYLKEKKRTLLQGELGNLYEGSFLLPKLSIRSRDSTIEMNLIMDLNMKRVMLH 120

Query: 111 EIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHV 150
           E++SI EEE A+V++    N  DR  +++ ++  I+ + +
Sbjct: 121 ELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQAIISRIGI 160

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5091553|gb|AAD39582.1|AC007067_22 T10O24.22 [Arabidopsis thaliana]

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 62/159 (38%), Positives = 95/159 (59%), Gaps = 10/159 (6%)

Query: 1   MAGANSSAAGSSS--RAQRNINEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYI 58
           M  A     G+SS  R QRN+ EK RRM MK L S L+S +    KL +P ++D ATSY+
Sbjct: 1   MGRAREIGEGNSSSLREQRNLREKDRRMRMKHLFSILSSHVSPTRKLPVPHLIDQATSYM 60

Query: 59  MHLQKNKESL-ERKKALLKGD--DHTEPSV----MNITTSGSTLEVNLICGLN-RNFMFH 110
           + L++N   L E+K+ LL+G+  +  E S     ++I +  ST+E+NLI  LN +  M H
Sbjct: 61  IQLKENVNYLKEKKRTLLQGELGNLYEGSFLLPKLSIRSRDSTIEMNLIMDLNMKRVMLH 120

Query: 111 EIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLH 149
           E++SI EEE A+V++    N  DR  +++ ++V   H +
Sbjct: 121 ELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQVPHPHAY 159

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125352|ref|XP_002329784.1| predicted protein [Populus trichocarpa] gi|222870846|gb|EEF07977.1| predicted protein [Populus trichocarpa]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 64/152 (42%), Positives = 82/152 (53%), Gaps = 19/152 (12%)

Query: 11  SSSRAQRNINEKHRRMLMKDLISQLASLIPSNSK----LSMPQILDDATSYIMHLQKNKE 66
           SSSR  R   E++RR  MK L SQL SL+P  S     LS+P  LD+A SYI  LQ N E
Sbjct: 6   SSSRTDRKTIERNRRNQMKALYSQLNSLVPHQSSREPVLSLPDQLDEAASYIKRLQTNLE 65

Query: 67  SLERKKALLKGDDHTEPSVMN---------------ITTSGSTLEVNLICGLNRNFMFHE 111
            ++ KK  L G +    + M+               I  +GSTLEV LI GL+  FMF+E
Sbjct: 66  RMKEKKDNLMGTERKNYASMSSCNGTTTGLRSPQIEIRETGSTLEVVLITGLDGQFMFNE 125

Query: 112 IISILEEEAAEVINVTRFNSGDRVIFSVQSKV 143
            I +L EE AE+IN +     D V  ++ SKV
Sbjct: 126 TIRVLHEEGAEIINASFSVVEDTVFHTIHSKV 157

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508667|ref|XP_003523076.1| PREDICTED: uncharacterized protein LOC100790403 [Glycine max]

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 60/162 (37%), Positives = 93/162 (57%), Gaps = 17/162 (10%)

Query: 6   SSAAGSSSRAQRNINEKHRRMLMKDLISQLASLIPSN-----SKLSMPQ--ILDDATSYI 58
           +S +  SS+  R   EK+RR+ MK L  QL+SLIP N     SKL + Q   LD A  YI
Sbjct: 6   ASTSTESSKLDRKTIEKNRRIHMKSLCHQLSSLIPPNLKPAKSKLMLGQRDQLDLAARYI 65

Query: 59  MHLQKNKESLERKK--ALLKGDD--------HTEPSVMNITTSGSTLEVNLICGLNRNFM 108
            H+ +  E L+R+K   +   DD         ++  ++ +   GS++EV L+ GLN+ FM
Sbjct: 66  KHMNERIEKLKRQKEQVMSNNDDRKMFNNNVESKLPIVELRDLGSSIEVMLVSGLNKAFM 125

Query: 109 FHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYITHLHV 150
            +E+IS+LEEE AEV+  +    GD++ + V ++V I+ + V
Sbjct: 126 LYEVISVLEEEGAEVVTASFSTVGDKIFYVVHAQVKISRVGV 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147863541|emb|CAN79761.1| hypothetical protein VITISV_038226 [Vitis vinifera]

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/132 (38%), Positives = 82/132 (62%), Gaps = 9/132 (6%)

Query: 17  RNINEKHRRMLMKDLISQLASLIP--SNSKLSMPQILDDATSYIMHLQKNKESLERKKAL 74
           RN  E++RRM MKDL S+LA LIP     + S+  +L+ A +Y+  LQ+  E L++++ L
Sbjct: 12  RNALERNRRMYMKDLFSKLAYLIPIQPGPRSSLHXLLNQAIAYVKELQERIEMLKQRRQL 71

Query: 75  LKGDDH-------TEPSVMNITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVT 127
           L+G  H       +   V+++   G  LE+ LI GLN NF  H++I++L EEAAEV++V+
Sbjct: 72  LEGTHHDAAGISGSMSPVVSLRDLGFILELCLITGLNENFTLHQVINVLLEEAAEVVDVS 131

Query: 128 RFNSGDRVIFSV 139
               G R+ +++
Sbjct: 132 YSTVGHRIFYTI 143

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	152
TAIR|locus:505006117	181	AT1G10585 [Arabidopsis thalian	0.868	0.729	0.314	5e-12
TAIR|locus:4515102513	174	AT1G10586 [Arabidopsis thalian	0.868	0.758	0.278	8.4e-10
TAIR|locus:2133089	190	AT4G20970 "AT4G20970" [Arabido	0.519	0.415	0.373	2.9e-07
UNIPROTKB|Q941Z7	248	P0431G06.13-1 "BHLH transcript	0.532	0.326	0.340	6.3e-05
UNIPROTKB|Q948F6	298	OSJNBa0049O12.18 "Putative SPA	0.368	0.187	0.357	0.00041
TAIR|locus:2026629	596	EGL3 "AT1G63650" [Arabidopsis	0.335	0.085	0.411	0.00054
TAIR|locus:2035237	590	AT1G01260 "AT1G01260" [Arabido	0.539	0.138	0.310	0.00087
TAIR|locus:2074865	231	HEC2 "AT3G50330" [Arabidopsis	0.388	0.255	0.333	0.0009
TAIR|locus:2046198	318	FRU "AT2G28160" [Arabidopsis t	0.335	0.160	0.372	0.00098
TAIR|locus:2155543	241	HEC1 "HECATE 1" [Arabidopsis t	0.361	0.228	0.339	0.00098

TAIR|locus:505006117 AT1G10585 [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 44/140 (31%), Positives = 74/140 (52%)

Query:    19 INEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESL-ERKKALLKG 77
             + EK RRM MK L S L+S +    KL +P ++D ATSY++ L++N   L E+K+ LL+G
Sbjct:    21 LREKDRRMRMKHLFSILSSHVSPTRKLPVPHLIDQATSYMIQLKENVNYLKEKKRTLLQG 80

Query:    78 D--DHTEPSVM----NITTSGSTLEVNLICGLN-RNFMFHXXXXXXXXXXXXXXNVTRFN 130
             +  +  E S +    +I +  ST+E+NLI  LN +  M H              +    N
Sbjct:    81 ELGNLYEGSFLLPKLSIRSRDSTIEMNLIMDLNMKRVMLHELVSIFEEEGAQVMSANLQN 140

Query:   131 SGDRVIFSVQSKVYITHLHV 150
               DR  +++ ++  I+ + +
Sbjct:   141 LNDRTTYTIIAQAIISRIGI 160

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0006865 "amino acid transport" evidence=RCA

TAIR|locus:4515102513 AT1G10586 [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 39/140 (27%), Positives = 70/140 (50%)

Query:    19 INEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESL-ERKKALLKG 77
             + EK RRM MK L S L+S +    +L +PQ++D A SY++ L++    L E K+ +L G
Sbjct:    21 LREKERRMRMKHLFSILSSHVSPTRRLPVPQLIDQAVSYMIQLKEKVNYLNEMKRRMLGG 80

Query:    78 D--DHTEPSVM----NITTSGSTLEVNLICGLN-RNFMFHXXXXXXXXXXXXXXNVTRFN 130
             +  + +E S +    +I +  S +E+NL+  LN +  M H              +    N
Sbjct:    81 EVKNRSEGSSLLPKLSIRSLDSIIEMNLVMDLNMKGVMLHKLVSVFEEEGAQVMSANLQN 140

Query:   131 SGDRVIFSVQSKVYITHLHV 150
               DR  +++ ++  I  + +
Sbjct:   141 LNDRTFYTIIAQAIICRIGI 160

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2133089 AT4G20970 "AT4G20970" [Arabidopsis thaliana (taxid:3702)]

 Score = 117 (46.2 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 31/83 (37%), Positives = 51/83 (61%)

Query:    21 EKHRRMLMKDLISQLASLIPSNSK---LSMPQILDDATSYIMHLQKNKESL-ERKKALLK 76
             EK+RRM MK L S+L SL+P +S    L++P  LD+A +YI  LQ N E   ERK+ L+ 
Sbjct:    20 EKNRRMQMKSLYSELISLLPHHSSTEPLTLPDQLDEAANYIKKLQVNVEKKRERKRNLVA 79

Query:    77 GDDHTEPSVMNITTSGSTLEVNL 99
                  + + +  ++  S+++V++
Sbjct:    80 TTTLEKLNSVGSSSVSSSVDVSV 102

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0050832 "defense response to fungus" evidence=IEP

UNIPROTKB|Q941Z7 P0431G06.13-1 "BHLH transcription factor-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 100 (40.3 bits), Expect = 6.3e-05, P = 6.3e-05
 Identities = 30/88 (34%), Positives = 43/88 (48%)

Query:    21 EKHRRMLMKDLISQLASLIPS---NSKLSMPQILDDATSYIMHLQKNKESLERKKALLKG 77
             E+ RR  + +L S L +L+P      KLS+P  +     YI  LQK  E+LERKK  L  
Sbjct:    77 ERDRRKQLNELYSSLRALLPDADHTKKLSIPTTVSRVLKYIPELQKQVENLERKKKELTT 136

Query:    78 DDHT--EPSVMN--ITTSGSTLEVNLIC 101
                T  +P V+   + + G    V+  C
Sbjct:   137 TSTTNCKPGVLGSQLMSEGMAPIVSATC 164

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q948F6 OSJNBa0049O12.18 "Putative SPATULA" [Oryza sativa (taxid:4530)]

 Score = 94 (38.1 bits), Expect = 0.00041, P = 0.00041
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query:    19 INEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKAL 74
             ++EK RR  + + +  L SLIP++SK     +LDDA  Y+  LQ   + L  +  L
Sbjct:    39 LSEKRRRSRINEKMKALQSLIPNSSKTDKASMLDDAIEYLKQLQLQVQMLSMRNGL 94

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2026629 EGL3 "AT1G63650" [Arabidopsis thaliana (taxid:3702)]

 Score = 97 (39.2 bits), Expect = 0.00054, P = 0.00054
 Identities = 21/51 (41%), Positives = 29/51 (56%)

Query:    19 INEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLE 69
             ++EK RR  + +    L S+IPS SK+    ILDD   Y+  LQK  + LE
Sbjct:   408 LSEKKRREKLNERFMTLRSIIPSISKIDKVSILDDTIEYLQDLQKRVQELE 458

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0009957 "epidermal cell fate specification" evidence=RCA;IMP

GO:0001708 "cell fate specification" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0009913 "epidermal cell differentiation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0016570 "histone modification" evidence=RCA

GO:0048449 "floral organ formation" evidence=RCA

TAIR|locus:2035237 AT1G01260 "AT1G01260" [Arabidopsis thaliana (taxid:3702)]

 Score = 95 (38.5 bits), Expect = 0.00087, P = 0.00087
 Identities = 27/87 (31%), Positives = 42/87 (48%)

Query:    21 EKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKGDDH 80
             E+ RR  +      L S++P+ SK+    +L DA SYI  L    + +E ++  L G   
Sbjct:   438 ERQRREKLNQRFYALRSVVPNISKMDKASLLGDAVSYINELHAKLKVMEAERERL-GYSS 496

Query:    81 TEP----SVMNITTSGSTLEVNLICGL 103
               P    S +N+ TSG  + V + C L
Sbjct:   497 NPPISLDSDINVQTSGEDVTVRINCPL 523

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009694 "jasmonic acid metabolic process" evidence=RCA

GO:0009753 "response to jasmonic acid stimulus" evidence=RCA

TAIR|locus:2074865 HEC2 "AT3G50330" [Arabidopsis thaliana (taxid:3702)]

 Score = 89 (36.4 bits), Expect = 0.00090, P = 0.00090
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query:    22 KHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKGDDHT 81
             +HRR  + + I  L  L+P  +K+    +LD+A  Y+  L+K  +SLE + A++ G   T
Sbjct:   135 RHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKKQVQSLE-EHAVVNGGGMT 193

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

GO:0080126 "ovary septum development" evidence=IGI

TAIR|locus:2046198 FRU "AT2G28160" [Arabidopsis thaliana (taxid:3702)]

 Score = 91 (37.1 bits), Expect = 0.00098, P = 0.00098
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query:    19 INEKHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLE 69
             I+E+ RR  MKD +  L SL+P+ +K+    I+ DA  Y+  LQ   + L+
Sbjct:   134 ISERRRRGRMKDKLYALRSLVPNITKMDKASIVGDAVLYVQELQSQAKKLK 184

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010039 "response to iron ion" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0034756 "regulation of iron ion transport" evidence=IMP

GO:0071281 "cellular response to iron ion" evidence=IEP

GO:0071369 "cellular response to ethylene stimulus" evidence=IEP

GO:0071732 "cellular response to nitric oxide" evidence=IEP

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

TAIR|locus:2155543 HEC1 "HECATE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 89 (36.4 bits), Expect = 0.00098, P = 0.00098
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query:    22 KHRRMLMKDLISQLASLIPSNSKLSMPQILDDATSYIMHLQKNKESLERKKALLKG 77
             +HRR  + + I  L  L+P  +K+    +LD+A  Y+  L+K  +SLE ++A++ G
Sbjct:   138 RHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKKQVQSLE-EQAVVTG 192


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.131   0.362    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      152       121   0.00091  102 3  11 22  0.47    30
                                                     29  0.49    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  540 (57 KB)
  Total size of DFA:  108 KB (2074 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  15.07u 0.11s 15.18t   Elapsed:  00:00:01
  Total cpu time:  15.07u 0.11s 15.18t   Elapsed:  00:00:01
  Start:  Sat May 11 13:28:58 2013   End:  Sat May 11 13:28:59 2013

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

GO:0048445 "carpel morphogenesis" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	152
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-08
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	6e-07
smart00353	53	smart00353, HLH, helix loop helix domain	7e-07

>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain

 Score = 47.5 bits (114), Expect = 2e-08
 Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS--NSKLSMPQILDDATSYIMHLQ 62
          R   N  E+ RR  + D   +L  L+P+  N KLS  +IL  A  YI HLQ
Sbjct: 2  RKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 43.7 bits (104), Expect = 6e-07
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 11 SSSRAQRNINEKHRRMLMKDLISQLASLIPS---NSKLSMPQILDDATSYIMHLQKNKE 66
           S R   N+ E+ RR  + D   +L SL+P+   + KLS  +IL  A  YI  LQ+  +
Sbjct: 2  KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins. Length = 60

>gnl|CDD|197674 smart00353, HLH, helix loop helix domain

 Score = 43.7 bits (104), Expect = 7e-07
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 18 NINEKHRRMLMKDLISQLASLIP---SNSKLSMPQILDDATSYIMHLQKNKES 67
          N  E+ RR  + +   +L SL+P    N KLS  +IL  A  YI  LQ+  + 
Sbjct: 1  NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	152
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.54
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.53
smart00353	53	HLH helix loop helix domain.	99.48
KOG1318	411	consensus Helix loop helix transcription factor EB	98.83
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.72
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.56
PLN03217	93	transcription factor ATBS1; Provisional	98.44
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.39
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.31
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.2
KOG0561	373	consensus bHLH transcription factor [Transcription	97.96
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.85
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.65
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.34
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.33
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.25
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.1
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.05
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.01
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	96.96
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	96.65
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.52
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	96.5
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.8
KOG4395	285	consensus Transcription factor Atonal, contains HT	95.69
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	95.61
KOG3898	254	consensus Transcription factor NeuroD and related	95.41
PRK05007	884	PII uridylyl-transferase; Provisional	95.07
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	94.96
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	94.95
PRK04374	869	PII uridylyl-transferase; Provisional	94.92
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	94.82
KOG3910	632	consensus Helix loop helix transcription factor [T	94.57
PRK05092	931	PII uridylyl-transferase; Provisional	94.51
PRK03059	856	PII uridylyl-transferase; Provisional	94.37
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.34
PRK03381	774	PII uridylyl-transferase; Provisional	94.29
PRK03381	774	PII uridylyl-transferase; Provisional	94.17
PRK01759	854	glnD PII uridylyl-transferase; Provisional	93.79
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	93.65
PRK01759	854	glnD PII uridylyl-transferase; Provisional	93.07
PRK00275	895	glnD PII uridylyl-transferase; Provisional	92.83
PRK05007	884	PII uridylyl-transferase; Provisional	92.64
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	92.54
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	92.48
PRK03059	856	PII uridylyl-transferase; Provisional	92.44
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	92.42
PRK05092	931	PII uridylyl-transferase; Provisional	92.3
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	92.19
PRK04374	869	PII uridylyl-transferase; Provisional	91.87
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	91.37
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	91.21
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	90.83
PRK00194	90	hypothetical protein; Validated	90.67
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	90.47
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	90.38
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	90.06
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	89.9
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	89.74
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	89.31
PRK04435	147	hypothetical protein; Provisional	88.44
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	87.34
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	87.29
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	87.04
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	86.55
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	86.35
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	85.69
KOG3582	856	consensus Mlx interactors and related transcriptio	85.4
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	85.27
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	84.32
cd02116	60	ACT ACT domains are commonly involved in specifica	83.11
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	83.06
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	82.85
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	82.31
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	81.31
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	81.1

>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt)

Probab=99.54  E-value=1.5e-14  Score=92.50  Aligned_cols=50  Identities=40%  Similarity=0.569  Sum_probs=47.5

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC-----CCCChhhHHHHHHHHHHHHH
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN-----SKLSMPQILDDATSYIMHLQ   62 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-----~K~~~~~il~~Ai~YIk~L~   62 (152)
                      +|..|+..||+||..||+.|..|+.+||..     .|.|+++||..||+||++||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            478999999999999999999999999987     78999999999999999997

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....

>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

Probab=99.53  E-value=1.9e-14  Score=92.69  Aligned_cols=54  Identities=39%  Similarity=0.549  Sum_probs=51.4

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHH
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      ..+..|+..||+||.+||+.|..|++++|..   .|+|+++||..|++||+.|++.+
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999998   89999999999999999999876

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and

>smart00353 HLH helix loop helix domain

Probab=99.48  E-value=9.5e-14  Score=87.71  Aligned_cols=49  Identities=39%  Similarity=0.569  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhhHHHHHHHHHHHHHHHHH
Q 045349           18 NINEKHRRMLMKDLISQLASLIPS---NSKLSMPQILDDATSYIMHLQKNKE   66 (152)
Q Consensus        18 ~~~ER~RR~~m~~~~~~LrsllP~---~~K~~~~~il~~Ai~YIk~L~~~v~   66 (152)
                      +..||+||.+||+.|..|++++|.   ..|.|+++||..|++||+.|+++++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999995   4799999999999999999999875

>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]

Probab=98.83  E-value=5.1e-09  Score=91.21  Aligned_cols=59  Identities=31%  Similarity=0.398  Sum_probs=53.4

Q ss_pred             CCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHH
Q 045349           10 GSSSRAQRNINEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQKNKESL   68 (152)
Q Consensus        10 ~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~~v~~L   68 (152)
                      ...+|..||+.||+||..+|+.+..|..|||..    .|+.|..||.-+++||+.||+..++.
T Consensus       230 dr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~  292 (411)
T KOG1318|consen  230 DRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRA  292 (411)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHH
Confidence            356789999999999999999999999999988    68889999999999999998877633

>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]

Probab=98.72  E-value=5.6e-08  Score=79.33  Aligned_cols=65  Identities=31%  Similarity=0.370  Sum_probs=55.3

Q ss_pred             CCCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCC-hhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 045349            9 AGSSSRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLS-MPQILDDATSYIMHLQKNKESLERKKA   73 (152)
Q Consensus         9 ~~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~-~~~il~~Ai~YIk~L~~~v~~L~~~k~   73 (152)
                      ++.+.|..||..||+||.++++.|..|+.+||..  .+.. ...||..|..||+.|+....+.....+
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e  122 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIE  122 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHH
Confidence            5677899999999999999999999999999988  4444 699999999999999877655554433

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.56  E-value=2.5e-07  Score=73.32  Aligned_cols=61  Identities=31%  Similarity=0.426  Sum_probs=53.7

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045349           14 RAQRNINEKHRRMLMKDLISQLASLIPSN-------SKLSMPQILDDATSYIMHLQKNKESLERKKAL   74 (152)
Q Consensus        14 ~~~h~~~ER~RR~~m~~~~~~LrsllP~~-------~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~   74 (152)
                      |..|--+||+||..+|.-|..|..|||..       .|.+++-||..||+||..|...+.+-+.+...
T Consensus        63 r~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~  130 (229)
T KOG1319|consen   63 RRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVST  130 (229)
T ss_pred             HHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77899999999999999999999999977       38999999999999999998877666655443

>PLN03217 transcription factor ATBS1; Provisional

Probab=98.44  E-value=5.6e-07  Score=62.86  Aligned_cols=54  Identities=28%  Similarity=0.490  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHHHhcCCCC------CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 045349           25 RMLMKDLISQLASLIPSN------SKLSMPQILDDATSYIMHLQKNKESLERKKALLKGD   78 (152)
Q Consensus        25 R~~m~~~~~~LrsllP~~------~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l~~~   78 (152)
                      -++|+++.++|+.|+|..      +|.+.+-+|.|+.+||+.|+.+|+.|.++..+|...
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            478999999999999976      688999999999999999999999999999887654

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]

Probab=98.39  E-value=4.5e-07  Score=84.68  Aligned_cols=59  Identities=25%  Similarity=0.364  Sum_probs=52.8

Q ss_pred             CCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHH
Q 045349            6 SSAAGSSSRAQRNINEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQKN   64 (152)
Q Consensus         6 ~~~~~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~~   64 (152)
                      +.+....+|..|+.+||+||++||..+..|.++||..    -|+||..||..||.+|+.+++.
T Consensus        13 ~d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   13 SDSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             ccchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            3444566789999999999999999999999999987    6999999999999999998875

>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]

Probab=98.31  E-value=2.8e-07  Score=76.00  Aligned_cols=54  Identities=28%  Similarity=0.453  Sum_probs=48.0

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC--------CCCChhhHHHHHHHHHHHHHHHH
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN--------SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--------~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      .++..|-+.||+||.+||+.+..|+.|||..        +|+.|++||.-|++|++.|+...
T Consensus        31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~   92 (250)
T KOG4304|consen   31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ   92 (250)
T ss_pred             HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence            3456677899999999999999999999955        68999999999999999998754

>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]

Probab=98.20  E-value=1.4e-06  Score=70.49  Aligned_cols=62  Identities=34%  Similarity=0.405  Sum_probs=54.4

Q ss_pred             CCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 045349           10 GSSSRAQRNINEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQKNKESLERK   71 (152)
Q Consensus        10 ~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~~v~~L~~~   71 (152)
                      ....+..+|..||+|=+.+|..|..||.+||..    +|.+|.++|..||.||..|++-++.-+..
T Consensus       106 ~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  106 TSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            455678889999999999999999999999965    78999999999999999999888665543

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.96  E-value=7.3e-06  Score=69.20  Aligned_cols=55  Identities=33%  Similarity=0.479  Sum_probs=47.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHHHH
Q 045349           14 RAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNKESL   68 (152)
Q Consensus        14 ~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v~~L   68 (152)
                      |..-|-.||+|=+-+|.-|..||+|+|..  .|.+|+-||..+.+||.+|+..--+|
T Consensus        61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            34446689999999999999999999988  89999999999999999997654433

>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]

Probab=97.85  E-value=5.5e-05  Score=62.46  Aligned_cols=62  Identities=21%  Similarity=0.267  Sum_probs=51.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhc-CCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           14 RAQRNINEKHRRMLMKDLISQLASL-IPSN-SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        14 ~~~h~~~ER~RR~~m~~~~~~Lrsl-lP~~-~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      |..-.+.||+|=++.|+.|.+|..- .|+. .++.|..||..||.||..||.-++++.+....+
T Consensus       119 RKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  119 RKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            4444589999999999999999643 4555 799999999999999999999999998765533

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.65  E-value=3.3e-05  Score=73.07  Aligned_cols=64  Identities=33%  Similarity=0.457  Sum_probs=57.4

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLERKKAL   74 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~   74 (152)
                      ..+|..||+.|++-|--+|++...|+.++|.. .|..++..+..||+||++|+..-+.|....+.
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~  338 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENAS  338 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhh
Confidence            57899999999999999999999999999988 79999999999999999998877766655443

>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.34  E-value=0.0016  Score=44.15  Aligned_cols=41  Identities=7%  Similarity=0.037  Sum_probs=37.7

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .+++|+|++|.++|.++||+|..|.+++.|+++..+|.+.-
T Consensus         9 ~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d   49 (72)
T cd04895           9 ARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTD   49 (72)
T ss_pred             CCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEEC
Confidence            57899999999999999999999999999999888877764

This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains

Probab=97.33  E-value=0.0017  Score=43.07  Aligned_cols=47  Identities=15%  Similarity=0.197  Sum_probs=39.1

Q ss_pred             eEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEee-CCeEEEEEEEEE
Q 045349           96 EVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNS-GDRVIFSVQSKV  143 (152)
Q Consensus        96 ~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~-~~~v~~ti~~qv  143 (152)
                      +|.+.| .+++|+|+++..+|..+|++|++|.+.+. ++.++.+|...-
T Consensus         3 ~i~v~~-~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~   50 (73)
T cd04900           3 EVFIYT-PDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLD   50 (73)
T ss_pred             EEEEEe-cCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEEC
Confidence            455555 47899999999999999999999999877 688888877753

This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.25  E-value=0.0027  Score=42.82  Aligned_cols=45  Identities=20%  Similarity=0.265  Sum_probs=38.8

Q ss_pred             EEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe-eCCeEEEEEEEEE
Q 045349           98 NLICGLNRNFMFHEIISILEEEAAEVINVTRFN-SGDRVIFSVQSKV  143 (152)
Q Consensus        98 ~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~-~~~~v~~ti~~qv  143 (152)
                      .+.| .+++++|+++..+|..+|++|++|.+++ .++.++.+|...-
T Consensus         4 ei~~-~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d   49 (76)
T cd04927           4 KLFC-SDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITD   49 (76)
T ss_pred             EEEE-CCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeC
Confidence            3444 4789999999999999999999999986 8899998888864

This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.10  E-value=0.0039  Score=42.61  Aligned_cols=45  Identities=16%  Similarity=0.209  Sum_probs=39.6

Q ss_pred             EEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           99 LICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        99 ~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      +.| +.++|+|++|..+|-++|++|.+|.+++.|+++..+|..+-.
T Consensus         6 V~~-~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~   50 (75)
T cd04897           6 VQC-RDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHK   50 (75)
T ss_pred             EEe-CCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcC
Confidence            344 578999999999999999999999999999998888877653

This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.05  E-value=0.0056  Score=40.65  Aligned_cols=47  Identities=13%  Similarity=0.155  Sum_probs=39.0

Q ss_pred             eEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           96 EVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        96 ~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .+.+.+ .+++++|++|..+|.++|++|+++.+.+.++.++.+|+.+-
T Consensus         3 ri~V~~-~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~   49 (72)
T cd04926           3 RLELRT-EDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTD   49 (72)
T ss_pred             EEEEEE-CCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEEC
Confidence            455544 46889999999999999999999999888888778777754

This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.01  E-value=0.0049  Score=42.11  Aligned_cols=46  Identities=9%  Similarity=0.042  Sum_probs=39.2

Q ss_pred             EEecCCCcchHHHHHHHHHHCCcEEEEEEEE--eeCCeEEEEEEEEEcc
Q 045349           99 LICGLNRNFMFHEIISILEEEAAEVINVTRF--NSGDRVIFSVQSKVYI  145 (152)
Q Consensus        99 ~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s--~~~~~v~~ti~~qv~~  145 (152)
                      ++| ..++|+|++|.++|.++|++|.+|.++  +.|+++..+|.....+
T Consensus         5 v~a-~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~~~g   52 (75)
T cd04896           5 IRC-VDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQSDG   52 (75)
T ss_pred             EEe-CCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEeCCC
Confidence            344 478999999999999999999999999  9999988877774333

This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=96.96  E-value=0.0069  Score=40.47  Aligned_cols=43  Identities=14%  Similarity=0.325  Sum_probs=38.2

Q ss_pred             ecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349          101 CGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus       101 ~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .+.+++++|++|..+|..+|++|++|.+++.++.++.+|.+.-
T Consensus         6 ~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d   48 (74)
T cd04925           6 TGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRD   48 (74)
T ss_pred             EECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEc
Confidence            3457899999999999999999999999999999888887763

This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04928 ACT_TyrKc Uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains

Probab=96.65  E-value=0.016  Score=38.85  Aligned_cols=47  Identities=9%  Similarity=0.148  Sum_probs=38.6

Q ss_pred             eEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe-eCCeEEEEEEEEE
Q 045349           96 EVNLICGLNRNFMFHEIISILEEEAAEVINVTRFN-SGDRVIFSVQSKV  143 (152)
Q Consensus        96 ~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~-~~~~v~~ti~~qv  143 (152)
                      +|.+.| +.++++|.++..+|..+||+|++|.+.+ .++.++.+|.+.-
T Consensus         3 eI~V~~-~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d   50 (68)
T cd04928           3 EITFAA-GDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTG   50 (68)
T ss_pred             EEEEEE-CCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEec
Confidence            565655 4789999999999999999999999865 4677888877764

This CD includes a novel, yet uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.52  E-value=0.0015  Score=50.52  Aligned_cols=54  Identities=30%  Similarity=0.387  Sum_probs=48.4

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHH
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      .++.-||..||+|-.-+|+.|..||..+|..  .|.|+...|.-|.-||..|-+-+
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            3578899999999999999999999999977  89999999999999999886543

>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains

Probab=96.50  E-value=0.026  Score=36.26  Aligned_cols=42  Identities=14%  Similarity=0.150  Sum_probs=37.3

Q ss_pred             cCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349          102 GLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus       102 ~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      ..+++++|.+|..+|.+++++|.++.+.+.++.++.+|+++.
T Consensus         7 ~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~   48 (70)
T cd04899           7 ALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTD   48 (70)
T ss_pred             EcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEEC
Confidence            347789999999999999999999999998888888888775

This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.80  E-value=0.16  Score=48.84  Aligned_cols=61  Identities=16%  Similarity=0.102  Sum_probs=48.6

Q ss_pred             CCceEEEEEeCC--eeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           82 EPSVMNITTSGS--TLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        82 ~~p~V~v~~~g~--~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      ..|.|.+....+  ...|.+ +..+++|+|++|..+|..+|++|++|.+++.|+.+..+|.+.-
T Consensus       800 ~~~~V~i~~~~~~~~T~i~V-~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d  862 (895)
T PRK00275        800 FPTQVTISNDAQRPVTVLEI-IAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITD  862 (895)
T ss_pred             CCCEEEEEECCCCCeEEEEE-EECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEEC
Confidence            456777776443  233444 4457899999999999999999999999999999998888865

>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]

Probab=95.69  E-value=0.016  Score=48.11  Aligned_cols=56  Identities=27%  Similarity=0.310  Sum_probs=49.4

Q ss_pred             CCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHH
Q 045349           10 GSSSRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        10 ~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      .+..+..-|..||+|=..+|..|..||-.+|..   .|.++-..|.-|-.||--|-..+
T Consensus       171 ~~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  171 NSHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             HHhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            345567778999999999999999999999988   78999999999999999887665

>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD

Probab=95.61  E-value=0.14  Score=32.42  Aligned_cols=46  Identities=13%  Similarity=0.200  Sum_probs=36.5

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      +.+.| .++++.|.++..+|.++|+.|.++.+.+.++.....|++.-
T Consensus         3 l~i~~-~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~   48 (70)
T cd04873           3 VEVYA-PDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTD   48 (70)
T ss_pred             EEEEe-CCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEEC
Confidence            44444 46789999999999999999999999887776666666554

This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t

>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]

Probab=95.41  E-value=0.0084  Score=49.61  Aligned_cols=53  Identities=30%  Similarity=0.382  Sum_probs=46.1

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHH
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      .|..-|..||+|=-.+|+.|..||.++|..   .|++|..+|.-|-+||..|++-.
T Consensus        72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~  127 (254)
T KOG3898|consen   72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL  127 (254)
T ss_pred             hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence            345557899999999999999999999944   79999999999999999998654

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.07  E-value=0.1  Score=49.99  Aligned_cols=60  Identities=13%  Similarity=0.144  Sum_probs=46.0

Q ss_pred             CceEEEEEeCCe--eeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           83 PSVMNITTSGST--LEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g~~--~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .|.|.+....+.  -.+.+++ .+++|+|++|.++|.++|++|.+|-++|.|+++..+|.++-
T Consensus       795 ~~~V~~d~~~s~~~TvlEV~a-~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~  856 (884)
T PRK05007        795 PTEVSFLPTHTDRRSYMELIA-LDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILAT  856 (884)
T ss_pred             CCEEEEccCCCCCeEEEEEEe-CCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEc
Confidence            456766644332  1233344 57899999999999999999999999999999888777754

>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A

Probab=94.96  E-value=0.21  Score=33.27  Aligned_cols=44  Identities=14%  Similarity=0.224  Sum_probs=36.9

Q ss_pred             ecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349          101 CGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus       101 ~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      .|.+++|.++.+..+|.++|.++++++.++.++.+...+.+...
T Consensus         8 ~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~   51 (76)
T PF13740_consen    8 VGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP   51 (76)
T ss_dssp             EEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES
T ss_pred             EecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC
Confidence            45688999999999999999999999999999998887777765

>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold

Probab=94.95  E-value=0.28  Score=30.57  Aligned_cols=36  Identities=17%  Similarity=0.353  Sum_probs=31.0

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCC
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGD  133 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~  133 (152)
                      |.+.|. +++|.|.++..+|.++|++|.++...+.++
T Consensus         3 v~v~~~-drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    3 VRVIVP-DRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             EEEEEE-TSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             EEEEcC-CCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            444554 789999999999999999999999988876

ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....

>PRK04374 PII uridylyl-transferase; Provisional

Probab=94.92  E-value=0.18  Score=48.41  Aligned_cols=62  Identities=13%  Similarity=0.137  Sum_probs=48.4

Q ss_pred             CCceEEEEEeCC--eeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           82 EPSVMNITTSGS--TLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        82 ~~p~V~v~~~g~--~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      ..|.|.+....+  ...|.+++ ..++|+|++|..+|.++|++|++|.++|.++++..+|.++-.
T Consensus       782 ~~~~V~~~~~~~~~~t~leI~a-~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~  845 (869)
T PRK04374        782 FAPRVEFSESAGGRRTRISLVA-PDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDE  845 (869)
T ss_pred             CCCeEEEeecCCCCeEEEEEEe-CCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECC
Confidence            346677765443  22344444 578999999999999999999999999999999988888753

>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A

Probab=94.82  E-value=0.32  Score=32.26  Aligned_cols=43  Identities=12%  Similarity=0.195  Sum_probs=34.8

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEee--CCeEEEEEEEEEcc
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNS--GDRVIFSVQSKVYI  145 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~--~~~v~~ti~~qv~~  145 (152)
                      .+++|+|.+|..++.+.|+.|.+.++...  ++....+|.+++.+
T Consensus        14 ~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d   58 (80)
T PF13291_consen   14 EDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKD   58 (80)
T ss_dssp             E--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESS
T ss_pred             EcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECC
Confidence            46789999999999999999999999884  56777888888754

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=94.57  E-value=0.035  Score=50.13  Aligned_cols=56  Identities=20%  Similarity=0.239  Sum_probs=47.0

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHH
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQKNKESL   68 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~~v~~L   68 (152)
                      +|+..|+.||-|-..+|+.|..|-...-..    +...|--||..|+.-|-.|+++|.+-
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            467788999999999999999998765322    56678889999999999999999764

>PRK05092 PII uridylyl-transferase; Provisional

Probab=94.51  E-value=0.25  Score=47.58  Aligned_cols=60  Identities=12%  Similarity=0.129  Sum_probs=47.5

Q ss_pred             CceEEEEEeCC--eeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           83 PSVMNITTSGS--TLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g~--~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .|.|.+....+  ...|.+.+ .+++|+|++|..+|.++|++|.+|.+.+.++++..+|.+..
T Consensus       830 ~~~V~~~~~~s~~~t~i~I~~-~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d  891 (931)
T PRK05092        830 PPRVTIDNEASNRFTVIEVNG-RDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTD  891 (931)
T ss_pred             CCEEEEeeCCCCCeEEEEEEE-CCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeC
Confidence            46677765443  23344444 57899999999999999999999999999999988888865

>PRK03059 PII uridylyl-transferase; Provisional

Probab=94.37  E-value=0.28  Score=46.90  Aligned_cols=58  Identities=14%  Similarity=0.122  Sum_probs=45.6

Q ss_pred             CceEEEEEeC--CeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEE
Q 045349           83 PSVMNITTSG--STLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQS  141 (152)
Q Consensus        83 ~p~V~v~~~g--~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~  141 (152)
                      .|.|.+....  ....|.+++ .+++|+|++|..+|..+|++|++|.+++.|+.+..+|.+
T Consensus       773 ~~~V~~~~~~~~~~T~i~V~a-~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V  832 (856)
T PRK03059        773 TPRVDLRPDERGQYYILSVSA-NDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI  832 (856)
T ss_pred             CceEEEEEcCCCCEEEEEEEe-CCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            4456665533  233454444 578999999999999999999999999999999888877

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.34  E-value=1.4  Score=41.92  Aligned_cols=61  Identities=10%  Similarity=0.036  Sum_probs=46.4

Q ss_pred             CceEEEEEe--CCeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEE-eeCCeEEEEEEEEEc
Q 045349           83 PSVMNITTS--GSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRF-NSGDRVIFSVQSKVY  144 (152)
Q Consensus        83 ~p~V~v~~~--g~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s-~~~~~v~~ti~~qv~  144 (152)
                      .|.|.+...  ....+|.+++ .+++++|++|..+|..+|++|++|.++ +.++.++.+|.++-.
T Consensus       655 ~~~v~~~~~~~~~~t~i~V~~-~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~  718 (850)
T TIGR01693       655 GPLALIDGTRPSGGTEVFIYA-PDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDL  718 (850)
T ss_pred             CCEEEEeccCCCCeEEEEEEe-CCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECC
Confidence            455555432  2344565555 478999999999999999999999998 778888888887753

This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.

>PRK03381 PII uridylyl-transferase; Provisional

Probab=94.29  E-value=0.31  Score=46.07  Aligned_cols=60  Identities=13%  Similarity=0.077  Sum_probs=46.8

Q ss_pred             CceEEEEEeCC--eeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           83 PSVMNITTSGS--TLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g~--~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .|.|.+....+  ...|.+. ...++|+|++|-.+|.++|++|++|.+++.++.+..+|.++-
T Consensus       694 ~~~v~~~~~~~~~~t~i~V~-a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d  755 (774)
T PRK03381        694 PPRVLWLDGASPDATVLEVR-AADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTG  755 (774)
T ss_pred             CcEEEEEECCCCCeEEEEEE-eCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEEC
Confidence            44566655433  2344444 457899999999999999999999999999999988888764

>PRK03381 PII uridylyl-transferase; Provisional

Probab=94.17  E-value=0.37  Score=45.64  Aligned_cols=60  Identities=10%  Similarity=0.125  Sum_probs=46.9

Q ss_pred             CceEEEEEe-CCeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           83 PSVMNITTS-GSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~-g~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .|.|.+... .+..+|.++| .+++++|++|..+|..+|++|++|++.+.++.++.+|.+.-
T Consensus       587 ~~~v~~~~~~~~~~~V~V~~-~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~  647 (774)
T PRK03381        587 GVHVEIAPADPHMVEVTVVA-PDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSP  647 (774)
T ss_pred             CCEEEEeeCCCCeEEEEEEe-cCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEEC
Confidence            455655433 3555676655 47899999999999999999999999987888888777764

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=93.79  E-value=0.28  Score=46.93  Aligned_cols=60  Identities=12%  Similarity=0.156  Sum_probs=45.8

Q ss_pred             CceEEEEEeCCe--eeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           83 PSVMNITTSGST--LEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g~~--~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .|.|.+....+.  -.+.+++ .+++|+|++|..+|.++|++|.+|-++|.++++..+|.+.-
T Consensus       770 ~~~V~~dn~~s~~~T~iev~a-~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~  831 (854)
T PRK01759        770 KTEVRFLNEEKQEQTEMELFA-LDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTN  831 (854)
T ss_pred             CCEEEEccCCCCCeEEEEEEe-CCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEEC
Confidence            456666554332  1233343 57899999999999999999999999999999887777754

>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains

Probab=93.65  E-value=0.54  Score=31.42  Aligned_cols=47  Identities=9%  Similarity=0.173  Sum_probs=39.5

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      +.+.| +.++|.+.+|-..|.++|.+|++++....++.++..+.+.+.
T Consensus         4 ltv~g-~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~   50 (77)
T cd04893           4 ISALG-TDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS   50 (77)
T ss_pred             EEEEe-CCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec
Confidence            33444 578999999999999999999999999988888887777654

This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=93.07  E-value=0.75  Score=44.05  Aligned_cols=60  Identities=12%  Similarity=0.195  Sum_probs=46.7

Q ss_pred             CceEEEEEeC--CeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe-eCCeEEEEEEEEE
Q 045349           83 PSVMNITTSG--STLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFN-SGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g--~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~-~~~~v~~ti~~qv  143 (152)
                      .|.|.+....  ...+|.++| ..++|+|++|..+|..+|++|++|.+.+ .++.++.+|.+.-
T Consensus       664 ~~~V~i~~~~~~~~t~V~V~~-~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d  726 (854)
T PRK01759        664 DLLVKISNRFSRGGTEIFIYC-QDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTE  726 (854)
T ss_pred             CCEEEEEecCCCCeEEEEEEe-cCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeC
Confidence            4566665433  344565655 4789999999999999999999999876 7889888888764

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=92.83  E-value=0.74  Score=44.33  Aligned_cols=50  Identities=4%  Similarity=0.042  Sum_probs=41.1

Q ss_pred             CeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEE-EeeCCeEEEEEEEEE
Q 045349           93 STLEVNLICGLNRNFMFHEIISILEEEAAEVINVTR-FNSGDRVIFSVQSKV  143 (152)
Q Consensus        93 ~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~-s~~~~~v~~ti~~qv  143 (152)
                      +..+|.+.|. +++++|+++..+|..+|++|++|.+ ++.+|.++-+|.+.-
T Consensus       703 ~~t~V~V~~~-DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d  753 (895)
T PRK00275        703 GGTQIFIYAP-DQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLD  753 (895)
T ss_pred             CeEEEEEEeC-CCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeC
Confidence            4567777664 7899999999999999999999997 455677888887764

>PRK05007 PII uridylyl-transferase; Provisional

Probab=92.64  E-value=0.89  Score=43.72  Aligned_cols=60  Identities=12%  Similarity=0.187  Sum_probs=45.3

Q ss_pred             CceEEEEEeC--CeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeC-CeEEEEEEEEE
Q 045349           83 PSVMNITTSG--STLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSG-DRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g--~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~-~~v~~ti~~qv  143 (152)
                      .|.|.+....  ...+|.++| ..++++|++|..+|..+|++|++|.+.+.+ +.++.+|.+.-
T Consensus       688 ~p~V~i~~~~~~~~t~V~V~a-~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d  750 (884)
T PRK05007        688 KPLVLLSKQATRGGTEIFIWS-PDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLE  750 (884)
T ss_pred             CCeEEEEecCCCCeEEEEEEe-cCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEEC
Confidence            4566665533  455666655 578999999999999999999999987655 48877777654

>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains

Probab=92.54  E-value=1.2  Score=27.80  Aligned_cols=42  Identities=14%  Similarity=0.212  Sum_probs=32.1

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEee-----CCeEEEEEEEEEc
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNS-----GDRVIFSVQSKVY  144 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~-----~~~v~~ti~~qv~  144 (152)
                      .+++|.|.+|++.|.+.|++|.+.++...     ++.....|.+.+.
T Consensus         6 ~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~   52 (73)
T cd04886           6 PDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETR   52 (73)
T ss_pred             CCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeC
Confidence            46789999999999999999999887664     2445555555553

This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.

>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=92.48  E-value=0.4  Score=45.80  Aligned_cols=62  Identities=15%  Similarity=0.125  Sum_probs=46.5

Q ss_pred             CCceEEEEEeCCe-eeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           82 EPSVMNITTSGST-LEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        82 ~~p~V~v~~~g~~-~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      ..|.|.+....+. ..+.-+....++|+|..+-.+|.+++|++.+|.++++|.++..+|....
T Consensus       777 i~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~  839 (867)
T COG2844         777 IPPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTD  839 (867)
T ss_pred             cCCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEec
Confidence            3577777654322 2222233467899999999999999999999999999999876666554

>PRK03059 PII uridylyl-transferase; Provisional

Probab=92.44  E-value=0.64  Score=44.53  Aligned_cols=60  Identities=12%  Similarity=0.172  Sum_probs=46.1

Q ss_pred             CceEEEEEe--CCeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEE-eeCCeEEEEEEEEE
Q 045349           83 PSVMNITTS--GSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRF-NSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~--g~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s-~~~~~v~~ti~~qv  143 (152)
                      .|-|-++..  .+..+|.+.|. +++++|+++..+|..+|++|++|.+. +.+|.++.+|.+.-
T Consensus       665 ~~~v~~~~~~~~~~~~v~i~~~-d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~  727 (856)
T PRK03059        665 TPIVRARLSPAGEGLQVMVYTP-DQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLD  727 (856)
T ss_pred             CCeEEEEecCCCCeEEEEEEec-CCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeC
Confidence            344445443  34567877664 78999999999999999999999984 56778888888764

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=92.42  E-value=0.64  Score=44.25  Aligned_cols=60  Identities=15%  Similarity=0.128  Sum_probs=45.9

Q ss_pred             CceEEEEEeCCe--eeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           83 PSVMNITTSGST--LEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g~~--~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .|.|.+....+.  -.|.+ .+..++|+|++|.++|.++|++|.++.+++.++++..+|.++.
T Consensus       766 ~~~V~~d~~~s~~~t~~~v-~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~  827 (850)
T TIGR01693       766 PPRVTILNTASRKATIMEV-RALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTD  827 (850)
T ss_pred             CCeEEEccCCCCCeEEEEE-EECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEEC
Confidence            456666654432  22333 4457899999999999999999999999999998877777764

This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.

>PRK05092 PII uridylyl-transferase; Provisional

Probab=92.30  E-value=1.1  Score=43.15  Aligned_cols=60  Identities=13%  Similarity=0.256  Sum_probs=46.1

Q ss_pred             CceEEEEEeC--CeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe-eCCeEEEEEEEEE
Q 045349           83 PSVMNITTSG--STLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFN-SGDRVIFSVQSKV  143 (152)
Q Consensus        83 ~p~V~v~~~g--~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~-~~~~v~~ti~~qv  143 (152)
                      .|.|.++...  +..+|.++|. .++++|.+|..+|..+|++|++|.+.+ .++.++.+|.++-
T Consensus       719 ~~~v~~~~~~~~~~t~v~I~~~-Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~  781 (931)
T PRK05092        719 PLATEVRPDPARGVTEVTVLAA-DHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQD  781 (931)
T ss_pred             CcEEEEEecCCCCeEEEEEEeC-CCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEEC
Confidence            3566665543  4567777664 789999999999999999999999876 5777777777654

>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains

Probab=92.19  E-value=1.6  Score=28.02  Aligned_cols=42  Identities=14%  Similarity=0.222  Sum_probs=33.9

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeC-CeEEEEEEEEEc
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSG-DRVIFSVQSKVY  144 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~-~~v~~ti~~qv~  144 (152)
                      .+++|.|.+|..++.+.|.+|.+.+..... +.....|.+++.
T Consensus         7 ~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~   49 (74)
T cd04887           7 PNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAP   49 (74)
T ss_pred             CCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcC
Confidence            367899999999999999999999987764 555566666664

The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK04374 PII uridylyl-transferase; Provisional

Probab=91.87  E-value=1.4  Score=42.36  Aligned_cols=51  Identities=16%  Similarity=0.245  Sum_probs=42.3

Q ss_pred             CCeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe-eCCeEEEEEEEEE
Q 045349           92 GSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFN-SGDRVIFSVQSKV  143 (152)
Q Consensus        92 g~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~-~~~~v~~ti~~qv  143 (152)
                      .+..+|.+.|. +++++|++|..+|..+|++|++|.+.+ .+|.++.+|.+.-
T Consensus       688 ~~~~~v~v~~~-d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~  739 (869)
T PRK04374        688 NDALEVFVYSP-DRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLP  739 (869)
T ss_pred             CCeEEEEEEeC-CCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeC
Confidence            35567877664 789999999999999999999999876 5778888888754

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=91.37  E-value=0.24  Score=44.12  Aligned_cols=43  Identities=28%  Similarity=0.295  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHH
Q 045349           19 INEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHL   61 (152)
Q Consensus        19 ~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L   61 (152)
                      -+-|.||++=|.-|+.|..++|-.    +-.||++++.-|..|||.-
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            344999999999999999999977    6799999999999999864

>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains

Probab=91.21  E-value=1.3  Score=29.02  Aligned_cols=34  Identities=12%  Similarity=0.239  Sum_probs=29.4

Q ss_pred             EEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeC
Q 045349           98 NLICGLNRNFMFHEIISILEEEAAEVINVTRFNSG  132 (152)
Q Consensus        98 ~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~  132 (152)
                      .+.| ..++|++.+|-+.|.++|++|.+.+..+.+
T Consensus         3 ~v~g-~D~~Giv~~it~~l~~~~~nI~~~~~~~~~   36 (81)
T cd04869           3 EVVG-NDRPGIVHEVTQFLAQRNINIEDLSTETYS   36 (81)
T ss_pred             EEEe-CCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence            3444 578999999999999999999999998876

This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in

>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein

Probab=90.83  E-value=0.8  Score=31.09  Aligned_cols=47  Identities=6%  Similarity=0.123  Sum_probs=37.6

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      |.+.| .+++|.+++|.+.|-++|+++++.+..+.++.++..+.+...
T Consensus         4 l~i~g-~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~   50 (88)
T cd04872           4 ITVVG-KDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDIS   50 (88)
T ss_pred             EEEEc-CCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeC
Confidence            44444 578999999999999999999999988877776666666543

This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK00194 hypothetical protein; Validated

Probab=90.67  E-value=0.85  Score=30.93  Aligned_cols=47  Identities=6%  Similarity=0.160  Sum_probs=37.1

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      +.+.| .+++|.+.++...|.++|++|++.+..+.++.++..+.+...
T Consensus         6 ltv~g-~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~   52 (90)
T PRK00194          6 ITVIG-KDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDIS   52 (90)
T ss_pred             EEEEc-CCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEec
Confidence            44444 578999999999999999999999988877766665555553

>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase)

Probab=90.47  E-value=1.5  Score=28.60  Aligned_cols=44  Identities=14%  Similarity=0.199  Sum_probs=32.0

Q ss_pred             ecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349          101 CGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus       101 ~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      .+..++|.+.+|-+.|.++|+++++.+..+..+.-.+.+.+++.
T Consensus         5 ~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~   48 (74)
T cd04875           5 SCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFE   48 (74)
T ss_pred             EcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEE
Confidence            34578999999999999999999999987532222244444443

This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB)

Probab=90.38  E-value=1.4  Score=28.93  Aligned_cols=42  Identities=12%  Similarity=0.247  Sum_probs=34.0

Q ss_pred             EecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEE
Q 045349          100 ICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQS  141 (152)
Q Consensus       100 ~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~  141 (152)
                      +.|..++|.+.++-++|.++|+++.+.+.+..++.+...+.+
T Consensus         4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v   45 (75)
T cd04870           4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILV   45 (75)
T ss_pred             EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEE
Confidence            346788999999999999999999999988888764443333

The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a

Probab=90.06  E-value=2.8  Score=26.08  Aligned_cols=35  Identities=9%  Similarity=0.319  Sum_probs=27.9

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeC
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSG  132 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~  132 (152)
                      +.+.+ .+++|.|.+++..|.+++++|.+.+....+
T Consensus         3 l~i~~-~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~   37 (72)
T cd04874           3 LSIIA-EDKPGVLRDLTGVIAEHGGNITYTQQFIER   37 (72)
T ss_pred             EEEEe-CCCCChHHHHHHHHHhCCCCEEEEEEeccC
Confidence            34444 367899999999999999999998876653

a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein

Probab=89.90  E-value=2  Score=28.08  Aligned_cols=41  Identities=15%  Similarity=0.323  Sum_probs=30.8

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEE
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSV  139 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti  139 (152)
                      +.+.+ .+++|+|.+|+.++.++++.+.+.++.+. +.+.+++
T Consensus         3 l~I~~-~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~l~i   43 (74)
T cd04877           3 LEITC-EDRLGITQEVLDLLVEHNIDLRGIEIDPK-GRIYLNF   43 (74)
T ss_pred             EEEEE-EccchHHHHHHHHHHHCCCceEEEEEecC-CeEEEEe
Confidence            33444 36789999999999999999999998775 4433433

ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence

>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH)

Probab=89.74  E-value=2.4  Score=27.59  Aligned_cols=43  Identities=7%  Similarity=0.017  Sum_probs=33.8

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCC-eEEEEEEEEEcc
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGD-RVIFSVQSKVYI  145 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~-~v~~ti~~qv~~  145 (152)
                      .+++|.|.++++.|.++|+.+++..+.+..+ .--|.|...+.+
T Consensus         7 ~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~   50 (75)
T cd04880           7 KNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEG   50 (75)
T ss_pred             CCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEEC
Confidence            3578999999999999999999998888765 344665555543

ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech

>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a

Probab=89.31  E-value=2.8  Score=26.87  Aligned_cols=42  Identities=7%  Similarity=0.177  Sum_probs=31.5

Q ss_pred             CCcchHHHHHHHHHHCCcEEEEEEEEee-CCeEEEEEEEEEcc
Q 045349          104 NRNFMFHEIISILEEEAAEVINVTRFNS-GDRVIFSVQSKVYI  145 (152)
Q Consensus       104 ~~~~~l~~il~~Le~~gL~Vv~a~~s~~-~~~v~~ti~~qv~~  145 (152)
                      ++++.+.+|+..|.++|++|...+.+.. ++.....|.+.+..
T Consensus         9 d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~   51 (76)
T cd04888           9 HRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTST   51 (76)
T ss_pred             CCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCc
Confidence            5689999999999999999999987653 34444555555543

a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK04435 hypothetical protein; Provisional

Probab=88.44  E-value=3.1  Score=31.46  Aligned_cols=55  Identities=9%  Similarity=0.265  Sum_probs=40.8

Q ss_pred             eCCeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe-eCCeEEEEEEEEEccc
Q 045349           91 SGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFN-SGDRVIFSVQSKVYIT  146 (152)
Q Consensus        91 ~g~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~-~~~~v~~ti~~qv~~s  146 (152)
                      .|..+.+.+.+. +++|.|.+|+..|.+.|++|.+.+.+. .++....+|.+.+...
T Consensus        66 ~~r~vtL~i~l~-Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~  121 (147)
T PRK04435         66 KGKIITLSLLLE-DRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSM  121 (147)
T ss_pred             CCcEEEEEEEEe-cCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCCh
Confidence            555555666553 568999999999999999999988654 3566667777776544

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]

Probab=87.34  E-value=0.61  Score=43.79  Aligned_cols=41  Identities=27%  Similarity=0.356  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHH
Q 045349           20 NEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMH   60 (152)
Q Consensus        20 ~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~   60 (152)
                      +=|.||.+=|+-|+.|.-+||..    +-+||++|+.-||.|++-
T Consensus        53 AARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   53 AARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            45889999999999999999966    689999999999999873

>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains

Probab=87.29  E-value=2.5  Score=26.11  Aligned_cols=40  Identities=20%  Similarity=0.333  Sum_probs=29.7

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeC--CeEEEEEEEE
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSG--DRVIFSVQSK  142 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~--~~v~~ti~~q  142 (152)
                      .+++|.|.++++.|.++|++|.+...+...  +...+.|..+
T Consensus         7 ~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve   48 (65)
T cd04882           7 PDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE   48 (65)
T ss_pred             CCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC
Confidence            367899999999999999999877765543  4444544443

Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=87.04  E-value=0.67  Score=42.61  Aligned_cols=38  Identities=34%  Similarity=0.436  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHH
Q 045349           22 KHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIM   59 (152)
Q Consensus        22 R~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk   59 (152)
                      ++-|+++|.-+..|.||||..    +|.||-++|.-++.|++
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            456889999999999999977    89999999999999975

>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate

Probab=86.55  E-value=4.7  Score=24.59  Aligned_cols=40  Identities=15%  Similarity=0.142  Sum_probs=31.2

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeC-CeEEEEEEEE
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSG-DRVIFSVQSK  142 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~-~~v~~ti~~q  142 (152)
                      .+++|.|.++.+.|.++|++|.+......+ +..+..|...
T Consensus         6 ~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~   46 (56)
T cd04889           6 ENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFS   46 (56)
T ss_pred             CCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEEC
Confidence            367899999999999999999888876655 5555555443

Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A

>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH)

Probab=86.35  E-value=4.6  Score=24.74  Aligned_cols=39  Identities=8%  Similarity=0.017  Sum_probs=30.8

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeC--CeEEEEEEE
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSG--DRVIFSVQS  141 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~--~~v~~ti~~  141 (152)
                      .++++.+.+++..|.++|++|.+..+...+  +....++.+
T Consensus         7 ~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v   47 (71)
T cd04879           7 KDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV   47 (71)
T ss_pred             cCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc
Confidence            356789999999999999999999987754  555555544

ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active

>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme

Probab=85.69  E-value=6.4  Score=26.00  Aligned_cols=43  Identities=7%  Similarity=0.030  Sum_probs=33.8

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCC-eEEEEEEEEEcc
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGD-RVIFSVQSKVYI  145 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~-~v~~ti~~qv~~  145 (152)
                      .+++|.|.++++.|.++|+++++..+.+..+ .-.|+|.++...
T Consensus         9 ~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~   52 (80)
T cd04905           9 PNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEG   52 (80)
T ss_pred             CCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEEC
Confidence            3578999999999999999999998877643 445666666653

The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi

>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]

Probab=85.40  E-value=0.26  Score=46.22  Aligned_cols=60  Identities=20%  Similarity=0.230  Sum_probs=49.4

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC-----CCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN-----SKLSMPQILDDATSYIMHLQKNKESLERK   71 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-----~K~~~~~il~~Ai~YIk~L~~~v~~L~~~   71 (152)
                      ++.+.|.-+|.+||...+-.|..|.++.-+.     .|++.+.-+...+.||..++.+...+.++
T Consensus       650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e  714 (856)
T KOG3582|consen  650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEE  714 (856)
T ss_pred             CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchh
Confidence            4577899999999999999999999988655     57888888999999999887766555544

>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains

Probab=85.27  E-value=5.9  Score=25.17  Aligned_cols=32  Identities=13%  Similarity=0.156  Sum_probs=27.4

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCCe
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGDR  134 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~  134 (152)
                      .+++|.|.+++..|.+.|++|.+......++.
T Consensus         9 ~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~   40 (66)
T cd04908           9 ENKPGRLAAVTEILSEAGINIRALSIADTSEF   40 (66)
T ss_pred             cCCCChHHHHHHHHHHCCCCEEEEEEEecCCC
Confidence            36789999999999999999999987766564

Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.

>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains

Probab=84.32  E-value=6.4  Score=23.22  Aligned_cols=40  Identities=15%  Similarity=0.302  Sum_probs=30.2

Q ss_pred             CCcchHHHHHHHHHHCCcEEEEEEEEeeC-CeEEEEEEEEE
Q 045349          104 NRNFMFHEIISILEEEAAEVINVTRFNSG-DRVIFSVQSKV  143 (152)
Q Consensus       104 ~~~~~l~~il~~Le~~gL~Vv~a~~s~~~-~~v~~ti~~qv  143 (152)
                      ++++.+.++++.|.++++++.+......+ +...+.+...+
T Consensus         7 ~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~   47 (71)
T cd04876           7 DRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEV   47 (71)
T ss_pred             ccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEE
Confidence            56789999999999999999999887655 43434444443

ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i

>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme

Probab=83.11  E-value=6  Score=21.96  Aligned_cols=29  Identities=21%  Similarity=0.454  Sum_probs=25.0

Q ss_pred             CCcchHHHHHHHHHHCCcEEEEEEEEeeC
Q 045349          104 NRNFMFHEIISILEEEAAEVINVTRFNSG  132 (152)
Q Consensus       104 ~~~~~l~~il~~Le~~gL~Vv~a~~s~~~  132 (152)
                      ++++.+.+++..|..+|+.+...+....+
T Consensus         7 ~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           7 DRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             CCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            45788999999999999999999886643

Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p

>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=83.06  E-value=3.9  Score=39.31  Aligned_cols=57  Identities=11%  Similarity=0.178  Sum_probs=46.0

Q ss_pred             EEEEEeCCeeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEE-eeCCeEEEEEEEEE
Q 045349           86 MNITTSGSTLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRF-NSGDRVIFSVQSKV  143 (152)
Q Consensus        86 V~v~~~g~~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s-~~~~~v~~ti~~qv  143 (152)
                      ++++....+.+|++.|. .++.+|+.+..++...|++|++|++. +-+|..+.||.+.-
T Consensus       676 ~~~r~~~~~teV~V~a~-d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~  733 (867)
T COG2844         676 ISVRPHSGGTEVFVYAP-DRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLE  733 (867)
T ss_pred             eeecccCCceEEEEEcC-CCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEec
Confidence            34555666679999885 67899999999999999999999974 45677998887663

>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH)

Probab=82.85  E-value=4.1  Score=25.74  Aligned_cols=42  Identities=12%  Similarity=0.175  Sum_probs=32.4

Q ss_pred             cCCCcchHHHHHHHHHHCCcEEEEEEEEe--eCCeEEEEEEEEE
Q 045349          102 GLNRNFMFHEIISILEEEAAEVINVTRFN--SGDRVIFSVQSKV  143 (152)
Q Consensus       102 ~~~~~~~l~~il~~Le~~gL~Vv~a~~s~--~~~~v~~ti~~qv  143 (152)
                      ..+++|.+.++.+.|.++|+++.+..+..  .++...+.|.+..
T Consensus         6 ~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~   49 (73)
T cd04902           6 NTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDE   49 (73)
T ss_pred             eCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCC
Confidence            34678999999999999999998887655  3466666666543

The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden

>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria

Probab=82.31  E-value=11  Score=24.28  Aligned_cols=29  Identities=14%  Similarity=0.170  Sum_probs=25.5

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEee
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNS  131 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~  131 (152)
                      .+++|.|.++++.|.++|++|++......
T Consensus         7 ~d~pG~L~~l~~~i~~~g~nI~~i~~~~~   35 (72)
T cd04884           7 EDKPGTLKPVVDTLREFNARIISILTAFE   35 (72)
T ss_pred             cCCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence            36789999999999999999999987664

This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=81.31  E-value=1.4  Score=34.29  Aligned_cols=46  Identities=24%  Similarity=0.252  Sum_probs=32.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHH
Q 045349           17 RNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQ   62 (152)
Q Consensus        17 h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~   62 (152)
                      +-..||.|-+.+++.|.-|+.|+|..  ++++.--.|.-+..||..|.
T Consensus        26 r~~~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~d   73 (173)
T KOG4447|consen   26 RQRKERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSLD   73 (173)
T ss_pred             hhHHHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhHH
Confidence            33469999999999999999999977  33333233555556665553

>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH)

Probab=81.10  E-value=6.6  Score=25.86  Aligned_cols=42  Identities=7%  Similarity=0.005  Sum_probs=33.1

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeE-EEEEEEEEc
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGDRV-IFSVQSKVY  144 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v-~~ti~~qv~  144 (152)
                      .+++|.|+++|..+...|+++.+..+-+..+.. -|.|...+.
T Consensus         8 ~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~   50 (74)
T cd04904           8 KEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCE   50 (74)
T ss_pred             CCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEE
Confidence            457899999999999999999999998876543 355555554

ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-12
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	3e-11
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	1e-10
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-10
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	4e-09
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-07
4f3l_A	361	Mclock, circadian locomoter output cycles protein	5e-04

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Length = 88

 Score = 58.9 bits (143), Expect = 1e-12
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIP---SNSKLSMPQILDDATSYIMHLQKNKESLER 70
          R   N+ E+ RR  +K     L   IP   +N K     IL  AT+YI+ +Q  ++ L  
Sbjct: 7  RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS 66

Query: 71 KKALLK 76
          ++ LL+
Sbjct: 67 EEDLLR 72

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Length = 83

 Score = 55.1 bits (133), Expect = 3e-11
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS--NSKLSMPQILDDATSYIMHLQKNKESLERK 71
          RA  N  E+ RR  +KD    L   +PS    K S  QILD AT YI ++++   + ++ 
Sbjct: 3  RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 62

Query: 72 KALLK 76
             LK
Sbjct: 63 IDDLK 67

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 53.5 bits (129), Expect = 1e-10
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS--NSKLSMPQILDDATSYIMHLQKNKESLERK 71
          RA  N  E+ RR  +KD    L   +PS    K S  QILD AT YI ++++   + ++ 
Sbjct: 13 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 72

Query: 72 KALLK 76
             LK
Sbjct: 73 IDDLK 77

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82

 Score = 53.2 bits (128), Expect = 2e-10
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS-NSKLSMPQILDDATSYIMHLQKNKESLERKK 72
          R   N  EK  R  + D I +L  L+    +KL+   +L  A  YI  LQ + + L+++ 
Sbjct: 7  RTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN 66

Query: 73 ALLK 76
            L+
Sbjct: 67 LSLR 70

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 49.4 bits (118), Expect = 4e-09
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 13 SRAQRNINEKHRRMLMKDLISQLASLIP---SNSKLSMPQILDDATSYIMHLQKNKESLE 69
          SR+  N  EK+RR  ++  + +L  L+P    +S+ +   +L  A  +I  L+ +     
Sbjct: 1  SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV 60

Query: 70 RKKALLK 76
           +   L+
Sbjct: 61 HQIDQLQ 67

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 45.0 bits (107), Expect = 2e-07
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS------NSKLSMPQILDDATSYIMHLQKNKE 66
          RAQ N  E+ RR  + + I QL+ +IP        S  S   IL  A+ YI  L+++  
Sbjct: 6  RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYI 58
          + R  RN +EK RR     LI +L S++P N  K+    +L  +  ++
Sbjct: 11 AKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFL 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.73
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.7
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.7
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.69
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.66
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.62
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.6
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.59
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.56
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.52
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.5
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.47
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.45
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.08
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.06
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.94
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.67
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.35
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	94.51
2nyi_A	195	Unknown protein; protein structure initiative, PSI	94.07
1u8s_A	192	Glycine cleavage system transcriptional repressor,	93.88
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	91.39
3he4_B	46	Synzip5; heterodimeric coiled-coil, de novo protei	83.22
2nyi_A	195	Unknown protein; protein structure initiative, PSI	82.52
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	80.21

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C

Probab=99.73  E-value=8.9e-18  Score=115.59  Aligned_cols=65  Identities=29%  Similarity=0.430  Sum_probs=60.9

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLERKKALLK   76 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   76 (152)
                      .++..|+.+||+||..||+.|..|+++||.. .|+|+++||.+||+||++|+++++.|+.+.+.|.
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~   70 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4688999999999999999999999999998 8999999999999999999999999999877653

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1

Probab=99.70  E-value=2.7e-17  Score=112.50  Aligned_cols=66  Identities=35%  Similarity=0.449  Sum_probs=61.6

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNKESLERKKALLK   76 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   76 (152)
                      ..+|..|+..||+||..||+.|..|+++||..  .|+|+++||..||+||++|++++++|+.+.+.|.
T Consensus        10 ~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A           10 ADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35689999999999999999999999999987  6999999999999999999999999999988663

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=99.70  E-value=3.6e-17  Score=112.45  Aligned_cols=63  Identities=35%  Similarity=0.445  Sum_probs=58.7

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      +|..||..||+||..||+.|..|+++||..  .|+|+++||..||+||+.|++++++|+.+++.+
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L   66 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999975  899999999999999999999999998877655

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=99.69  E-value=7.6e-17  Score=110.60  Aligned_cols=63  Identities=25%  Similarity=0.323  Sum_probs=58.6

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      +|..||..||+||..||+.|..|+++||..   .|.++++||..|++||++|+++.++|..+++.+
T Consensus         1 ~R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L   66 (80)
T 1nlw_A            1 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (80)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999965   799999999999999999999999999887755

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1

Probab=99.66  E-value=2.4e-16  Score=109.87  Aligned_cols=63  Identities=32%  Similarity=0.423  Sum_probs=57.3

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      +|..||..||+||..||+.|..|+++||..   .|+|+++||..||+||+.|+++.+.+..+++.+
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L   71 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            588999999999999999999999999986   699999999999999999999988877665543

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1

Probab=99.62  E-value=1.4e-16  Score=104.65  Aligned_cols=53  Identities=34%  Similarity=0.465  Sum_probs=49.3

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhhHHHHHHHHHHHHHHHH
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN-------SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-------~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      +|.+|+.+||+||..||..|..|++|||..       +|.+++++|+.||+||++||+++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999999999999954       57899999999999999999865

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1

Probab=99.60  E-value=2.5e-16  Score=103.55  Aligned_cols=55  Identities=36%  Similarity=0.504  Sum_probs=50.7

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCCC------CCChhhHHHHHHHHHHHHHHHH
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSNS------KLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~~------K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      ..++..|+.+||+||..||+.|..|++|||...      |+|+++||..||+||++|+++.
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999873      7899999999999999999764

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.59  E-value=1.5e-15  Score=102.01  Aligned_cols=60  Identities=28%  Similarity=0.464  Sum_probs=54.9

Q ss_pred             CCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHH
Q 045349           10 GSSSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLE   69 (152)
Q Consensus        10 ~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-~K~~~~~il~~Ai~YIk~L~~~v~~L~   69 (152)
                      ..++|..|+.+||+||.+||+.|..|++|||.. .|+||++||..||+||+.||+++.=|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            456789999999999999999999999999975 699999999999999999999886553

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.56  E-value=7.5e-15  Score=107.28  Aligned_cols=62  Identities=26%  Similarity=0.473  Sum_probs=52.9

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQKNKESLERKK   72 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k   72 (152)
                      ..++..|+.+||+||..||+.|..|++|||..    .|+++++||..||+||+.|+++++.|+...
T Consensus        25 ~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           25 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999976    489999999999999999999999998754

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.52  E-value=4e-15  Score=101.13  Aligned_cols=58  Identities=22%  Similarity=0.311  Sum_probs=48.9

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCC-ChhhHHHHHHHHHHHHHHHHHHHH
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN---SKL-SMPQILDDATSYIMHLQKNKESLE   69 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~-~~~~il~~Ai~YIk~L~~~v~~L~   69 (152)
                      .+|..||..||+||..+|+.|..|+.+||..   .|. +|.+||..||+||+.|++.+++++
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999952   565 899999999999999999998875

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=99.50  E-value=4e-14  Score=92.11  Aligned_cols=55  Identities=27%  Similarity=0.344  Sum_probs=50.9

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHH
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNKE   66 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v~   66 (152)
                      ++|..||..||+|+..||+.|..||.+||..   .|+||.++|..||+||..|++.++
T Consensus         1 ~rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            1 SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999976   699999999999999999998763

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.47  E-value=1.8e-14  Score=97.26  Aligned_cols=54  Identities=31%  Similarity=0.375  Sum_probs=49.5

Q ss_pred             CCCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHH
Q 045349           10 GSSSRAQRNINEKHRRMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQK   63 (152)
Q Consensus        10 ~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~   63 (152)
                      -...+..|+.+||+||.+||+.|..|++|||..    .|+||++||..||+||+.|+.
T Consensus         6 ~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            6 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            345689999999999999999999999999965    799999999999999999974

>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B*

Probab=99.45  E-value=7.1e-14  Score=93.09  Aligned_cols=55  Identities=25%  Similarity=0.324  Sum_probs=50.7

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHH
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      ...|..||..||+|+..||+.|..||.+||..  .|+||..+|..||+||..|++.+
T Consensus        10 ~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            34678899999999999999999999999976  79999999999999999999865

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.08  E-value=1.3e-10  Score=97.26  Aligned_cols=57  Identities=25%  Similarity=0.457  Sum_probs=42.2

Q ss_pred             CCCCCchhhhhHHHHHHHHHHHHHHHHHHhcCC-CCCCCChhhHHHHHHHHHHHHHHH
Q 045349            8 AAGSSSRAQRNINEKHRRMLMKDLISQLASLIP-SNSKLSMPQILDDATSYIMHLQKN   64 (152)
Q Consensus         8 ~~~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP-~~~K~~~~~il~~Ai~YIk~L~~~   64 (152)
                      .....+|..|+.+||+||.+||..|..|++||| ...|+||++||..||.||+.++.-
T Consensus         7 ~~~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A            7 DKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             ------------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            345778999999999999999999999999999 448999999999999999999753

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.06  E-value=3.4e-11  Score=79.90  Aligned_cols=46  Identities=28%  Similarity=0.320  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHH
Q 045349           18 NINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQK   63 (152)
Q Consensus        18 ~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~   63 (152)
                      +..||+|+..||+.|..||.+||..   .|+||..+|..||+||..||+
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            4679999999999999999999977   799999999999999999985

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.94  E-value=6.6e-10  Score=93.98  Aligned_cols=57  Identities=30%  Similarity=0.355  Sum_probs=49.7

Q ss_pred             CCCCCCchhhhhHHHHHHHHHHHHHHHHHHhcCC----CCCCCChhhHHHHHHHHHHHHHH
Q 045349            7 SAAGSSSRAQRNINEKHRRMLMKDLISQLASLIP----SNSKLSMPQILDDATSYIMHLQK   63 (152)
Q Consensus         7 ~~~~~~~~~~h~~~ER~RR~~m~~~~~~LrsllP----~~~K~~~~~il~~Ai~YIk~L~~   63 (152)
                      ......+|..|+.+||+||.+||..|..|++|||    ...|+||++||..||.|||.|+.
T Consensus         7 ~~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B            7 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             cchhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            3445678999999999999999999999999999    45899999999999999999874

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=98.67  E-value=4.2e-08  Score=69.19  Aligned_cols=48  Identities=33%  Similarity=0.406  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHH
Q 045349           20 NEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNKES   67 (152)
Q Consensus        20 ~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v~~   67 (152)
                      .||+|-..||+.|..||.+||..   .|+||..+|.-||+||..|++-+++
T Consensus        32 ~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           32 DPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            35888899999999999999975   7999999999999999999998854

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=98.35  E-value=1.3e-06  Score=59.93  Aligned_cols=47  Identities=28%  Similarity=0.479  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHhcCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 045349           25 RMLMKDLISQLASLIPSN----SKLSMPQILDDATSYIMHLQKNKESLERK   71 (152)
Q Consensus        25 R~~m~~~~~~LrsllP~~----~K~~~~~il~~Ai~YIk~L~~~v~~L~~~   71 (152)
                      |-.+|+.+..|..|||..    .|++|.+||..|++||++||+..+.+.+.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~   54 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   54 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999965    68999999999999999999887776653

>1zpv_A ACT domain protein; structural genomics, PSI, protein structure INIT midwest center for structural genomics, MCSG, unknown funct; 1.90A {Streptococcus pneumoniae} SCOP: d.58.18.7

Probab=94.51  E-value=0.39  Score=31.24  Aligned_cols=49  Identities=2%  Similarity=0.001  Sum_probs=38.5

Q ss_pred             eEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEcc
Q 045349           96 EVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVYI  145 (152)
Q Consensus        96 ~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~~  145 (152)
                      .+.+.| .+++|.+.+|..+|.++|.+|.+.+....++..+..+.+.+.+
T Consensus         7 ~l~v~~-~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~~   55 (91)
T 1zpv_A            7 IITVVG-KDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSDE   55 (91)
T ss_dssp             EEEEEE-SCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEESS
T ss_pred             EEEEEE-CCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeCC
Confidence            344444 4789999999999999999999999888777666666666543

>2nyi_A Unknown protein; protein structure initiative, PSI, center for eukaryotic structural genomics, CESG, structural genomics; 1.80A {Galdieria sulphuraria}

Probab=94.07  E-value=0.31  Score=36.93  Aligned_cols=49  Identities=16%  Similarity=0.099  Sum_probs=39.9

Q ss_pred             eeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           95 LEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        95 ~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      +.|.+.| ..++|++..|...|.++|++|++++..+..+.++.++.+...
T Consensus         6 ~~ltv~~-~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~~~   54 (195)
T 2nyi_A            6 FVVSVAG-SDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVSLN   54 (195)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES
T ss_pred             EEEEEEe-CCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEEec
Confidence            3455555 478999999999999999999999999888887766666543

>1u8s_A Glycine cleavage system transcriptional repressor, putative; structural genomics, protein structure initiative (PSI), domain swapping; 2.45A {Vibrio cholerae} SCOP: d.58.18.5 d.58.18.5

Probab=93.88  E-value=0.36  Score=36.10  Aligned_cols=48  Identities=10%  Similarity=0.182  Sum_probs=39.8

Q ss_pred             eeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349           95 LEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus        95 ~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      +.|.++| .+++|++.+|..+|.++|++|++++..+.++.++.++.+..
T Consensus         7 ~~itv~~-~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~~   54 (192)
T 1u8s_A            7 LVITAVG-TDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG   54 (192)
T ss_dssp             EEEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEc-CCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEec
Confidence            3455556 47899999999999999999999999888888777777654

>2ko1_A CTR148A, GTP pyrophosphokinase; homodimer, alpha+beta, transferase, structural genomics, PSI-2, protein structure initiative; NMR {Chlorobaculum tepidum} PDB: 3ibw_A

Probab=91.39  E-value=1.3  Score=28.12  Aligned_cols=41  Identities=10%  Similarity=0.079  Sum_probs=32.6

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEE
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKV  143 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv  143 (152)
                      .+++|.|.+|..+|.+.|++|.+.+....++.....+...+
T Consensus        13 ~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~~   53 (88)
T 2ko1_A           13 EDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIFV   53 (88)
T ss_dssp             ECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEEE
T ss_pred             ECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEEE
Confidence            46889999999999999999999999876664344455544

>3he4_B Synzip5; heterodimeric coiled-coil, de novo protein; 2.46A {Artificial gene}

Probab=83.22  E-value=1.5  Score=25.61  Aligned_cols=27  Identities=22%  Similarity=0.409  Sum_probs=21.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           49 QILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        49 ~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      +.+.+--+||++|+++-.+|+.-++.+
T Consensus         3 ntvkelknyiqeleernaelknlkehl   29 (46)
T 3he4_B            3 NTVKELKNYIQELEERNAELKNLKEHL   29 (46)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHhHHHHhHHHHH
Confidence            346778899999999999998776644

>2nyi_A Unknown protein; protein structure initiative, PSI, center for eukaryotic structural genomics, CESG, structural genomics; 1.80A {Galdieria sulphuraria}

Probab=82.52  E-value=4.6  Score=30.25  Aligned_cols=36  Identities=8%  Similarity=0.168  Sum_probs=30.6

Q ss_pred             eEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeC
Q 045349           96 EVNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSG  132 (152)
Q Consensus        96 ~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~  132 (152)
                      -+.+.| ..++|+++.|-..|-++|++|.+++..+.+
T Consensus        95 iltv~g-~DrpGiva~Vt~~La~~g~nI~~~~~~t~~  130 (195)
T 2nyi_A           95 ELYVEG-PDSEGIVEAVTAVLAKKGANIVELETETLP  130 (195)
T ss_dssp             EEEEEE-ECCTTHHHHHHHHHHHTTCEEEEEEEEEEE
T ss_pred             EEEEEe-CCCcCHHHHHHHHHHHcCCCEEEceeeecc
Confidence            355555 478999999999999999999999988765

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=80.21  E-value=5.3  Score=28.19  Aligned_cols=34  Identities=12%  Similarity=0.236  Sum_probs=29.3

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEee
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNS  131 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~  131 (152)
                      +.+.|. ++.|++.+|+.+|.+.++++.++++.+.
T Consensus         3 ~~v~~~-dr~g~l~~i~~~l~~~~~ni~~~~~~~~   36 (190)
T 2jhe_A            3 LEVFCE-DRLGLTRELLDLLVLRGIDLRGIEIDPI   36 (190)
T ss_dssp             EEEEEC-SCTTHHHHHHHHHHHTTCCEEEEEEETT
T ss_pred             EEEEEe-cCCcHHHHHHHHHHHcCCCeEEEEEecC
Confidence            455564 6789999999999999999999999775

---

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	152
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-11
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	5e-10
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	2e-09
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	5e-09
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	2e-08
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-07
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	3e-06
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	7e-06

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.9 bits (132), Expect = 2e-11
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIP---SNSKLSMPQILDDATSYIMHLQKNKESLER 70
          R   N+ E+ RR  +K     L   IP   +N K     IL  AT+YI+ +Q  ++ L  
Sbjct: 7  RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS 66

Query: 71 KKALLK 76
          ++ LL+
Sbjct: 67 EEDLLR 72

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.7 bits (121), Expect = 5e-10
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 13 SRAQRNINEKHRRMLMKDLISQLASLIPSNS---KLSMPQILDDATSYIMHLQKNKESLE 69
          SR+  N  EK+RR  ++  + +L  L+P      + +   +L  A  +I  L+ +     
Sbjct: 1  SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV 60

Query: 70 RKKALLK 76
           +   L+
Sbjct: 61 HQIDQLQ 67

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 2e-09
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS--NSKLSMPQILDDATSYIMHLQKNKESLERK 71
          RA  N  E+ RR  +KD    L   +PS    K S  QILD AT YI ++++   + ++ 
Sbjct: 3  RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 62

Query: 72 KALLK 76
             LK
Sbjct: 63 IDDLK 67

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 5e-09
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 11 SSSRAQRNINEKHRRMLMKDLISQLASLIPS-NSKLSMPQILDDATSYIMHLQKNKESLE 69
             R   N  EK  R  + D I +L  L+    +KL+   +L  A  YI  LQ + + L+
Sbjct: 4  GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

Query: 70 RKKALLK 76
          ++   L+
Sbjct: 64 QENLSLR 70

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.0 bits (109), Expect = 2e-08
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIP-------SNSKLSMPQILDDATSYIMHLQKNKE 66
          R      E+ RR  +   + +LASLIP        ++  S    ++ A  YI HLQ+N  
Sbjct: 3  RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

Query: 67 S 67
          +
Sbjct: 63 T 63

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 1e-07
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 14 RAQRNINEKHRRMLMKDLISQLASLIPS------NSKLSMPQILDDATSYIMHLQKNKE 66
          RAQ N  E+ RR  + + I QL+ +IP        S  S   IL  A+ YI  L+++  
Sbjct: 6  RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (95), Expect = 3e-06
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 25 RMLMKDLISQLASLIPS-NSKLSMPQILDDATSYIMHLQKNKESLERKKALLK 76
          R  + D I +L  L+   ++K+    +L  A  YI +LQ+    L ++  +LK
Sbjct: 1  RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK 53

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 7e-06
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSNS--KLSMPQILDDATSYIMHLQK 63
          +  R    + E+ R   + +    L     SN   +L   +IL +A  YI  LQ 
Sbjct: 10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQA 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	152
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.71
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.68
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.64
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.63
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.51
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	94.01
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	93.43
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	89.78
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	89.35
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	88.97
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	85.51
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	81.66

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.7e-17  Score=111.43  Aligned_cols=63  Identities=25%  Similarity=0.323  Sum_probs=58.4

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      .|..||..||+||..||+.|..|+++||..   .|+|+++||..||+||+.|+++++.|..+++.+
T Consensus         1 ~R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L   66 (79)
T d1nlwa_           1 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQL   66 (79)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            378999999999999999999999999976   689999999999999999999999998887655

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.6e-17  Score=111.96  Aligned_cols=64  Identities=30%  Similarity=0.422  Sum_probs=59.9

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~-~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      .+|..|+.+||+||..||+.|..|+++||.. .|+|+++||..||+||++|+++++.|..+.+.+
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~l   69 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4688999999999999999999999999987 799999999999999999999999999887654

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.5e-17  Score=111.33  Aligned_cols=64  Identities=31%  Similarity=0.412  Sum_probs=58.7

Q ss_pred             CchhhhhHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           12 SSRAQRNINEKHRRMLMKDLISQLASLIPSN---SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        12 ~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~---~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      .+|..|+.+||+||..||+.|..|+++||+.   .|+|+++||..||+||+.|++++++|..+++.+
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   71 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3678999999999999999999999999965   689999999999999999999999998877654

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=8.8e-17  Score=108.74  Aligned_cols=63  Identities=35%  Similarity=0.445  Sum_probs=57.9

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNKESLERKKALL   75 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l   75 (152)
                      +|..|+..||+||.+||+.|..|+++||..  .|+|+++||..||+||+.|+++++.|..+.+.+
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l   66 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999965  799999999999999999999999998876543

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.64  E-value=8.4e-17  Score=103.92  Aligned_cols=53  Identities=34%  Similarity=0.465  Sum_probs=49.3

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhcCCC-------CCCCChhhHHHHHHHHHHHHHHHH
Q 045349           13 SRAQRNINEKHRRMLMKDLISQLASLIPS-------NSKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        13 ~~~~h~~~ER~RR~~m~~~~~~LrsllP~-------~~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      +|..|+.+||+||.+||+.|..|+++||.       ..|+|+++||..||+||++||+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            57899999999999999999999999994       279999999999999999999865

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.2e-16  Score=104.87  Aligned_cols=56  Identities=25%  Similarity=0.321  Sum_probs=51.7

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhhHHHHHHHHHHHHHHHHH
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSN--SKLSMPQILDDATSYIMHLQKNKE   66 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~--~K~~~~~il~~Ai~YIk~L~~~v~   66 (152)
                      ..++..|+..||+||..||+.|..|+++||..  .|+|+++||..||+||++||+.++
T Consensus        10 ~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            45678999999999999999999999999986  689999999999999999998764

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.5e-15  Score=97.40  Aligned_cols=55  Identities=36%  Similarity=0.504  Sum_probs=50.0

Q ss_pred             CCchhhhhHHHHHHHHHHHHHHHHHHhcCCCC------CCCChhhHHHHHHHHHHHHHHHH
Q 045349           11 SSSRAQRNINEKHRRMLMKDLISQLASLIPSN------SKLSMPQILDDATSYIMHLQKNK   65 (152)
Q Consensus        11 ~~~~~~h~~~ER~RR~~m~~~~~~LrsllP~~------~K~~~~~il~~Ai~YIk~L~~~v   65 (152)
                      ..+|..|+..||+||..||+.|..|+++||..      .|+|++.||..|++||++||++.
T Consensus         3 ~~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            35688999999999999999999999999965      49999999999999999998753

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=2.8e-14  Score=91.40  Aligned_cols=52  Identities=29%  Similarity=0.430  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHhcCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 045349           25 RMLMKDLISQLASLIPSN-SKLSMPQILDDATSYIMHLQKNKESLERKKALLK   76 (152)
Q Consensus        25 R~~m~~~~~~LrsllP~~-~K~~~~~il~~Ai~YIk~L~~~v~~L~~~k~~l~   76 (152)
                      |.+||+.|..|+++||+. .|+|+++||.+||+||+.|++++++|+++...+.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567999999999999987 6999999999999999999999999999877553

>d1u8sa1 d.58.18.5 (A:2-87) putative transcriptional repressor VC2159 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Glycine cleavage system transcriptional repressor
domain: putative transcriptional repressor VC2159
species: Vibrio cholerae [TaxId: 666]

Probab=94.01  E-value=0.19  Score=31.78  Aligned_cols=47  Identities=11%  Similarity=0.219  Sum_probs=39.4

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      |.++ |.+++|.+.++...|-+.|.+|++++...+++.+.+.+.+...
T Consensus         8 itv~-G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~   54 (86)
T d1u8sa1           8 ITAV-GTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGS   54 (86)
T ss_dssp             EEEE-EECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEEC
T ss_pred             EEEE-eCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcC
Confidence            4444 4688999999999999999999999999999987777666654

>d1zpva1 d.58.18.7 (A:1-83) UPF0237 protein SP0238 {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: SP0238-like
domain: UPF0237 protein SP0238
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=93.43  E-value=0.34  Score=30.12  Aligned_cols=47  Identities=2%  Similarity=0.039  Sum_probs=38.4

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEEEEEEc
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSVQSKVY  144 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti~~qv~  144 (152)
                      +.++| ..++|+++.|-..|-++|.+|.+++-.+.++.++..+.+.+.
T Consensus         5 itv~g-~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~~   51 (83)
T d1zpva1           5 ITVVG-KDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSD   51 (83)
T ss_dssp             EEEEE-SCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES
T ss_pred             EEEEc-CCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEEe
Confidence            34444 588999999999999999999999998888877666666553

>d2f06a2 d.58.18.11 (A:1-70) Hypothetical protein BT0572 {Bacteroides thetaiotaomicron [TaxId: 818]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: BT0572-like
domain: Hypothetical protein BT0572
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=89.78  E-value=1  Score=27.55  Aligned_cols=42  Identities=14%  Similarity=0.190  Sum_probs=33.5

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEEEE
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIFSV  139 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~ti  139 (152)
                      +.++.. +++|.|.++...|.+.|+++.+.++..-.+.-+.-|
T Consensus         6 isV~~e-NkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Ri   47 (70)
T d2f06a2           6 LSIFLE-NKSGRLTEVTEVLAKENINLSALCIAENADFGILRG   47 (70)
T ss_dssp             EEEEEC-SSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEE
T ss_pred             EEEEEe-CCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEE
Confidence            344444 689999999999999999999999888777655444

>d2f06a1 d.58.18.11 (A:71-141) Hypothetical protein BT0572 {Bacteroides thetaiotaomicron [TaxId: 818]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: BT0572-like
domain: Hypothetical protein BT0572
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=89.35  E-value=1  Score=27.36  Aligned_cols=35  Identities=11%  Similarity=0.107  Sum_probs=30.1

Q ss_pred             CCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeEEE
Q 045349          103 LNRNFMFHEIISILEEEAAEVINVTRFNSGDRVIF  137 (152)
Q Consensus       103 ~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v~~  137 (152)
                      .+++|.|.++++.|.+.|++|.....+..++.-+.
T Consensus         7 ~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~   41 (71)
T d2f06a1           7 PNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANV   41 (71)
T ss_dssp             ESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEE
T ss_pred             cCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEE
Confidence            46789999999999999999999998877776543

>d1u8sa2 d.58.18.5 (A:88-180) putative transcriptional repressor VC2159 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Glycine cleavage system transcriptional repressor
domain: putative transcriptional repressor VC2159
species: Vibrio cholerae [TaxId: 666]

Probab=88.97  E-value=1.3  Score=27.88  Aligned_cols=36  Identities=8%  Similarity=0.134  Sum_probs=30.4

Q ss_pred             eeeEEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEe
Q 045349           94 TLEVNLICGLNRNFMFHEIISILEEEAAEVINVTRFN  130 (152)
Q Consensus        94 ~~~V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~  130 (152)
                      .++|.+.|. .++|++.+|-..|-++|++|.+.+..+
T Consensus         6 tv~v~v~g~-DrpGIV~~it~~la~~~~nI~~l~t~~   41 (93)
T d1u8sa2           6 TVEVYVESD-DKLGLTEKFTQFFAQRQIGMASLSAQT   41 (93)
T ss_dssp             EEEEEEEES-CCTTHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             EEEEEEEEC-CCCCHHHHHHHHHHHcCCCchhhhccc
Confidence            456766664 789999999999999999999988755

>d1y7pa2 d.58.18.12 (A:2-78) Hypothetical protein AF1403, N-terminal domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: AF1403 N-terminal domain-like
domain: Hypothetical protein AF1403, N-terminal domain
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=85.51  E-value=0.76  Score=28.42  Aligned_cols=46  Identities=13%  Similarity=0.200  Sum_probs=29.6

Q ss_pred             EEEEecCCCcchHHHHHHHHHHCCcEEEEEEEEee-CCe--EEEEEEEEE
Q 045349           97 VNLICGLNRNFMFHEIISILEEEAAEVINVTRFNS-GDR--VIFSVQSKV  143 (152)
Q Consensus        97 V~~~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~-~~~--v~~ti~~qv  143 (152)
                      +.+.|. +++|+|.+|..++-+++..|.+.+.... ++.  +..+|..+.
T Consensus         4 i~i~~~-Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~   52 (77)
T d1y7pa2           4 LRIIAE-NKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEI   52 (77)
T ss_dssp             EEEEEE-CCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEE
T ss_pred             EEEEEe-cCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEc
Confidence            445554 6789999999999999999999997653 332  344555444

>d2qmwa2 d.58.18.3 (A:185-264) Prephenate dehydratase C-terminal domain {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phenylalanine metabolism regulatory domain
domain: Prephenate dehydratase C-terminal domain
species: Staphylococcus aureus [TaxId: 1280]

Probab=81.66  E-value=2.5  Score=26.14  Aligned_cols=46  Identities=0%  Similarity=-0.060  Sum_probs=35.0

Q ss_pred             EecCCCcchHHHHHHHHHHCCcEEEEEEEEeeCCeE-EEEEEEEEcc
Q 045349          100 ICGLNRNFMFHEIISILEEEAAEVINVTRFNSGDRV-IFSVQSKVYI  145 (152)
Q Consensus       100 ~~~~~~~~~l~~il~~Le~~gL~Vv~a~~s~~~~~v-~~ti~~qv~~  145 (152)
                      +.-.+++|-|.+++..+.++|++...-.+-+..+.. -|.|.+.+.+
T Consensus         7 ~~~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~~g   53 (80)
T d2qmwa2           7 TPMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQADS   53 (80)
T ss_dssp             EESSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEESC
T ss_pred             EeCCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEec
Confidence            333467899999999999999999999998876653 3555555543